Reviewer #3 (Public Review):

Summary:

Alexander et al. reported the gene-regulatory networks underpinning sex determination of murine primordial germ cells (PGCs) through single-nucleus multiomics, offering a detailed chromatin accessibility and gene expression map across three embryonic stages in both male (XY) and female (XX) mice. It highlights how regulatory element accessibility may precede gene expression, pointing to chromatin accessibility as a primer for lineage commitment before differentiation. Sexual dimorphism in these elements and gene expression increases over time, and the study maps transcription factors regulating sexually dimorphic genes in PGCs, identifying sex-specific enrichment in various transcription factors.

Strengths:

The study includes step-wise multiomic analysis with some computational approach to identify candidate TFs regulating XX and XY PGC gene expression, providing a detailed timeline of chromatin accessibility and gene expression during PGC development, which identifies previously unknown PGC subpopulations and offers a multimodal reference atlas of differentiating PGC clusters. Furthermore, the study maps a complex network of transcription factors associated with sex determination in PGCs, adding depth to our understanding of these processes.

Weaknesses:

While the multiomics approach is powerful, it primarily offers correlational insights between chromatin accessibility, gene expression, and transcription factor activity, without direct functional validation of identified regulatory networks.

Reviewer #1 (Public Review):

Summary:

In this study, the authors advance their previous findings on the role of the SLAM-SAP signaling pathway in the development and function of multiple innate-like gamma-delta T-cell subsets. Using a high throughput single-cell proteogenomics approach, the authors uncover SAP-dependent developmental checkpoints, and the role of SAP signaling in regulating the diversion of γδ T cells into the αβ T cell developmental pathway. Finally, the authors define TRGV4/TRAV13-4(DV7)-expressing T cells as a novel, SAP-dependent Vγ4 γδT1 subset.

Strengths:

This study furthers our understanding of the importance and complexity of the SLAM-SAP signaling pathway not only in the development of innate-like γδ T cells but also in how it potentially balances the γδ/αβ T cell lineage commitment. Additionally, this study reveals the role of SAP-dependent events in the generation of γδ TCR repertoire.

The conclusions of the study are supported by well-thought-out experiments and compelling data.

Weaknesses:

No major weaknesses in the study were identified.

Reviewer #2 (Public Review):

Summary:

Mistri et al explore the role of SLAM-SAP signaling in the developmental programming of innate-like gd T cell subsets. Using proteo-genomics, they determined that abrogation of SLAM-SAP signaling altered that programming, reducing some IL-17-producing subsets, including a novel Vγ4 γδT1 subset, and diverting gdTCR-expressing precursors to the ab fate. Altogether, this is a very thorough, thoughtfully interpreted study that adds significantly to our understanding of the contribution of the SLAM-SAP pathway to lineage specification. A particularly interesting element is the role of SLAM-SAP in preventing gd17 progenitors from switching fates and adopting the ab fate.

One thing to keep in mind in assessing the ultimate fate of the "ab wannabe cells" is that mechanisms exist to silence the gd TCR as cells differentiate to the DP stage and so their presence as diverted DP cells may not be evident by staining for gdTCR expression - and will only be evident transcriptomically.

Strengths:

This is an exceedingly well-designed and thorough study that significantly enriches our understanding of gd T cell development.

Weaknesses:

There are no major weaknesses identified by this reviewer.

Reviewer #2 (Public Review):

This work focuses on the biochemical features of the SARS-CoV-2 Nucleocapsid (N) protein, which condenses the large viral RNA genome inside the virus and also plays other roles in the infected cell. The N protein of SARS-CoV-2 and other coronaviruses is known to contain two globular RNA-binding domains, the NTD and CTD, flanked by disordered regions. The central disordered linker is particularly well understood: it contains a long SR-rich region that is extensively phosphorylated in infected cells, followed by a leucine-rich helical segment that was shown previously by these authors to promote N protein oligomerization.

In the current work, the authors analyze 5 million viral sequence variants to assess the conservation of specific amino acids and general sequence features in the major regions of the N protein. This analysis shows that disordered regions are particularly variable but that the general hydrophobic and charge character of these regions are conserved, particularly in the SR and leucine-rich regions of the central linker. The authors then construct a series of N proteins bearing the most prevalent mutations seen in the Delta and Omicron variants, and they subject these mutant proteins to a comprehensive array of biophysical analyses (temperature sensitivity, circular dichroism, oligomerization, RNA binding, and phase separation).

The results include a number of novel findings that are worthy of further exploration. Most notable are the analyses of the previously unstudied P31L mutation of the Omicron variant. The authors use ColabFold and sedimentation analysis to suggest that this mutation promotes self-association of the disordered N-terminal region and stimulates the formation of N protein condensates. Although the affinity of this interaction is low, it seems likely that this mutation enhances viral fitness by promoting N-terminal interactions. The work also addresses the impact of another unstudied mutation, D63G, that is located on the surface of the globular NTD and has no significant effect on the properties analyzed here, raising interesting questions about how this mutation enhances viral fitness. Finally, the paper ends with studies showing that another common mutant, R203K/G204R, disrupts phase separation and might thereby alter N protein function in a way that enhances viral fitness. These provocative results set the stage for in-depth analyses of these mutations in future work.

Reviewer #3 (Public Review):

Nguyen, Zhao et al. used bioinformatic analysis of mutational variants of SARS-CoV-2 Nucleocapsid (N) protein from the large genomic database of SARS-CoV-2 sequences to identify domains and regions of N where mutations are more highly represented, and computationally determined the effects of these mutations on the physicochemical properties of the protein. They found that the intrinsically disordered regions (IDRs) of N protein are more highly mutated than structured regions, and that these mutations can lead to higher variability in the physical properties of these domains. These computational predictions are compared to in vitro biophysical experiments to assess the effects of identified mutations on the thermodynamic stability, oligomeric state, particle formation, and liquid-liquid phase separation of a few exemplary mutants.

The paper is well written, easy to follow and the conclusions drawn are supported by the evidence presented. The analyses and conclusions are interesting and will be of value to virologists, cell biologists, and biophysicists studying SARS-CoV-2 function and assembly.

Reviewer #1 (Public Review):

Summary:

The authors were using an innovative technic to study the visual vigilance based on high-acuity vision, the fovea. Combining motion-capture features and visual space around the head, the authors were able to estimate the visual fixation of free-feeding pigeon at any moment. Simulating predator attacks on screens, they showed that 1) pigeons used their fovea to inspect predators cues, 2) the behavioural state (feeding or head-up) influenced the latency to use the fovea and 3) the use of the fovea decrease the latency to escape of both the individual that foveate the predators cues but also the other flock members.

Strengths:

The paper is very interesting, and combines innovative technic well adapted to study the importance of high-acuity vision for spotting a predator, but also of improving the behavioural response (escaping). The results are strong and the models used are well-adapted. This paper is a major contribution to our understanding of the use of visual adaptation in a foraging context when at risk. This is also a major contribution to the understanding of individual interaction in a flock.

Weaknesses:

I have identified only two weaknesses:

(1) The authors often mixed the methods and the results, Which reduces the readability and fluidity of the manuscript. I would recommend the authors to re-structure the manuscript.<br /> (2) In some parts, the authors stated that they reconstructed the visual field of the pigeon, which is not true. They identified the foveal positions, but not the visual fields, which involve different sectors (binocular, monocular or blind). Similarly, they sometimes mix-up the area centralis and the fovea, which are two different visual adaptations.

Reviewer #1 (Public Review):

Summary:

Plasmacytoid dendritic cells (pDCs) represent a specialized subset of dendritic cells (DCs) known for their role in producing type I interferons (IFN-I) in response to viral infections. It was believed that pDCs originated from common DC progenitors (CDP). However, recent studies by Rodrigues et al. (Nature Immunology, 2018) and Dress et al. (Nature Immunology, 2019) have challenged this perspective, proposing that pDCs predominantly develop from lymphoid progenitors expressing IL-7R and Ly6D. A minor subset of pDCs arising from CDP has also been identified as functionally distinct, exhibiting reduced IFN-I production but a strong capability to activate T-cell responses. On the other hand, clonal lineage tracing experiments, as recently reported by Feng et al. (Immunity, 2022), have demonstrated a shared origin between pDCs and conventional DCs (cDCs), suggesting a contribution of common DC precursors to the pDC lineage.

In this context, Araujo et al. investigated the heterogeneity of pDCs in terms of both development and function. Their findings revealed that approximately 20% of pDCs originate from lymphoid progenitors common to B cells. Using Mb1-Cre x Bcl11a floxed mice, the authors demonstrated that the development of this subset of pDCs, referred to as "B-pDCs," relied on the transcription factor BCL11a. Functionally, B-pDCs exhibited a diminished capacity to produce IFN-I in response to TLR9 agonists but secreted more IL-12 compared to conventional pDCs. Moreover, B-pDCs, either spontaneously or upon activation, exhibited increased expression of activation markers (CD80/CD86/MHC-II) and a heightened ability to activate T-cell responses in vitro compared to conventional pDCs. Finally, Araujo et al. characterized these B-pDCs at the transcriptomic level using bulk and single-cell RNA sequencing, revealing them as a unique subset of pDCs expressing certain B cell markers such as Mb1, as well as specific markers (Axl) associated with cells recently described as transitional DCs.

Thus, in contrast to previous findings, this study posits that a small proportion of pDCs derive from B cell-committed lymphoid progenitors, and this subset of B-pDCs exhibits distinct functional characteristics, being less specialized in IFN-I production but rather in T cell activation.

Strengths:

Previously, the same research group delineated the significance of BCL11a as a critical transcription factor in pDC development (Ippolito et al., PNAS, 2014). This study elucidates the precise stage during hematopoiesis at which BCL11a expression becomes essential for the emergence of a distinct subset of pDCs, substantiated by robust genetic evidence in vivo. Furthermore, it underscores the shared developmental origin between pDCs and B cells, reinforcing prior research in the field that suggests a lymphoid origin of pDCs. Finally, this work attributes specific functional properties to pDCs originating from these lymphoid progenitors shared with B cells, emphasizing the early imprinting of functional heterogeneity during their development.

Weaknesses:

The authors delineate a subset of pDCs dependent on the BCL11a transcription factor, originating from lymphoid progenitors, and compare it to conventional pDCs, which they suggest differentiate from common DC progenitors of myeloid origin. However, this interpretation lacks support from the authors' data. Their single-cell RNA sequencing data identifies cells corresponding to progenitors (Prog2), from which the majority of pDCs, termed conventional pDCs, likely originate. This progenitor cell population expresses Il7r, Siglech, and Ly6D, but not Csfr1. The authors describe this progenitor as resembling a "pro-pDC myeloid precursor," yet these cells align more closely with lymphoid (Il7r+) progenitors described by Rodrigues et al. (Nature Immunology, 2018) and Dress et al. (Nature Immunology, 2019). Furthermore, analysis of their Mb1 reporter mice reveals that only a fraction of common lymphoid progenitors (CLP) express YFP, giving rise to a fraction of YFP+ pDCs. However, this does not exclude the possibility that YFP- CLP could also give rise to pDCs. The authors could address this caveat by attempting to differentiate pDCs from both YFP+ and YFP- CLPs in vitro in the presence of FLT3L. Additionally, transfer experiments using these lymphoid progenitors could be conducted in vivo to assess their differentiation potential in competitive settings.

Using their Mb1-reporter mice, the authors demonstrate that YFP pDCs originating from lymphoid progenitors are functionally distinct from conventional pDCs, mostly in vitro, but their in vivo relevance remains unknown. It is crucial to investigate how Bcl11a conditional deficiency in Mb1-expressing cells affects the anti-viral immune response, for example, using the M-CoV infection model as described by Sulczewski et al. in Nature Immunology, 2023. Particularly, the authors suggest that their B-pDCs act as antigen-presenting cells involved in T-cell activation compared to conventional pDCs. However, these findings contrast with those of Rodrigues et al., who have shown that pDCs of myeloid origin are more effective than pDCs of lymphoid origin in activating T-cell responses. The authors should discuss these discrepancies in greater detail. It is also notable that B-PDCs acquire the expression of ID2 (Figure S3A), commonly a marker of conventional/myeloid DCs. The authors could analyze in more detail the acquisition of specific myeloid features (CD11c, CX3CR1) by this B-PDCs subset and discuss how the expression of ID2 may impair classical pDC features, as ID2 is a repressor of E2-2, a master regulator of pDC fate.

Finally, through the analysis of their single-cell RNA sequencing data, the authors show that the subset of B-pDCs they identified expresses Axl, confirmed at the protein level. Given this specific expression profile, the authors suggest that B-pDCs are related to a previously described subset of transitional DCs, which were reported to share a common developmental path with pDCs, (Sulczewski et al. in Nature Immunology, 2023). While intriguing, this observation requires further phenotypic and functional characterization to substantiate this claim.

Reviewer #2 (Public Review):

Summary:

The origin of plasmatoid dendritic cells and their subclasses continues to be a debated field, akin to any immune cell field that is determined through the expression of surface markers (relative to clear subclass separation based on functional biology and experimentation). In this context, in this manuscript by Araujo et al, the authors attempt to demonstrate that a subtype of pDCs comes from lymphoid origin due to the presence of some B cell gene expression markers. They nomenclature these cells as B-pDCs. Strikingly, pDCs function via expression of IFNa where as B-pDCs do not express IFNa - thereby raising the question of what are their physiological or pathophysiological properties. B-pDCs also express AXL, a marker not seen in mouse pDCs but observed in human pDCs. Overall, using a combination of gene expression profiling of immune cells isolated from mice via RNA-seq and single-cell profiling the authors propose that B-pDCs are a novel subtype of pDCs in mice that were not previously identified and characterized.

Weaknesses:

My two points of discussion about this manuscript are as follows.

(1) How new are these observations that pDCs could also originate from common lymphoid progenitors. This fact has been previously outlined by many laboratories including Shigematsu et al, Immunity 2004. These studies in the manuscript can be considered new based on the single-cell profiling presented, only if the further characterization of the isolated B-pDCs is performed at the functional biology level. Overlapping gene expression profiles are often seen in developing immune cell types- especially when only evaluated at the RNA expression level- and can lead to cell type complexity (and identification of new cell types) that are not biologically and functionally relevant.

(2) The authors hardly perform any experiments to interrogate the function of these B-pDCs. The discussion on this topic can be enhanced. Ideally, some biological experiments would confirm that B-pDCs are important.

Reviewer #1 (Public Review):

Summary:

C. elegans NHL-2 is a member of the conserved TRIM-NHL RNA binding protein family, with known functions in promoting small regulatory RNA function, including the conserved let-7 family microRNAs. Since NHL-2 promotes microRNA function, the authors seek to address if this function is due to direct binding of a mRNA target shared with the miRNA pathway. They successfully solve the crystal structure of NHL-2's NHL domain and discover residues Tyr935/Arg978 are required for RNA binding in vitro. In C. elegans, they establish that Tyr935/Arg978 are required for nhl-2 to promote let-7 microRNA function. Processing body (P body) size is increased in nhl-2 (Y935A R978A) and null mutants. The microRNA Argonautes, ALG-1 and ALG-2, also show increased binding to known let-7 mRNA targets in nhl-2 null mutants. Together these data suggest a lack of mRNA turnover in the absence of functional NHL-2. NHL-2 may function with CGH-1 and IFET-1 to promote let-7 miRISC function.

Strengths:

The authors successfully solve the structure of NHL-2's NHL domain. Although unable to crystalize it bound to RNA they are able to predict residues important for RNA binding based on charge, position and comparison with other known NHL domain structures crystalized with RNA. In vitro RNA binding assays confirm that Tyr935/Arg978 are required for RNA binding in vitro.

Weaknesses:

(1) In vivo, authors use a combination of established let-7 microRNA genetics and a 3' UTR reporter assay to establish that Tyr935/Arg978 are required for nhl-2 to promote let-7 microRNA function. However, they do not demonstrate that full length NHL-2 actually binds RNA directly in vivo in the Tyr935/Arg978 mutated background. While the presented genetic evidence suggests nhl(RBlf) acts much like the nhl-2 null, it is never demonstrated that full length NHL-2(RBlf) is actually RNA binding defective/dead in vivo. Yet several times in the text this is implied or stated. For example,<br /> o page 8, section title. "RNA binding is essential for NHL-2 function in heterochronic pathway"<br /> o page 9 - line 13-14. "Together, these data indicate that the RING and NHL domains are required for the normal function of NHL-2, but that the loss of RNA-binding activity has a more pronounced phenotype, suggesting that RNA-binding is critical for NHL-2 function."<br /> o page 11, line 3-4. "Together these experiments support the conclusion that... RNA binding is essential for its function"<br /> The language should be softened (e.g., page 8: "Residues required for RNA binding in vitro are required for NHL-2 function in heterochronic path") or additional experiments should be performed to support that NHL-2(RBlf) is in fact RNA binding defective/dead, like wild-type NHL-2 vs NHL-2(RBlf) RIP-qPCR for let-7 targets.

(2) Authors report that Processing body (P body) size is dependent on nhl-2 and the Tyr935/Arg978 residues. microRNA Argonautes, ALG-1 and ALG-2, also show increased binding to known let-7 mRNA targets in nhl-2 null mutants (unfortunately requirement of Tyr935/Arg978 is not tested). However total levels of these mRNAs are unchanged. Authors propose these data together support a role for nhl-2 in promoting microRNA target turnover. Unfortunately, it is unclear how increased P body size with no observed increase of microRNA target levels are to be resolved.

(3) The authors propose a model where NHL-2, CGH-1(DDX6) and IFET-1(eIF4E-transporter/4E-T) promote microRNA mediated translational repression and possibly turnover based on nhl-2-dependent IFET-1 interaction with ALG-1, cgh-1's synthetic interaction with both nhl-2 and ifet-1 to enhance let-7-mediated alae development, and conservation of known interactions between Dead Box helicases and eiF4A, which is supplemented by ALPHAFold modelling of IFET-1. The Boag lab previously characterized ifet-1 as a translational repressor required for germline P granule formation (Sengupta 2013 J Cell Sci). The role of NHL-2 RNA binding is unclear in this model as is any more molecular evidence of direct NHL-2, CGH-1 and IFET-1 interaction.

(4) In Figure 5, adult nhl-2(ok818) worms express the mCherry when the putative NHL-2 binding sites in the lin-28 3'UTR reporter are mutated. Couldn't this be interpreted as suggesting that the observed phenotype is nhl-2 independent? The authors mention this as an "interesting" observation in text, but I find it concerning. The authors should address this issue more directly. The reporter expression data needs to be quantified.

(5) I am frankly confused at the direction the manuscript takes in the Discussion section. The role of NHL-2 RNA binding, which has been the core of the paper, is seemingly disregarded and exchanged for what is mainly speculation about protein-protein level regulation with CGH-1 and IFET-1. This is all based on only a few pieces of data that do not include any analysis using the nhl-2(RBlf): nhl-2-dependent IFET-1 interaction with ALG-1, cgh-1's synthetic interaction with both nhl-2 and ifet-1 to enhance let-7-mediated alae development, and conservation of known interactions between Dead Box helicases and eiF4A, which is supplemented by ALPHAFold modelling of IFET-1. I'd strongly suggest reworking the text to better integrate IFET-1 or skip it and refocus the Discussion around the majority of the data characterizing NHL-2 RNA binding.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors provide structural analysis of the NHL domain for C. elegans NHL-2 and provide functional analysis of the NHL RNA binding domain. Their data support a model in which NHL-2 binding to mRNA targets through U rich motifs to promote miRISC regulation of translation and mRNA stability.

Strengths:

The authors present convincing data to describe the structure of the NHL-2 NHL domain along with functional analysis that supports an important role for two amino acids that are required for RNA binding activity. The function of these two amino acids were further studied through phenotypic assays to analyze their contribution to miRNA mediated regulation through the let-7 pathway. These data support an important role for RNA binding activity of NHL-2 in the regulation of miRNA dependent pathways. Genetic interactions support a role for the eIF4E binding protein IFET-1 in the miRISC activity.

Weaknesses:

The use of phenotypic assays to monitor let-7 pathway activity could be better explained so that the reader can more easily follow the significance of changes in alae formation or col-19::gfp expression.

The challenges of comparing expression levels using extrachromosomal arrays should be acknowledged.

The figure legends need to be revised to more clearly and accurately explain what is shown in the figures.

Reviewer #3 (Public Review):

Summary:

The manuscript by Saadat et al., examines the structure and function of the NHL-2 RNA binding domain in miRNA-mediated gene regulation in C. elegans. NHL-2 has previously been shown to function in miRNA and other smRNA pathways in C. elegans but its mechanism of action is unclear. The authors present a crystal structure that revealed candidate RNA binding residues. In vitro binding assays confirmed that these amino acids were required for RNA binding. The authors tested the importance of the RING and NHL domains in NHL-2 by mutating the endogenous gene using CRISPR and analyzing developmental and molecular effects in C. elegans. They concluded that the RNA binding domain of NHL-2 and co-factors, including CGH-1 and IFET-1, are important for the regulation of some miRNA targets in developing C. elegans.

Strengths:

The NHL-2 structural work and in vitro analyses of RNA binding activity are rigorous. The work is important for providing new structural information for an important post-transcriptional regulator.

Weaknesses:

The in vivo studies to better understand the role of NHL and several cofactors require further controls, replicates or better explanations of the methods and analyses in order to support the conclusions. In particular, protein levels of the mutant NHL-2 strains should be analyzed to rule out differences in expression contributing to the results; the reporter strategy would be improved by showing it is dependent on miRNA regulation, including an internal control and adding quantitative data; validation of similar levels of ALG-1 protein in the immunoprecipitation experiments would add confidence for the differences in levels of miRNA targets detected.

Reviewer #1 (Public Review):

Summary:

The "optorepressilator", an optically controllable genetic oscillator based on the famous E. coli 3-repressor (LacI, TetR, CI) oscillator "repressilator", was developed. An individual repressilator shows a stable oscillation of the protein levels with a relatively long period that extends a few doubling times of E. coli, but when many cells oscillate, their phases tend to desynchronize. The authors introduced an additional optically controllable promoter through a conformal change of CcaS protein and let it control how much additional CI is produced. By tightly controlling the leak from the added promoter, the authors successfully kept the original repressilator oscillation when the added promoter was not activated. In contrast, the oscillation was stopped by expressing the additional CI. Using this system, the authors showed that it is possible to synchronise the phase of the oscillation, especially when the activation happens as a short pulse at the right phase of the repressilator oscillation. The authors further show that, by changing the frequency of the short pulses, the repressilator was entrained to various ratios to the pulse period, and the author could reconstruct the so-called "Arnold tongues", the signature of entrainment of the nonlinear oscillator to externally added periodic perturbation. The behaviour is consistent with the simplified mathematical model that simulates the protein concentration using ordinary differential equations.

Strengths:

Optical control of the oscillation of the protein clock is a powerful and clean tool for studying the synthetic oscillator's response to perturbation in a well-controlled and tunable manner. The article utilizes the plate reader setup for population average measurements and the mother machine setup for single-cell measurements, and they compensate nicely to acquire necessary information.

Weaknesses:

The current paper added the optogenetically controlled perturbation to control the phase of oscillation and entrainment, but there are a few other works that add external perturbation to a collection of cells that individually oscillate to study phase shift and/or entrainment. The current paper lacks discussion about the pros and cons of the current system compared to previously analyzed systems.

Reviewer #2 (Public Review):

Summary:

In this manuscript by Cannarsa et. al., the authors describe the engineering of a light-entrainable synthetic biological oscillator in bacteria. It is based on an upgraded version of one of the first synthetic circuits to be constructed, the repressilator. The authors sought to make this oscillator entrainable by an external forcing signal, analogous to the way natural biological oscillators (like the circadian clock) are synchronized. They reasoned that an optogenetic system would provide a convenient and flexible means of manipulation. To this end, the authors exploited the CcaS-CcaA light-switchable system, which allows activation and deactivation of transcription by green and red light, respectively. They used this system to make the expression of one of the repressilator's transcription factors (lacI) light-controlled, from a construct separated from the main repressilator plasmid. This way, under red light the oscillator runs freely, but exposure to green light causes overexpression of the lacI, pushing the system into a specific state. Consequently, returning to red light will restore the oscillations from the same phase in all cells, effectively synchronizing the cell population.

After demonstrating the functionality of the basic concept, the authors combined modeling and experiments to show how periodic exposure to green light enables efficient entrainment, and how the frequency of the forcing signal affects the oscillatory behavior (detuning).

This work provides an important demonstration of engineering tunability into a foundational genetic circuit, expands the synthetic biology toolbox, and provides a platform to address critical questions about synchronization in biological oscillators. Due to the flexibility of the experimental system, it is also expected to provide a fertile ground for future testing of theoretical predictions regarding non-linear oscillators.

Strengths:

* The study provides a simple and elegant mechanism for the entertainment of a synthetic oscillator. The design relies on optogenetic proteins, which enable efficient experimentation compared to alternative approaches (like using chemical inducers). This way, a static culture (without microfluidics or change of growth media) can be easily exposed to flexible temporal sequences of the zeitgeber, and continuously measured through time.

* The study makes use of both plate-reader-based population-level readout and mother-machine single-cell measurements. Synchronization through entrainment is a single cell level phenomenon, but with a clear population-level manifestation. Thus, this experimental approach combination provides a strong validation to their system. At the same time, differences between the readout from the two systems have emerged, and provided a further opportunity for model refinement and testing.

* The authors correctly identified the main optimization goal, namely the effective leakiness of their construct even under red light. Then, they successfully overcame this issue using synthetic biology approaches.

* The work is supported by a simplified model of the repressilator, which provides a convenient analytical and numerical means to draw testable predictions. The model predictions are well aligned with the experimental evidence.

Weaknesses:

* Even after optimizing the expression level of the light-sensitive gene, the system is very sensitive, i.e., a very short exposure is sufficient to elicit the strongest entertainment. This limited dynamic range might hamper some model testing and future usage.

* As a result of the previous point, the system is entrained by transiently "breaking" the oscillator: each pulse of green light represents a Hopf bifurcation into a single attractor. it means that the system cannot oscillate in constant green light. In comparison, this is generally not the case for natural zeitgebers like light and temperature for the circadian rhythms. Extreme values might prevent oscillations (not necessarily due to breaking the core oscillator), but usually, free running is possible in a wide range of constant conditions. In some cases, the free-running period length will vary as a function of the constant value.

While the approach presented in this manuscript is valid, a comprehensive analysis of more subtle modes of repressilator entrainment could also be of value.

* The entire work makes use of a single intensity and single duration of the green pulse to force entrainment. While the model has clear predictions for how those modalities should affect entrainment, none of the experiments attempted to validate those predictions.

Reviewer #1 (Public Review):

The authors investigate the role of chirping in a species of weakly electric fish. They subject the fish to various scenarios and correlate the production of chirps with many different factors. They find major correlations between the background beat signals (continuously present during any social interactions) or some aspects of social and environmental conditions with the propensity to produce different types of chirps. By analyzing more specifically different aspects of these correlations they conclude that chirping patterns are related to navigation purposes and the need to localize the source of the beat signal (i.e. the location of the conspecific).

The study provides a wealth of interesting observations of behavior and much of this data constitutes a useful dataset to document the patterns of social interactions in these fish. Some data, in particular the high propensity to chirp in cluttered environments, raises interesting questions. Their main hypothesis is a useful addition to the debate on the function of these chirps and is worth considering and exploring further.

After the initial reviewers' comments, the authors performed a welcome revision of the way the results are presented. Overall the study has been improved by the revision. However, one piece of new data is perplexing to me. The new Figure 7 presents the results of a model analysis of the strength of the EI caused by a second fish to localize when the focal fish is chirping. From my understanding of this type of model, EOD frequency is not a parameter in the model since it evaluates the strength of the field at a given point in time. Therefore the only thing that matters is the phase relationship and strength of the EOD. Assuming that the second fish's EOD is kept constant and the phases relationship is also the same, the only difference during a chirp that could affect the result of the calculation is the potential decrease in EOD amplitude during the chirp. It is indeed logical that if the focal fish decreased its EOD amplitude the target fish's EOD becomes relatively stronger. Where things are harder to understand is why the different types of chirps (e.g. type 1 vs type 2) lead to the same increase in signal even though they are typically associated with different levels of amplitude modulations. Also, it is hard to imagine that a type 2 chirps that is barely associated with any decrease in EOD amplitude (0-10% maybe), would cause doubling of the EI strength. There might be something I don't understand but the authors should provide a lot more details on how this result is obtained and convince us that it makes sense.

Reviewer #2 (Public Review):

Studying Apteronotus leptorhynchus (the weakly electric brown ghost knifefish), the authors provide evidence that 'chirps' (brief modulations in the frequency and amplitude of the ongoing electric signal) function in active sensing (specifically homeoactive sensing) rather than communication. Chirping is a behavior that has been well studied, including numerous studies on the sensory coding of chirps and the neural mechanisms for chirp generation. Chirps are largely thought to function in communication behavior, so this alternative function is a very exciting possibility that could have a great impact on the field. The authors do provide convincing evidence that chirps may function in homeoactive sensing. However, their evidence arguing against a role for chirps in communication is not as strong, and fails to sufficiently consider the evidence from a large body of existing research. Ultimately, the manuscript presents very interesting data that is sure to stimulate discussion and follow-up studies, but it suffers from dismissing evidence in support of, or consistent with, a communicative function for chirps. The authors do acknowledge that chirps could function as both a communication and homeactive sensing signal, but it seems clear they wish to argue against the former and for the latter, and the evidence is not yet there to support this.

In the introduction, the authors state, "Since both chirps and positional parameters (such as size, orientation or motion) can only be detected as perturbations of the beat, and via the same electroreceptors, the inputs relaying both types of information are inevitably interfering." I disagree with this statement, which seems to be a key assumption. Both of these features certainly modulate the activity of electroreceptors, but that does not mean those modulations are ambiguous as to their source. You do not know whether the two types of modulations can be unambiguously decoded from electroreceptor afferent population activity.

My biggest issue with this manuscript is that it is much too strong in dismissing evidence that chirping correlates with context. In your behavioral observations, you found sex differences in chirping as well as differences between freely interacting and physically separated fish. Chirps tended to occur in close proximity to another fish. Your model of chirp variability found that environmental experience, social experience, and beat frequency (DF) are the most important factors explaining chirp variability. Are these not all considered behavioral or social context? Beat frequency (DF) in particular is heavily downplayed as being a part of "context" but it is a crucial part of the context, as it provides information about the identity of the fish you're interacting with. The authors show quite convincingly that the types of chirps produced do not vary with these contexts, but chirp rates do.

Further, in your playback experiments, fish responded differently to small vs. large DFs, males chirped more than females, type 2 chirps became more frequent throughout a playback, and rises tended to occur at the end of a playback. These are all examples of context-dependent behavior.

In the results, the authors state, "Overall, the majority of chirps were produced by male subjects, in comparable amounts regardless of environmental experience (resident, intruder or equal; Figure S1A,C), social status (dominant or subordinate; Figure S1B) or social experience (novel or experienced; Figure S1D)." This is not what is shown in Figure S1. S1A shows clear differences between resident vs. intruder males, S1B shows clear differences between dominant vs. subordinate males, and S1D shows clear differences between naïve and experienced males. The analysis shown in Figure 2 would seem to support this. Indeed, the authors state, "Overall, this analysis indicated that environmental and social experience, together with beat frequency (DF) are the most important factors explaining chirp variability."

The choice of chirp type varied widely between individuals but was relatively consistent within individuals across trials of the same experiment. The authors interpret this to mean that chirping does not vary with internal state, but is it not likely that the internal states of individuals are stable under stable conditions, and that individuals may differ in these internal states across the same conditions? Stable differences in communication signals between individuals are frequently interpreted as reflecting differences between those individuals in certain characteristics, which are being communicated by these signals.

I am not convinced of the conclusion drawn by the analysis of chirp transitions. The transition matrices show plenty of 1-2 and 2-1 transitions occurring. Further, the cross-correlation analysis only shows that chirp timing between individuals is not phase-locked at these small timescales. It is entirely possible that chirp rates are correlated between interacting individuals, even if their precise timing is not. Further, it is not clear to me how "transitions" were defined. The methods do not make this clear, and it is not clear to me how you can have zero chirp transitions between two individuals when those two individuals are both generating chirps throughout an interaction.

In the results, "Although all chirp types were used during aggressive interactions, these seemed to be rather less frequent in the immediate surround of the chirps (Figure 6A)." A lack of precise temporal correlation on short timescales does not mean there is no association between the two behaviors. An increased rate of chirping during aggression is still a correlation between the two behaviors, even if chirps and specific aggressive behaviors are not tightly time-locked.

In summary, it is simply too strong to say that chirping does not correlate with context, or to claim that there is convincing evidence arguing against a communication function of chirps. Importantly, however, this does not detract from your exciting and well-supported hypothesis that chirping functions in homeoactive sensing. A given EOD behavior could serve both communication and homeoactive sensing. I actually suspect this is quite common in electric fish (both gymnotiforms and mormyrids), and perhaps in other actively sensing species such as echolocating animals. The two are not mutually exclusive.

Reviewer #3 (Public Review):

Summary:

This important paper provides the best-to-date characterization of chirping in weakly electric fish using a large number of variables. These include environment (free vs divided fish, with or without clutter), breeding state, gender, intruder vs resident, social status, locomotion state and social and environmental experience, without and with playback experiments. It applies state-of-the-art methods for reducing the dimensionality of the data and finding patterns of correlation between different kinds of variables (factor analysis, K-means). The strength of the evidence, collated from a large number of trials with many controls, leads to the conclusion that the traditionally assumed communication function of chirps may be secondary to its role in environmental assessment and exploration that takes social context into account. Based on their extensive analyses, the authors suggest that chirps are mainly used as probes that help detect beats caused by other fish and as well as objects.

Strengths:

The work is based on completely novel recordings using interaction chambers. The amount of new data and associated analyses is simply staggering, and yet, well organized in presentation. The study further evaluates the electric field strength around a fish (via modelling with the boundary element method) and how its decay parallels the chirp rate, thereby relating the above variables to electric field geometry.

The main conclusions are that the lack of any significant behavioural correlates for chirping, and the lack of temporal patterning in chirp time series, cast doubt on a primary communication goal for most chirps. Rather, the key determinants of chirping are the difference frequency between two interacting conspecifics as well as individual subjects' environmental and social experience. The paper concludes that there is a lack of evidence for stereotyped temporal patterning of chirp time series, as well as of sender-receiver chirp transitions beyond the known increase in chirp frequency during an interaction.

These conclusions by themselves will be very useful to the field. They will also allow scientists working on other "communication" systems to perhaps reconsider and expand the goals of the probes used in those senses. A lot of data are summarized in this paper, with thorough referencing to past work.

The alternative hypotheses that arise from the work are that chirps are mainly used as environmental probes for better beat detection and processing and object localization, and in this sense are self-directed signals. This led to their prediction that environmental complexity ("clutter") should increase chirp rate, which is fact was revealed by their new experiments. The authors also argue that waveform EODs have less power across high spatial frequencies compared to pulse-type fish, with a resulting relatively impoverished power of resolution. Chirping in wave-type fish could temporarily compensate for the lower frequency resolution while still being able to resolve EOD perturbations with a good temporal definition (which pulse-type fish lack due to low pulse rates).

The authors also advance the interesting idea that the sinusoidal frequency modulations caused by chirps are the electric fish's solution to the minute (and undetectable by neural wetware) echo-delays available to it, due to the propagation of electric fields at the speed of light in water. The paper provides a number of experimental avenues to pursue in order to validate the non-communication role of chirps.

Weaknesses:

My main criticism is that the alternative putative role for chirps as probe signals that optimize beat detection could be better developed. The paper could be clearer as to what that means precisely, especially since beating - and therefore detection of some aspects of beating due to the proximity of a conspecific - most often precedes chirping. One meaning the authors suggest, tentatively, is that the chirps could enhance electrosensory responses to the beat, for example by causing beat phase shifts that remediate blind spots in the electric field of view.

A second criticism is that the study links the beat detection to underwater object localization. The paper does not significantly develop that line of thought given their data - the authors tread carefully here given the speculative aspect of this link. It is certainly possible that the image on the fish's body of an object in the environment will be slightly modified by introducing a chirp on the waveform, as this may enhance certain heterogeneities of the object in relation to its environment. The thrust of this argument derives mainly from the notion of Fourier analysis with pulse type fish EOD waveforms (see above, and radar theory more generally), where higher temporal frequencies in the beat waveform induced by the chirp will enable a better spatial resolution of objects. It remains to be seen whether experiments can show this to be significant.

Reviewer #1 (Public Review):

Summary:

The authors present tviblindi, a computational workflow for trajectory inference from molecular data at single-cell resolution. The method is based on (i) pseudo-time inference via expecting hitting time, (ii) sampling of random walks in a directed acyclic k-NN where edges are oriented away from a cell of origin w.r.t. the involved nodes' expected hitting times, and (iii) clustering of the random walks via persistent homology. An extended use case on mass cytometry data shows that tviblindi can be used elucidate the biology of T cell development.

Strengths:

- Overall, the paper is very well written and most (but not all, see below) steps of the tviblindi algorithm are explained well.

- The T cell biology use case is convincing (at least to me: I'm not an immunologist, only a bioinformatician with a strong interest in immunology).

Weaknesses:

- The main weakness of the paper is that a systematic comparison of tviblindi against other tools for trajectory inference (there are many) is entirely missing. Even though I really like the algorithmic approach underlying tviblindi, I would therefore not recommend to our wet-lab collaborators that they should use tviblindi to analyze their data. The only validation in the manuscript is the T cell development use case. Although this use case is convincing, it does not suffice for showing that the algorithms's results are systematically trustworthy and more meaningful (at least in some dimension) than trajectories inferred with one of the many existing methods.

- The authors' explanation of the random walk clustering via persistent homology in the Results (subsection "Real-time topological interactive clustering") is not detailed enough, essentially only concept dropping. What does "sparse regions" mean here and what does it mean that "persistent homology" is used? The authors should try to better describe this step such that the reader has a chance to get an intuition how the random walk clustering actually works. This is especially important because the selection of sparse regions is done interactively. Therefore, it's crucial that the users understand how this selection affects the results. For this, the authors must manage to provide a better intuition of the maths behind clustering of random walks via persistent homology.

- To motivate their work, the authors write in the introduction that "TI methods often use multiple steps of dimensionality reduction and/or clustering, inadvertently introducing bias. The choice of hyperparameters also fixes the a priori resolution in a way that is difficult to predict." They claim that tviblindi is better than the original methods because "analysis is performed in the original high-dimensional space, avoiding artifacts of dimensionality reduction." However, in the manuscript, tviblindi is tested only on mass cytometry data which has a much lower dimensionality than scRNA-seq data for which most existing trajectory inference methods are designed. Since tviblindi works on a k-NN graph representation of the input data, it is unclear if it could be run on scRNA-seq data without prior dimensionality reduction. For this, cell-cell distances would have to be computed in the original high-dimensional space, which is problematic due to the very high dimensionality of scRNA-seq data. Of course, the authors could explicitly reduce the scope of tviblindi to data of lower dimensionality, but this would have to be stated explicitly.

- Also tviblindi has at least one hyper-parameter, the number k used to construct the k-NN graphs (there are probably more hidden in the algorithm's subroutines). I did not find a systematic evaluation of the effect of this hyper-parameter.

Reviewer #2 (Public Review):

Summary: In Deconstructing Complexity: A Computational Topology Approach to Trajectory Inference in the Human Thymus with tviblindi, Stuchly et al. propose a new trajectory inference algorithm called tviblindi and a visualization algorithm called vaevictis for single-cell data. The paper utilizes novel and exciting ideas from computational topology coupled with random walk simulations to align single cells onto a continuum. The authors validate the utility of their approach largely using simulated data and establish known protein expression dynamics along CD4/CD8 T cell development in thymus using mass cytometry data. The authors also apply their method to track Treg development in single-cell RNA-sequencing data of human thymus.

The technical crux of the method is as follows: The authors provide an interactive tool to align single cells along a continuum axis. The method uses expected hitting time (given a user input start cell) to obtain a pseudotime alignment of cells. The pseudotime gives an orientation/direction for each cell, which is then used to simulate random walks. The random walks are then arranged/clustered based on the sparse region in the data they navigate using persistent homology.

Strengths:<br /> The notion of using persistent homology to group random walks to identify trajectories in the data is novel.<br /> The strength of the method lies in the implementation details that make computationally demanding ideas such as persistent homology more tractable for large scale single-cell data. This enables the authors to make the method more user friendly and interactive allowing real-time user query with the data.

Weaknesses:<br /> The interactive nature of the tool is also a weakness, by allowing for user bias leading to possible overfitting for a specific data.

The main weakness of the method is lack of benchmarking the method on real data and comparison to other methods. Trajectory inference is a very crowded field with many highly successful and widely used algorithms, the two most relevant ones (closest to this manuscript) are not only not benchmarked against, but also not sited. Including those that specifically use persistent homology to discover trajectories (Rizvi et.al. published Nat Biotech 2017). Including those that specifically implement the idea of simulating random walks to identify stable states in single-cell data (e.g. CellRank published in Lange et.al Nat Meth 2022), as well as many trajectory algorithms that take alternative approaches. The paper has much less benchmarking, demonstration on real data and comparison to the very many other previous trajectory algorithms published before it. Generally speaking, in a crowded field of previously published trajectory methods, I do not think this one approach will compete well against prior work (especially due to its inability to handle the noise typical in real world data (as was even demonstrated in the little bit of application to real world data provided).

Beyond general lack of benchmarking there are two issues that give me particular concern. As previously mentioned, the algorithm is highly susceptible to user bias and overfitting. The paper gives the example (Figure 4) of a trajectory which mistakenly shows that cells may pass from an apoptotic phase to a different developmental stage. To circumvent this mistake, the authors propose the interactive version of tviblindi that allows users to zoom in (increase resolution) and identify that there are in fact two trajectories in one. In this case, the authors show how the author can fix a mistake when the answer is known. However, the point of trajectory inference is to discover the unknown. With so much interactive options for the user to guide the result, the method is more user/bias driven than data-driven. So a rigorous and quantitative discussion of robustness of the method, as well as how to ensure data-driven inference and avoid over-fitting would be useful.

Second, the paper discusses the benefit of tviblindi operating in the original high dimensions of the data. This is perhaps adequate for mass cytometry data where there is less of an issue of dropouts and the proteins may be chosen to be large independent. But in the context of single-cell RNA-sequencing data, the massive undersampling of mRNA, as well as high degree of noise (e.g. ambient RNA), introduces very large degree of noise so that modeling data in the original high dimensions leads to methods being fit to the noise. Therefore ALL other methods for trajectory inference work in a lower dimension, for very good reason, otherwise one is learning noise rather than signal. It would be great to have a discussion on the feasibility of the method as is for such noisy data and provide users with guidance. We note that the example scRNA-seq data included in the paper is denoised using imputation, which will likely result in the trajectory inference being oversmoothed as well.

Reviewer #3 (Public Review):

Summary:<br /> Stuchly et al. proposed a single-cell trajectory inference tool, tviblindi, which was built on a sequential implementation of the k-nearest neighbor graph, random walk, persistent homology and clustering, and interactive visualization. The paper was organized around the detailed illustration of the usage and interpretation of results through the human thymus system.

Strengths:<br /> Overall, I found the paper and method to be practical and needed in the field. Especially the in-depth, step-by-step demonstration of the application of tviblindi in numerous T cell development trajectories and how to interpret and validate the findings can be a template for many basic science and disease-related studies. The videos are also very helpful in showcasing how the tool works.

Weaknesses:<br /> I only have a few minor suggestions that hopefully can make the paper easier to follow and the advantage of the method to be more convincing.<br /> (1) The "Computational method for the TI and interrogation - tviblindi" subsection under the Results is a little hard to follow without having a thorough understanding of the tviblindi algorithm procedures. I would suggest that the authors discuss the uniqueness and advantages of the tool after the detailed introduction of the method (moving it after the "Connectome - a fully automated pipeline".<br /> Also, considering it is a computational tool paper, inevitably, readers are curious about how it functions compared to other popular trajectory inference approaches. I did not find any formal discussion until almost the end of the supplementary note (even that is not cited anywhere in the main text). Authors may consider improving the summary of the advantages of tviblindi by incorporating concrete quantitative comparisons with other trajectory tools.<br /> (2) Regarding the discussion in Figure 4 the trajectory goes through the apoptotic stage and reconnects back to the canonical trajectory with counterintuitive directionality, it can be a checkpoint as authors interpret using their expert knowledge, or maybe a false discovery of the tool. Maybe authors can consider running other algorithms on those cells and see which tracks they identify and if the directionality matches with the tviblindi.<br /> (3) The paper mainly focused on mass cytometry data and had a brief discussion on scRNA-seq. Can the tool be applied to multimodality data such as CITE-seq data that have both protein markers and gene expression? Any suggestions if users want to adapt to scATAC-seq or other epigenomic data?

Reviewer #3 (Public Review):

Summary:

This work investigates the computational consequences of assemblies containing both excitatory and inhibitory neurons (E/I assembly) in a model with parameters constrained by experimental data from the telencephalic area Dp of zebrafish. The authors show how this precise E/I balance shapes the geometry of neuronal dynamics in comparison to unstructured networks and networks with more global inhibitory balance. Specifically, E/I assemblies lead to the activity being locally restricted onto manifolds - a dynamical structure in between high-dimensional representations in unstructured networks and discrete attractors in networks with global inhibitory balance. Furthermore, E/I assemblies lead to smoother representations of mixtures of stimuli while those stimuli can still be reliably classified, and allow for more robust learning of additional stimuli.

Strengths:

Since experimental studies do suggest that E/I balance is very precise and E/I assemblies exist, it is important to study the consequences of those connectivity structures on network dynamics. The authors convincingly show that E/I assemblies lead to different geometries of stimulus representation compared to unstructured networks and networks with global inhibition. This finding might open the door for future studies for exploring the functional advantage of these locally defined manifolds, and how other network properties allow to shape those manifolds.

The authors also make sure that their spiking model is well-constrained by experimental data from the zebrafish pDp. Both spontaneous and odor stimulus triggered spiking activity is within the range of experimental measurements. But the model is also general enough to be potentially applied to findings in other animal models and brain regions.

Weaknesses:

I find the point about pattern completion a bit confusing. In Fig. 3 the authors argue that only the Scaled I network can lead to pattern completion for morphed inputs since the output correlations are higher than the input correlations. For me, this sounds less like the network can perform pattern completion but it can nonlinearly increase the output correlations. Furthermore, in Suppl. Fig. 3 the authors show that activating half the assembly does lead to pattern completion in the sense that also non-activated assembly cells become highly active and that this pattern completion can be seen for Scaled I, Tuned E+I, and Tuned I networks. These two results seem a bit contradictory to me and require further clarification, and the authors might want to clarify how exactly they define pattern completion.

The authors argue that Tuned E+I networks have several advantages over Scaled I networks. While I agree with the authors that in some cases adding this localized E/I balance is beneficial, I believe that a more rigorous comparison between Tuned E+I networks and Scaled I networks is needed: quantification of variance (Fig. 4G) and angle distributions (Fig. 4H) should also be shown for the Scaled I network. Similarly in Fig. 5, what is the Mahalanobis distance for Scaled I networks and how well can the Scaled I network be classified compared to the Tuned E+I network? I suspect that the Scaled I network will actually be better at classifying odors compared to the E+I network. The authors might want to speculate about the benefit of having networks with both sources of inhibition (local and global) and hence being able to switch between locally defined manifolds and discrete attractor states.

At a few points in the manuscript, the authors use statements without actually providing evidence in terms of a Figure. Often the authors themselves acknowledge this, by adding the term "not shown" to the end of the sentence. I believe it will be helpful to the reader to be provided with figures or panels in support of the statements.

Reviewer #1 (Public Review):

Summary:

Meissner-Bernard et al present a biologically constrained model of telencephalic area of adult zebrafish, a homologous area to the piriform cortex, and argue for the role of precisely balanced memory networks in olfactory processing.

This is interesting as it can add to recent evidence on the presence of functional subnetworks in multiple sensory cortices. It is also important in deviating from traditional accounts of memory systems as attractor networks. Evidence for attractor networks has been found in some systems, like in the head direction circuits in the flies. However, the presence of attractor dynamics in other modalities, like sensory systems, and their role in computation has been more contentious. This work contributes to this active line of research in experimental and computational neuroscience by suggesting that, rather than being represented in attractor networks and persistent activity, olfactory memories might be coded by balanced excitation-inhibitory subnetworks.

Strengths:

The main strength of the work is in: (1) direct link to biological parameters and measurements, (2) good controls and quantification of the results, and (3) comparison across multiple models.

(1) The authors have done a good job of gathering the current experimental information to inform a biological-constrained spiking model of the telencephalic area of adult zebrafish. The results are compared to previous experimental measurements to choose the right regimes of operation.<br /> (2) Multiple quantification metrics and controls are used to support the main conclusions and to ensure that the key parameters are controlled for - e.g. when comparing across multiple models.<br /> (3) Four specific models (random, scaled I / attractor, and two variant of specific E-I networks - tuned I and tuned E+I) are compared with different metrics, helping to pinpoint which features emerge in which model.

Weaknesses:

Major problems with the work are: (1) mechanistic explanation of the results in specific E-I networks, (2) parameter exploration, and (3) the functional significance of the specific E-I model.

(1) The main problem with the paper is a lack of mechanistic analysis of the models. The models are treated like biological entities and only tested with different assays and metrics to describe their different features (e.g. different geometry of representation in Fig. 4). Given that all the key parameters of the models are known and can be changed (unlike biological networks), it is expected to provide a more analytical account of why specific networks show the reported results. For instance, what is the key mechanism for medium amplification in specific E/I network models (Fig. 3)? How does the specific geometry of representation/manifolds (in Fig. 4) emerge in terms of excitatory-inhibitory interactions, and what are the main mechanisms/parameters? Mechanistic account and analysis of these results are missing in the current version of the paper.

(2) The second major issue with the study is a lack of systematic exploration and analysis of the parameter space. Some parameters are biologically constrained, but not all the parameters. For instance, it is not clear what the justification for the choice of synaptic time scales are (with E synaptic time constants being larger than inhibition: tau_syn_i = 10 ms, tau_syn_E = 30 ms). How would the results change if they are varying these - and other unconstrained - parameters? It is important to show how the main results, especially the manifold localisation, would change by doing a systematic exploration of the key parameters and performing some sensitivity analysis. This would also help to see how robust the results are, which parameters are more important and which parameters are less relevant, and to shed light on the key mechanisms.

(3) It is not clear what the main functional advantage of the specific E-I network model is compared to random networks. In terms of activity, they show that specific E-I networks amplify the input more than random networks (Fig. 3). But when it comes to classification, the effect seems to be very small (Fig. 5c). Description of different geometry of representation and manifold localization in specific networks compared to random networks is good, but it is more of an illustration of different activity patterns than proving a functional benefit for the network. The reader is still left with the question of what major functional benefits (in terms of computational/biological processing) should be expected from these networks, if they are to be a good model for olfactory processing and learning.<br /> One possibility for instance might be that the tasks used here are too easy to reveal the main benefits of the specific models - and more complex tasks would be needed to assess the functional enhancement (e.g. more noisy conditions or more combination of odours). It would be good to show this more clearly - or at least discuss it in relation to computation and function.

Reviewer #2 (Public Review):

Summary:

The authors conducted a comparative analysis of four networks, varying in the presence of excitatory assemblies and the architecture of inhibitory cell assembly connectivity. They found that co-tuned E-I assemblies provide network stability and a continuous representation of input patterns (on locally constrained manifolds), contrasting with networks with global inhibition that result in attractor networks.

Strengths:

The findings presented in this paper are very interesting and cutting-edge. The manuscript effectively conveys the message and presents a creative way to represent high-dimensional inputs and network responses. Particularly, the result regarding the projection of input patterns onto local manifolds and continuous representation of input/memory is very Intriguing and novel. Both computational and experimental neuroscientists would find value in reading the paper.

Weaknesses:

Intuitively, classification (decodability) in discrete attractor networks is much better than in networks that have continuous representations. This could also be shown in Figure 5B, along with the performance of the random and tuned E-I networks. The latter networks have the advantage of providing network stability compared to the Scaled I network, but at the cost of reduced network salience and, therefore, reduced input decodability. The authors may consider designing a decoder to quantify and compare the classification performance of all four networks.

Networks featuring E/I assemblies could potentially represent multistable attractors by exploring the parameter space for their reciprocal connectivity and connectivity with the rest of the network. However, for co-tuned E-I networks, the scope for achieving multistability is relatively constrained compared to networks employing global or lateral inhibition between assemblies. It would be good if the authors mentioned this in the discussion. Also, the fact that reciprocal inhibition increases network stability has been shown before and should be cited in the statements addressing network stability (e.g., some of the citations in the manuscript, including Rost et al. 2018, Lagzi & Fairhall 2022, and Vogels et al. 2011 have shown this).

Providing raster plots of the pDp network for familiar and novel inputs would help with understanding the claims regarding continuous versus discrete representation of inputs, allowing readers to visualize the activity patterns of the four different networks. (similar to Figure 1B).

Reviewer #2 (Public Review):

Summary:

This manuscript reports interesting findings about the navigational behavior of mice. The authors have dissected this behavior in various components using a sophisticated behavioral maze and statistical analysis of the data. ​

Strengths:

The results are solid and they support the main conclusions, which will be of considerable value to many scientists.

Weaknesses:

Figure 1: In some trials the mice seem to be doing thigmotaxis, walking along the perimeter of the maze. This is perhaps due to the fear of the open arena. But, these paths along the perimeter would significantly influence all metrics of navigation, e.g. the distance or time to reward. Perhaps analysis can be done that treats such behavior separately and the factors it out from the paths that are away from the perimeter. 

Figure 1c: the color axis seems unusual. Red colors indicate less frequently visited regions (less than 25%) and white corresponds to more frequently visited places (>25%)? Why use such a binary measure instead of a graded map as commonly done?

Some figures use linear scale and others use logarithmic scale. Is there a scientific justification? For example, average latency is on a log scale and average speed is on a linear scale, but both quantify the same behavior. The y-axis in panel 1-I is much wider than the data. Is there a reason for this? Or can the authors zoom into the y-axis so that the reader can discern any pattern?<br /> <br /> 1F shows no significant reduction in distance to reward. Does that mean there is no improvement with experience and all the improvement in the latency is due to increasing running speed with experience?

Figure 3: The distance traveled was reduced by nearly 10-fold and speed increased by by about 3fold. So, the time to reach the reward should decrease by only 3 fold (t=d/v) but that too reduced by 10fold. How does one reconcile the 3fold difference between the expected and observed values? 

Figure 4: The reader is confused about the use of a binary color scheme here for the checking behavior: gray for a large amount of checking, and pink for small. But, there is a large ellipse that is gray and there are smaller circles that are also gray, but these two gray areas mean very different things as far as the reader can tell. Is that so? Why not show the entire graded colormap of checking probability instead of such a seemingly arbitrary binary depiction? 

Figure 4C: What would explain the large amount of checking behavior at the perimeter? Does that occur predominantly during thigmotaxis? 

Was there a correlation between the amount of time spent by the animals in a part of the maze and the amount of reward checking? Previous studies have shown that the two behaviors are often positively correlated, e.g. reference 20 in the manuscript.  How does this fit with the path integration hypothesis? 

"Scratches and odor trails were eliminated by washing and rotating the maze floor between trials." Can one eliminate scratches by just washing the maze floor? Rotation of the maze floor between trials can make these cues unreliable or variable but will not eliminate them. Ditto for odor cues.

"Possible odor gradient cues were eliminated by experiments where such gradients were prevented with vacuum fans (Fig. S6E)" What tests were done to ensure that these were *eliminated* versus just diminished? 

"Probe trials of fully trained mice resulted in trajectories and initial hole checking identical to that of regular trials thereby demonstrating that local odor cues are not essential for spatial learning." As far as the reader can tell, probe trials only eliminated the food odor cues but did not eliminate all other odors. If so, this conclusion can be modified accordingly. <br /> The interpretation of direction selectivity is a bit tricky. At different places in this manuscript, this is interpreted as a path integration signal that encodes goal location, including the Consync cells. However, studies show that (e.g. Acharya et al. 2016) direction selectivity in virtual reality is comparable to that during natural mazes, despite large differences in vestibular cues and spatial selectivity. How would one reconcile these observations with path integration interpretation? 

The manuscript would be improved if the speculations about place cells, grid cells, BTSP, etc. were pared down. I could easily imagine the outcome of these speculations to go the other way and some claims are not supported by data. "We note that the cited experiments were done with virtual movement constrained to 1D and in the presence of landmarks. It remains to be shown whether similar results are obtained in our unconstrained 2D maze and with only self-motion cues available." There are many studies that have measured the evolution of place cells in non-virtual mazes, look up papers from the 1990s. Reference 43 reports such results in a 2D virtual maze.

Reviewer #1 (Public Review):

Assessment:

This important work advances our understanding of navigation and path integration in mammals by using a clever behavioral paradigm. The paper provides compelling evidence that mice are able to create and use a cognitive map to find "short cuts" in an environment, using only the location of rewards relative to the point of entry to the environment and path integration, and need not rely on visual landmarks.

Summary:

The authors have designed a novel experimental apparatus called the 'Hidden Food Maze (HFM)' and a beautiful suite of behavioral experiments using this apparatus to investigate the interplay between allothetic and idiothetic cues in navigation. The results presented provide a clear demonstration of the central claim of the paper, namely that mice only need a fixed start location and path integration to develop a cognitive map. The experiments and analyses conducted to test the main claim of the paper -- that the animals have formed a cognitive map -- are conclusive. While I think the results are quite interesting and sound, one issue that needs to be addressed is the framing of how landmarks are used (or not), as discussed below, although I believe this will be a straightforward issue for the authors to address.

Strengths:

The 90-degree rotationally symmetric design and use of 4 distal landmarks and 4 quadrants with their corresponding rotationally equivalent locations (REL) lends itself to teasing apart the influence of path integration and landmark-based navigation in a clever way. The authors use a really complete set of experiments and associated controls to show that mice can use a start location and path integration to develop a cognitive map and generate shortcut routes to new locations.

Weaknesses:

I have two comments. The second comment is perhaps major and would require rephrasing multiple sentences/paragraphs throughout the paper.

(1) The data clearly indicate that in the hidden food maze (HFM) task mice did not use external visual "cue cards" to navigate, as this is clearly shown in the errors mice make when they start trials from a different start location when trained in the static entrance condition. The absence of visual landmark-guided behavior is indeed surprising, given the previous literature showing the use of distal landmarks to navigate and neural correlates of visual landmarks in hippocampal formation. While the authors briefly mention that the mice might not be using distal landmarks because of their pretraining procedure - I think it is worth highlighting this point (about the importance of landmark stability and citing relevant papers) and elaborating on it in greater detail. It is very likely that mice do not use the distal visual landmarks in this task because the pretraining of animals leads to them not identifying them as stable landmarks. For example, if they thought that each time they were introduced to the arena, it was "through the same door", then the landmarks would appear to be in arbitrary locations compared to the last time. In the same way, we as humans wouldn't use clouds or the location of people or other animate objects as trusted navigational beacons. In addition, the animals are introduced to the environment without any extra-maze landmarks that could help them resolve this ambiguity. Previous work (and what we see in our dome experiments) has shown that in environments with 'unreliable' landmarks, place cells are not controlled by landmarks - https://www.sciencedirect.com/science/article/pii/S0028390898000537, https://pubmed.ncbi.nlm.nih.gov/7891125/. This makes it likely that the absence of these distal visual landmarks when the animal first entered the maze ensured that the animal does not 'trust' these visual features as landmarks.

(2) I don't agree with the statement that 'Exogenous cues are not required for learning the food location'. There are many cues that the animal is likely using to help reduce errors in path integration. For example, the start location of the rat could act as a landmark/exogenous cue in the sense of partially correcting path integration errors. The maze has four identical entrances (90-degree rotationally symmetric). Despite this, it is entirely plausible that the animal can correct path integration errors by identifying the correct start entrance for a given trial, and indeed the distance/bearing to the others would also help triangulate one's location. Further, the overall arena geometry could help reduce PI error. For example, with a food source learned to be "near the middle" of the arena, the animal would surely not estimate the position to be near the far wall (and an interesting follow-on experiment would be to have two different-sized, but otherwise nearly identical arenas). As the rat travels away from the start location, small path integration errors are bound to accumulate, these errors could be at least partially corrected based on entrance and distal wall locations. If this process of periodically checking the location of the entrance to correct path integration errors is done every few seconds, path integration would be aided 'exogenously' to build a cognitive map. While the original claim of the paper still stands, i.e. mice can learn the location of a hidden food size when their starting point in the environment remains constant across trials. I would advise rewording portions of the paper, including the discussion throughout the paper that states claims such as "Exogenous cues are not required for learning the food location" to account for the possibility that the start and the overall arena geometry could be used as helpful exogenous cues to correct for path integration errors.

Reviewer #3 (Public Review):

Summary:

How is it that animals find learned food locations in their daily life? Do they use landmarks to home in on these learned locations or do they learn a path based on self-motion (turn left, take ten steps forward, turn right, etc.). This study carefully examines this question in a well-designed behavioral apparatus. A key finding is that to support the observed behavior in the hidden food arena, mice appear to not use the distal cues that are present in the environment for performing this task. Removal of such cues did not change the learning rate, for example. In a clever analysis of whether the resulting cognitive map based on self-motion cues could allow a mouse to take a shortcut, it was found that indeed they are. The work nicely shows the evolution of the rodent's learning of the task, and the role of active sensing in the targeted reduction of uncertainty of food location proximal to its expected location.

Strengths:

A convincing demonstration that mice can synthesize a cognitive map for the finding of a static reward using body frame-based cues. This shows that the uncertainty of the final target location is resolved by an active sensing process of probing holes proximal to the expected location. Showing that changing the position of entry into the arena rotates the anticipated location of the reward in a manner consistent with failure to use distal cues.

Weaknesses:

The task is low stakes, and thus the failure to use distal cues at most costs the animal a delay in finding the food; this delay is likely unimportant to the animal. Thus, it is unclear whether this result would generalize to a situation where the animal may be under some time pressure, urgency due to food (or water) restriction, or due to predatory threat. In such cases, the use of distal cues to make locating the reward robust to changing start locations may be more likely to be observed.

Reviewer #1 (Public Review):

The paper submitted by Yogesh and Keller explores the role of cholinergic input from the basal forebrain (BF) in the mouse primary visual cortex (V1). The study aims to understand the signals conveyed by BF cholinergic axons in the visual cortex, their impact on neurons in different cortical layers, and their computational significance in cortical visual processing. The authors employed two-photon calcium imaging to directly monitor cholinergic input from BF axons expressing GCaMP6 in mice running through a virtual corridor, revealing a strong correlation between BF axonal activity and locomotion. This persistent activation during locomotion suggests that BF input provides a binary locomotion state signal. To elucidate the impact of cholinergic input on cortical activity, the authors conducted optogenetic and chemogenetic manipulations, with a specific focus on L2/3 and L5 neurons. They found that cholinergic input modulates the responses of L5 neurons to visual stimuli and visuomotor mismatch, while not significantly affecting L2/3 neurons. Moreover, the study demonstrates that BF cholinergic input leads to decorrelation in the activity patterns of L2/3 and L5 neurons.

This topic has garnered significant attention in the field, drawing the interest of many researchers actively investigating the role of BF cholinergic input in cortical activity and sensory processing. The experiments and analyses were thoughtfully designed and conducted with rigorous standards, providing evidence of layer-specific differences in the impact of cholinergic input on neuronal responses to bottom-up (visual stimuli) and top-down inputs (visuomotor mismatch).

Reviewer #2 (Public Review):

The manuscript investigates the function of basal forebrain cholinergic axons in mouse primary visual cortex (V1) during locomotion using two-photon calcium imaging in head-fixed mice. Cholinergic modulation has previously been proposed to mediate the effects of locomotion on V1 responses. The manuscript concludes that the activity of basal forebrain cholinergic axons in visual cortex provides a signal which is more correlated with binary locomotion state than locomotion velocity of the animal and finds no evidence for modulation of cholinergic axons by locomotion velocity. Cholinergic axons did not seem to respond to grating stimuli or visuomotor prediction error. Optogenetic stimulation of these axons increased the amplitude of responses to visual stimuli and decreased the response latency of layer 5 excitatory neurons, but not layer 2/3 neurons. Moreover, optogenetic or chemogenetic stimulation of cholinergic inputs reduced pairwise correlation of neuronal responses. These results provide insight into the role of cholinergic modulation to visual cortex and demonstrate that it affects different layers of visual cortex in a distinct manner. The experiments are well executed and the data appear to be of high quality. However, further analyses may be required to fully support some of the study's conclusions. Specifically, the analyses of the effects of locomotion and stimulation of cholinergic inputs present grand averages of responses across all neurons, and therefore may mask heterogeneity across layer 2/3 and layer 5 neurons.

Reviewer #2 (Public Review):

Summary:

The current work describes a set of behavioral tasks to explore individual differences in the preferred perceptual and motor rhythms. Results show a consistent individual preference for a given perceptual and motor frequency across tasks and, while these were correlated, the latter is slower than the former one. Additionally, the adaptation accuracy to rate changes is proportional to the amount of rate variation and, crucially, the amount of adaptation decreases with age.

Strengths:

Experiments are carefully designed to measure individual preferred motor and perceptual tempo. Furthermore, the experimental design is validated by testing the consistency across tasks and test-retest, what makes the introduced paradigm a useful tool for future research.<br /> The obtained data is rigorously analyzed using a diverse set of tools, each adapted to the specificities across the different research questions and tasks.<br /> This study identifies several relevant behavioral features: (i) each individual shows a preferred and reliable motor and perceptual tempo and, while both are related, the motor is consistently slower than the pure perceptual one; (ii) the presence of hysteresis in the adaptation to rate variations; and (iii) the decrement of this adaptation with age. All these observations are valuable for the auditory-motor integration field of research, and they could potentially inform existing biophysical models to increase their descriptive power.

Weaknesses:

To get a better understanding of the mechanisms underlying the behavioral observations, it would have been useful to compare the observed pattern of results with simulations done with existing biophysical models. However, this point is addressed if the current study is read along with this other publication of the same research group: Kaya, E., & Henry, M. J. (2024, February 5). Modeling rhythm perception and temporal adaptation: top-down influences on a gradually decaying oscillator. https://doi.org/10.31234/osf.io/q9uvr

Reviewer #2 (Public Review):

This manuscript asks how different forms of selection affect the patterns of genetic diversity in microbial populations. One popular metric used to infer signatures of selection is dN/dS, the ratio of nonsynonymous to synonymous distances between two genomes. Previous observations across many bacterial species have found dN/dS decreases with dS, which is a proxy for the divergence time. The most common interpretation of this pattern was proposed by Rocha et al. (2006), who suggested the excess in nonsynonymous mutations on short divergence times represent transient deleterious mutations that have not yet been purged by selection.

In this study, the authors propose an alternative model based on the population structure of human gut bacteria, in which dN is dominated by selective sweeps of SNPs that revert previous mutations within local populations. The authors argue that contrary to standard population genetics models, which are based on the population dynamics of large eukaryotes, the large populations in the human gut mean that reversions may be quite common and may have a large impact on evolutionary dynamics. They show that such a model can fit the decrease of dN/dS in time at least as well as the purifying selection model.

Strengths

The main strength of the manuscript is to show that adaptive sweeps in gut microbial populations can lead to small dN/dS. While previous work has shown that using dN/dS to infer the strength of selection within a population is problematic (see Kryazhimskiy and Plotkin, 2008, cited in the paper) the particular mechanism proposed by the authors is new to my knowledge. In addition, despite the known caveats, dN/dS values are still routinely reported in studies of microbial evolution, and so their interpretation should be of considerable interest to the community.

The authors provide compelling justification for the importance of adaptive reversions and make a good case that these need to be carefully considered by future studies of microbial evolution. The authors show that their model can fit the data as well as the standard model based on purifying selection and the parameters they infer appear to be plausible given known data. More generally, I found the discussion on the implications of traditional population genetics models in the context of human gut bacteria to be a valuable contribution of the paper.

Weaknesses

The authors argue that the purifying selection model would predict a gradual loss in fitness via Muller's ratchet. This is true if recombination is ignored, but this assumption is inconsistent with the data from Garud, et al. (2019) cited in the manuscript, who showed a significant linkage decrease in the bacteria also used in this study.

I also found that the data analysis part of the paper added little new to what was previously known. Most of the data comes directly from the Garud et al. study and the analysis is very similar as well. Even if other appropriate data may not currently be available, I feel that more could be done to test specific predictions of the model with more careful analysis.

Finally, I found the description of the underlying assumptions of the model and the theoretical results difficult to understand. I could not, for example, relate the fitting parameters nloci and Tadapt to the simulations after reading the main text and the supplement. In addition, it was not clear to me if simulations involved actual hosts or how the changes in selection coefficients for different sites was implemented. Note that these are not simply issues of exposition since the specific implementation of the model could conceivably lead to different results. For example, if the environmental change is due to the colonization of a different host, it would presumably affect the selection coefficients at many sites at once and lead to clonal interference. Related to this point, it was also not clear that the weak mutation strong selection assumption is consistent with the microscopic parameters of the model. The authors also mention that "superspreading" may somehow make a difference to the probability of maintaining the least loaded class in the purifying selection model, but what they mean by this was not adequately explained.

Reviewer #1 (Public Review):

This study makes a substantial contribution to our understanding of the molecular evolutionary dynamics of microbial genomes by proposing a model that incorporates relatively frequent adaptive reversion mutations. In many ways, this makes sense from my own experience with evolutionary genomic data of microbes, where reversions are surprisingly familiar as evidence of the immense power of selection in large populations.

One criticism is the reliance on one major data set of B. fragilis to test fits of these models, but this is relatively minor in my opinion and can be caveated by discussion of other relevant datasets for parallel investigation.

Another point is that this problem isn't as new as the manuscript indicates, see for example https://journals.asm.org/doi/10.1128/aem.02002-20.

Nonetheless, the paper succeeds by both developing theory and offering concrete parameters to illustrate the magnitudes of the problems that distinguish competing ideas, for example, the risk of mutational load posed in the absence of frequent back mutation.

Reviewer #3 (Public Review):

The diversity of bacterial species in the human gut microbiome is widely known, but the extensive diversity within each species is far less appreciated. Strains found in individuals on opposite sides of the globe can differ by as little as handfuls of mutations, while strains found in an individual's gut, or in the same household, might have a common ancestor tens of thousands of years ago. What are the evolutionary, ecological, and transmission dynamics that established and maintain this diversity?

The time, T, since the common ancestor of two strains, can be directly inferred by comparing their core genomes and finding the fraction of synonymous (non-amino acid changing) sites at which they differ: dS. With the per-site per-generation mutation rate, μ, and the mean generation times roughly known, this directly yields T (albeit with substantial uncertainty of the generation time.) A traditional way to probe the extent to which selection plays a role is to study pairs of strains and compare the fraction of non-synonymous (amino acid or stop-codon changing) sites, dN, at which the strains differ with their dS. Small dN/dS, as found between distantly related strains, is attributed to purifying selection against deleterious mutations dominating over mutations that have driven adaptive evolution. Large dN/dS as found in laboratory evolution experiments, is caused by beneficial mutations that quickly arise in large bacterial populations, and, with substantial selective advantages, per generation, can rise to high abundance fast enough that very few synonymous mutations arise in the lineages that take over the population.

A number of studies (including by Lieberman's group) have analyzed large numbers of strains of various dominant human gut species and studied how dN/dS varies. Although between closely related strains the variations are large -- often much larger than attributable to just statistical variations -- a systematic trend from dN/dS around unity or larger for close relatives to dN/dS ~ 0.1 for more distant relatives has been found in enough species that it is natural to conjecture a general explanation.<br /> The conventional explanation is that, for close relatives, the effects of selection over the time since they diverged has not yet purged weakly deleterious mutations that arose by chance -- roughly mutations with sT<1 -- while since the common ancestor of more distantly related strains, there is plenty of time for most of those that arose to have been purged.

Torrillo and Lieberman have carried out an in-depth -- sophisticated and quantitative -- analysis of models of some of the evolutionary processes that shape the dependence of dN/dS on dS -- and hence on their divergence time, T. They first review the purifying selection model and show that -- even ignoring its inability to explain dN/dS > 1 for many closely related pairs -- the model has major problems explaining the crossover from dN/dS somewhat less than unity to much smaller values as dS goes through -- on a logarithmic scale -- the 10^-4 range. The first problem, already seen in the infinite-population-size deterministic model, is that a very large fraction of non-synonymous mutations would have to have deleterious s's in the 10^-5 per generation range to fit the data (and a small fraction effectively neutral). As the s's are naturally expected (at least in the absence of quantitative analysis to the contrary) to be spread out over a wide range on a logarithmic scale of s, this seems implausible. But the authors go further and analyze the effects of fluctuations that occur even in the very large populations: ~ >10^12 bacteria per species in one gut, and 10^10 human guts globally. They show that Muller's ratchet -- the gradual accumulation of weakly deleterious mutations that are not purged by selection - leads to a mutational meltdown with the parameters needed to fit the purifying selection model. In particular, with N_e the "effective population size" that roughly parametrizes the magnitude of stochastic birth-death and transition fluctuations, and U the total mutation rate to such deleterious mutations this occurs for U/s > log(sN_e) which they show would obtain with the fitted parameters.

Torrillo and Lieberman promise an alternate model: that there are a modest number of "loci" at which conditionally beneficial mutations can occur that are beneficial in some individual guts (or other environmental conditions) at some times, but deleterious in other (or the same) gut at other times. With the ancestors of a pair of strains having passed through one too many individuals and transmissions, it is possible for a beneficial mutation to occur and rise in the population, only later to be reverted by the beneficial inverse mutation. With tens of loci at which this can occur, they show that this process could explain the drop of dN/dS from short times -- in which very few such mutations have occurred -- to very long times by which most have flipped back and forth so that a random pair of strains will have the same nucleotide at such sites with 50% probability. Their qualitative analysis of a minimally simple model of this process shows that the bacterial populations are plenty big enough for such specific mutations to occur many times in each individual's gut, and with modest beneficials, to takeover. With a few of these conditionally beneficial mutations or reversions occurring during an individuals lifetime, they get a reasonably quantitative agreement with the dN/dS vs dS data with very few parameters. A key assumption of their model is that genetically exact reversion mutations are far more likely to takeover a gut population -- and spread -- than compensatory mutations which have a similar phenotypic-reversion effect: a mutation that is reverted does not show up in dN, while one that is compensated by another shows up as a two-mutation difference after the environment has changed twice.

Strengths:

The quantitative arguments made against the conventional purifying selection model are highly compelling, especially the consideration of multiple aspects that are usually ignored, including -- crucially -- how Muller's ratchet arises and depends on the realistic and needed-to-fit parameters; the effects of bottlenecks in transmission and the possibility that purifying selection mainly occurs then; and complications of the model of a single deleterious s, to include a distribution of selective disadvantages. Generally, the author's approach of focusing on the simplest models with as few as possible parameters (some roughly known), and then adding in various effects one-by-one, is outstanding and, in being used to analyze environmental microbial data, exceptional.

The reversion model the authors propose and study is a simple general one and they again explore carefully various aspects of it -- including dynamics within and between hosts -- and the consequent qualitative and quantitative effects. Again, the quantitive analysis of almost all aspects is exemplary. Although it is hard to make a compelling guess of the number of loci that are subject to alternating selection on the needed time-scales (years to centuries) they make a reasonable argument for a lower bound in terms of the number of known invertible promoters (that can genetically switch gene expression on and off).

Weaknesses:

The primary weakness of this paper is one that the author's are completely open about: the assumption that, collectively, any of possibly-many compensatory mutations that could phenotypically revert an earlier mutation, are less likely to arise and takeover local populations than the exact specific reversion mutation. While detailed analysis of this is, reasonably enough, beyond the scope of the present paper, more discussion of this issue would add substantially to this work. Quantitatively, the problem is that even a modest number of compensatory mutations occurring as the environmental pressures change could lead to enough accumulation of non-synonymous mutations that they could cause dN/dS to stay large -- easily >1 -- to much larger dS than is observed. If, say, the appropriate locus is a gene, the number of combinations of mutations that are better in each environment would play a role in how large dN would saturate to in the steady state (1/2 of n_loci in the author's model). It is possible that clonal interference between compensatory and reversion mutations would result in the mutations with the largest s -- eg, as mentioned, reversion of a stop codon -- being much more likely to take over, and this could limit the typical number of differences between quite well-diverged strains. However, the reversion and subsequent re-reversion would have to both beat out other possible compensatory mutations -- naively less likely. I recommend that a few sentences in the Discussion be added on this important issue along with comments on the more general puzzle -- at least to this reader! -- as to why there appear to be so little adaptive genetic changes in core genomes on time scales of human lifetimes and civilization.

An important feature of gut bacterial evolution that is now being intensely studied is only mentioned in passing at the end of this paper: horizontal transfer and recombination of core genetic material. As this tends to bring in many more mutations overall than occur in regions of a pair of genomes with asexual ancestry, the effects cannot be neglected. To what extent can this give rise to a similar dependence of dN/dS on dS as seen in the data? Of course, such a picture begs the question as to what sets the low dN/dS of segments that are recombined --- often from genetic distances comparable to the diameter of the species.

Reviewer #1 (Public Review):

The impact of this paper is that it shows conclusively the bone defects caused by ninein depletion, albeit transient defects, which has been indirectly deduced in past studies. The paper is largely descriptive including the cytoskeletal analysis of osteoclasts thus it remains unclear how ninein reduction causes bone defects and why this defect is transient. The Discussion includes several unfounded potential mechanisms that really need to be thoroughly analyzed to gain a mechanistic understanding of the bone defects in ninein-null mice.

Other points:<br /> Data showing normal osteoblasts in ninein-null mice was qualitative and requires further in-depth analysis and quantification of osteoblast and osteocyte presence and activity in ninein del/del mice to strengthen the study.

In ninein knock-out mice, reduced TRAP+ve multinuclear cells were observed (Figure 6A and 6B). However, the magnitude of difference (about 5% decrease in multinucleated cells) is not consistent with the skeletal deformities reported in Figures 2-4, potentially suggesting the contribution of additional mechanisms.

The fusion assay in Figure 6C needs further clarification. How was the syncytia perimeter defined to measure cell surface? The x-axis suggests that there are syncytia that contain up to 160 nuclei at day 3. How were the nuclei differentially stained and quantified?

Some text needs clarification. For instance, "On days 3 and 4, we found only about half as many large syncytia in cultures from ninein-deleted mice, compared to controls, but on day 5 large syncytia lacking ninein exceeded 90% of control levels. Altogether, this suggests that fusion deficiencies are a transient phenomenon in in vitro-induced adult osteoclasts. On later days of culture, fusion efficiency started to diminish." What is the definition of "large syncytia"? Is the fusion index increase by day 5 diminished in later days? A graph of the syncytia size/ nuclei number or fusion index in the above-mentioned days will be helpful.

Assessment of resorption was qualitative in Figure 6E and since the fusion deficiencies are transient, quantification of a corresponding resorption activity is needed. This should be described in the Materials and Methods section.

Further experiments are needed to show connections between reduced centrosome clustering and reduced osteoclast formation as there is no evidence to date that suggest centrosome clustering is required for cell fusion. Multi-color live imaging and dynamic analysis can be used to determine if the ninein deficient cells show defective movement/migration/ fusion dynamics.

Quantification of the % of multinucleated osteoclasts that contain clustered and dispersed centrosomes is needed.

Reviewer #2 (Public Review):

The paper by Gilbert et al. is well-written in a detailed format and the authors are candid in their data interpretation by acknowledging that the described ninein bone defects are mild, transient, and do not lead to major long-lasting defects in adulthood.

The main strength of the study is presenting a novel link between a centrosomal protein and osteoclasts in the mouse. However, the majority of the work is dedicated to describing the premature ossification phenotype and less attention is paid to how a centrosomal protein affects osteoclast proliferation, survival, and/or differentiation into mature osteoclasts.

Based on the decrease in the number of osteoclasts (Fig 5E, G, and also per coverslip after 2 days in culture), the authors suggest that the loss of ninein impacts osteoclast proliferation. First, proliferation can be directly quantified using Ki67 staining or EdU incorporation. Second, other interpretations are also plausible and can also be experimentally tested. These include less adhesion and attachment of the mutants to the coverslips, but perhaps more relevant in vivo is cell death of the ninein mutant osteoclasts. It has been established that the loss of centrosome function activates p53-dependent cell death and osteoclasts might be a vulnerable cell population. Quantifying p53 immunoreactivity and/or cell death in osteoclasts might help clarify the phenotype of osteoclast reduction.

Reviewer #3 (Public Review):

Ninein is a centrosome protein that has been implicated in microtubule anchorage and centrosome cohesion. Mutations in the human ninein gene have been linked to Seckel syndrome and a rare form of skeletal dysplasia. However, the role of ninein in skeletal development remains unknown. Here, we describe a ninein knockout mouse with advanced endochondral ossification during embryonic development. Although the long bones maintain a regular size, the absence of ninein delays the formation of the bone marrow cavity in the prenatal tibia. Likewise, intramembranous ossification in the skull is more developed, leading to a premature closure of the interfrontal suture. We demonstrate that ninein is strongly expressed in osteoclasts of control mice and that its absence reduces the fusion of precursor cells into syncytial osteoclasts. As a consequence, ninein-deficient osteoclasts have a reduced capacity to resorb bone. At the cellular level, the absence of ninein interferes with<br /> centrosomal microtubule organization, reduces centrosome cohesion, and provokes the loss of centrosome clustering in multinucleated mature osteoclasts. We propose that centrosomal ninein is important for osteoclast fusion, to enable a functional balance between bone-forming osteoblasts and bone-resorbing osteoclasts during skeletal development.

Reviewer #1 (Public Review):

Summary:

Previous work in humans and non-human animals suggests that during offline periods following learning, the brain replays newly acquired information in a sequential manner. The present study uses a MEG-based decoding approach to investigate the nature of replay/reactivation during a cued recall task directly following a learning session, where human participants are trained on a new sequence of 10 visual images embedded in a graph structure. During retrieval, participants are then cued with two items from the learned sequence, and neural evidence is obtained for the simultaneous or sequential reactivation of future sequence items. The authors find evidence for both sequential and clustered (i.e., simultaneous) reactivation. Replicating previous work, low-performing participants tend to show sequential, temporally segregated reactivation of future items, whereas high-performing participants show more clustered reactivation. Adding to previous work, the authors show that an image's reactivation strength varies depending on its proximity to the retrieval cue within the graph structure.

Strengths:

As the authors point out, work on memory reactivation has largely been limited to the retrieval of single associations. Given the sequential nature of our real-life experiences, there is clearly value in extending this work to structured, sequential information. State-of-the-art decoding approaches for MEG are used to characterize the strength and timing of item reactivation. The manuscript is very well written with helpful and informative figures in the main sections. The task includes an extensive localizer with 50 repetitions per image, allowing for stable training of the decoders and the inclusion of several sanity checks demonstrating that on-screen items can be decoded with high accuracy.

Weaknesses:

Of major concern, the experiment is not optimally designed for analysis of the retrieval task phase, where only 4 min of recording time and a single presentation of each cue item are available for the analyses of sequential and non-sequential reactivation. In their revision, the authors include data from the learning blocks in their analysis. These blocks follow the same trial structure as the retrieval task, and apart from adding more data points could also reveal a possible shift from sequential to clustered reactivation as learning of the graph structure progresses. The new analyses are not entirely conclusive, maybe given the variability in the number of learning blocks that participants require to reach the criterion. In principle, they suggest that reactivation strength increases from learning (pre-rest) to final retrieval (post-rest).

On a more conceptual note, the main narrative of the manuscript implies that sequential and clustered reactivation are mutually exclusive, such that a single participant would show either one or the other type. With the analytic methods used here, however, it seems possible to observe both types of reactivation. For example, the observation that mean reactivation strength (across the entire trial, or in a given time window of interest) varies with graph distance does not exclude the possibility that this reactivation is also sequential. In fact, the approach of defining one peak time window of reactivation may bias towards simultaneous, graded reactivation. It would be helpful if the authors could clarify this conceptual point. A strong claim that the two types of reactivation are mutually exclusive would need to be substantiated by further evidence, for instance, a suitable metric contrasting "sequenceness" vs "clusteredness".

On the same point, the non-sequential reactivation analyses use a time window of peak decodability that is determined based on the average reactivation of all future items, irrespective of graph distance. In a sequential forward cascade of reactivations, it could be assumed that the reactivation of near items would peak earlier than the reactivation of far items. In the revised manuscript, the authors now show the "raw" timecourses of item decodability at different graph distances, clearly demonstrating their peak reactivation times, which show convincingly that reactivation for near and far items occurs at very similar time points. The question that remains, therefore, is whether the method of pre-selecting a time window of interest described above could exert a bias towards finding clustered reactivation.

Reviewer #2 (Public Review):

Summary:

The authors investigate replay (defined as sequential reactivation) and clustered reactivation during retrieval of an abstract cognitive map. Replay and clustered reactivation were analysed based on MEG recordings combined with a decoding approach. While the authors state to find evidence for both, replay and clustered reactivation during retrieval, replay was exclusively present in low performers. Further, the authors show that reactivation strength declined with an increasing graph distance.

Strengths:

The paper raises interesting research questions, i.e., replay vs. clustered reactivation and how that supports retrieval of cognitive maps. The paper is well written, well structured and easy to follow. The methodological approach is convincing and definitely suited to address the proposed research questions.

The paper is a great combination between replicating previous findings (Wimmer et al. 2020) with a new experimental approach but at the same time presenting novel evidence (reactivation strength declines as a function of graph distance).

What I also want to positively highlight is their general transparency. For example, they pre-registered this study but with a focus on a different part of the data and outlined this explicitly in the paper.

The paper has very interesting findings. However, there are some shortcomings, especially in the experimental design. These are shortly outlined below but are also openly and in detail discussed by the authors.

Weaknesses:

The individual findings are interesting. However, due to some shortcomings in the experimental design they cannot be profoundly related to each other. For example, the authors show that replay is present in low but not in high performers with the assumption that high performers tend to simultaneously reactivate items. But then, the authors do not investigate clustered reactivation (= simultaneous reactivation) as a function of performance due to a low number of retrieval trials and ceiling performance in most participants.<br /> As a consequence of the experimental design, some analyses are underpowered (very low number of trials, n = ~10, and for some analyses, very low number of participants, n = 14).

Reviewer #4 (Public Review):

Summary:

Although previous research suggested that noradrenergic glutamatergic signaling could influence respiratory control, the work performed by Chang and colleagues reveals that excitatory (specifically Vglut2) neurons is dynamically and widely expressed throughout the central noradrenergic system, but it is not significantly crucial to change baseline breathing as well the hypercapnia and hypoxia ventilatory responses. The central point that will make a significant change in the field is how NA-glutamate transmission may influence breathing control and the dysfunction of NA neurons in respiratory disorders.

Strengths:

There are several strengths such as the comprehensive analysis of Vglut1, Vglut2, and Vglut3 expression in the central noradrenergic system and the combined measurements of breathing parameters in conscious unrestrained mice.

Other considerations :

These results strongly suggest that glutamate may not be necessary for modulating breathing under normal conditions or even when faced with high levels of carbon dioxide (hypercapnia) or low oxygen levels (hypoxia). This finding is unexpected, considering many studies have underscored glutamate's vital role in respiratory regulation, more so than catecholamines. This leads us to question the significance of catecholamines in controlling respiration. Moreover, if glutamate is not essential for this function, we need to explore its role in other physiological processes such as sympathetic nerve activity (SNA), thermoregulation, and sensory physiology.

Reviewer #1 (Public Review):

Summary:

Chang et al. provide glutamate co-expression profiles in the central noradrenergic system and test the requirement of Vglut2-based glutamatergic release in respiratory and metabolic activity under physiologically relevant gas challenges. Their experiments show that conditional deletion of Vglut2 in NA neurons does not impact steady-state breathing or metabolic activity in room air, hypercapnia, or hypoxia. Their observations challenge the importance of glutamatergic signaling from Vglut2 expressing NA neurons in normal respiratory homeostasis in conscious adult mice.

Strengths:

The comprehensive Vglut1, Vglut2, and Vglut3 co-expression profiles in the central noradrenergic system and the combined measurements of breathing and oxygen consumption are two major strengths of this study. Observations from these experiments provide previously undescribed insights into (1) expression patterns for subtypes of the vesicular glutamate transporter protein in the noradrenergic system and (2) the dispensable nature of Vglut2-dependent glutamate signaling from noradrenergic neurons to breathing responses to physiologically relevant gas challenges in adult conscious mice.

Weaknesses:

Although the cellular expression profiles for the vesicular glutamate transporters are provided, the study does not document that glutamatergic-based signaling originating from noradrenergic neurons is evident at the cellular level under normal, hypoxic, and/or hypercapnic conditions. The authors effectively recognize this issue and appropriately discuss their findings in this context.

Reviewer #2 (Public Review):

The authors characterized the recombinase-based cumulative fate maps for vesicular glutamate transporters (Vglut1, Vglut2 and Vglut3) expression and compared those maps to their real-time expression profiles in central NA neurons by RNA in situ hybridization in adult mice. Authors have revealed a new and intriguing expression pattern for Vglut2, along with an entirely uncharted co-expression domain for Vglut3 within central noradrenergic neurons. Interestingly, and in contrast to previous studies, the authors demonstrated that glutamatergic signaling in central noradrenergic neurons does not exert any influence on breathing and metabolic control either under normoxic/normocapnic conditions or after chemoreflex stimulation. Also, they showed for the first-time the Vglut3-expressing NA population in C2/A2 nuclei. In addition, they were also able to demonstrate Vglut2 expression in anterior NA populations, such as LC neurons, by using more refined techniques, unlike previous studies.

A major strength of the study is the use of a set of techniques to investigate the participation of NA-based glutamatergic signaling in breathing and metabolic control. The authors provided a full characterization of the recombinase-based cumulative fate maps for Vglut transporters. They performed real-time mRNA expression of Vglut transporters in central NA neurons of adult mice. Further, they evaluated the effect of knocking down Vglut2 expression in NA neurons using a DBH-Cre; Vglut2cKO mice on breathing and control in unanesthetized mice. Finally, they injected the AAV virus containing Cre-dependent Td tomato into LC of v-Glut2 Cre mice to verify the VGlut2 expression in LC-NA neurons. A very positive aspect of the article is that the authors combined ventilation with metabolic measurements. This integration holds particular significance, especially when delving into the exploration of respiratory chemosensitivity. Furthermore, the sample size of the experiments is excellent.<br /> Despite the clear strengths of the paper, some weaknesses exist. It is not clear in the manuscript if the experiments were performed in males and females and if the data were combined. I believe that the study would have benefited from a more comprehensive analysis exploring the sex specific differences. The reason I think this is particularly relevant is the developmental disorders mentioned by the authors, such as SIDS and Rett syndrome, which could potentially arise from disruptions in central noradrenergic (NA) function, exhibit varying degrees of sex predominance. Moreover, some of the noradrenergic cell groups are sexually dimorphic. For instance, female Wistar rats exhibit a larger LC size and more LC-NA neurons than male subjects (Pinos et al., 2001; Garcia-Falgueras et al., 2005). More recently, a detailed transcriptional profiling investigation has unveiled the identities of over 3,000 genes in the LC. This revelation has highlighted significant sexual dimorphisms, with more than 100 genes exhibiting differential expression within LC-NA neurons at the transcript level. Furthermore, this investigation has convincingly showcased that these distinct gene expression patterns have the capacity to elicit disparate behavioral responses between sexes (Mulvey et al., 2018). Therefore, the authors should compare the fate maps, Vglut transporters in males and females, at least considering LC-NA neurons. Even in the absence of identified sex differences, this information retains significant importance.<br /> An important point well raised by the authors is that although suggestive, these experiments do not definitively rule out that NA-Vglut2 based glutamatergic signaling has a role in breathing control. Subsequent experiments will be necessary to validate this hypothesis.

An improvement could be made in terms of measuring body temperature. Opting for implanted sensors over rectal probes would circumvent the need to open the chamber, thereby preventing alterations in gas composition during respiratory measurements. Further, what happens to body temperature phenotype in these animals under different gas exposures? These data should be included in the Tables.

Is it plausible that another neurotransmitter within NA neurons might be released in higher amounts in DBH-Cre; Vglut2 cKO mice to compensate for the deficiency in glutamate and prevent changes in ventilation?

Continuing along the same line of inquiry is there a possibility that Vglut2 cKO from NA neurons not only eliminates glutamate release but also reduces NA release? A similar mechanism was previously found in VGLUT2 cKO from DA neurons in previous studies (Alsio et al., 2011; Fortin et al., 2012; Hnasko et al., 2010). Additionally, does glutamate play a role in the vesicular loading of NA? Therefore, could the lack of effect on breathing be explained by the lack of noradrenaline and not glutamate?

Reviewer #3 (Public Review):

This study described changes in membrane excitability and Na+ and K+ current amplitudes of sympathetic motor neurons in culture. The findings indicate that neurons isolated from aged animals show increased membrane excitability manifested as increased firing rates in response to electrical stimulation and changes in related membrane properties including depolarized resting membrane potential, increased rheobase, and spontaneous firing. By contrast, neuron cultures from young mice show little to no spontaneous firing and relatively low firing rates in response to current injection. These changes in excitability correlate with reductions in the magnitude of KCNQ currents in neurons cultured from aged mice compared to neurons from cultured from young mice. The authors conclude that aging promotes hyperexcitability of sympathetic motor neurons through changes in KCNQ channels.

The electrophysiological cataloging of the neuronal properties is well done, and the experiments are performed using perforated patch recordings which preserves the internal constituents of neurons, providing confidence that the effects seen are not due to washout of regulators from the cells. The main weakness is that this study is a descriptive tabulation of changes in the electrophysiology of neurons in culture, and the effects shown are correlative rather than establishing causality. Pharmacological support is provided indicating that blockade or enhancement of KCNQ reverses the changes in excitability, but the specifics of the effects and relevance to intact preparations are unclear. Additional experiments in slice cultures would provide greater significance on the potential relevance of the findings for intact preparations.

Reviewer #1 (Public Review):

Summary:

The authors study age-related changes in the excitability and firing properties of sympathetic neurons, which they ascribe to age-related changes in the expression of KCNQ (Kv7, "M-type") K+ currents in rodent sympathetic neurons, whose regulation by GPCRs has been most thoroughly studied for over 40 years.

Strengths:

The strengths include the rigor of the current-clamp and voltage-clamp experiments and the lovely, crisp presentation of the data, The separation of neurons into tonic, phasic and adapting classes is also interesting, and informative. The ability to successfully isolate and dissociate peripheral ganglia from such older animals is also quite rare and commendable! There is much useful detail here.

Weaknesses:

Whereas the description of the data are very nice and useful, the manuscript does not provide much in the way of mechanistic insights. As such, the effect is more of an epi-phenomenon of unclear insight, and the authors cannot ascribe changes in signaling mechanisms, such as that of M1 mAChRs to the phenomena that is supported by data.

Reviewer #2 (Public Review):

Summary:

This research shows compelling and detailed evidence showing that aging influences intrinsic membrane properties of peripheral sympathetic motor neurons, which become hyperexcitable. The authors found that sympathetic motor neurons from old mice exhibit increased firing rates (spontaneous and evoked), more depolarized membrane resting potential, and increased rheobase. Furthermore, the study investigates cellular mechanisms underlying age-associated hyperexcitability and shows solid evidence supporting that a decreased activity of KCNQ channels during aging is a major contributor to the increased excitability of sympathetic old neurons. All conclusions of this paper are well supported by the data.

Strengths:

Detailed and rigorous analysis of electrical responses of peripheral sympathetic motor neurons using electrophysiology (perforated patch and whole-cell recordings). The study identifies a decrease in KCNQ current as a cellular mechanism behind age-induced hyperexcitability in sympathetic motor neurons.

Weaknesses:

None, the revised version of the manuscript has addressed all my concerns.

Reviewer #1 (Public Review):

Summary:

The authors constructed a novel HSV-based therapeutic vaccine to cure SIV in a primate model. The novel HSV vector is deleted for ICP34.5. Evidence is given that this protein blocks HIV reactivation by interference with the NFkappaB pathway. The deleted construct supposedly would reactivate SIV from latency. The SIV genes carried by the vector ought to elicit a strong immune response. Together the HSV vector would elicit a shock and kill effect. This is tested in a primate model.

Strengths and weaknesses:

(1) Deleting ICP34.5 from the HSV construct has a very strong effect on HIV reactivation. Why is no eGFP readout given in Figure 1C as for WT HSV? The mechanism underlying increased activation by deleting ICP34.5 is only partially explored. Overexpression of ICP34.5 has a much smaller effect (reduction in reactivation) than deletion of ICP34.5 (strong activation); so the story seems incomplete.

(2) No toxicity data are given for deleting ICP34.5. How specific is the effect for HIV reactivation? An RNA seq analysis is required to show the effect on cellular genes.

(3) The primate groups are too small and the results to variable to make averages. In Figure 5, the group with ART and saline has two slow rebounders. It is not correct to average those with a single quick rebounder. Here the interpretation is NOT supported by the data.

Discussion

HSV vectors are mainly used in cancer treatment partially due to induced inflammation. Whether these are suitable to cure PLWH without major symptoms is a bit questionable to me and should at least be argued for.

Reviewer #2 (Public Review):

Summary:

In this article, Wen et. al. describe the development of a 'proof-of-concept' bi-functional vector based on HSV-deltaICP-34.5's ability to purge latent HIV-1 and SIV genomes from cells. They show that co-infection of latent J-lat T-cell lines with an HSV-deltaICP-34.5 vector can reactivate HIV-1 from a latent state. Over- or stable expression of ICP 34.5 ORF in these cells can arrest latent HIV-1 genomes from transcription, even in the presence of latency reversal agents. ICP34.5 can co-IP with- and de-phosphorylate IKKa/b to block its interaction with NF-k/B transcription factor. Additionally, ICP34.5 can interact with HSF1 which was identified by mass-spec. Thus, the authors propose that the latency reversal effect of HSV-deltaICP-34.5 in co-infected JLat cells is due to modulatory effects on the IKKa/b-NF-kB and PP1-HSF-1 pathway.

Next, the authors cleverly construct a bifunctional HSV-based vector with deleted ICP34.5 and 47 ORFs to purge latency and avoid immunological refluxes, and additionally, expand the application of this construct as a vaccine by introducing SIV genes. They use this 'vaccine' in mouse models and show the expected SIV-immune responses. Experiments in rhesus macaques (RM), further elicit the potential for their approach to reactivate SIV genomes and at the same time block their replication by antibodies. What was interesting in the SIV experiments is that the dual-functional vector vaccine containing sPD1- and SIV Gag/Env ORFs effectively delayed SIV rebound in RMs and in some cases almost neutralized viral DNA copy detection in serum. Very promising indeed, however, there are some questions I wish the authors had explored to get answers to, detailed below.

Overall, this is an elegant and timely work demonstrating the feasibility of reducing virus rebound in animals, with the potential to expand to clinical studies. The work was well-written, and sections were clearly discussed.

Strengths:

The work is well designed, rationale explained, and written very clearly for lay readers.

Claims are adequately supported by evidence and well-designed experiments including controls.

Weaknesses:

(1) While the mechanism of ICP34.5 interaction and modulation of the NF-kB and HSF1 pathways are shown, this only proves ICP34.5 interactions but does not give away the mechanism of how the HSV-deltaICP-34.5 vector purges HIV-1 latency. What other components of the vector are required for latency reversal? Perhaps serial deletion experiments of the other ORFs in the HSV-deltaICP-34.5 vector might be revealing.

(2) The efficacy of the HSV vaccine vectors was evaluated in Rhesus Macaque model animals. Animals were chronically infected with SIV (a parent of HIV), treated with ART, challenged with bi-functional HSV vaccine or controls, and discontinued treatment, and the resulting virus burden and immune responses were monitored. The animals showed SIV Gag and Env-specific immune responses, and delayed virus rebound (however rebound is still there), and below-detection viral DNA copies. What would make a more convincing argument to this reviewer will be data to demonstrate that after the bi-functional vaccine, the animals show overall reduction in the number of circulating latent cells. The feasibility of obtaining such a result is not clearly demonstrated.

(3) The authors state that the reduced virus rebound detected following bi-functional vaccine delivery is due to latent genomes becoming activated and steady-state neutralization of these viruses by antibody response. This needs to be demonstrated. Perhaps cell-culture experiments from specimens taken from animals might help address this issue. In lab cultures one could create environments without antibody responses, under these conditions one would expect a higher level of viral loads to be released in response to the vaccine in question.

(4) How do the authors imagine neutralizing HIV-1 envelope epitopes by a similar strategy? A discussion of this point may also help.

(5) I thought the empty HSV-vector control also elicited somewhat delayed kinetics in virus rebound and neutralization, can the authors comment on why this is the case?

Reviewer #2 (Public Review):

Summary:

This is an interesting and well-performed study that develops a new modeling approach (MoA-HMM) to simultaneously characterize reinforcement learning parameters of different RL agents, as well as latent behavioral states that differ in the relative contributions of those agents to the animal's choices. They performed this study in rats trained to perform the two-step task. While the major advance of the paper is developing and rigorously validating this novel technical approach, there are also a number of interesting conceptual advances. For instance, humans performing the two-step task are thought to exhibit a trade-off between model-free and model-based strategies. However, the MoA-HMM did not reveal such a trade-off in the rats, but instead suggested a trade-off between model-based exploratory vs. exploitative strategies. Additionally, the firing rates of neurons in the orbitofrontal cortex (OFC) reflected latent behavioral states estimated from the HMM, suggesting that (1) characterizing dynamic behavioral strategies might help elucidate neural dynamics supporting behavior, and (2) OFC might reflect the contributions of one or a subset of RL agents that are preferentially active or engaged in particular states identified by the HMM.

Strengths:

The claims were generally well-supported by the data. The model was validated rigorously and was used to generate and test novel predictions about behavior and neural activity in OFC. The approach is likely to be generally useful for characterizing dynamic behavioral strategies.

Weaknesses:

There were a lot of typos and some figures were mis-referenced in the text and figure legends.

Reviewer #1 (Public Review):

Summary:

Motivated by the existence of different behavioral strategies (e.g. model-based vs. model-free), and potentially different neural circuits that underlie them, Venditto et al. introduce a new approach for inferring which strategies animals are using from data. In particular, they extend the mixture of agents (MoA) framework to accommodate the possibility that the weighting among different strategies might change over time. These temporal dynamics are introduced via a hidden Markov model (HMM), i.e. with discrete state transitions. These state transition probabilities and initial state probabilities are fit simultaneously along with the MoA parameters, which include decay/learning rate and mixture weightings, using the EM algorithm. The authors test their model on data from Miller et al., 2017, 2022, arguing that this formulation leads to (1) better fits and (2) improved interpretability over their original model, which did not include the HMM portion. Lastly, they claim that certain aspects of OFC firing are modulated by the internal state as identified by the MoA-HMM.

Strengths:

The paper is very well written and easy to follow, especially for one with a significant modeling component. Furthermore, the authors do an excellent job explaining and then disentangling many threads that are often knotted together in discussions of animal behavior and RL: model-free vs. model-based choice, outcome vs. choice-focused, exploration vs. exploitation, bias, preservation. Each of these concepts is quantified by particular parameters of their models. Model recovery (Fig. 3) is mostly convincing and licenses their fits to animal behavior later (although see below). While the specific claims made about behavior and neural activity are not especially surprising (e.g. the animals begin a session, in which rare vs. common transitions are not yet known, in a more exploratory mode), the MoA-HMM framework seems broadly applicable to other tasks in the field and useful for the purpose of quantification here.

Weaknesses:

The authors sometimes seem to equivocate on to what extent they view their model as a neural (as opposed to merely behavioral) description. For example, they introduce their paper by citing work that views heterogeneity in strategy as the result of "relatively independent, separable circuits that are conceptualized as supporting distinct strategies, each potentially competing for control." The HMM, of course, also relates to internal states of the animal. Therefore, the reader might come away with the impression that the MoA-HMM is literally trying to model dynamic, competing controllers in the brain (e.g. basal ganglia vs. frontal cortex), as opposed to giving a descriptive account of their emergent behavior. If the former is really the intended interpretation, the authors should say more about how they think the weighting/arbitration mechanism between alternative strategies is implemented, and how it can be modulated over time. If not, they should make this clearer.

Second, while the authors demonstrate that model recovery recapitulates the weight dynamics and action values (Fig. 3), the actual parameters that are recovered are less precise (Fig. 3 Supplement 1). The authors should comment on how this might affect their later inferences from behavioral data. Furthermore, it would be better to quantify using the R^2 score between simulated and recovered, rather than the Pearson correlation (r), which doesn't enforce unity slope and zero intercept (i.e. the line that is plotted), and so will tend to exaggerate the strength of parameter recovery.

Finally, the authors are very aware of the difficulties associated with long-timescale (minutes) correlations with neural activity, including both satiety and electrode drift, so they do attempt to control for this using a third-order polynomial as a time regressor as well as interaction terms (Fig. 7 Supplement 1). However, on net there does not appear to be any significant difference between the permutation-corrected CPDs computed for states 2 and 3 across all neurons (Fig. 7D). This stands in contrast to the claim that "the modulation of the reward effect can also be seen between states 2 and 3 - state 2, on average, sees a higher modulation to reward that lasts significantly longer than modulation in state 3," which might be true for the neuron in Fig. 7C, but is never quantified. Thus, while I am convinced state modulation exists for model-based (MBr) outcome value (Fig. 7A-B), I'm not convinced that these more gradual shifts can be isolated by the MoA-HMM model, which is important to keep in mind for anyone looking to apply this model to their own data.

Joint Public Review:

Summary:

The paper explores chemosensory behaviour in surface and cave morphs and F2 hybrids in the Mexican cave fish Astyanax mexicanus. The authors develop a new behavioural assay for the long-term imaging of individual fish in a parallel high-throughput setup. The authors first demonstrate that the different morphs show different basal exploratory swimming patterns and that these patterns are stable for individual fish. Next, the authors test the attraction of fish to various concentrations of alanine and other amino acids. They find that the cave morph is a lot more sensitive to chemicals and shows directional chemotaxis along a diffusion gradient of amino acids. Surface fish, although can detect the chemicals, do not show marked chemotaxis behaviour and have an overall lower sensitivity. These differences have been reported previously but the authors report longer-term observations on many individual fish of both morphs and their F2 hybrids. The data also indicate that the observed behaviour is a quantitative genetic trait. The approach presented will allow the mapping of genes contribution to these traits. The work will be of general interest to behavioural neuroscientists and those interested in olfactory behaviours and the individual variability in behavioural patterns.

Strengths:

The authors provide a large dataset of swimming behaviour for surface fish and cave fish and also their F2 hybrids, demonstrating large differences in chemosensory behaviour and indicating that this is a quantitative genetic trait.

One strength of the paper is the development of a new and improved setup for the behavioural imaging of individual fish for extended periods and under chemosensory stimulation. The authors show that cave fish need up to 24 h of habituation to display a behavioural pattern that is consistent and unlikely to be due to the stressed state of the animals. The setup also uses relatively large tanks that allows the build-up of chemical gradients.

With their new system, the authors could generate cleaner results without mechanical disturbances. The authors characterize multiple measurements to score the odour response behaviours and also developed a new personality analysis. Their conclusion that cave fish evolved as a specialist to sense alanine and histidine among 6 tested amino acids was well supported by their data.

Weaknesses:

Further work will be needed to pinpoint the nature of the genetic changes and neurobiological mechanisms that underlie the differences between the two forms and the large individual variation of behaviours.<br /> The authors did not measure the concentrations of alanine and other amino acids in the local cave water and surface water.

Reviewer #1 (Public Review):

Summary:

The manuscript aims to provide insights into the mediators and mechanisms underlying tardigrade radiation tolerance. The authors start by assessing the effect of ionizing radiation (IR) on the tardigrade lab species, H. exemplaris, as well as the ability of this organism to recover from this stress - specifically they look at DNA double and single strand breaks. They go on to characterize the response of H. exemplaris and two other tardigrade species to IR at the transcriptomic level. Excitingly, the authors identify a novel gene/protein called TDR1 (tardigrade DNA damage response protein 1). They carefully assess the induction of expression/enrichment of this gene/protein using a combination of transcriptomics and biochemistry - even going so far as to use a translational inhibitor to confirm the de novo production of this protein. TDR1 binds DNA in vitro and co-localizes with DNA in tardigrades.

Reverse genetics in tardigrades is difficult, thus the authors use a heterologous system (human cells) to express TDR1 in. They find that when transiently expressed TDR1 helps improve human cell resistance to IR.

This work is a masterclass in integrative biology incorporating a holistic set of approaches spanning next-gen sequencing, organismal biology, biochemistry, and cell biology. I think the importance of the findings is suitable and honestly, I find very little to critique in their experimental approaches.

Overall, I find this to be one of the more compelling papers on tardigrade stress-tolerance I have read.

Reviewer #3 (Public Review):

Summary:

This paper describes transcriptomes from three tardigrade species with or without treatment with ionizing radiation (IR). The authors show that IR produces numerous single strand and double strand breaks as expected and that these are substantially repaired within 4-8 hours. Treatment with IR induces strong upregulation of transcripts from numerous DNA repair proteins, and from the newly described protein TDR1 with homologs in both Hypsibioidea and Macrobiotoidea supefamilies. The authors show that TDR1 transcription produces newly translated TDR1 protein, which can bind DNA and co-localizes with DNA in the nucleus. At higher concentrations TDR appears to form aggregates with DNA, which might be relevant to a possible function in DNA damage repair. When introduced into human U2OS cells treated with the radiomimetic drug bleomycin, TDR1 reduces the number of double-strand breaks as detected by gamma H2AX spots. This paper will be of interest to the DNA repair field and to radiobiologists.

Strengths:

The paper is well-written and provides solid evidence of the upregulation of DNA repair enzymes after irradiation of tardigrades, as well as upregulation of the TRD1 protein. The reduction of gamma-H2A.X spots in U2OS cells after expression of TRD1 supports a role in a DNA damage.

Weaknesses:<br /> Genetic tools are still being developed in tardigrades, so there is no mutant phenotype to support a DNA repair function for TRD1, but this may be available soon.

Reviewer #4 (Public Review):

In this study, Anoud et al. show convincing results of genes involved in the radio-resistance of tardigrades. With transcriptomics, they found many genes involved in DNA repair pathways to be overexpressed after ionizing radiation. In addition, they found RNF146 coding for a ubiquitin ligase, and genes of the AMNP family. Finally, they more deeply characterized one upregulated gene that they named TDR1 (Tardigrade DNA damage Response 1) which seems specific to tardigrades. With proteomics they verified these results. They show that TDR1 binds DNA in vitro and co-localize with DNA in tardigrades. Because of the difficulties of carrying reverse genetics in tardigrades, the authors showed in vitro that human cells expressing TDR1 led to a reduced number of phospho-H2AX foci (indicating DNA damages) when treated with Bleomycin. Based on these results, the authors suggested that TDR1 interacts with DNA and might regulate chromosomal organization and favors DNA repair.

Strengths:

The paper provides solid evidence of the upregulation of DNA repair enzymes after irradiation of tardigrades, as well as upregulation of the TRD1 protein.

The reduction of gamma-H2A.X spots in U2OS cells after expression of TRD1 supports a role in a DNA damage.

The shown interaction of TDR1 with DNA.

Weaknesses:

No reverse genetics to support a DNA repair function for TRD1, even if I recognize that these remain difficult to carry in tardigrades.

No pulse field electrophoresis gels to show DNA damages in tardigrades, which remain apparently challenging to perform in tardigrades.

After revision, the manuscript gained in structure, and in precision.

Overall, the manuscript provides valuable and convincing results contributing to our knowledge of tardigrade radio resistance. While reverse genetics remain difficult to carry in tardigrades, the authors used the alternative approach to investigate TDR1 function in vitro in human cells.

This study illustrates integrative biology as it combines a set of different methodologies including next-generation sequencing, transcriptomic and proteomic analyses, immunohistochemistry, immunolabelling, in vitro assays and SEM. According to me, the quality and importance of the results make it of interest to the fields of DNA repair, radiobiology, and radio resistance.

Reviewer #2 (Public Review):

Summary:

The paper presents PPI-hotspot a method to predict PPI-hotspots. Overall, it could be useful but serious concerns about the validation and benchmarking of the methodology make it difficult to predict its reliability.

Strengths:

Develops an extended benchmark of hot-spots.

Weaknesses:

(1) Novelty seems to be just in the extended training set. Features and approaches have been used before.

(2) As far as I can tell the training and testing sets are the same. If I am correct, it is a fatal flaw.

(3) Comparisons should state that: SPOTONE is a sequence (only) based ML method that uses similar features but is trained on a smaller dataset. FTmap I think predicts binding sites, I don't understand how it can be compared with hot spots. Suggesting superiority by comparing with these methods is an overreach.

(4) Training in the same dataset as SPOTONE, and then comparing results in targets without structure could be valuable.

(5) The paper presents as validation of the prediction and experimental validation of hotspots in human eEF2. Several predictions were made but only one was confirmed, what was the overall success rate of this exercise?

Reviewer #1 (Public Review):

Summary:

The paper describes a program developed to identify PPI-hot spots using the free protein structure and compares it to FTMap and SPOTONE, two webservers that they consider as competitive approaches to the problem. On the positive side, I appreciate the effort in providing a new webserver that can be tested by the community but have two major concerns as follows.

(1) The comparison to the FTMap program is wrong. The authors misinterpret the article they refer to, i.e., Zerbe et al. "Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces" J. Chem. Inf. Model. 52, 2236-2244, (2012). FTMap identifies hot spots that bind small molecular ligands. The Zerbe et al. article shows that such hot spots tend to interact with hot spot residues on the partner protein in a protein-protein complex (emphasis on "partner"). Thus, the hot spots identified by FTMap are not the hot spots defined by the authors. In fact, because the Zerbe paper considers the partner protein in a complex, the results cannot be compared to the results of Chen et al. This difference is missed by the authors, and hence the comparison of the FTMap is invalid. I did not investigate the comparison to SPOTONE, and hence have no opinion.

(2) Chen et al. use a number of usual features in a variety of simple machine-learning methods to identify hot spot residues. This approach has been used in the literature for more than a decade. Although the authors say that they were able to find only FTMap and SPOTONE as servers, there are dozens of papers that describe such a methodology. Some examples are given here: (Higa and Tozzi, 2009; Keskin, et al., 2005; Lise, et al., 2011; Tuncbag, et al., 2009; Xia, et al., 2010). There are certainly more papers. Thus, while I consider the web server as a potentially useful contribution, the paper does not provide a fundamentally novel approach.

Higa, R.H. and Tozzi, C.L. Prediction of binding hot spot residues by using structural and evolutionary parameters. Genet Mol Biol 2009;32(3):626-633.

Keskin, O., Ma, B.Y. and Nussinov, R. Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues. J Mol Biol 2005;345(5):1281-1294.

Lise, S., et al. Predictions of Hot Spot Residues at Protein-Protein Interfaces Using Support Vector Machines. PLoS One 2011;6(2).

Tuncbag, N., Gursoy, A. and Keskin, O. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 2009;25(12):1513-1520.

Xia, J.F., et al. APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics 2010;11:174.

Strengths:<br /> A new web server was developed for detecting protein-protein interaction hot spots.

Weaknesses:<br /> The comparison to FTMap results is wrong. The method is not novel.

Reviewer #2 (Public Review):

Summary:

This article has characterized the mouse Schlemm's canal expression profile using a comprehensive approach based on sorted SEC, LEC, and BEC total RNA-Seq, scRNA-Seq, and snRNA-Seq to enrich the selection of SECs. The study has successfully profiled genome-wide gene expression using sorted SECs, demonstrating that SECs have a closer similarity to LECs than BECs. The combined scRNA- and snRNA-Seq data with deep coverage of gene expression led to the successful identification of many novel biomarkers for inner wall SECs, outer wall SECs, collector channel ECs, and pericytes. In addition, the study also identified two novel states of inner wall SECs separated by new markers. The study provides significant novel information about the biology and expression profile of SECs in the inner and outer walls. It is of great significance to have this novel, convincing, and comprehensive study led by leading researchers published in this journal.

Strengths:

This is a comprehensive study using various data to support the expression characterization of mouse SECs. First, the study profiled genome-wide expression using sorted SECs, LECs, and BECs from the same tissue/organ to identify the similarities and differences among the three types of cells. Second, snRNA-Seq was applied to enrich the number of SECs from mouse ocular tissues significantly. Increased sampling of SECs and other cells led to more comprehensive coverage and characterization of cells, including pericytes. Third, the combined scRNA- and snRNA-Seq data analyses increase the power to further characterize the subtle differences within SECs, leading to identifying the expression markers of Inner and Outer wall SECs, collector channel ECs, and distal region cells. Fourth, the identified unique markers were validated for RNA and protein expression in mouse ocular tissues. Fifth, the study explored how the IOP- and glaucoma-associated genes are expressed in the ScRNA- and snRNA-Seq data, providing potential connections of these GWAS genes with IOP and glaucoma. Sixth, the initial pathway and network analyses generated exciting hypotheses that could be tested in other independent studies.

Weaknesses:

A few minor weaknesses have been noted. First, since snRNA-Seq and scRNA-Seq generated different coverage of expressed genes in the cells, how did the combined analyses balance the un-equal sequencing coverage and missing data points in the snRNA-Seq data? Second, the RNA/protein validation of selected SEC molecular markers was done using mouse anterior segment tissues. It would be more helpful to examine whether these molecular markers for SECs could work well in human SECs. Third, the effort to characterize the GWAS-identified IOP- and glaucoma-associated genes is exciting but with limited new information. Additional work could be performed to prioritize these genes.

Reviewer #1 (Public Review):

Summary:

Balasubramanian et al. characterized the cell types comprising mouse Schlemm's canal (SC) using bulk and single-cell RNA sequencing (scRNA-seq). The results identify expression patterns that delineate the SC inner and outer wall cells and two inner wall 'states'. Further analysis demonstrates expression patterns of glaucoma-associated genes and receptor-ligand pairs between SEC's and neighboring trabecular meshwork.

Strengths:

While mouse SC has been profiled in previous scRNA-seq studies (van Zyl et al 2020, Thomson et al 2021), these data provide higher resolution of SC cell types, particularly endothelial cell (SEC) populations. SC is an important regulator of anterior chamber outflow and has important consequences for glaucoma.

Weaknesses:

(1) Since SC has previously been characterized in mouse, human, and other species by scRNA-seq in other studies, this study would benefit from more direct comparisons to published datasets. For example, Table 4 could be expanded to list the SC cell numbers profiled in each study. Expression patterns highlighted in this study could be independently verified by plotting in publicly available mouse SC datasets. Further, a comparison to human expression patterns would assess whether type-specific expression patterns are conserved. Alternatively, an integrated analysis could be performed. Indeed, the authors mention that an integrated analysis was attempted but the data is not shown. It is unclear if this was because of a lack of agreement between datasets or other reasons.

(2) Figure 1 presents bulk RNA seq results comparing SEC, BEC, and LEC expression patterns. These populations were isolated using cell surface markers and enrichment by FACS. Since each EC population is derived from the same sample, the accuracy of this data hinges on the purity of enrichment. However, a reference is not given for this method and it is not clear how purity was validated. The authors later note that marker Emcn, which was used to identify BECs, is also expressed in SECs and LECs at lower levels. It should be demonstrated that these populations are clearly separated by flow cytometry.

(3) Bulk RNA-seq analysis infers similarity from the number of DEGs between samples, however, this is not a robust indicator. A correlation analysis should be run to verify conclusions.

(4) Figures 2-4 present three different datasets targeting the same tissue: 1) C57bl/6j scRNA-seq, 2) C57bl/6j snRNA-seq, 3) 129/sj scRNA-seq. Integrated analysis comparing datasets #1 to #2 and #3 is also presented. Integration methods are not described beyond 'normalization for cell numbers'. It is unclear if additional alignment methods were used. Integration across each of these datasets needs careful consideration, especially since different filtering methods were used (e.g. <20% mito in scRNA-seq and <5% in snRNA-seq). Improper integration could affect the ability to cluster or exaggerate differences between cell/types and states. It would be useful to demonstrate the contribution of different samples and datasets to each cell type/state to verify that these are not driven by batch effects, mouse strain, or collection platform.

(5) IW1 and IW2 are not well separated, and it is unclear if these represent truly different cell states. Figure 5b shows the staining of CCL21A and describes expression in the 'posterior portion' but in the image there are no DAPI+ nuclei in the anterior portion, suggesting the sampling in this section is different from Figure 5a. This would be improved by co-staining NPNT and CCL21A to demonstrate specificity.

(6) The substructures observed within clusters in sc/snRNA-seq data suggest that overall profiling may still not be comprehensive. This should be noted in the discussion.

Reviewer #1 (Public Review):

Summary:

This work by Leclercq and colleagues performed metabolomics on biospecimens collected from 96 patients diagnosed with several types of alcohol use disorders (AUD). The authors discovered strong alterations in circulating glycerophospholipids, bile acids, and some gut microbe-derived metabolites in AUD patients compared to controls. An exciting part of this work is that metabolomics was also performed in frontal cortex of post-mortem brains and cerebrospinal fluid of heavy alcohol users, and some of the same metabolites were seen to be altered in the central nervous system. This is an important study that will form the basis for hypothesis generation around diet-microbe-host interactions in alcohol use disorder. The work is done in a highly rigorous manner, and the rigorously collected human samples are a clear strength of this work. Overall, many new insights may be gained by this work, and it is poised to have a high impact on the field.

Strengths:

(1) The rigorously collected patient-derived samples.

(2) There is high rigor in the metabolomics investigation.

(3) Statistical analyses are well-described and strong.

(4) An evident strength is the careful control of taking blood samples at the same time of the day to avoid alterations in meal- and circadian-related fluctuations in metabolites.

Weaknesses:

(1) Some validation in animal models of ethanol exposure compared to pair-fed controls would help strengthen causal relationships between metabolites and alterations in the CNS.

(2) The classification of "heavy alcohol users" based on autopsy reports may not be that accurate.

(3) The fact that most people with alcohol use disorder choose to drink over eating food, there needs to be some more discussion around how dietary intake (secondary to heavy drinking) most likely has a significant impact on the metabolome.

Reviewer #2 (Public Review):

The authors carried out the current studies with the justification that the biochemical mechanisms that lead to alcohol addiction are incompletely understood. The topic and question addressed here are impactful and indeed deserve further research. To this end, a metabolomics approach toward investigating the metabolic effects of alcohol use disorder and the effect of alcohol withdrawal in AUD subjects is valuable. However, it is primarily descriptive in nature, and these data alone do not meet the stated goal of investigating biochemical mechanisms of alcohol addiction. The current work's most significant limitation is the cross-sectional study design, though inadequate description and citation of the underlying methodological approaches also hampers interest.

Most of the data are cross-sectional in the study design, i.e., alcohol use disorder vs controls. However, it is well established that there is a high degree of interpersonal variation with metabolism, and further, there is somewhat high intra-personal variation in metabolism over time. This means that the relatively small cohort of subjects is unlikely to reflect the broader condition of interest (AUD/withdrawal). The authors report a comparison of a later time-point after alcohol withdrawal (T2) vs. the AUD condition. However, without replicative time points from the control subjects it is difficult to assess how much of these changes are due to withdrawal vs the intra-personal variation described above. Overall, there is not enough experimental context to interpret these findings into a biological understanding. For example, while several metabolites are linked with AUD and associated with microbiome or host metabolism based on existing literature, it's unclear from the current study what function these changes have concerning AUD, if any. The authors also argue that alcohol withdrawal shifts the AUD plasma metabolic fingerprint towards healthy controls (line 153). However, this is hard to assess based on the plots provided since the change in the direction of the orange data subset is considers AUD T2 vs T1. In contrast, AUD T2 vs Control would represent the claimed shift. To support these claims, the authors would better support their argument by showing this comparison as well as showing all experimental groups (including control subjects) in their multi-dimensional model (e.g., PCA). The authors attempt to extend the significance of their findings by assessing post-mortem brain tissues from AUD subjects; however, the finding that many of the metabolites changed in T2/T1 are also present in AUD brain tissues is interesting; however, not strongly supporting of the authors' claims that these metabolites are markers of AUD (line 173). Concerning the plasma cohort itself, it is unclear how the authors assessed for compliance with alcohol withdrawal or whether the subjects' blood-alcohol levels were independently verified.

The second area of concern is the need for more description of the analytical methodology, the lack of metabolite identification validation evidence, and related statistical questions. The authors cite reference #59 regarding the general methodology. However, this reference from their group is a tutorial/review/protocol-focused resource paper, and it is needs to be clarified how specific critical steps were actually applied to the current plasma study samples given the range of descriptions provided in the citations. The authors report a variety of interesting metabolites, including their primary fragment intensities, which are appreciated (Supplementary Table 3), but no MS2 matching scores are provided for level 2 or 3 hits. Further, level 1 hits under their definition are validated by an in-house standard, but no supporting data are provided besides this categorization. Finally, a common risk in such descriptive studies is finding spurious associations, especially considering many factors described in the current work. These include AUD, depression, anxiety, craving, withdrawal, etc. The authors describe the use of BH correction for multiple-hypothesis testing. However, this approach only accounts for the many possible metabolite association tests within each comparison (such as metabolites vs depression). It does not account for the multi-variate comparisons to the many behavior/clinical factors described above. The authors should employ one of several common strategies, such as linear mixed effects models, for these types of multi-variate assessments.

Reviewer #1 (Public Review):

Summary:

Arman Angaji and his team delved into the intricate world of tumor growth and evolution, utilizing a blend of computer simulations and real patient data from liver cancer.

Strengths:

Their analysis of how mutations and clones are distributed within tumors revealed an interesting finding: tumors don't just spread from their edges as previously believed. Instead, they expand both from within and the edges simultaneously, suggesting a unique growth mode. This mode naturally indicates that external forces may play a role in cancer cells dispersion within the tumor. Moreover, their research hints at an intriguing phenomenon - the high death rate of progenitor cells and extremely slow pace in growth in the initial phase of tumor expansion. Understanding this dynamic could significantly impact our comprehension of cancer development.

Weaknesses:

It's important to note, however, that this study relies on specific computer models, metrics derived from inferred clones, and a limited number of patient data. While the insights gained are promising, further investigation is essential to validate these findings. Nonetheless, this work opens up exciting avenues for comprehending the evolution of cancers.

Reviewer #2 (Public Review):

Summary:

The article uses a cell-based model to investigate how mutations and cells spread throughout a tumour. The paper uses published data and the proposed model to understand how growth and death mechanisms lead to the observed data. This work provides an insight into the early stages of tumour development. From the work provided here, the results are solid, showing a thorough analysis. However, the work has not fully specified the model, which can lead to some questions around the model's suitability. The article is well-written and presents a very suitable and rigorous analysis to describe the data. The authors did a particularly nice job of the discussion and decision of their "metrics of interest", though this is not the main aim of this work.

Strengths:

Due to the particularly nice and tractable cell-based model, the authors are able to perform a thorough analysis to compare the published data to that simulated with their model. They then used their computational model to investigate different growth mechanisms of volume growth and surface growth. With this approach, the authors are able to compare the metric of interest (here, the direction angle of a new mutant clone, the dispersion of mutants throughout the tumour) to quantify how the different growth models compare to the observed data. The authors have also used inference methods to identify model parameters based on the data observed. The authors performed a rigorous analysis and have chosen the metrics in an appropriate manner to compare the different growth mechanisms.

Weaknesses:

The work contained within this article considers a single cell-based model. While ideally, this is sufficient, results from simulated multi-cellular systems can often be sensitive to the model choice. Performing this work with various other standard models would strengthen the results significantly. This is, however, not an easy task.

Context:

Improved mechanistic understanding into the early developmental stages of tumours will further assist in disease treatment and quantification. Understanding how readily and quickly a tumour is evolving is key to understanding how it will develop and progress. This work provides a solid example as to how this can be achieved with data alongside simulated models.

Reviewer #2 (Public Review):

Summary:

The authors Fu et al., developed polymer models that combine loop extrusion with attractive interactions to best describe Hi-C population average data. They analyzed Hi-C data of the MYC locus as an example and developed an optimization strategy to extract the parameters that best fit this average Hi-C data.

Strengths:

The model has an intuitive nature and the authors masterfully fitted the model to predict relevant biology/Hi-C methodology parameters. This includes loop extrusion parameters, the need for self-interaction with specific energies, and the time and distance parameters expected for Hi-C capture.

Weaknesses:

(1) We are no longer in the age in which the community only has access to population average Hi-C. Why was only the population average Hi-C used in this study?

Can single-cell data: i.e. single-cell Hi-C/Dip-C data or chromatin tracing data (i.e. see Tan et al Science 2018 - for Dip-C, Bintu et al Science 2018, Su et al Cell 2020 for chromatin tracing, etc.) or even 2 color DNA FISH data (used here only as validation) better constrain these models? At the very least the simulations themselves could be used to answer this essential question.

I am expecting that the single-cell variance and overall distributions of distances between loci might better constrain the models, and the authors should at least comment on it.

(2) The authors claimed "Our parameter optimization can be adapted to build biophysical models of any locus of interest. Despite the model's simplicity, the best-fit simulations are sufficient to predict the contribution of loop extrusion and domain interactions, as well as single-cell variability from Hi-C data. Modeling dynamics enables testing mechanistic relationships between chromatin dynamics and transcription regulation. As more experimental results emerge to define simulation parameters, updates to the model should further increase its power." The focus on the Myc locus in this study is too narrow for this claim. I am expecting at least one more locus for testing the generality of this model.

Reviewer #1 (Public Review):

Summary:

The authors of this study aim to use an optimization algorithm approach, based on the established Nelder-Mead method, to infer polymer models that best match input bulk Hi-C contact data. The procedure infers the best parameters of a generic polymer model that combines loop-extrusion (LE) dynamics and compartmentalization of chromatin types driven by weak biochemical affinities. Using this and DNA FISH, the authors investigate the chromatin structure of the MYC locus in leukemia cells, showing that loop extrusion alone cannot explain local pathogenic chromatin rearrangements. Finally, they study the locus single-cell heterogeneity and time dynamics.

Strengths:

-The optimization method provides a fast computational tool that speeds up the parameter search of complex chromatin polymer models and is a good technical advancement.

-The method is not restricted to short genomic regions, as in principle it can be applied genome-wide to any input Hi-C dataset, and could be potentially useful for testing predictions on chromatin structure.

Weaknesses:

(1) The optimization is based on the iterative comparison of simulated and Hi-C contact matrices using the Spearman correlation. However, the inferred set of the best-fit simulation parameters could sensitively depend on such a specific metric choice, questioning the robustness of the output polymer models. How do results change by using different correlation coefficients?

(2) The best-fit contact threshold of 420nm seems a quite large value, considering that contact probabilities of pairs of loci at the mega-base scale are defined within 150nm (see, e.g., Bintu et al. Science (2018) and Takei et al. Science (2021)).

(3) In their model, the authors consider the presence of LE anchor sites at Hi-C TAD boundaries. Do they correspond to real, experimentally found CTCF sites located at genomic positions, or they are just assumed? A track of CTCF peaks of the considered chromatin loci would be needed.

(4) In the model, each TAD is assigned a specific energy affinity value. Do the different domain types (i.e., different colors) have a mutually attractive energy? If so, what is its value and how is it determined? The simulated contact maps (e.g., Figure 2C) seem to allow attractions between different blocks, yet this is unclear.

(5) To substantiate the claim that the simulations can predict heterogeneity across single cells, the authors should perform additional analyses. For instance, they could plot the histograms (models vs. experiments) of the TAD2-TAD4 distance distributions and check whether the models can recapitulate the FISH-observed variance or standard deviation. They could also add other testable predictions, e.g., on gyration radius distributions, kurtosis, all-against-all comparison of single-molecule distance matrices, etc,.

(6) The authors state that loop extrusion is crucial for enhancer function only at large distances. How does that reconcile, e.g., with Mach et al. Nature Gen. (2022) where LE is found to constrain the dynamics of genomically close (150kb) chromatin loci?

Reviewer #1 (Public Review):

Summary:

This study explores the neural control of muscle by decomposing the firing activity of constituent motor units from the grid of surface electromyography (EMG) in the Tibialis (TA) Anterior and Vastus Lateralis (VL) during isometric contractions. The study involves extensive samples of motor units across the broadest range of voluntary contraction intensities up to 80% of MVC. The authors examine the rate coding of the population of motor units, which describes the instantaneous firing rate of each motor unit as a function of muscle force. This relationship is characterized by a natural logarithm function that delineates two distinct phases: an initial phase with a steep acceleration in firing rate, particularly pronounced in low-threshold motor units, and a subsequent modest linear increase in firing rate, more significant in high-threshold motor units.

Strengths:

The study makes a significant contribution to the field of neuromuscular physiology by providing a detailed analysis of motor unit behavior during muscle contractions in a few ways.

(1) The significance lies in its comprehensive framework of motor unit activity during isometric contractions in a broad range of intensities, providing insights into the non-linear relationship between the firing rate and the muscle force. The extensive sample of motor units across the pool confirms the observation in animal studies in which the spinal motoneuron exhibits a discharge consisting of distinct phases in response to synaptic currents, under the influence of persistent inward currents. As such, it is now reasonable to state the human motor units across the pool are also under the control of gain modulation via some neuromodulatory effects in addition to synaptic inputs arising from ionotropic effects.

(2) The firing scheme across the entire motoneuron pool revealed in this study reconciles the discrepancy in firing organization under debate; i.e., whether it is 'onion skin' like or not (Heckman and Enoka 2012). The onion skin like model states that the low threshold motor units discharge higher than high threshold motor units and have been held for a long time because the firing behaviors were examined in a partial range of contraction force range due to technical limitations. This reconciliation is crucial because it is fundamental to modelling the organization of motor unit recruitment and rate coding to achieve a desired force generation to advance our understanding of motor control.

(3) The extensive data collection with a novel blind source separation algorithm on the expanded number of channels of surface EMG signal provides a robust dataset that enhances the reliability and validity of findings, setting a new standard for empirical studies in the field.

Collectively, this study fills several knowledge gaps in the field and advances our understanding of the mechanism underlying the isometric force generation.

Weaknesses:

Although the findings and claims based on them are mostly well aligned, some accounts of the methods and claims need to be clarified.

(1) The authors examine the input-output function of a motor unit by constructing models, using force as an input and discharge rate as an output. It sounds circular, or the other way around to use the muscle force as an input variable, because the muscle force is the result of motor unit discharges, not the cause that elicits the discharges. More specifically, as a result of non-linear interactions of synchronous and/or asynchronous discharges of a population of a given motoneuron pool that give rise to transient increase/maintenance in twitch force, the gross muscle force is attained. I acknowledge that it is extremely challenging experimentally to measure synaptic currents impinging upon the spinal motoneurons in human subjects and the author has an assumption that the force could be used as a proxy of synaptic currents. However, it is necessary to explicitly provide the caveats and rationale behind that. Force could be used as the input variable for modelling.

2) The authors examine the firing organizations in TA and VL in this study without explicit purposes and rationale for choosing these muscles. The lack of accounts makes it hard for the readers to interpret the data presented, particularly in terms of comparing the results from the different muscles.

(3) In the methods, the author described the manual curation process after applying the blind source separation algorithm. For the readers to understand the whole process of decomposition and to secure rigor and robustness of the analyses, it would be necessary to provide details on what exact curation is performed with what criteria.

(4) In Figure 3, the early recruited units tend to become untraceable in the higher range of contraction. This is more pronounced in the muscle VL. This limitation would ambiguate the whole firing curve along the force axis and therefore limitation and the applicability in the different muscles needs to be discussed.

(5) It is unclear how commonly the notion "the long-held belief that rate coding is similar across motor units from the same pool" is held among the community without a reference. Different firing organizations have been modelled and discussed in the seminal paper by Fuglevand et al. (1993), and as far as I understand, the debate has not converged to a specific consensus. As such, any reference would be required to support the claim the notion is widely recognized.

(6) The authors claim that the firing behavior as a function of force is well characterized by a natural logarithmic function, which consists of initial steep acceleration followed by a modest increase in firing rate. Arguably the gain modulation in firing rate could be attributed to a neuromodulatory effect on the spinal motoneuron, which has been suggested by a number of animal studies. However, the complexity of the interactions between ionotropic and neuromodulatory inputs to motoneurons may require further elucidation to fully understand the mechanisms of neural control; it is possible to consider the differential acceleration among different threshold motor units as a differential combinatory effect of ionotropic and neuromodulatory inputs, but it is not trivially determined how differentially or systematically the inputs are organized. Likewise, the authors make an account for the difference in firing rate between TA and VL in terms of different amounts or balances of excitatory and inhibitory inputs to the motoneuron pool, but again this could be explained by other factors, such as a different extent of neuromodulatory effects. To determine the complexity of the interactions, further studies will be warranted.

(7) It is unclear with the account " ... the bandwidth of muscle force is < 10Hz during isometric contraction" in the manuscript alone, and therefore, it is difficult to understand the following claim. It appears very interesting and crucial for motor unit discharge and force generation and maintenance because it would pose a question of why the discharge rate of most motor units is higher than 10Hz, despite the bandwidth being so limited, but needs to be elaborated.

(References)

Heckman, C. J. & Enoka, R. M. Motor unit. Comprehensive Physiology 2, 2629-2682 (2012).

Fuglevand, A. J., Winter, D. A. & Patla, A. E. Models of recruitment and rate coding organization in motor-unit pools. J Neurophysiol 70, 2470-2488 (1993).

Reviewer #2 (Public Review):

Summary:

The motivation for this study is to provide a comprehensive assessment of motor unit firing rate responses of entire pools during isometric contractions. The authors have used new quantitative methods to extract more unique motor units across contractions than prior studies. This was achieved by recording muscle fibre action potentials from four high-density surface electromyogram (HDsEMG) arrays (Caillet et al., 2023), quantifying residual EMG comparing the recorded and data-based simulation (Figure 1A-B), and developing a metric to compare the spatial identification for each motor unit (Figure 1D-E). From identified motor units, the authors have provided a detailed characterization of recruitment and firing rate responses during slow voluntary isometric contractions in the vastus lateralis and tibialis anterior muscles up to 80% of maximum intensity. In the lower limb, it is interesting how lower threshold motor units have firing rate responses that saturate, whereas higher threshold units that presumably produce higher muscle contractile forces continue to increase their firing rate. In many ways, these results agree with the rate coding of motor units in the extensor digitorum communis muscle (Monster and Chan, 1977). The paper is detailed, and the analyses are well explained. However, there are several points that I think should be addressed to strengthen the paper.

General comments:

(1) The authors claim they have measured the complete rate coding profiles of motor units in the vastus lateralis and tibialis anterior muscles. However, this study quantified rate coding during slow and prolonged voluntary isometric contractions whereas the function of rate coding during movements (Grimby and Hannerz, 1977) or more complex isometric contractions (Cutsem and Duchateau, 2005; Marshall et al., 2022) remains unexplored. For example, supraspinal inputs may not scale the same way across low and higher threshold motor units, or between muscles (Devanne et al., 1997), making the response of firing rates to increasing isometric contraction force less clear. Conceptually, the authors focus on the literature on intrinsic motoneurone properties, but in vivo, other possibilities are that descending supraspinal drive, spinal network dynamics, and afferent inputs have different effects across motor unit sizes, muscles, and types of contractions. Also, the influence from local muscles that act as synergists (e.g., vastii muscles for the vastus lateralis, and peroneal muscles that evert the foot for the tibialis anterior) or antagonists (coactivation during higher contraction intensities would stiffen the joint) may provide differential forms of proprioceptive feedback across motor pools.

(2) The evidence that the entire motor unit pool was recorded per muscle is not clear. There appears to be substantial residual EMG (Figure 1B), signal cancellation of smaller motor units (lines 172-176), some participants had fewer than 20 identified motor units, and contractions never went above 80% of MVC. Also, to my understanding, there remains no gold-standard in awake humans to estimate the total motor unit number in order to determine if the entire pool was decomposed. Furthermore, using four HDsEMG arrays also raises questions about how some channels were placed over non-target muscles, and if motor units were decomposed from surrounding synergists.

(3) The authors claim (Abstract L51; Discussion L376) that a commonly held view in the field is that rate coding is similar across motor units from the same pool. Perhaps this is in reference to some studies that have carefully assessed lower threshold motor units during lower force ramp contractions (e.g., Fuglevand et al., 2015; Revill and Fuglevand, 2017). However, a more complete integration of the literature exploring motor unit firing rate responses during rapid isometric contractions, comparing different muscles and contraction intensities would be helpful. From Figure 3, the range of rate coding in the tibialis anterior (~7-40 Hz) is greater than the vastus lateralis (~5-22 Hz) muscle across contraction levels. In agreement with other studies, the range of rate coding within some muscles is different than others (Kirk et al., 2021) and during maximal intensity (Bellemare et al., 1983) or rapid contractions (Desmedt and Godaux, 1978). Likewise, within a motor pool, there is a diversity of firing rate responses across motor units of different sizes as a function of isometric force (Monster and Chan, 1977; Desmedt and Godaux, 1977; Kukula and Clamann, 1981; Del Vecchio et al., 2019; Marshall et al., 2022). A strength of this paper is how firing rate responses are quantified across a wide range of motor unit recruitment thresholds and between two muscles. I suggest improving clarity for the general reader, especially in the motivation for testing two lower limb muscles, and elaborating on some of the functional implications.

Reviewer #3 (Public Review):

Summary:

This is an interesting manuscript that uses state-of-the-art experimental and simulation approaches to quantify motor unit discharge patterns in the human TA and VL. The non-linear profiles of motor unit discharge were calculated and found to have an initial acceleration phase followed by an attenuation phase. Lower threshold motor units had a larger gain of the initial acceleration whereas the higher threshold motor unit had a higher gain in the attenuation phase. These data represent a technical feat and are important for understanding how humans generate and control voluntary force.

Strengths:<br /> The authors used rigorous, state-of-the-art analyses to decompose and validate their motor unit data during a wide range of voluntary efforts.

The analyses are clearly presented, applied, and visualized.

The supplemental data provides important transparency.

Weaknesses:

The number of participants and muscles tested are quite small - particularly given the constraints on yield. It is unclear if this will translate to other motor pools. The justification for TA and VL should be provided.

While an impressive effort was made to identify and track motor units across a range of contractions, it appears that a substantial portion of muscle force was not identified. Though high-intensity contractions are challenging to decompose - the authors are commended for their technical ability to record population motor unit discharge times with recruitment thresholds up to 75% of a participant's maximal voluntary contractions. However previous groups have seen substantial recruitment of motor units above 80% and even 90% maximum activation in the soleus. Given the innervation ratios of higher threshold motor units, if recruitment continued to 100%, the top quartile would likely represent a substantial portion of the traditional fast-fatigable motor units. It would be highly interesting to understand the recruitment and rate coding of the highest threshold motor units, at a minimum I would suggest using terms other than "entire range" or "full spectrum of recruitment thresholds"

The quantification of hysteresis using torque appears to make self-evident the observation that lower threshold motor units demonstrate less hysteresis with respect to torque. If there is motor unit discharge there will be force. I believe this limitation goes beyond the floor effects discussed in the manuscript. Traditionally, individuals have used the discharge of a lower threshold unit as the measure on which to apply hysteresis analyses to infer ion channel function in human spinal motoneurons.

The main findings are not entirely novel. See Monster and Chan 1977 and Kanosue et al 1979.

Reviewer #1 (Public Review):

Summary:

In this valuable study, the authors found that the macrolide drug rapamycin, which is an important pharmacological tool in the clinic and the research lab, is less specific than previously thought. They provide solid functional evidence that rapamycin activates TRPM8 and develop an NMR method to measure the specific binding of a ligand to a membrane protein.

Strengths:

The authors use a variety of complementary experimental techniques in several different systems, and their results support the conclusions drawn.

Weaknesses:

Controls are not shown in all cases, and a lack of unity across the figures makes the flow of the paper disjointed. The proposed location of the rapamycin binding pocket within the membrane means that molecular docking approaches designed for soluble proteins alone do not provide solid evidence for a rapamycin binding pocket location in TRPM8, but the authors are appropriately careful in stating that the model is consistent with their functional experiments.

Impact:

This work provides still more evidence for the polymodality of TRP channels, reminding both TRP channel researchers and those who use rapamycin in other contexts that the adjective "specific" is only meaningful in the context of what else has been explicitly tested.

Reviewer #2 (Public Review):

Summary:

Tóth and Bazeli et al. find rapamycin activates heterologously-expressed TRPM8 and dissociated sensory neurons in a TRPM8-dependent way with Ca2+-imaging. With electrophysiology and STTD-NMR, they confirmed the activation is through direct interaction with TRPM8. Using mutants and computational modeling, the authored localized the binding site to the groove between S4 and S5, different than the binding pocket of cooling agents such as menthol. The hydroxyl group on carbon 40 within the cyclohexane ring in rapamycin is indispensable for activation, while other rapalogs with its replacement, such as everolimus, still bind but cannot activate TRPM8. Overall, the findings provide new insights into TRPM8 functions and may indicate previously unknown physiological effects or therapeutic mechanisms of rapamycin.

Strengths:

The authors spent extensive effort on demonstrating that the interaction between TRPM8 and rapamycin is direct. The evidence is solid. In probing the binding site and the structural-function relationship, the authors combined computational simulation and functional experiments. It is very impressive to see that "within" a rapamycin molecule, the portion shared with everolimus is for "binding", while the hydroxyl group in the cyclohexane ring is for activation. Such detailed dissection represents a successful trial in the computational biology-facilitated, functional experiment-validated study of TRP channel structural-activity relationship. The research draws the attention of scientists, including those outside the TRP channel field, to previously neglected effects of rapamycin, and therefore the manuscript deserves broad readership.

Weaknesses:

The significance of the research could be improved by showing or discussing whether a similar binding pocket is present in other TRP channels, and hence rapalogs might bind to or activate these TRP channels. Additionally, while the finding on TRPM8 is novel, it is worthwhile to perform more comprehensive pharmacological characterization, including single-channel recording and a few more mutant studies to offer further insight into the mechanism of rapamycin binding to S4~S5 pocket driving channel opening. It is also necessary to know if rapalogs have independent or synergistic effects on top of other activators, including cooling agents and lower temperature, and their dependence on regulators such as PIP2.

Additional discussion that might be helpful:

The authors did confirm that rapamycin does not activate TRPV1, TRPA1 and TRPM3. But other TRP channels, particularly other structurally similar TRPM channels, should be discussed or tested. Alignment of the amino acid sequences or structures at the predicted binding pocket might predict some possible outcomes. In particular, rapamycin is known to activate TRPML1 in a PI(3,5)P2-dependent manner, which should be highlighted in comparison among TRP channels (PMID: 35131932, 31112550).

Reviewer #3 (Public Review):

Summary:

Rapamycin is a macrolide of immunologic therapeutic importance, proposed as a ligand of mTOR. It is also employed as in essays to probe protein-protein interactions.<br /> The authors serendipitously found that the drug rapamycin and some related compounds, potently activate the cationic channel TRPM8, which is the main mediator of cold sensation in mammals. The authors show that rapamycin might bind to a novel binding site that is different from the binding site for menthol, the prototypical activator of TRPM8. These solid results are important to a wide audience since rapamycin is a widely used drug and is also employed in essays to probe protein-protein interactions, which could be affected by potential specific interactions of rapamycin with other membrane proteins, as illustrated herein.

Strengths:

The authors employ several experimental approaches to convincingly show that rapamycin activates directly the TRPM8 cation channel and not an accessory protein or the surrounding membrane. In general, the electrophysiological, mutational and fluorescence imaging experiments are adequately carried out and cautiously interpreted, presenting a clear picture of the direct interaction with TRPM8. In particular, the authors convincingly show that the interactions of rapamycin with TRPM8 are distinct from interactions of menthol with the same ion channel.

Weaknesses:

The main weakness of the manuscript is the NMR method employed to show that rapamycin binds to TRPM8. The authors developed and deployed a novel signal processing approach based on subtraction of several independent NMR spectra to show that rapamycin binds to the TRPM8 protein and not to the surrounding membrane or other proteins. While interesting and potentially useful, the method is not well developed (several positive controls are missing) and is not presented in a clear manner, such that the quality of data can be assessed and the reliability and pertinence of the subtraction procedure evaluated.

Reviewer #1 (Public Review):

The authors studied how hippocampal connectivity gradients across the lifespan, and how these relate to memory function and neurotransmitter distributions. They observed older age with less distinct transitions and observed an association between gradient de-differentiation and cognitive decline.

This is overall an innovative and interesting study to assess gradient alterations across the lifespan and its associations to cognition.

The paper is well-written, and the methods appear sound and thoughtful. There are several strengths, including the inclusion of two independent cohorts, the use of gradient mapping and alignment techniques, and an overall sound statistical and analysis framework. There are several areas for potential improvements in the paper, and these are listed below:

(1) The reported D1 associations appear a bit post-hoc in the current work and I was unclear why the authors specifically focussed on dopamine here, as other transmitter systems are similar present at the level of the hippocampus and implicated in aging.

Moreover, the authors may be aware that multiple PET tracers are somewhat challenged in the mesiotemporal region. Is this the case for the D1 receptor as well? The hippocampus is a small and complex structure, and PET more of a low res technique so one would want to highlight and discuss the limitations of the correlations with PET maps here and/or evaluate whether the analysis adds necessary findings to the study.

From my (perhaps somewhat biased) perspective, it might be valuable to instead or in addition look at measures of hippocampal microstructure and how these relate to the functional aging effects. This could be done, if available, using data from the same subjects (eg based on quantitative MRI contrasts and/or structural MRI) and/or using contextualization findings as implemented in eg hippomaps.readthedocs.io

(2) Can the authors clarify why they did not replicate based on cohorts that are more widely used in the community and open access, such as CamCAN and/or HCP-Aging? It might connect their results with other studies if an attempt was made to also show that findings persist in either of these repositories.

(3) The authors applied TSM and related these parameters to topographic changes in the gradients. I was wondering whether and how such an approach controls for autocorrelation present in both the PET map and gradients. Could the authors clarify?

(4) The TSM approach quantifies the gradients in terms of x/y/z direction in a cartesian coordinate system. Wouldn't a shape intrinsic coordinate system in the hippocampus also be interesting, and perhaps even be more efficient to look at here (see eg DeKraker 2022 eLife or Paquola et al 2020 eLife)?

Reviewer #2 (Public Review):

Summary:

This paper derives the first three functional gradients in the left and right hippocampus across two datasets. These gradient maps are then compared to dopamine receptor maps obtained with PET, associated with age, and linked to memory. Results reveal links between dopamine maps and gradient 2, age with gradients 1 and 2, and memory performance.

Strengths:

This paper investigates how hippocampal gradients relate to aging, memory, and dopamine receptors, which are interesting and important questions. A strength of the paper is that some of the findings were replicated in a separate sample.

Weaknesses

The paper would benefit from added clarification on the number of models/comparisons for each test. Furthermore, it would be helpful to clarify whether or not multiple comparison correction was performed and - if so - what type or - if not - to provide a justification. The manuscript would furthermore benefit from code sharing and clarifying which results did/did not replicate.

Reviewer #3 (Public Review):

Summary:

In this study, the authors analyzed the complex functional organization of the hippocampus using two separate adult lifespan datasets. They investigated how individual variations in the detailed connectivity patterns within the hippocampus relate to behavioral and molecular traits. The findings confirm three overlapping hippocampal gradients and reveal that each is linked to established functional patterns in the cortex, the arrangement of dopamine receptors within the hippocampus, and differences in memory abilities among individuals. By employing multivariate data analysis techniques, they identified older adults who display a hippocampal gradient pattern resembling that of younger individuals and exhibit better memory performance compared to their age-matched peers. This underscores the behavioral importance of maintaining a specific functional organization within the hippocampus as people age.

Strengths:

The evidence supporting the conclusions is overall compelling, based on a unique dataset, rich set of carefully unpacked results, and an in-depth data analysis. Possible confounds are carefully considered and ruled out.

Weaknesses:

No major weaknesses. The transparency of the statistical analyses could be improved by explicitly (1) stating what tests and corrections (if any) were performed, and (2) justifying the elected statistical approaches. Further, some of the findings related to the DA markers are borderline statistically significant and therefore perhaps less compelling but they line up nicely with results obtained using experimental animals and I expect the small effect sizes to be largely related to the quality and specificity of the PET data rather than the derived functional connectivity gradients.

Reviewer #1 (Public Review):

Summary:

This study reports single-cell RNA sequencing results of lung adenocarcinoma, comparing 4 treatment-naive and 5 post-neoadjuvant chemotherapy tumor samples.<br /> The authors claim that there are metabolic reprogramming in tumor cells as well as stromal and immune cells after chemotherapy.<br /> The most significant findings are in the macrophages that there are more pro-tumorigenic cells after chemotherapy, i.e. CD45+CD11b+ARG+ cells. In the treatment-naive samples, more anti-tumorigenic CD45+CD11b+CD86+ macrophages are found. They sorted each population and performed functional analyses.

Strengths:

Comparison of the treatment-naive and post-chemotherapy samples of lung adenocarcinoma.

Weaknesses:

(1) Lengthy descriptive clustering analysis, with indistinct direct comparisons between the treatment-naive and the post-chemotherapy samples.<br /> (2) No statistical analysis was performed for the comparison.<br /> (3) Difficult to match data to the text.<br /> (4) ARG1 is a cytosolic enzyme that can be detected by intracellular staining after fixation. It is unclear how the staining and sorting was performed to measure function of sorted cells.

Reviewer #2 (Public Review):

In this study, Huang et al. performed a scRNA-seq analysis of lung adenocarcinoma (LUAD) specimens from 9 human patients, including 5 who received neoadjuvant chemotherapy (NCT), and 4 without treatment (control). The new data was produced using 10 × Genomics technology and comprises 83622 cells, of which 50055 and 33567 cells were derived from the NCT and control groups, respectively. Data was processed via R Seurat package, and various downstream analyses were conducted, including CNV, GSVA, functional enrichment, cell-cell interaction, and pseudotime trajectory analyses. Additionally, the authors performed several experiments for in vitro and in vivo validation of their findings, such as immunohistochemistry, immunofluorescence, flow cytometry, and animal experiments.

The study extensively discusses the heterogeneity of cell populations in LUAD, comparing the samples with and without chemotherapy. However, there are several shortcomings that diminish the quality of this paper:

• The number of cells included in the dataset is limited, and the number of patients from different groups is low, which may reduce the attractiveness of the dataset for other researchers to reuse. Additionally, there is no metadata on patients' clinical characteristics, such as age, sex, history of smoking, etc., which would be valuable for future studies.<br /> • Several crucial details about the data analysis are missing: How many PCs were used for reduction? Which versions of Seurat/inferCNV/other packages were used? Why monocle2 was used and not monocle3 or other packages? Also, the authors use R version 3.6.1, and the current version is 4.3.2.<br /> • It seems that the authors may lack a fundamental understanding of scRNA-seq data processing and the functions of Seurat. For instance, they state, 'Next, we classified cell types through dimensional reduction and unsupervised clustering via the Seurat package.' However, dimensional reduction and unsupervised clustering are not methods for cell classification. Typically, cell types are classified using marker genes or other established methods.<br /> "Therefore, to identify subclusters within each of these nine major cell types, we performed principal component analysis" (Line 127). Principal component analysis is a method for dimensionality reduction, not cell clustering.<br /> The authors did not mention the normalization or scaling of the data, which are crucial steps in scRNA-seq data preprocessing.<br /> • Numerous style and grammar mistakes are present in the main text. For instance, certain sections of the methods are written in the present tense, suggesting that parts of a protocol were copied without text editing. Furthermore, some sections of the introduction are written in the past tense when the present tense would be more suitable. Clusters are inconsistently referred to by numbers or cell types, leading to confusion. Additionally, the authors frequently use the term "evolution" when describing trajectory analysis, which may not be appropriate. Overall, significant revisions to the main text are required.<br /> • Some figures are not mentioned in order or are not referenced in the text at all, such as Figure 5l (where it is also unclear how the authors selected the root cells). Additionally, many figures have text that is too small to be read without zooming in. Overall, the quality of the figures is inconsistent and sometimes very poor.<br /> • At times, the authors' statements are incomplete (ex. Lines 67-69, Line 177, Line 629, Lines 646-648 and 678).

The results section lacks clarity on several points:<br /> • The authors state that "myofibroblasts exclusively originated from the control group". However, pathways up-regulated in myofibroblasts (such as glycolysis) were enhanced after chemotherapy, as indicated by GSVA score. Similarly, why are some clusters of TAMs from the control group associated with pathways enriched in chemotherapy group?<br /> • Further explanation is necessary regarding the distinctions between malignant and non-malignant cells, as well as regarding the upregulation of metabolism-related pathways in fibroblasts from the NCT group. Additionally, clarification is needed regarding why certain TAMs from the control group are associated with pathways enriched in the chemotherapy group.<br /> • In the section titled 'Chemo-driven Pro-mac and Anti-mac Metabolic Reprogramming Exerted Diametrically Opposite Effects on Tumor Cells': The markers selected to characterize the anti- and pro-macrophages are commonly employed for describing M1 or M2 polarization. It is uncertain whether this new classification into anti- and pro-macrophages is necessary. Additionally, it should be noted that pro-macrophages are anti-inflammatory, while anti-macrophages are pro-inflammatory, which could lead to confusion. M2 macrophages are already recognized for their role in stimulating tumor relapse after chemotherapy.<br /> • The authors suggest that there is "reprogramming of CD8+ cytotoxic cells" following chemotherapy (Line 409). It remains unclear whether they imply the reprogramming of other CD8+ T cells into cytotoxic cells. While it is indicated that cytotoxic cells from the control group differ from those in the NCT group and that NCT cytotoxic T cells exhibit higher cytotoxicity, the authors did not assess the expression of NK and NK-like T cell markers (aside from NKG7), which may possess greater cytotoxic potential than CD8+ cytotoxic cells. This could also elucidate why cytotoxic cells from the NCT and control groups are positioned on separate branches in trajectory analysis. Overall, with 22.5k T cells in the dataset, only 3 subtypes were identified, suggesting a need for improved cell annotations by the authors.

Reviewer #1 (Public Review):

In this manuscript, Molnar, Suranyi and colleagues have probed the genomic stability of Mycobacterium smegmatis in response to several anti-tuberculosis drugs as monotherapy and in combination. Unlike the study by Nyinoh and McFaddden http://dx.doi.org/10.1002/ddr.21497 (which should be cited), the authors use a sub-lethal dose of antibiotic. While this is motivated by sound technical considerations, the biological and therapeutic rationale could be further elaborated. The results the authors obtain are in line with papers examining the genomic mutation rate in vitro and from patient samples in Mycobacterium tuberculosis, in vitro in Mycobacterium smegmatis and in vitro in Mycobacterium tuberculosis (although the study by HL David (PMID: 4991927) is not cited). The results are confirmatory of previous studies. It is therefore puzzling why the authors propose the opposite hypothesis in the paper (i.e antibiotic exposure should increase mutation rates) merely to tear it down later. This straw-man style is entirely unnecessary. The results on the nucleotide pools are interesting, but the statistically significant data is difficult to identify as presented, and therefore the new biological insights are unclear. Finally, the authors show that a fluctuation assay generates mutations with higher frequencies that the genetic stability assays, confirming the well-known effect of phenotypic antibiotic resistance.

Reviewer #2 (Public Review):

In this study, the authors assess whether selective pressure from drug chemotherapy influences the emergence of drug resistance through the acquisition of genetic mutations or phenotypic tolerance. I commend the authors on their approach of utilizing the mutation accumulation (MA) assay as a means to answer this and whole genome sequencing of clones from the assay convincingly demonstrates low mutation rates in Mycobacteria when exposed to sub-inhibitory concentrations of antibiotics. Also, quantitative PCR highlighted the upregulation of DNA repair genes in Mycobacteria following drug treatment, implying the preservation of genomic integrity via specific repair pathways.

Even though the findings stem from M. smegmatis exposure to antibiotics under in vitro conditions, this is still relevant in the context of the development of drug resistance so I can see where the authors' train of thought was heading in exploring this. However, I think important experiments to perform to more fully support the conclusion that resistance is largely associated with phenotypic rather than genetic factors would have been to either sequence clones from the ciprofloxacin tolerance assay (to show absence/ minimal genetic mutations) or to have tested the MIC of clones from the MA assay (to show an increase in MIC). There seems to be a disconnect between making these conclusions from experiments conducted under different conditions, or perhaps the authors can clarify why this was done. With regards to the sub-inhibitory drug concentration applied, there is significant variation in the viability as calculated by CFUs following the different treatments and there is evidence that cell death greatly affects the calculation of mutation rate (PMCID: PMC5966242). For instance, the COMBO treatment led to 6% viability whilst the INH treatment led to 80% cell viability. Are there any adjustments made to take this into account? It would also be useful to the reader to include a supplementary table of the SNPs detected from the lineages of each treatment - to determine if at any point rifampicin treatment led to mutations in rpoB, isoniazid to katG mutations, etc. Overall, while this study is tantalizingly suggestive of phenotypic tolerance playing a leading role in drug resistance (and perhaps genetic mutations a sub-ordinate role) a more substantial link is needed to clarify this.

Reviewer #3 (Public Review):

Summary:

This manuscript describes how antibiotics influence genetic stability and survival in Mycobacterium smegmatis. Prolonged treatment with first-line antibiotics did not significantly impact mutation rates. Instead, adaptation to these drugs appears to be mediated by upregulation of DNA repair enzymes. While this study offers robust data, findings remain correlative and fall short of providing mechanistic insights.

Strengths:

The strength of this study is the use of genome-wide approaches to address the specific question of whether or not mycobacteria induce mutagenic potential upon antibiotic exposure.

Weaknesses:

The authors suggest that the upregulation of DNA repair enzymes ensures a low mutation rate under drug pressure. However, this suggestion is based on correlative data, and there is no mechanistic validation of their speculations in this study.

Furthermore, as detailed below, some of the statements made by the authors are not substantiated by the data presented in the manuscript.

Finally, some clarifications are needed for the methodologies employed in this study. Most importantly, reduced colony growth should be demonstrated on agar plates to indicate that the drug concentrations calculated from liquid culture growth can be applied to agar surface growth. Without such validations, the lack of induced mutation could simply be due to the fact that the drug concentrations used in this study were insufficient.

Reviewer #1 (Public Review):

Summary:

In the work: "Endosomal sorting protein SNX4 limits synaptic vesicle docking and release" Josse Poppinga and collaborators addressed the synaptic function of Sortin-Nexin 4 (SNX4). Employing a newly developed in vitro KO model, with live imaging experiments, electrophysiological recordings, and ultrastructural analysis, the authors evaluate modifications in synaptic morphology and function upon loss of SNX4. The data demonstrate increased neurotransmitter release and alteration in synapse ultrastructure with a higher number of docked vesicles and shorter AZ. The evaluation of the presynaptic function of SNX4 is of relevance and tackles an open and yet unresolved question in the field of presynaptic physiology.

Strengths:

The sequential characterization of the cellular model is nicely conducted and the different techniques employed are appropriate for the morpho-functional analysis of the synaptic phenotype and the derived conclusions on SNX4 function at presynaptic site. The authors succeeded in presenting a novel in vitro model that resulted in chronical deletion of SNX4 in neurons. A convincing sequence of experimental techniques is applied to the model to unravel the role of SNX4, whose functions in neuronal cells and at synapses are largely unknown. The understanding of the role of endosomal sorting at the presynaptic site is relevant and of high interest in the field of synaptic physiology and in the pathophysiology of the many described synaptopathies that broadly result in loss of synaptic fidelity and quality control at release sites.

Weaknesses:

The flow of the data presentation is mostly descriptive with several consistent morphological and functional modifications upon SNX loss. The paper would benefit from a wider characterization that would allow us to address the physiological roles of SNX4 at the synaptic site and speculate on the underlying molecular mechanisms. In addition, due to the described role of SNX4 in autophagy and the high interest in the regulation of synaptic autophagy in the field of synaptic physiology, an initial evaluation of the autophagy phenotype in the neuronal SNX4KO model is important, and not to be only restricted to the discussion section.

Reviewer #2 (Public Review):

Summary:

SNX4 is thought to mediate recycling from endosomes back to the plasma membrane in cells. In this study, the authors demonstrate the increases in the amounts of transmitter release and the number of docked vesicles by combining genetics, electrophysiology, and EM. They failed to find evidence for its role in synaptic vesicle cycling and endocytosis, which may be intuitively closer to the endosome function.

Strengths:

The electrophysiological data and EM data are in principle, convincing, though there are several issues in the study.

Weaknesses:

It is unclear why the increase in the amounts of transmitter release and docked vesicles happened in the SNX4 KO mice. In other words, it is unclear how the endosomal sorting proteins in the end regulate or are connected to presynaptic, particularly the active zone function.

Reviewer #3 (Public Review):

Summary:

The study aims to determine whether the endosomal protein SNX4 performs a role in neurotransmitter release and synaptic vesicle recycling. The authors exploited a newly generated conditional knockout mouse to allow them to interrogate the SNX4 function. A series of basic parameters were assessed, with an observed impact on neurotransmitter release and active zone morphology. The work is interesting, however as things currently stand, the work is descriptive with little mechanistic insight. There are a number of places where the data appear to be a little preliminary, and some of the conclusions require further validation.

Strengths:

The strengths of the work are the state-of-the-art methods to monitor presynaptic function.

Weaknesses:

The weaknesses are the fact that the work is largely descriptive, with no mechanistic insight into the role of SNX4. Further weaknesses are the absence of controls in some experiments and the design of specific experiments.

Reviewer #2 (Public Review):

Summary:

The paper entitled "Goal-directed motor actions drive acetylcholine dynamics in sensory cortex" aims to characterize the dynamics of cholinergic signaling in sensory cortex during perceptual behavior. The authors showed that acetylcholine release in S1 was linked to goal-directed motor actions rather than sensory input or reward delivery, a pattern also observed in the auditory cortex (A1). This release was specifically associated with whisking and licking and was potentiated by training. The results contribute to a better understanding of neuromodulator actions. That said, several aspects of the manuscript could benefit from improved writing, data presentation, and statistical analysis.

Strengths:

The evidence provided is clear to link ACh response to different task-related events. Implementing two different tasks to show generality is appreciated. Important control analysis is included.

Weaknesses:

The quantification of ACh signal differences across different trial types or between expert and early-training mice is lacking. Although statistical significance is occasionally mentioned, the indication of significance in figures seems rare. For example, in Figures 5A and E, it is difficult to tell when p is < 0.05. Based on the sentence "small, but significant increase on Hits over False Alarm trials (Figure 5A, S Figure 4A)" there is indeed a time point where the difference is significant, and more details should be added (when and the p-value).

For Figure 5D, it seems like there is no significant difference between Hit and False alarm trials, however, for the trials with 1 or 2 lick there appears to be a difference. Is it due to a lack of power? Moreover, in Figure 5 H the first licks also seem to differ.

Linear regression: the coefficient of determination (R²) is absent, in Figures 4E, F, and 6B, H, making it hard to evaluate the goodness of the fitting.

Similar comments apply to Figure 7: the lack of quantitative comparisons between the coefficients of first lick and other regressors, and between early and expert training, as well as the change in goodness of fit by removing a regressor.

The writing of the introduction and discussion could be improved to enhance readability, and the manuscript could improve its discussion on orofacial movement and acetylcholine release by citing relevant studies demonstrating the association between neuronal activity and orofacial/body movements.

Reviewer #1 (Public Review):

Summary:

This study aimed at gaining a better comprehension of the functional role of acetylcholine release within the sensory cortex. To this end, the authors measured the dynamics of cortical acetylcholine release using two-photon imaging of the GRAB-Ach3.0 fluorescent sensor, either in the mouse primary somatosensory cortex (S1), throughout the learning of a whisker-dependent object position discrimination task, or in the primary auditory cortex (A1) of mice engaged in a specific sound signal detection task.

The illustrated results suggest that variations in acetylcholine release tend to be associated, in the primary sensory areas, with goal-directed actions (whisking in the case of the object position discrimination task, and more strongly with licking), rather than with sensory inputs or rewards. They also indicate that the variations in cholinergic signal specifically associated with licking increase with learning.

Strengths:

The impact of cholinergic inputs on cortical function has intrigued neuroscientists for many decades due to the complexity of its mode of action on the molecular and cellular points of view.

Being able to image the dynamics of cortical cholinergic release in vivo on mice engaged in goal-directed tasks has moved this field into a really exciting phase, where it becomes possible to draw links between specific behavioral features and local variations of cholinergic release in given cortical areas.

This study is therefore particularly timely, it provides a set of precious and original data. Globally the experiments were rigorously designed, and the illustrated quantifications and analyses follow high standards. This work therefore constitutes a valuable contribution to this field of research and could be of interest to a large audience.

Weaknesses:

Although the manuscript reports very interesting links between behavior and cortical cholinergic release, the study remains correlative and is devoid of experiments allowing to link causally cholinergic cortical inputs with motor actions, and more globally to gauge their impact on learning and execution of the tasks. Since the nature of the link between goal-directed motor actions and acetylcholine dynamics is not really clarified here, the word "drive" in the title of the paper, which may have a causal connotation should be replaced (especially since acetylcholine-related signal fluctuations seems often to precede motor actions).

As high-speed videography of the C2 whisker was achieved during the object position discrimination task, it seems that the whisker curvature changes could have been quantified in addition to the whisker angle. This would allow appreciation of how acetylcholine related signals vary according to both whisker-related motor output and sensory input, hereby providing clearer support for the assertion that acetylcholine levels are "related to motor actions rather than sensory inputs".

The data set related to the auditory task is used here to support the claim that licks rather than rewards are linked to variations of fluorescence of the cholinergic sensor in sensory cortices. These data seem very interesting indeed but are shown here in a very incomplete manner (a figure illustrating the learning curves of the 6 recorded animals, and acetylcholine dynamics during the four types of trials would be very welcome). If the animals were placed on a treadmill and the locomotion measured, together with pupil size, during the task as in Gee et al., BioRxiv 2022, one could ask how these other motor activities are linked with acetylcholine dynamics in A1. By comparing the impact of goal-directed actions versus motor activities accompanying more global state transitions on acetylcholine dynamics, these data could provide a particularly valuable contribution to this study. They could in addition rule out potential confounding factors regarding the claim that cholinergic dynamics are here mainly linked to first licks.

Coming back to the whisker-dependent object localization task, if cholinergic-related signals have been recorded during the "no whisker sessions", analyzing these data would be very useful in the scope of this study. Indeed, during these sessions, the animals were not naive, since they went through the learning of the task, but could not resolve it anymore, still they most probably kept on licking upon the pole-in and/or pole-out cues. In these sessions, the licking is fully dissociated from tactile sensory inputs, and for this reason it would be particularly interesting to see how the fluorescence varies with first licks. In addition, plotting these sessions in Figure 6C would be informative. Indeed, if the increase of cholinergic signals with performance comes progressively due to changes in the internal state of the animal and/or plasticity mechanisms, first lick related cholinergic signal variations could remain high despite the decrease of performance in these sessions.

Finally, because the functional role of cortical cholinergic release is a hot topic, a few recent studies addressing this question with slightly different approaches in the visual cortex would be worth mentioning, at least in the discussion, as well as a recent study focusing on motor learning, which revealed an apparent decrease of acetylcholine dynamics associated with goal-directed motor actions upon learning.

Reviewer #2 (Public Review):

Summary:

While many studies have explored the impacts of pathogens on hosts, the effect of hosts on pathogens has received less attention. In this manuscript, Wang et al. utilize Drosophila melanogaster and an opportunistic pathogen, Serratia marcescens, to explore how the host impacts pathogenicity. Beginning with an observation that larval presence and density impacted microbial growth in fly vials (which they assess qualitatively as the amount of 'slick' and quantitatively as microbial load/CFUs), the authors focus on the impact of axenic/germ-free larvae on an opportunistic pathogen S. marcescens. Similar to their observations with general microbial load, they find that larvae reduce the presence of a pinkish slick of Sm, indicative of its secondary metabolite prodigiosin. The presence of larvae alters prodigiosin production, pathogen load, pathogen cellular morphology, and virulence, and this effect is through transcriptional and metabolic changes in the pathogen. Overall, they observe a loss of virulence factors/pathways and an increase in pathways contributing to growth. Given the important role the host plays in this lifestyle shift, the authors then examined host features that might influence these effects, focusing on the role of antimicrobial peptides (Amps). The authors combine the use of synthetic Amps and an Amp-deficient fly line and conclude much of the larval inhibitory effect is due to their production of AMPs.

Strengths:

This is a very interesting question and the use of Drosophila-Serratia marcescens is a great model to explore these interactions and effects.

The authors have an interesting and compelling phenotype and are asking a unique question on the impact of the host on the pathogen. The use of microbial transcriptomics and metabolomics is a strength, especially in order to assess these impacts on the pathogen level and at single-cell level to capture heterogeneity.

Weaknesses:

Overall, the writing style in the manuscript makes it difficult to fully understand and appreciate the data and its interpretation.

The data on the role of AMPs would benefit from strengthening. Some of the arguments in the text of that section are also counterintuitive. The authors show that AMP larvae have a reduced impact on Sm as compared to wt larvae, but it seems less mild of an effect than that observed with wt excreta (assuming the same as secreta in Figures 7, should be corrected or harmonized). Higher doses of AMPs give a phenotype similar to wt larvae, but a lower dose (40 ng/ul) gives phenotypes more similar to controls. The authors argue that this data suggests AMPs are the factor responsible for much of the inhibition, but their data seems more to support that it's synergistic- you seem to still need larvae (or some not yet defined feature larvae make, although secreta/excreta was not sufficient) + AMPs to see similar effects as wt. Based on positioning and color scheme guessing that AMP 40ng/ul was used in Figures 7D-H, but could not find this detail in the text, methods, or figure legend and it should be indicated. This section does not seem to be well supported by the provided data, and this inconsistency greatly dampened this reviewer's enthusiasm for the paper.

Reviewer #1 (Public Review):

Summary:

In this work, Wang and colleagues used Drosophila-Serratia as a host-microbe model to investigate the impact of the host on gut bacteria. The authors showed that Drosophila larvae reduce S. marcescens abundance in the food likely due to a combination of mechanical force and secretion of antimicrobial peptides. S. marcescens exposed to Drosophila larvae lost virulence to flies and could promote larval growth similar to typical Drosophila gut commensals. These phenotypic changes were reflected in the transcriptome and metabolome of bacteria, suggesting that the host could drive the switch from pathogenicity to commensalism in bacteria. Further, the authors used single-cell bacterial RNA-seq to demonstrate the heterogeneity in gut bacterial populations.

Strengths:

This is a valuable work that addresses an important question of the effect of the host on its gut microbes. The authors could convincingly demonstrate that gut bacteria are strongly affected by the host with important consequences for both interacting partners. Moreover, the authors used state-of-the-art bacterial single-cell RNA-seq to reveal heterogeneity in host-associated commensal populations.

Weaknesses:

Some of the conclusions are not fully supported by the data.

Specifically, in lines 142-143, the authors claim that larva antagonizes the pathogenicity of S. marcescens based on the survival data. I do not fully agree with this statement. An alternative possibility could be that, since there are fewer S. marcescens in larvae-processed food, flies receive a lower pathogen load and consequently survive. Can the authors rule this out?

Also, the authors propose that Drosophila larvae induce a transition from pathogenicity to commensalism in S. marcescens and provide nice phenotypic and transcriptomic data supporting this claim. However, is it driven only by transcriptional changes? Considering high mutation rates in bacteria, it is possible that S. marcescens during growth in the presence of larvae acquired mutations causing all the observed phenotypic and transcriptional changes. To test this possibility, the authors could check how long S. marcescens maintains the traits it acquires during growth with Drosophila. If these traits persist after reculturing isolated bacteria, it is very likely they are caused by genome alterations, if not - likely it is a phenotypic switch driven by transcriptional changes.

Reviewer #3 (Public Review):

In this study, Wang and coworkers established a model of Drosophila-S. marcescens interactions and thoroughly examined host-microbe bidirectional interactions. They found that:

(1) Drosophila larvae directly impact microbial aggregation and density;<br /> (2) Drosophila larvae affect microbial metabolism and cell wall morphology, as evidenced by reduced prodigiosin production and EPS production, respectively;<br /> (3) Drosophila larvae attenuate microbial virulence;<br /> (4) Drosophila larvae modulate the global transcription of microbes for adaptation to the host;<br /> (5) Microbial single-cell RNA sequencing (scRNA-seq) analysis revealed heterogeneity in microbial pathogenicity and growth;<br /> (6) AMPs are key factors controlling microbial virulence phenotypes.

Taken together, they concluded that host immune factors such as AMPs are directly involved in the pathogen-to-commensal transition by altering microbial transcription.

General comments:

In general, this study is intriguing as it demonstrates that host immune effectors such as AMPs can serve as critical factors capable of modulating microbial transcription for host-microbe symbiosis. However, several important questions remain unanswered. One such question is: What is the mechanism by which AMPs modulate the pathogen-to-commensal transition? One hypothesis suggests that antimicrobial activity may influence microbial physiology, subsequently modulating transcription for the transition from pathogen to commensal. In this context, it is imperative to test various antibiotics with different modes of action (e.g., targeting the cell wall, transcription, or translation) at sub-lethal concentrations to determine whether sub-lethal doses of antimicrobial activity are sufficient to induce the pathogen-to-commensal transition.

Reviewer #1 (Public Review):

In this study, the authors explore the implications of two types of rhythmic inhibition - "gamma" (30-80 Hz) and "beta"(13-30Hz) - for synaptic integration. They study this in a multi-compartmental model L5 pyramidal neuron with Poisson excitation and rhythmic inhibition (16 Hz and 64 Hz), applied either to the perisomatic or apical tuft regions in the neuron. They find that 64 Hz inhibition applied to the cell body is effective in phasic modulation of AP generation, while 16 Hz inhibition applied to the apical tufts is effective in phasic modulation of dendritic spikes (in addition to APs). Switching the location of the two kinds of rhythmic inhibition reduces the overall excitability, but is not effective in phasic modulation of either dendritic spikes and weakly so for somatic APs.

Strengths:

The effect of the timescale of rhythmic inhibition on synaptic integration is an interesting question, since a) rhythmic spiking is most strongly evident in inhibitory population, b) rhythmic spiking is modulated by behavioral states and the sensory environment. The methods are clear and the data are well-presented. The study systematically explores the effect of two frequencies of rhythmic inhibition in a biophysically detailed model. The study considers not only idealized rhythmic inhibition but also the bursty kind that is observed in in-vivo conditions. Both distributed and clustered excitatory synaptic organization are simulated, which covers the two extremes of the spatial organization of excitatory inputs in-vivo.

Weaknesses:

SOM+ interneurons such as Martinotti cells target the apical tufts of pyramidals in the cortex. Since interneurons in general are strongly implicated in mediating rhythmic population activity over a range of timescales, it is quite appropriate to study the consequence of rhythmic inhibition provided by SOM+ interneurons for synaptic integration, including the phenomenon of dendritic spikes. However, using conclusions from a singular study (ref 22) to identify the beta band as the rhythm mediated by SOM+ is not very accurate. SOM+ interneurons have been implicated in regulating rhythms centered just below 30 Hz (refs 22, 21). It is a range that lies in the grey zone of the traditional definition of beta and gamma. However, it is significantly higher than the 16 Hz rhythms explored in this study. It thus remains unknown how a 25-30 Hz rhythmic inhibition (that has an experimentally suggested role for dendrite targeting SOM+ INs) in apical tufts regulates dendritic spikes.

Distal dendritic inhibition has been previously shown to be more effective in controlling dendritic spikes. However, given the slow timescale of dendritic spikes, it can be hypothesized that high-frequency rhythmic inhibition would be ineffective in entraining the dendritic spikes either in distal or proximal location, as demonstrated by 4H and 5F, and vice versa. A computational study can take this further by exploring the robustness of this hypothesis. By sticking to a single-frequency definition of what constitutes Gamma (64 Hz) and Beta (16 Hz) inhibition, the current exploration does support the core hypothesis. However, given the temporal dynamics of dendritic spikes, it is valuable to learn, for example, the upper bound of "Beta" range (13-30Hz) inhibition that fails to phasically modulate them. In addition to the reason stated in the earlier paragraph, Alpha band activity (8-12 Hz), has been implicated (e.g. van Kerkoerle, 2014) in signaling of inter-areal feedback to the superficial layer in the cortex, potentially targeting apical tufts of pyramidals from multiple layers and resulting in alpha-range rhythmic inhibition. To make the findings significant, it might therefore be more pertinent to understand the consequences of ~10Hz rhythmic inhibition (in addition to the ~25-30 Hz Beta/Gamma) in the apical tufts for phasic modulation of dendritic spikes.

The differential effect of Gamma and Beta range inhibition on basal and apical excitatory clusters is not convincing from the information provided. The basal cluster appears to overlap with perisomatic inhibitory synapses. The description in the methods does not have enough information to negate the visual perception (ln 979-81). With this understanding, it is not surprising that the correlation between excitation and APs is high (during the trough of gamma) for basal and not apical excitation. A more comparable scenario would be a more distal location of the basal excitatory cluster.

Reviewer #2 (Public Review):

Summary:

The manuscript illustrates how spatial targeting (perisomatic vs distal, apical, and basal dendritic) and timing of inhibition are crucial to distinct effects on neuronal integration and show that beta and gamma oscillations differentially engage dendritic spiking mechanisms.

Strengths:

The strength of this study lies in the integrative biophysical modelling of a layer 5 pyramidal neuron by bringing together in vitro and in vivo observations.

Weaknesses:

The weaknesses are probably in some of the parameterizations of inhibitory synaptic dynamics. A unitary peak conductance of 1nS is very high for inhibitory synapses. This high value could invariably skew some of the network-level predictions. The authors could obtain specific parameters from the Neocortical Collaboration Portal (https://bbp.epfl.ch/nmc-portal/microcircuit.html), which is an incredible resource for cortical neurons and synapses.

Reviewer #3 (Public Review):

Summary:

The authors consider several known aspects of PV and SOM interneurons and tie them together into a coherent single-cell model that demonstrates how the aspects interact. These aspects are:<br /> (1) While SOM interneurons target distal parts of pyramidal cell dendrites, PV interneurons target perisomatic regions.<br /> (2) SOM interneurons are associated with beta rhythms, PV interneurons with gamma rhythms.<br /> (3) Clustered excitation on dendrites can trigger various forms of dendritic spikes independent of somatic spikes. The main finding is that SOM and PV interneurons are not simply associated with beta and gamma frequencies respectively, but that their ability to modulate the activity of a pyramidal cell "works best" at their assigned frequencies. For example, distally targeting SOM interneurons are ideally placed to precisely modulate dendritic Ca-spikes when their firing is modulated at beta frequencies or timed relative to excitatory inputs. Outside those activity regimes, not only is modulation weakened, but overall firing reduced.

Strengths:

I think the greatest strength is the model itself. While the various individual findings were largely known or strongly expected, the model provides a coherent and quantitative picture of how they come together and interact.

The paper also powerfully demonstrates that an established view of "subtractive" vs. "divisive" inhibition may be too soma-focused and provide an incomplete picture in cells with dendritic nonlinearities giving rise to a separate, non-somatic all-or-nothing mechanism (Ca-spike).

Weaknesses:

While the authors overall did an admirable job of simulating the neuron in an in-vivo-like activity regime, I think it still provides an idealized picture that it optimized for the generation of the types of events the authors were interested in. That is not a problem per se - studying a mechanism under idealized conditions is a great advantage of simulation techniques - but this should be more clearly characterized. Specifics on this are very detailed and will follow in the comments to authors.

What disappointed me a bit was the lack of a concise summary of what we learned beyond the fact that beta and gamma act differently on dendritic integration. The individual paragraphs of the discussion often are 80% summary of existing theories and only a single vague statement about how the results in this study relate. I think a summarizing schematic or similar would help immensely.

Orthogonal to that, there were some points where the authors could have offered more depth on specific features. For example, the authors summarized that their "results suggest that the timescales of these rhythms align with the specialized impacts of SOM and PV interneurons on neuronal integration". Here they could go deeper and try to explain why SOM impact is specialized at slower time scales. (I think their results provide enough for a speculative outlook.)

Beyond that, the authors invite the community to reappraise the role of gamma and beta in coding. This idea seems to be hindered by the fact that I cannot find a mention of a release of the model used in this work. The base pyramidal cell model is of course available from the original study, but it would be helpful for follow-up work to release the complete setup including excitatory and inhibitory synapses and their activation in the different simulation paradigms used. As well as code related to that.

Impact:

Individually, most results were at least qualitatively known or at least expected. However, demonstrating that beta-modulation of dendritic events and gamma-modulation of soma spiking can work together, at the same time and in the same model can lead to highly valuable follow-up work. For example, by studying how top-down excitation onto apical compartments and bottom-up excitation on basal compartments interacts with the various rhythms; or what the impact of silencing of SOM neurons by VIP interneuron activation entails. But this requires - again - public release of the model and the code controlling the simulation setups.

Beyond that, the authors clearly demonstrated that a single compartment, i.e., only a soma-focused view is too simple, at least when beta is considered. Conversely, the authors were able to describe the impact of most things related to the apical dendrite on somatic spiking as "going through" the Ca-spike mechanism. Therefore, the setup may serve as the basis of constraining simplified two-compartment models in the future.

Reviewer #1 (Public Review):

Summary:

In this paper, Kalidini and Crevecoeur ask why sequential movements are sometimes coarticulated. To answer this question, first, they modified a standard optimal controller to perform consecutive reaches to two targets (T1 and T2). They investigated the optimal solution with and without a constraint on the endpoint's velocity in the via target (T1). They observed that the controller coarticulates the movements only when there is no constraint on the speed at the via-point. They characterized coarticulation in two ways: First, T2 affected the curvature of the first reach in unperturbed reaches. Second, T2 affected corrective movements in response to a mechanical perturbation of the first reach.

Parallel to the modeling work, they ran the same experiment on human participants. The participants were instructed to either consider T1 as via point (go task) or to slow down in T1 and then continue to T2 (stop task). Mirroring the simulation results, they observed coarticulation only in the go task. Interestingly, in the go task, when the initial reach was occasionally perturbed, the long-latency feedback responses differed for different T2 targets, suggesting that the information about the final target was already present in the motor circuits that mediate the long-latency response. In summary, they conclude that coarticulation in sequential tasks depends on instruction, and when coarticulation happens, the corrections in earlier segments of movement reflect the entirety of the coarticulated sequence.

Evaluation

Among many strengths of this paper, most notably, the results and the experiment design are grounded in, and guided by the optimal control simulation. The methods and procedures are appropriate and standard. The results and methods are explained sufficiently and the paper is written clearly. The results on modulation of long-latency response based on future goals are interesting and of broad interest for future experiments on motor control in sequential movement. However, I find the authors' framing of these results, mostly in the introduction section, somewhat complicated.

The current version of the introduction motivates the study by suggesting that "coarticulation and separation of sub-movement [in sequential movements] have been formulated as distinct hypotheses" and this apparent distinction, which led to contradictory results, can be resolved by Optimal Feedback Control (OFC) framework in which task-optimized control gains control coarticulation. This framing seems complicated for two main reasons. First, the authors use chunking and coarticulation interchangeably. However, as originally proposed by (Miller 1956), the chunking of the sequence items may fully occur at an abstract level like working memory, with no motoric coarticulation of sequence elements at the level of motor execution. In this scenario, sequence production will be faster due to the proactive preparation of sequence elements. This simple dissociation between chunking and coarticulation may already explain the apparent contradiction between the previous works mentioned in the introduction section. Second, the authors propose the OFC as a novel approach for studying neural correlates of sequence production. While I agree that OFC simulations can be highly insightful as a normative model for understanding the importance of sequence elements, it is unclear to me how OFCs can generate new hypotheses regarding the neural implementation of sequential movements. For instance, if the control gains are summarizing the instruction of the task and the relevance of future targets, it is unclear in which brain areas, or how these control gains are implemented. I believe the manuscript will benefit from making points more clear in the introduction and the discussion sections.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors examine the question of whether discrete action sequences and coarticulated continuous sequential actions can be produced from the same controller, without having to derive separate control policies for each sequential movement. Using modeling and behavioral experiments, the authors demonstrate that this is indeed possible if the constraints of the policy are appropriately specified. These results are of interest to those interested in motor sequences, but it is unclear whether these findings can be interpreted to apply to the control of sequences more broadly (see weaknesses below).

Strengths:

The authors provide an interesting and novel extension of the stochastic optimal control model to demonstrate how different temporal constraints can lead to either individual or coarticulated movements. The authors use this model to make predictions about patterns of behavior (e.g., in response to perturbations), which they then demonstrate in human participants both by measuring movement kinematics as well as EMG. Together this work supports the authors' primary claims regarding how changes in task instructions (i.e., task constraints) can result in coarticulated or separated movement sequences and the extent to which the subsequent movement goal affects the planning and control of the previous movement.

Weaknesses:

I reviewed a prior version of this manuscript, and appreciate the authors addressing many of my previous comments. However, there are some concerns, particularly with regard to how the authors interpret their findings.

(1) It would be helpful for the authors to discuss whether they think there is a fundamental distinction between a coarticulated sequence and a single movement passing through a via point (or equivalently, avoiding an obstacle). The notion of a coarticulated sequence brings with it the notion of sequential (sub)movements and temporal structure, whereas the latter can be treated as more of a constraint on the production of a single continuous movement. If I am interpreting the authors' findings correctly it seems they are suggesting that these are not truly different kinds of movements at the level of a control policy, but it would be helpful for the authors to clarify this claim.

(2) The authors' model clearly shows that each subsequent target only influences the movement of one target back, but not earlier ones (page 7 lines 199-204). This stands in contrast to the paper they cite from Kashefi 2023, in which those authors clearly show that people account for at least 2 targets in the future when planning/executing the current movement. It would be useful to know whether this distinction arises because of a difference in experimental methodology, or because the model is not capturing something about human behavior.

(3) In my prior review I raised a concern that the authors seem to be claiming that because they can use a single control policy for both coarticulated and separated movement sequences, there need not be any higher-level or explicit specification of whether the movements are sequential. While much of that language has been removed, it still appears in a few places (e.g., p. 13, lines 403-404). As previously noted, the authors' control policy can generate both types of movements as long as the proper constraints are provided to the model. However, these constraints must be specified somewhere (potentially explicitly, as the authors do by providing them as task instructions). Moreover, in typical sequence tasks, although some movements become coarticulated, people also tend to form chunks with distinct chunk boundaries, which presumably means that there is at least some specification of the sequential ordering of these chunks that must exist (otherwise the authors' model might suggest that people can coarticulate forever without needing to exhibit any chunk boundaries). Hence the authors should limit themselves to the narrow claim that a single control policy can lead to separated or coarticulated movements given an appropriate set of constraints, but acknowledge that their work cannot speak to where or how those constraints are specified in humans (i.e., that there could still be an explicit sequence representation guiding coarticulation).

Reviewer #3 (Public Review):

Summary:

In this study the authors tested for alterations in selection intensity across ~13,000 protein coding genes along the gorilla lineage in order to test the hypothesis that the evolution of a polygynous social system resulted in relaxed selective constraint through a reduction in sperm competition. Of these genes, 578 exhibited signatures of relaxed purifying selection that were enriched for functions in male germ cells including meiosis and sperm biology. These genes were also more likely expressed in male germ cells and to contain deleterious mutations. Functional analysis of genes not previously implicated in male reproduction identified 41 new genes essential to male fertility in a Drosophila model. Moreover, genes under relaxed selective constraint in the gorilla lineage were more likely to contain loss of function variants in a cohort of infertile men. The authors conclude their results support the hypothesis that the emergence of a polygynous social system may have reduced the degree of selective pressures exerted through sperm competition.

Strengths:

(1) The identification of novel genes involved in spermatogenesis using signatures of relaxed selective constraint coupled to in vivo RNAi in Drosophila is very exciting and offers a proof of principal as to the power of evolutionarily-informed functional genomics that has been largely underutilized.

Weaknesses:

(1) The analysis is restricted to protein-coding regions of genes that have single, orthologous sequences spanning 261 mammalian species, and as such is a non-random set of 13,310 genes that have higher evolutionary conservation. While this approach is necessary for the analyses being performed, it excludes non-coding regions, recently duplicated genes/gene families, and rapidly evolving genes, which are all likely subject to stronger selection as compared to evolutionarily conserved genes (and gene regions). Thus, the conclusions of relaxed selective constraint as being pervasive is likely missing a large number of the most strongly selected genes, among which have repeatedly been shown to include sex and reproduction related genes. Would the results be similar if the set of orthologous genes were restricted to the primate lineage, as it may include more rapidly evolving genes?

(2) The identification of genes showing relaxed selection along the gorilla lineage, which are overrepresented in male reproduction, supports the hypothesis that the emergency of polygyny resulted in relaxed sperm competition and is the driving force behind their observations. However, there is no control group to support that polygyny is the driving force. To more fully test this hypothesis the authors should consider contrasting their findings to observations for other species whereby polygyny did not evolve (or a gradation between). Ideally this could be integrated into RELAX-Scan comparisons, but even a semi-qualitative observation could be made for lineages more often having shared signatures of relaxed constraint across the 576 genes identified in gorilla.

(3) The comparisons of infertile human males to a large number of presumably healthy males from a separate cohort can lead to genetic differences related to population structure and/or differences in study recruitment as compared to infertility, and care must be taken to avoid confounding in any association study before drawing conclusions. Population structure is likely to occur in human cohorts and is more likely to affect patterns of rare variation, even when controls are ascertained using similar enrollment criteria, geographic regions, racial/ethnic and national identities. In this study, the MERGE cohort upon a quick search appears to be largely recruited from Germany, vs. the control cohort gnomeAD is a more cosmopolitan study including somewhat diverse ancestries. Thus, it is likely the infertile vs. control cohort has existing genetic differences unrelated to the phenotype.

Reviewer #1 (Public Review):

This manuscript describes the pattern of relaxed selection observed at spermatogenesis genes in gorillas, presumably due to the low sperm competition associated with single-male polygyny. The analyses to detect patterns of selection are very thorough, as are the follow up analyses to characterize the function of these genes. Furthermore, the authors take the extra steps of in vivo determination of function with a Drosophila model.

This is an excellent paper. It addresses the interesting phenomenon of relaxation of selection as a genomic signal of reproductive strategies using multiple computational approaches and follow-up analyses by pulling in data from GO, mouse knockouts, human infertility database, and even Drosophila RNAi experiments. I really appreciate the comprehensive and creative approach to analyze and explore the data. As far as I can tell, the analyses were performed soundly and statistics are appropriate. The Introduction and Discussion sections are thoughtful and well-written. I have no major criticisms of the manuscript.

The main area that I would suggest for improvement is in the "Caveats and Limitations" section of the Discussion. Currently, the first paragraph of this section states the obvious that genetic manipulation of gorillas is not feasible. Beyond a reminder to the reader that this was a rationale for the Drosophila work, it isn't really adding much insight. The second paragraph is a brief discussion of the directionality of change. I think it comes across as overly simplistic, with a sort of "well, we can never know" feel. Obviously, there are plenty of researchers who do model change to infer direction and causation, and there are plenty of published papers attempting to do so with respect to mating systems in primates.

I do not think the authors need to remove these paragraphs, but I do encourage them to turn the "Caveats and Limitations" section into something more meaningful by addressing limitations of the work that was actually done rather than limitations of hypothetical things that were not done. A few areas come to mind. First, the authors should discuss the effect of gene-tree vs species-tree inconsistencies in the analyses, which could affect the identification of gorilla-specific amino acid changes and/or the dN/dS estimates. Incomplete lineage sorting is very common in primates including the gorilla-chimp-human splits (Rivas-González et al. 2023). It would be nice to hear the authors' thoughts on how that might affect their analyses. Second, the dN/dS-based analyses assume the neutrality of synonymous substitutions. Of course, that assumption is not completely true; it might be true enough, and the authors should at least note it as a caveat. Third, and potentially related, is the consideration that these protein-coding genes may be functioning in other ways such as via antisense transcription. The genes under relaxed selection may be on their way to becoming pseudogenes and evolving as such at the sequence level, but many pseudogenes continue to be transcribed sense or anti-sense in a regulatory purpose. I don't think there is a way to incorporate this into the authors' analyses but it would be nice to see it acknowledged as a caveat or limitation.

Reviewer #2 (Public Review):

Summary:

Bowman and colleagues have compiled a large comparative genomic dataset to examine the molecular evolution of genes in mammals, with the primary goal of identifying how changes in the gorilla mating system have shaped the evolution of spermatogenesis. They report several patterns pointing to signal of relaxed purifying selection on genes involved in male fertility, a pattern that they interpret as a response to changes in the mating system of gorillas. Many previous studies have used comparisons among species of primates and other mammals to understand how changes in mating systems have shaped the evolution or reproductive traits and genes. These collective works have provided some of the best evidence that changes in the form and intensity of sexual selection has had a strong effect on the evolution of male reproduction. The current study builds on this rich history by exploring molecular evolution of over 13,310 genes across 261 mammals. This very large phylogenetic dataset allows affords considerable power to characterize patterns of molecular evolution along the gorilla lineage. This allows for some added power relative to a previous study that interrogated the same lineage-specific patterns (Scally et al. 2021). They report a subset of genes showing evidence for either positive directional selection (less than 1% of genes) or relaxed purifying selection (4% of genes) in gorillas. Relaxed purifying selection is more common than positive selection, and genes showing signatures of relaxed constraint are enriched for spermatogenesis functions using various tests based on functional annotation or gene expression and infertility associations in humans and mice. The authors also report new functional data - the only original data in this study - using a high throughput genetic screen showing that some of these genes are also expressed in spermatogenesis in flies, and when perturbed they affect male fertility.

These results are interpreted as strong evidence that changes in mating system, specifically that loss of sperm competition, has shaped the evolution of male reproduction in gorillas. The authors argue that these discoveries illustrate, for the first time, the genome-wide effect of striking changes in mating behavior in gorillas on the genetic underpinnings of male reproduction and provide new candidates relevant to male fertility in humans. Support for these central conclusions is eroded by a lack of appropriate comparative contrasts needed clarify the uniqueness of these patterns to gorillas and, critically, establish a direct phylogenetic association with mating system or correlated reproductive traits.

Strengths:

The presentation is engaging, clear, and easy to follow throughout. I enjoyed reading the overall narrative and I think that the authors did a good job of presenting the details of male reproductive biology in an informative and accessible manner. Given the general interest in gorilla evolution, and the clear relevance to humans, studies of this scope on male reproductive biology are likely to be of broad interest to both evolutionary and reproductive biologists.

The reported signatures of molecular evolution in gorillas appear robust, well-executed, and supported by several lines of evidence that establish some links with male reproduction. The authors have presented a series of molecular evolution analyses that demonstrate both rigor and attention to analytical details and quality control. Although all the primary sequence data has been previously published by others, the compilation of a high-quality curated comparative dataset of this scale is impressive and inspires confidence in the underlying molecular results. Likewise, the incorporation of diverse other data from mice and humans helps shape the overall narrative. To my knowledge, this represents the most focused and detailed analysis of protein-coding evolution specific to gorillas to date (although parallel results from the landmark gorilla genome study - Scally et al. 2012 - are downplayed somewhat).

Likewise, the inclusion of new functional data from Drosophila establishes a subset of genes showing recent changes in molecular evolution in gorillas that appear to be both deeply conserved in animals and related to male fertility.

Weaknesses:

This study lacks the necessary comparative framework needed to ascribe any of the reported patterns to changes in the reproductive system of gorillas, or to really understand the uniqueness of these patterns relative to other species. Although wording is careful at times, the authors repeatedly ascribe the patterns they are finding directly to the specific changes in mating system biology that has occurred in gorillas. The general framing and significance rests on the central finding that "these data provide compelling evidence that reduced sperm competition in gorillas is associated with relaxed purifying selection on genes related to male reproductive function (Abstract)". No such association between variation in mating system or at any correlated reproductive traits and molecular evolution is ever directly tested let alone established as a clear statistical correlation. The massive comparative dataset is used to localize patterns of molecular evolution to the gorilla lineage and then these patterns are interpreted in the context of changes in mating system, as an assumption of the study not a direct result. Although basic information of the reproductive system (or correlates thereof) likely exists for many of the 261 species included here, this information is never used to test for a relationship between changes in positive or purifying selection and reproduction.

The lack of any such comparisons is especially curious given that there are many previous studies that have sought and established such connections for traits and/or genes in mammals (dozens now?), and especially great apes, before. This comparative approach is the gold standard to making claims linking mating system to molecular evolution and yet this is not pursued here. The authors are correct in that they provide a rigorous genome-wide analysis (but not at all for the first time, see Scally et al. 2012), but they skip this critical central step to rigorous inference in comparative genomics. This is essentially a broad comparative study, but the central conclusion (a direct link between mating system and molecular evolution) is speculative and not actually tested.

Note that despite the framing here, there are of course several aspects of lineage specific biology that undoubtedly shape molecular evolution of male reproduction and fertility but could be unrelated to sperm competition per se. For example, shift in operational sex ratios can have profound effects on effective population sizes and the efficacy of selection, which of course would be expected to change the intensity and direction of molecular evolution. Likewise, shifts in population size, structure, and diet all can affect molecular evolution and reproduction.

In the absence of a broad phylogenetically independent contrast (which would be really interesting here), the authors need to at least establish that there is indeed something noteworthy about the specific findings they report relative to other systems that have a different mating system. Such comparisons would be readily available within the great apes, especially compared to chimpanzees and bonobos (Pan). Most of the patterns are presented in such a way to suggest a clear connection between the result and the unique features of gorilla reproduction, but are these clearly outliers? Relaxed purifying selection is much more common than positive selection, is this result qualitatively or quantitatively unique to gorillas as implied (I would honestly be surprised if it was as this is a common outcome of these dn/ds-based tests)? Similar questions and the need for more context apply to the various enrichment tests. That genes involved in male reproduction evolve rapidly and that this reflects both relaxed constraint and positive selection is an exceptionally well-established pattern, as is enrichment for reproductive functions/expression of such genes in unbiased genome-wide screens (as cited by the authors, including in gorillas by Scally et al. 2012 who performed a very similar analysis albeit with some model advances used in the current study). Do chimpanzees or humans lack these specific signatures of relaxed constraint at reproductive genes or is it a much stronger enrichment in gorillas? Establishing these baseline comparisons would help a lot with interpretation of the core findings. A little bit of this is explored with the human comparisons but not in a parallel genome-wide manner that places the signatures in gorillas in context.

I had similar questions related to the high-throughput Drosophila screen. This is a creative and novel component of the study. However, I am unclear on how to interpret the results or the conclusions drawn from them. It is very interesting that a subset of genes showing relaxed constraint are conserved to Drosophila and that perturbation of some of these cause fertility issues. However, the conclusion that these genes reflect novel candidates not implicated in sperm biology is a bit overstated. Here implicated means genes with an annotated sterility phenotype in humans, mice, flies, or gorillas - specific annotations which are pretty limited at least in the mammalian systems. The entire design was conditioned on analyzing genes that were reliably expressed during Drosophila spermatogenesis, and then focusing on those. But the comparative set for the enrichment test was a random set of genes. Shouldn't the background be a random set of testis-expressed genes? I would say that genes that are reliably expressed during spermatogenesis in both mammals and flies are implicated in sperm biology and genetic manipulation of such genes would be expected to produce fertility phenotypes at some appreciable rate. So the result here adds some interesting data but it does not seem unexpected or significant as framed.

Reviewer #3 (Public Review):

Summary:

Hudaiberdiev and Ovcharenko investigate regions within the genome where a high abundance of DNA-associated proteins are located and identify DNA sequence features enriched in these regions, their conservation in evolution, and variation in disease. Using ChIP-seq binding profiles of over 1,000 proteins in three human cell lines (HepG2, K562, and H1) as a data source they're able to identify nearly 44,000 high-occupancy target loci (HOT) that form at promoter and enhancer regions, thus suggesting these HOT loci regulate housekeeping and cell identity genes. Their primary investigative tool is HepG2 cells, but they employ K562 and H1 cells as tools to validate these assertions in other human cell types. Their analyses use RNA pol II signal, super-enhancer, regular-enhancer, and epigenetic marks to support the identification of these regions. The work is notable, in that it identifies a set of proteins that are invariantly associated with high-occupancy enhancers and promoters and argues for the integration of these molecules at different genomic loci. These observations are leveraged by the authors to argue HOT loci as potential sites of transcriptional condensates, a claim that they are well poised to provide information in support of. This work would benefit from refinement and some additional work to support the claims.

Comments:

Condensates are thought to be scaffolded by one or more proteins or RNA molecules that are associated together to induce phase separation. The authors can readily provide from their analysis a check of whether HOT loci exist within different condensate compartments (or a marker for them). Generally, ChIPSeq signal from MED1 and Ronin (THAP11) would be anticipated to correspond with transcriptional condensates of different flavors, other coactivator proteins (e.g., BRD4), would be useful to include as well. Similarly, condensate scaffolding proteins of facultative and constitutive heterochromatin (HP1a and EZH2/1) would augment the authors' model by providing further evidence that HOT Loci occur at transcriptional condensates and not heterochromatin condensates. Sites of splicing might be informative as well, splicing condensates (or nuclear speckles) are scaffolded by SRRM/SON, which is probably not in their data set, but members of the serine arginine-rich splicing factor family of proteins can serve as a proxy-SRSF2 is the best studied of this set. This would provide a significant improvement to their proposed model and be expected since the authors note that these proteins occur at the enhancers and promoter regions of highly expressed genes.

It is curious that MAX is found to be highly enriched without its binding partner Myc, is Myc's signal simply lower in abundance, or is it absent from HOT loci? How could it be possible that a pair of proteins, which bind DNA as a heterodimer are found in HOT loci without invoking a condensate model to interpret the results?

Numerous studies have linked the physical properties of transcription factor proteins to their role in the genome. The authors here provide a limited analysis of the proteins found at different HOT-loci by employing go terms. Is there evidence for specific types of structural motifs, disordered motifs, or related properties of these proteins present in specific loci?

Condensates themselves possess different emergent properties, but it is a product of the proteins and RNAs that concentrate in them and not a result of any one specific function (condensates can have multiple functions!)

Transcriptional condensates serve as functional bodies. The notion the authors present in their discussion is not held by practitioners of condensate science, in that condensates exist to perform biochemical functions and are dissolved in response to satisfying that need, not that they serve simply as reservoirs of active molecules. For example, transcriptional condensates form at enhancers or promoters that concentrate factors involved in the activation and expression of that gene and are subsequently dissolved in response to a regulatory signal (in transcription this can be the nascently synthesized RNA itself or other factors). The association reactions driving the formation of active biochemical machinery within condensates are materially changed, as are the kinetics of assembly. It is unnecessary and inaccurate to qualify transcriptional condensates as depots for transcriptional machinery.

This work has the potential to advance the field forward by providing a detailed perspective on what proteins are located in what regions of the genome. Publication of this information alongside the manuscript would advance the field materially.

Reviewer #1 (Public Review):

Summary:

This study explores the sequence characteristics and features of high-occupancy target (HOT) loci across the human genome. The computational analyses presented in this paper provide information into the correlation of TF binding and regulatory networks at HOT loci that were regarded as lacking sequence specificity.

By leveraging hundreds of ChIP-seq datasets from the ENCODE Project to delineate HOT loci in HepG2, K562, and H1-hESC cells, the investigators identified the regulatory significance and participation in 3D chromatin interactions of HOT loci. Subsequent exploration focused on the interaction of DNA-associated proteins (DAPs) with HOT loci using computational models. The models established that the potential formation of HOT loci is likely embedded in their DNA sequences and is significantly influenced by GC contents. Further inquiry exposed contrasting roles of HOT loci in housekeeping and tissue-specific functions spanning various cell types, with distinctions between embryonic and differentiated states, including instances of polymorphic variability. The authors conclude with a speculative model that HOT loci serve as anchors where phase-separated transcriptional condensates form. The findings presented here open avenues for future research, encouraging more exploration of the functional implications of HOT loci.

Strengths:

The concept of using computational models to define characteristics of HOT loci is refreshing and allows researchers to take a different approach to identifying potential targets. The major strengths of the study lies in the very large number of datasets analyzed, with hundreds of ChIP-seq data sets for both HepG2 and K562 cells as part of the ENCODE project. Such quantitative power allowed the authors to delve deeply into HOT loci, which were previously thought to be artifacts.

Weaknesses:

While this study contributes to our knowledge of HOT loci, there are critical weaknesses that need to be addressed. There are questions on the validity of the assumptions made for certain analyses. The speculative nature of the proposed model involving transcriptional condensates needs either further validation or be toned down. Furthermore, some apparent contradictions exist among the main conclusions, and these either need to be better explained or corrected. Lastly, several figure panels could be better explained or described in the figure legends.

Reviewer #2 (Public Review):

Summary:

The paper 'Sequence characteristic and an accurate model of abundant hyperactive loci in human genome' by Hydaiberdiev and Ovcharenko offers comprehensive analyses and insights about the 'high-occupancy target' (HOT) loci in the human genome. These are considered genomic regions that overlap with transcription factor binding sites. The authors provided very comprehensive analyses of the TF composition characteristics of these HOT loci. They showed that these HOT loci tend to overlap with annotated promoters and enhancers, GC-rich regions, open chromatin signals, and highly conserved regions, and that these loci are also enriched with potentially causal variants with different traits.

Strengths:

Overall, the HOT loci' definition is clear and the data of HOT regions across the genome can be a useful dataset for studies that use HepG2 or K562 as a model. I appreciate the authors' efforts in presenting many analyses and plots backing up each statement.

Weaknesses:

It is noteworthy that the HOT concept and their signature characteristics as being highly functional regions of the genome are not presented for the first time here. Additionally, I find the main manuscript, though very comprehensive, long-winded and can be put in a shorter, more digestible format without sacrificing scientific content.

The introduction's mention of the blacklisted region can be rather misleading because when I read it, I was anticipating that we are uncovering new regulatory regions within the blacklisted region. However, the paper does not seem to address the question of whether the HOT regions overlap, if any, with the ENCODE blacklisted regions afterward. This plays into the central assessment that this manuscript is long-winded.

The introduction also mentioned that HOT regions correspond to 'genomic regions that seemingly get bound by a large number of TFs with no apparent DNA sequence specificity' (this point of 'no sequence specificity' is reiterated in the discussion lines 485-486). However, later on in the paper, the authors also presented models such as convolutional neural networks that take in one-hot-encoded DNA sequence to predict HOT performed really well. It means that the sequence contexts with potential motifs can still play a role in forming the HOT loci. At the same time, lines 59-60 also cited studies that "detected putative drive motifs at the core segments of the HOT loci". The authors should edit the manuscript to clarify (or eradicate) contradictory statements.

Reviewer #1 (Public Review):

Summary:

By using the biophysical chromosome stretching, the authors measured the stiffness of chromosomes of mouse oocytes in meiosis I (MI) and meiosis II (MII). This study was the follow-up of previous studies in spermatocytes (and oocytes) by the authors (Biggs et al. Commun. Biol. 2020: Hornick et al. J. Assist. Rep. and Genet. 2015). They showed that MI chromosomes are much stiffer (~10 fold) than mitotic chromosomes of mouse embryonic fibroblast (MEF) cells. MII chromosomes are also stiffer than the mitotic chromosomes. The authors also found that oocyte aging increases the stiffness of the chromosomes. Surprisingly, the stiffness of meiotic chromosomes is independent of meiotic chromosome components, Rec8, Stag3, and Rad21L. with aging.

Strengths:

This provides a new insight into the biophysical property of meiotic chromosomes, that is chromosome stiffness. The stiffness of chromosomes in meiosis prophase I is ~10-fold higher than that of mitotic chromosomes, which is independent of meiotic cohesin. The increased stiffness during oocyte aging is a novel finding.

Weaknesses:

A major weakness of this paper is that it does not provide any molecular mechanism underlying the difference between MI and MII chromosomes (and/or prophase I and mitotic chromosomes).

Reviewer #2 (Public Review):

This paper reports investigations of chromosome stiffness in oocytes and spermatocytes. The paper shows that prophase I spermatocytes and MI/MII oocytes yield high Young Modulus values in the assay the authors applied. Deficiency in each one of three meiosis-specific cohesins they claim did not affect this result and increased stiffness was seen in aged oocytes but not in oocytes treated with the DNA-damaging agent etoposide.

The paper reports some interesting observations which are in line with a report by the same authors of 2020 where increased stiffness of spermatocyte chromosomes was already shown. In that sense, the current manuscript is an extension of that previous paper, and thus novelty is somewhat limited. The paper is also largely descriptive as it does neither propose a mechanism nor report factors that determine the chromosomal stiffness.

There are several points that need to be considered.

(1) Limitations of the study and the conclusions are not discussed in the "Discussion" section and that is a significant gap. Even more so as the authors rely on just one experimental system for all their data - there is no independent verification - and that in vitro system may be prone to artefacts.

(2) It is somewhat unfortunate that they jump between oocytes and spermatocytes to address the cohesin question. Prophase I (pachytene) spermatocytes chromosomes are not directly comparable to MI or MII oocyte chromosomes. In fact, the authors report Young Modulus values of 3700 for MI oocytes and only 2700 for spermatocyte prophase chromosomes, illustrating this difference. Why not use oocyte-specific cohesin deficiencies?

(3) It remains unclear whether the treatment of oocytes with the detergent TritonX-100 affects the spindle and thus the chromosomes isolated directly from the Triton-lysed oocytes. In fact, it is rather likely that the detergent affects chromatin-associated proteins and thus structural features of the chromosomes.

(4) Why did the authors use mouse strains of different genetic backgrounds, CD-1, and C57BL/6? That makes comparison difficult. Breeding of heterozygous cohesin mutants will yield the ideal controls, i.e. littermates.

(5) How did the authors capture chromosome axes from STAG3-deficienct spermatocytes which feature very few if any axes? How representative are those chromosomes that could be captured?

Reviewer #3 (Public Review):

Summary:

Understanding the mechanical properties of chromosomes remains an important issue in cell biology. Measuring chromosome stiffness can provide valuable insights into chromosome organization and function. Using a sophisticated micromanipulation system, Liu et al. analyzed chromosome stiffness in MI and MII oocytes. The authors found that chromosomes in MI oocytes were ten-fold stiffer than mitotic ones. The stiffness of chromosomes in MI mouse oocytes was significantly higher than that in MII oocytes. Furthermore, the knockout of the meiosis-specific cohesin component (Rec8, Stag3, Rad21l) did not affect meiotic chromosome stiffness. Interestingly, the authors showed that chromosomes from old MI oocytes had higher stiffness than those from young MI oocytes. The authors claimed this effect was not due to the accumulated DNA damage during the aging process because induced DNA damage reduced chromosome stiffness in oocytes.

Strengths:

The technique used (isolating the chromosomes in meiosis and measuring their stiffness) is the authors' specialty. The results are intriguing and informative to the chromatin/chromosome and other related fields.

Weaknesses:

(1) How intact the measured chromosomes were is unclear.

(2) Some control data needs to be included.

(3) The paper was not well-written, particularly the Introduction section.

(4) How intact were the measured chromosomes? Although the structural preservation of the chromosomes is essential for this kind of measurement, the meiotic chromosomes were isolated in PBS with Triton X-100 and measured at room temperature. It is known that chromosomes are very sensitive to cation concentrations and macromolecular crowding in the environment (PMID: 29358072, 22540018, 37986866). It would be better to discuss this point.

Reviewer #1 (Public Review):

Summary:<br /> This paper addresses the important question of the neural mechanisms underlying interval discrimination. The authors develop a detailed and biologically plausible model based on a previously proposed theory of timing. The model proposes that the interval between two stimuli can be encoded in the state of the neuronal and synaptic properties, specifically those with time constants on the order of hundreds of milliseconds, such as short-term synaptic plasticity and GABAb currents. Based on biological parameters in the PFC the authors show that the model can account for interval discrimination for up to 750 ms. Furthermore, the model accounts for three well-established psychophysical properties of interval timing: the linear relation between objective and neural time, the scalar property/Weber's law, and dopaminergic modulation of timing (although this property is less robust). Of particular novelty is the demonstration of Weber's law, and an explanation of how many complex and nonlinear neuronal properties produce a linear relationship between the standard deviation of interval estimates and their mean.

This is an interesting paper that addresses a significant gap in the field. However, I have one major concern. As I understood the methods (and I may have misunderstood) it seems that the readout units are not operating in continuous time, and that interval discrimination relies in part on external information. Specifically, the readout units only look at the spike counts during the window delta_t_w. Thus, discrimination between 100 and 200 ms looks only at the spikes at 120-145 and 220-245, respectively, meaning that the experimenters are providing interval information for the readout of the intervals being discriminated. If this is indeed the case the model is fairly limited in biological plausibility and significantly dampens my enthusiasm for the paper.

Stimulus onset occurs at 1500 ms in order to allow the network to stabilize. Ideally, this value should be randomized across trials to ensure performance generalizes across initial states.

Why does StDev saturate? Is that because subjective time saturates as well?

The model captures the effect of D2 receptors observed in some timing studies, specifically and DR2 activation increases "clock" speed. In the discussion, it would be nice to explain that dopaminergic modulation of subjective timing is not as universally observed as the linear psychophysical law or the scalar property, and I believe somewhat controversial (e.g., Ward, ..., Balsam, 2009).

(NB: Regarding my potential concern that that the decoding was performed in discontinuous time, the authors have clarified that decoding was done in continuous time--i.e., each output unit was trained to respond to a given time bin of the target interval but exposed to all time bins of all intervals during testing. Thus confirming the robustness of their decoding procedure and model.)

Reviewer #2 (Public Review):

Summary:<br /> The paper explores a mathematical model of subsecond time perception, engaging with established theories such as the linear psychophysical law, Weber's law, and dopaminergic modulation of subjective durations. While it ambitiously attempts to confirm specific mechanisms of time perception and presents a comprehensive description of these mechanisms, the work is presented as data-driven but its empirical backing and model generalization capabilities are questionable. The title's implication of a robust empirical foundation is misleading, as the main figures do not reflect empirical data directly but rather model outputs aligned with general trends in psychophysical studies. This disjunction raises concerns about the model's applicability and the strength of the claims made regarding time perception mechanisms.

Strengths:<br /> (1) The paper describes specific mechanisms of time perception, providing a theoretical examination of linear psychophysical law, Weber's law, and dopaminergic modulation. This aspect is valuable for readers seeking a theoretical understanding of temporal perception.

(2) The authors describe a range of psychophysical studies and theories, attempting to position their model within the broader scientific discourse on time perception.

Weaknesses:<br /> (1) Lack of Empirical Data: The absence of two things: 1) quantification of error between model and empirical data with interpretation of what this degree of error means, and 2) clear comparisons between model and empirical data in all figures and tables, to substantiate the model's predictions stands out. The reliance on general trends rather than specific empirical studies undermines the strength and reliability of the model's claims. The paper would benefit from quantitative and qualitative simulations of results from specific, large-sample studies to anchor the model's predictions in concrete empirical evidence.

(2) Methodological Ambiguities: The training and testing procedures lack robust checks for generalization, leading to potential overfitting issues. Clarifications are needed on whether and how the model reaches a steady state before stimulation and the implications of the chosen model time constants in the absence of stimulation. The overlap between training (50ms) and testing (25ms) steps and the implications for model generalization need validation with "traditional" parameter fitting protocols, such as formal model cross-validation across well-defined datasets and splits, as well as evaluations to understand and assess potential overfitting.

(3) Inadequate Visualization of Empirical Data: References to empirical data are vague and not directly visualized alongside model outputs. Future iterations should include empirical data, not general trends from psychophysics, in figures for a clear comparison.

(4) Limitations in Model Scope and Dynamics: The exploration of limitations is narrowly focused on interval length and noise. Expanding the model limitations to consider isochronous pulse processing and the emergence of limit-cycle behaviors after prolonged stimulation would provide a more comprehensive understanding of the model's capabilities and limitations. Additionally, the justification for using \(N_{Poisson}\) as a proxy for more connections is unclear and warrants a more direct approach. Adding more units to a truly data-driven model should be trivial.

(5) Omissions and Redundancies: Certain omissions, such as the lack of a condition in Figure 7A or missing references to relevant models and reviews, detract from the paper's thoroughness. Moreover, some statements and terms like "internal clock" are used without a clear mechanistic definition within the model.

Guidance for Readers<br /> Readers should approach this paper as a theoretical exploration into the mechanisms of subsecond-time perception. The model offers a detailed theoretical framework that engages with established laws and theories in time perception. However, it's crucial to note the model's reliance on general trends and its lack of direct empirical backing. The findings should be interpreted as a hypothesis-generating exercise rather than conclusive evidence.

Reviewer #1 (Public Review):

The study by Prieto et al. faces the increasingly serious problem of bacterial resistance to antimicrobial agents. This work has an important element of novelty proposing a new approach to control antibiotic resistance spread by plasmids. Instead of targeting the resistance determinant, plasmid-borne proteins are used as antigens to be bound by specific nanobodies (Nbs). Once bound plasmid transfer was inhibited and Salmonella infection blocked. This in-depth study is quite detailed and complex, with many experiments (9 figures with multiple panels), rigorously carried out. Results fully support the authors' conclusions. Specifically, the authors investigated the role of two large molecular weight proteins (RSP and RSP2) encoded by the IncHI1 derivative-plasmid R27 of Salmonella. These proteins have bacterial Ig-like (Big) domains and are expressed on the cell surface, creating the opportunity for them to serve as immunostimulatory antigens. Using a mouse infection model, the authors showed that RSP proteins can properly function as antigens, in Salmonella strains harboring the IncHI1 plasmid. The authors clearly showed increased levels of specific IgG and IgA antibodies against these RSP proteins proteins in different tissues of immunized animals. In addition, non-immunized mice exhibited Salmonella colonization in the spleen and much more severe disease than immunized ones.

However, the strength of this work is the selection and production of nanobodies (Nbs) that specifically interact with the extracellular domain of RSP proteins. The procedure to obtain Nbs is lengthy and complicated and includes the immunization of dromedaries with purified RPS and the construction of a VHH (H-chain antibody variable region) library in E. coli. As RSP is expressed on the surface of E. coli, specific Nbs were able to agglutinate Salmonella strains harboring the p27 plasmid encoding the RSP proteins.<br /> The authors demonstrated that Nbs-RSP reduced the conjugation frequency of p27 thus limiting the diffusion of the amp resistance harbored by the plasmid. This represents an innovative and promising strategy to fight antibiotic resistance, as it is not blocked by the mechanism that determines, in the specific case, the amp resistance of p27 but it targets an antigen associated with HincHI- derivative plasmids. Thus, RPS vaccination could be effective not only against Salmonella but also against other enteric bacteria. A possible criticism could be that Nbs against RSP proteins reduce the severity of the disease but do not completely prevent the infection by Salmonella.

Reviewer #2 (Public Review):

Summary:

This manuscript aims to tackle the antimicrobial resistance through the development of vaccines. Specifically, the authors test the potential of the RSP protein as a vaccine candidate. The RSP protein contains bacterial Ig-like domains that are typically carried in IncHl1 plasmids like R27. The extracellular location of the RSP protein and its role in the conjugation process makes it a good candidate for a vaccine. The authors then use Salmonella carrying an IncHl plasmid to test the efficacy of the RSP protein as a vaccine antigen in providing protection against infection of antibiotic-resistant bacteria carrying the IncHl plasmid. The authors found no differences in total IgG or IgA levels, nor in pro-inflammatory cytokines between immunized and non-immunized mice. They however found differences in specific IgG and IgA, attenuated disease symptoms, and restricted systemic infection.

The manuscript also evaluates the potential use of nanobodies specifically targeting the RSP protein by expressing it in E. coli and evaluating their interference in the conjugation of IncHl plasmids. The authors found that E. coli strains expressing RSP-specific nanobodies bind to Salmonella cells carrying the R27 plasmid thereby reducing the conjugation efficacy of Salmonella.

Strengths:

- The main strength of this manuscript is that it targets the mechanism of transmission of resistance genes carried by any bacterial species, thus making it broad.

- The experimental setup is sound and with proper replication.

Weaknesses:

- The two main experiments, evaluating the potential of the RSP protein and the effects of nanobodies on conjugation, seem as parts of two different and unrelated strategies.

- The survival rates shown in Figure 1A and Figure 3A for Salmonella pHCM1 and non-immunized mice challenged with Salmonella, respectively, are substantially different. In the same figures, the challenge of immunized mice and Salmonella pHCM1 and mice challenged with Salmonella pHCM1 with and without ampicillin are virtually the same. While this is not the only measure of the effect of immunization, the inconsistencies in the resulting survival curves should be addressed by the authors more thoroughly as they can confound the effects found in other parameters, including total and specific IgG and IgA, and pro-inflammatory cytokines.

- Overall the results are inconsistent and provide only partial evidence of the effectiveness of the RSP protein as a vaccine target.

- The conjugative experiments use very long conjugation times, making it harder to asses if the resulting transconjugants are the direct result of conjugation or just the growth of transconjugants obtained at earlier points in time. While this could be assessed from the obtained results, it is not a direct or precise measure.

- While the potential outcomes of these experiments could be applied to any bacterial species carrying this type of plasmids, it is unclear why the authors use Salmonella strains to evaluate it. The introduction does a great job of explaining the importance of these plasmids but falls short in introducing their relevance in Salmonella.

Reviewer #1 (Public Review):

Summary:

This is a nice paper taking a broad range of aspects and endpoints into account. The effect of GAHT in girls has been nicely worked out. Changes in Sertoli and peritubular cells appear valid, less strong evidence is provided for Leydig cell development. The recovery of SSCs appears an overjudgement and should be rephrased. The multitude and diversity of datasets appear a strength and a weakness as some datasets were not sufficiently critically reviewed and a selection of highlights provides a certain bias to the interpretation and conclusion of the study.

The authors need to indicate that the subset of data on SSCs has been reported previously (Human Reprod 36: 5-15 (2021) and is simply re-incorporated in the present paper. as Fig. 1C. There are sufficient new results to publish the remaining datasets as a separate paper. Authors could refer to the SSC data with reference to the previous publication.

Strengths:

The patient cohort is impressive and is nicely characterized. Here, histological endpoints and endocrine profiles were analyzed appropriately for most endpoints. The paper is well-written and has many new findings.

Weaknesses:

The patients and controls are poorly separated in regard to pubertal status. Here additional endpoints (e.g. Tanner status) would have been helpful especially as the individual patient history is unknown. Pre- and peri-puberty is a very rough differentiation. The characterization and evaluation of Leydig cells is the weakest histological endpoint. Here, additional markers may be required. Fig. 1 suffers from suboptimal micrograph quality.

Reviewer #2 (Public Review):

Summary:

The study is devoted to the deep investigation of the spermatogonial stem cell (SSC) niche in trans women after gender-affirming hormone therapy (GAHT). Both cellular structure and functionality of the niche were studied. The authors evidently demonstrated that all cellular components of SSC niche were affected by hormone therapy. Interestingly, the signs of "rejuvenation" within the niche were also observed indicating the possible reverse to the immature condition.

Strengths:

The obtained findings are important for the better understanding of hormonal regulation of testis and SSC niche and provide some clues for using the biomaterials from these specific and even unique donors for biomedical research.

Weaknesses:

This study has some limitations. Many studies can't be done using the testes cells of trans women, since their cells are significantly different from adult man cells and less from prepubertal and pubertal cells. The authors themselves identify some of the limitations: this material is suitable only for studying prepubertal processes in the testis. However, the authors also report large variability in data due to different hormonal therapy regimens and, apparently, age. Accordingly, not all material obtained from trans women can also be used for studies of prepubertal processes.

Reviewer #1 (Public Review):

Summary:

In this report, Yu et al ascribe potential tumor suppressive functions to the non-core regions of RAG1/2 recombinases. Using a well-established BCR-ABL oncogene-driven system, the authors model the development of B cell acute lymphoblastic leukemia in mice and found that RAG mutants lacking non-core regions show accelerated leukemogenesis. They further report that the loss of non-core regions of RAG1/2 increases genomic instability, possibly caused by increased off-target recombination of aberrant RAG-induced breaks. The authors conclude that the non-core regions of RAG1 in particular not only increases the fidelity of VDJ recombination, but may also influence the recombination "range" of off-target joints, and that in the absence of the non-core regions, mutant RAG1/2 (termed cRAGs) catalyze high levels of off-target recombination leading to the development of aggressive leukemia.

Strengths:

The authors used a genetically defined oncogene-driven model to study the effect of RAG non-core regions have on leukemogenesis. The animal studies were well performed and generally included a good number of mice. Therefore, the finding that cRAG expression led to development of more aggressive BCR-ABL+ leukemia compared to fRAG is solid. The authors also present some nice analyses that characterize the (genomic) nature of aggressive leukemia that develop in the absence of RAG non-core regions.

Weaknesses:

The paper relies on cRAG1/2 overexpression, an experimental limitation that needs to be taken into consideration when extrapolating the physiological relevance of the findings.

Reviewer #1 (Public Review):

Summary:<br /> The study claims to explore plant microbiome engineering using host-mediated selection as a strategy to enhance rice growth and drought tolerance.

Strengths:

The authors have derived and identified simplified microbiomes from wild microbial communities of rice fields, deserts, and serpentine seep soils by selecting microbiomes from plants with desired phenotypes across generations. Metagenome-assembled genomes revealed enriched functions, such as glycerol-3-phosphate and iron transport, known to mediate plant-microbe interactions during drought.

Weaknesses:

The findings demonstrate the efficacy of host-mediated microbiome selection, but the engineering part for enhancing rice performance under drought-stress conditions has not been provided. The proposed mechanisms rely on correlations but not direct experimental proofs.

Reviewer #2 (Public Review):

Summary:

In this study, Styer et al. impose artificial selection on root-associated microbiomes to increase drought tolerance in rice plants using different soils as starting microbiomes. Using NDVI and biomass as a proxy for plant health, they find that iterative passaging of the microbiomes of the best-performing plants increased plant resilience to drought stress in a soil-dependent manner. The study makes use of numerous controls. The authors survey the microbiota of the plants across generations, using an array of interesting analyses to characterize their observations. Firstly, the authors find that the acquired microbiomes are divergent towards the beginning of the selection experiment, but nearly converge later suggesting that the selected communities become more similar over time. One reason is that the diversity of the microbiomes severely decreases after only one or two generations of selection AND that microbes from each inoculation source appear to easily disperse across the experiment, leading to microbiome homogeneity. The authors then present an analysis to correlate ASVs with the NDVI and Biomass over the course of the experiment (using the rice soil selection lines) to develop hypotheses about which ASVs may impact plant traits.

Strengths:

The authors set out to refine the understanding of microbiome artificial selection, a topic of recent interest to the plant microbiome field. The authors use an established approach (Mueller et al), expanding upon it by including multiple starting soil inocula to ask whether the strength of selection varies by input microbiome. This is an important and novel question. Using drought resilience as measured by NDVI and plant biomass to select upon was a wise choice for this type of study, given their relative ease and quickness to assess. The inclusion of several types of controls, multiple selection lines, and several starting soil inocula showed a thoughtful experimental design. The analyses were diverse, non-standard, and attempted to address microbiome dynamics on multiple fronts. I am not necessarily convinced by some of the conclusions (see below), however, I think this study examines an important and exciting topic in the area of plant microbiomes. I predict the findings of the experiments will inform a wide audience of researchers attempting similar studies and be helpful in their designs.

Weaknesses:

Although the controls were well designed, the dispersal of the microbiomes erased the utility of the sterile inoculated (SI) controls, at least from my reading of the manuscript. Perhaps the original intent of the SI plants was to contrast the selected microbiomes vs axenic plants to show that plant resilience to drought increased generation after generation. If the controls had worked properly under my presumed scenario, this would allow the authors to account for batch variation across the generations (due to slight differences in MS media prep, water quality, etc.). Instead, the SI lines acquired microbes from the experiment and never appeared to significantly deviate from the SL plants. The dispersal of the microbes amongst soils and selection lines also minimizes any conclusions that can be made about the different starting inocula and how prone to selection they may be.

Reviewer #3 (Public Review):

Summary:

In this work, Styer et al. explore host selection as a means for recruiting microbes that may aid their host under stressful conditions, in this case under drought stress, as an alternative to target-SynCom design. They do so by subjecting rice plants to several generations of soil transplantation, and by using the most successful rice plants as donors for the next generation. By using several NGS approaches and very thorough bioinformatics analysis, the authors identify potential microbial taxa and the associated functions enriched in the conditions of interest.

Strengths:

In general, I think this approach was very much needed in the field as an alternative to SynComs, which are still not readily usable in croplands. This work sets the grounds for future similar approaches, using different stresses and different host plants.

In this work, the experimental setup is well thought-through and well-replicated. In addition, an exhaustive set of preliminary experiments was performed before deciding on the final panel of soils to use and scoring methodology. The figures are clear and well-explained.

Weaknesses:

One of the more unexpected results is that sterile/non-inoculated calcined clay also tends to enrich similar microbes, and the authors did extensive work exploring possible sources and microbial dispersal within the growth chamber. In a future experiment, the work would benefit from including a truly sterile control (same growth chamber but completely isolated from possible contaminations). In this regard, the reader may get to wonder whether these efforts are necessary at all (selection experiments), since plants seem to get from their environment what they need to survive. This is discussed across the paper but not directly addressed and I think the manuscript would benefit from a clear argument for or against this idea.

Reviewer #1 (Public Review):

Summary:

This short report shows that the transcription factor gene mirror is specifically expressed in the posterior region of the butterfly wing imaginal disk, and uses CRISPR mosaic knock-outs to show it is necessary to specify the morphological features (scales, veins, and surface) of this area.

Strengths:

The data and figures support the conclusions. The article is swiftly written and makes an interesting evolutionary comparison to the function of this gene in Drosophila. Based on the data presented, it can now be established that mirror likely has a similar selector function for posterior-wing identity in a plethora of insects.

Weaknesses:

This first version has minor terminological issues regarding the use of the terms "domains" and "compartment".

Reviewer #2 (Public Review):

This is a short and unpretentious paper. It is an interesting area and therefore, although much of this area of research was pioneered in flies, extending basic findings to butterflies would be worthwhile. Indeed, there is an intriguing observation but it is technically flawed and these flaws are serious.

The authors show that mirror is expressed at the back of the wing in butterflies (as in flies). They present some evidence that is required for the proper development of the back of the wing in butterflies (a region dubbed the vannus by the ancient guru Snodgrass). But there are problems with that evidence. First, concerning the method, using CRISP they treat embryos and the expectation is that the mirror gene will be damaged in groups of cell lineages, giving a mosaic animal in which some lines of cells are normal for mirror and others are not. We do not know where the clones or patches of cells that are defective for mirror are because they are not marked. Also, we do not know what part of the wing is wild type and what part is mutant for mirror. When the mirror mutant cells colonise the back of the wing and that butterfly survives (many butterflies fail to develop), the back of the wing is altered in some selected butterflies. This raises a second problem: we do not know whether the rear of the wing is missing or transformed. From the images, the appearance of the back of the wing is clearly different from the wild type, but is that due to transformation or not? And then I believe we need to know specifically what the difference is between the rear of the wing and the main part. What we see is a silvery look at the back that is not present in the main part, is it the structure of the scales? We are not told. There are other problems. Mirror is only part of a group of genes in flies and in flies both iroquois and mirror are needed to make the back of the wing, the alula (Kehl et al). What is known about iro expression in butterflies?

In flies, mirror regulates a late and local expression of dpp that seems to be responsible for making the alula. What happens in butterflies? Would a study of the expression of Dpp in wildtype and mirror compromised wings be useful?

Thus, I find the paper to be disappointing for a general journal as it does little more than claim what was discovered in Drosophila is at least partly true in butterflies. Also, it fails to explain what the authors mean by "wing domains" and "domain specification". They are not alone, butterfly workers, in general, appear vague about these concepts, their vagueness allowing too much loose thinking.

Since these matters are at the heart of the purpose and meaning of the work reported here, we readers need a paper containing more critical thought and information. I would like to have a better and more logical introduction and discussion.

The authors do define what they mean by the vannus of the wing. In flies the definition of compartments is clear and abundantly demonstrated, with gene expression and requirement being limited precisely to sets of cells that display lineage boundaries. It is true that domains of gene expression in flies, for example of the iroquois complex, which includes mirror, can only be related to patterns with difficulty. Some recap of what is known plus the opinion of the authors on how they interpret papers on possible lineage domains in butterflies might also be useful as the reader, is no wiser about what the authors might mean at the end of it!

The references are sometimes inappropriate. The discovery of the AP compartments should not be referred to Guillen et al 1995, but to Morata and Lawrence 1975. Proofreading is required.

Reviewer #3 (Public Review):

Summary:

The manuscript by Chatterjee et al. examines the role of the mirror locus in patterning butterfly wings. The authors examine the pattern of mirror expression in the common buckeye butterfly, Junonia coenia, and then employ CRISPR mutagenesis to generate mosaic butterflies carrying clones of mirror mutant cells. They find that mirror is expressed in a well-defined posterior sector of final-instar wing discs from both hindwings and forewings and that CRISPR-injected larvae display a loss of adult wing structures presumably derived from the mirror expressing region of hindwing primordium (the case for forewings is a bit less clear since the mirror domain is narrower than in the hindwing, but there also do seem to be some anomalies in posterior regions of forewings in adults derived from CRISPR injected larvae). The authors conclude that the wings of these butterflies have at least three different fundamental wing compartments, the mirror domain, a posterior domain defined by engrailed expression, and an anterior domain expressing neither mirror nor engrailed. They speculate that this most posterior compartment has been reduced to a rudiment in Drosophila and thus has not been adequately recognized as such a primary regional specialization.

Critique:

This is a very straightforward study and the experimental results presented support the key claims that mirror is expressed in a restricted posterior section of the wing primordium and that mosaic wings from CRISPR-injected larvae display loss of adult wing structures presumably derived from cells expressing mirror (or at least nearby). The major issue I have with this paper is the strong interpretation of these findings that lead the authors to conclude that mirror is acting as a high-level gene akin to engrailed in defining a separate extreme posterior wing compartment. To place this claim in context, it is important in my view to consider what is known about engrailed, for which there is ample evidence to support the claim that this gene does play a very ancestral and conserved function in defining posterior compartments of all body segments (including the wing) across arthropods.

(1) Engrailed is expressed in a broad posterior domain with a sharp anterior border in all segments of virtually all arthropods examined (broad use of a very good pan-species anti-En antibody makes this case very strong).

(2) In Drosophila, marked clones of wing cells (generated during larval stages) strictly obey a straight anterior-posterior border indicating that cells in these two domains do not normally intermix, thus, supporting the claim that a clear A/P lineage compartment exists.

In my opinion, mirror does not seem to be in the same category of regulator as engrailed for the following reasons:

(1) There is no evidence that I am aware of, either from the current experiments, or others that the mirror expression domain corresponds to a clonal lineage compartment. It is also unclear from the data shown in this study whether engrailed is co-expressed with mirror in the posterior-most cells of J. coenia wing discs. If so, it does not seem justified to infer that mirror acts as an independent determinant of the region of the wing where it is expressed.

(2) Mirror is not only expressed in a posterior region of the wing in flies but also in the ventral region of the eye. In Drosophila, mirror mutants not only lack the alula (derived approximately from cells where mirror is expressed), but also lack tissue derived from the ventral region of the eye disc (although this ventral tissue loss phenotype may extend beyond the cells expressing mirror).

In summary, it seems most reasonable to me to think of mirror as a transcription factor that provides important development information for a diverse set of cells in which it can be expressed (posterior wing cells and ventral eye cells) but not that it acts as a high-level regulator as engrailed.

Recommendation:

While the data provided in this succinct study are solid and interesting, it is not clear to me that these findings support the major claim that mirror defines an extreme posterior compartment akin to that specified by engrailed. Minimally, the authors should address the points outlined above in their discussion section and greatly tone down their conclusion regarding mirror being a conserved selector-like gene dedicated to establishing posterior-most fates of the wing. They also should cite and discuss the original study in Drosophila describing the mirror expression pattern in the embryo and eye and the corresponding eye phenotype of mirror mutants: McNeill et al., Genes & Dev. 1997. 11: 1073-1082; doi:10.1101/gad.11.8.1073.

Reviewer #2 (Public Review):

Summary:

Invasive fungal infections are very difficult to treat with limited drug options. With the increasing concern of the drug resistance, developing antifungal vaccine is a high priority. In this study, authors studied the metal metabolism in Candida albicans by testing some chelators, including EDTA, to block the metal acquisition and metabolism by the fungus. Interestingly, they found EDTA treated yeast cells grew poorly in vitro and non-pathogenic in vivo in a murine model. Mice immunized by EDTA-treated Candida (CAET) were protected against challenge with wild type Candida cells. RNA-Seq analysis to survey the gene expression profile in response to EDTA treatment in vitro revealed upregulation of genes in metal homeostasis and down regulation of ribosome biogenesis. They also revealed an induction of both pro- and anti-inflammatory cytokines involved in Th1, Th2 and Th17 host immune response in response to CAET immunization. Overall, this is an interesting study with a translational potential.

Strengths:

The main strength of the report is that authors identified a potential whole cell live vaccine strain that can provide a full protection against candidiasis. Abundant data both on in vitro phenotype, gene expression profile and host immune response have been presented.

Weaknesses:

A weakness is that the immune mechanism of CAET mediated host protection remain unclear. The immune data is somewhat confusing. Authors only checked cytokines and chemokines in blood. The immune response in infected tissues and antibody response may be investigated.

Another potential concern is that using live wild type Candida cells treated with EDTA may still have chance to evolve and become infectious, considering that these treated cells still proliferate in vivo. Some of the gene regulation profiles may be transit and subjected to reverse, adding to the safety concern.

Reviewer #3 (Public Review):

Summary:

The authors are trying to find a vaccine solution for invasive candidiasis.

Strengths:

The testing of the antifungal activity of EDTA on Candida is not new as many other papers have examined this effect. The novelty here is on the use of this such EDTA treated strain as a vaccine to protect against a secondary challenge with wild-type Candida.

Weaknesses:

However, data presented in Fig. 5 and in Fig. 6 are not convincing and need further experimental controls and analysis as the authors do not show a time-dependent effect on the CFU of their vaccine formulation. Specific points are below.

Methodology used is also an issue. As it stands, the impact is minor, if any.

Comments on revised version:

The data provided in the revised paper are simply not satisfactory and do not give confidence that a rigorous design and methodologies were used to obtain the results illustrated in this paper.

Reviewer #1 (Public Review):

(1) Napthylamine (1NA), an industrial reagent used in the manufacturing of dyes and pesticides is harmful to humans and the environment. In the current manuscript, the authors report the successful isolation of a Pseudomonas strain from a former naphthylamine manufacturing site that is capable of degrading 1NA. Using genetic and enzymatic analysis they identified the initial stages of 1NA degradation and the enzymes responsible for downstream processing of 1,2-dihydroxynapthalene and Salicylate. The authors determined the molecular structure of NpaA1, the first enzyme in the pathway responsible for glutamylation of 1NA. NpaA1 has a border substrate specificity compared to previously characterized enzymes involved in aromatic amine degradation. They carried out structural comparison of NpaA1 with glutamine synthase structures, alfa-fold models of similar enzymes and put forth hypothesis to explain the broad substrate specificity of NpaA1.

The manuscript is well written and easy to understand. The authors carried out careful genetic analysis to identify the genes/enzymes responsible for degradation of 1NA to catechol. They characterized the first enzyme in the pathway, NpaA1 which is responsible glutamylation of 1NA. and determined the molecular structure of apo-NpaA1, NpaA1 - AMPPNP complex and Npa1 - ADP - Met-Sox-P complex using X-ray crystallography.<br /> The proposed mechanism of broad substrate specificity of NpaA1, however, is based on comparison of 1NA docked NpaA1 structure with St-GS (Glutamate synthase) and Alphafold2 predicted model of AtdA1 from an aniline degrading strain of Acinetobacter sp. Lack of molecular structure or mutational studies to back the proposed mechanism makes it difficult to agree with the proposed mechanism.

Reviewer #2 (Public Review):

Microbial degradation of synthetic organic compounds is the basis of bioremediation. Biodegradation of 1NA has not been previously reported. The report describes a complete study of 1NA biodegradation by a new isolate Pseudomonas sp. strain JS3066. The study includes the enrichment and isolation of the 1NA-degrading bacterium Pseudomonas sp. strain JS3066, the identification of the genes and enzymes involved in 1NA degradation, and the detailed characterization of γ-glutamylorganoamide synthetase by using biochemical and structural analysis. In the discussion, the potential evolution of 1NA degradation pathway, the similarity and difference between γ-glutamylorganoamide synthetase and glutamine synthetase, and the significance were explained. The conclusions were well supported by the results presented.

Reviewer #1 (Public Review):

This study offers good evidence pointing to a genetic basis for Arabidopsis thaliana's response to elevated CO2 (eCO2) levels and its subsequent impact on the leaf ionome. The natural variation analyses in the study support the hypothesis that genetic factors, rather than local adaptation, guide the influence of eCO2 on the ionome of rosette leaves in Arabidopsis.

Comments on current version:

I appreciate the revisions and the effort the authors have made.

Most of the abstract now accurately reflects the results and methods. It would be nice to have a few more technical details in the abstract, such as:<br /> * What was the CO2 level?<br /> * Which gene was identified?

I still have a problem with this sentence:

"The elevation of atmospheric CO2 leads to a decline in plant mineral content, which might pose a significant threat to food security in the coming decades."

The authors provide a wide range of published studies that support this statement. I fully agree that this is what the literature suggests. However, I think the literature has asked the wrong question.

In general, these studies addressed the question: Given no time for adaptation, do plants grown under high CO2 have a different mineral composition? The answer is yes.

But a more important question is: Can plants and food crops adapt in time? I believe the strength of this study is that it tests this, and it suggests that the answer is yes. I also think there is a lot of unpublished results and greenhouse breeding success that supports the contention that most plants can adapt to the CO2.

"The artificial elevation of atmospheric CO2 leads to a physiological response and decline in plant mineral content, which might pose a significant threat to food security in the coming decades if plants cannot adapt."

It needs to be made clear throughout the paper when high CO2 levels lead to low mineral composition. These are all artificial manipulations without allowing the plants to adapt to the new environment.

"The elevation of atmospheric CO2 concentration leads to a decline in the mineral composition of C3 plants (Gojon et al., 2023)." - this is well supported in artificial environments.

Do wild plants have fewer minerals in their leaves today compared to plants in 1950? This would be great evidence and framing for this experiment.

Crop plants having lower nitrogen and different mineral compositions over time is substantially a product of breeders initially increasing inputs and then, over the last decade, selecting for higher input efficiency.

At the end of the introduction or the beginning of the results, please define why the CO2 level was chosen and its context as being at the high end of current predictions.

"According to the literature, this results in a 20-25% reduction in vitamin C or lycopene and requires a significantly higher nitrogen and water intake to reach expected sugar levels (Doddrell H (2023), Horticulture Research). In addition, the negative effect of elevated CO2 on tomato nutrient content seems to have significant repercussions on nutrition-health properties (Boufeldja (2023), Molecules)."

Thank you for sharing these reviews. These suggest to me that breeders favored the 80% yield bump over other traits. Either there was no breeding, or the breeding focused on other traits. It is important to mention that breeders should include mineral nutrition in their selection index while they maximize yield. Simpler breeding strategies can sometimes heavily favor one trait over others, but cattle breeders today regularly use selection indices that incorporate weights for two dozen traits.

This study provides nice evidence that an annual weed species is likely to be able to adapt easily to high eCO2. Whether perennial species will be able to adapt in time is clearly a topic that needs to be investigated.

Reviewer #2 (Public Review):

The research uses a large collection of Arabidopsis thaliana accessions from various geographic scales to investigate the natural genetic variation underlying the response of ionome (elemental) composition to elevated CO2 (eCO2), a concern for future food security. While most accessions show a decrease in elemental accumulation, the authors demonstrate a wide variety of responses to eCO2 across the diversity of Arabidopsis, including lines that increase elemental content in eCO2. The demonstration of genetic diversity in eCO2 response is a significant contribution to our understanding of this important phenomenon.

Comments on revised version:

The authors made significant improvements in the manuscript from the original preprint, and the conclusions are now well supported by the evidence presented.

Reviewer #1 (Public Review):

Summary:

Zai et al test if songbirds can recover the capacity to sing auditory targets without singing experience or sensory feedback. Past work showed that after the pitch of targeted song syllables are driven outside of birds' preferred target range with external reinforcement, birds revert to baseline (i.e. restore their song to their target). Here the authors tested the extent to which this restoration occurs in muted or deafened birds. If these birds can restore, this would suggest an internal model that allows for sensory-to-motor mapping. If they cannot, this would suggest that learning relies entirely on feedback dependent mechanisms, e.g. reinforcement learning (RL). The authors find that deafened birds exhibit moderate but significant restoration, consistent with the existence of a previously under-appreciated internal model in songbirds.

Strengths:

The experimental approach of studying vocal plasticity in deafened or muted birds is innovative, technically difficult and perfectly suited for the question of feedback-independent learning. The finding in Figure 4 that deafened birds exhibit subtle but significant plasticity toward restoration of their pre-deafening target is surprising and important for the songbird and vocal learning fields, in general.

In this revision, the authors suitably addressed confusion about some statistical methods related to Fig. 4, where the main finding of vocal plasticity in deafened birds was presented.

There remain minor issues in the presentation early in the results section and in Fig. 4 that should be straightforward to clarify in the revision.

Reviewer #3 (Public Review):

Summary:

Zai et al. test whether birds can modify their vocal behavior in a manner consistent with planning. They point out that while some animals are known to be capable of volitional control of vocalizations, it has been unclear if animals are capable of planning vocalizations-that is, modifying vocalizations towards a desired target without the need to learn this modification by practising and comparing sensory feedback of practised behavior to the behavioral target. They study zebra finches that have been trained to shift the pitch of song syllables away from their baseline values. It is known that once this training ends, zebra finches have a drive to modify pitch so that it is restored back to its baseline value. They take advantage of this drive to ask whether birds can implement this targeted pitch modification in a manner that looks like planning, by comparing the time course and magnitude of pitch modification in separate groups of birds who have undergone different manipulations of sensory and motor capabilities. A key finding is that birds who are deafened immediately before the onset of this pitch restoration paradigm, but after they have been shifted away from baseline, are able to shift pitch partially back towards their baseline target. In other words, this targeted pitch shift occurs even when birds don't have access to auditory feedback, which argues that this shift is not due to reinforcement-learning-guided practice, but is instead planned based on the difference between an internal representation of the target (baseline pitch) and current behavior (pitch the bird was singing immediately before deafening).

The authors present additional behavioral studies arguing that this pitch shift requires auditory experience of song in its state after it has been shifted away from baseline (birds deafened early on, before the initial pitch shift away from baseline, do not exhibit any shift back towards baseline), and that a full shift back to baseline requires auditory feedback. The authors synthesize these results to argue that different mechanisms operate for small shifts (planning, which does not need auditory feedback) and large shifts (through a mechanism that requires auditory feedback).

The authors also make a distinction between two kinds of planning: covert-not requiring any motor practice and overt-requiring motor practice but without access to auditory experience from which target mismatch could be computed. They argue that birds plan overtly, based on these deafening experiments as well as an analogous experiment involving temporary muting, which suggests that indeed motor practice is required for pitch shifts.

Strengths:

The primary finding (that partially restorative pitch shift occurs even after deafening) rests on strong behavioral evidence. It is less clear to what extent this shift requires practice, since their analysis of pitch after deafening takes the average over within the first two hours of singing. If this shift is already evident in the first few renditions then this would be evidence for covert planning. Technical hurdles, such as limited sample sizes and unstable song after surgical deafening, make this difficult to test. (Similarly, the authors could test whether the first few renditions after recovery from muting already exhibit a shift back towards baseline.)

This work will be a valuable addition to others studying birdsong learning and its neural mechanisms. It documents features of birdsong plasticity that are unexpected in standard models of birdsong learning based on reinforcement and are consistent with an additional, perhaps more cognitive, mechanism involving planning. As the authors point out, perhaps this framework offers a reinterpretation of the neural mechanisms underlying a prior finding of covert pitch learning in songbirds (Charlesworth et al., 2012).

A strength of this work is the variety and detail in its behavioral studies, combined with sensory and motor manipulations, which on their own form a rich set of observations that are useful behavioral constraints on future studies.

Weaknesses:

The argument that pitch modification in deafened birds requires some experience hearing their song in its shifted state prior to deafening (Fig. 4) is solid but has an important caveat. Their argument rests on comparing two experimental conditions: one with and one without auditory experience of shifted pitch. However, these conditions also differ in the pitch training paradigm: the "with experience" condition was performed using white noise training, while the "without experience" condition used "lights off" training (Fig. 4A). It is possible that the differences in ability for these two groups to restore pitch to baseline reflects the training paradigm, not whether subjects had auditory experience of the pitch shift. Ideally, a control study would use one of the training paradigms for both conditions, which would be "lights off" or electrical stimulation (McGregor et al. 2022), since WN training cannot be performed in deafened birds. In the Discussion, in response to this point, the authors point out that birds are known to recover their pitch shift if those shifts are driven using electrical stimulation as reinforcement (McGregor et al. 2022); however, it is arguably still relevant to know whether a similar recovery occurs for the "lights off" paradigm used here.

Reviewer #3 (Public Review):

Summary:

The goal of this paper is to characterize an anti-diuretic signaling system in insects using Drosophila melanogaster as a model. Specifically, the authors wished to characterize a role of ion transport peptide (ITP) and its isoforms in regulating diverse aspects of physiology and metabolism. The authors combined genetic and comparative genomic approaches with classical physiological techniques and biochemical assays to provide a comprehensive analysis of ITP and its role in regulating fluid balance and metabolic homeostasis in Drosophila. The authors further characterized a previously unrecognized role for Gyc76C as a receptor for ITPa, an amidated isoform of ITP, and in mediating the effects of ITPa on fluid balance and metabolism. The evidence presented in favor of this model is very strong as it combines multiple approaches and employs ideal controls. Taken together, these findings represent an important contribution to the field of insect neuropeptides and neurohormones and have strong relevance for other animals.

Strengths:

Many approaches are used to support their model. Experiments were well-controlled, used appropriate statistical analyses, and were interpreted properly and without exaggeration.

Weaknesses:

No major weaknesses were identified by this reviewer. More evidence to support their model would be gained by using a loss-of-function approach with ITPa, and by providing more direct evidence that Gyc76C is the receptor that mediates the effects of ITPa on fat metabolism. However, these weaknesses do not detract from the overall quality of the evidence presented in this manuscript, which is very strong.

Reviewer #1 (Public Review):

Summary:

In Drosophila melanogaster, ITP has functions on feeding, drinking, metabolism, excretion, and circadian rhythm. In the current study, the authors characterized and compared the expression of all three ITP isoforms (ITPa and ITPL1&2) in the CNS and peripheral tissues of Drosophila. An important finding is that they functionally characterized and identified Gyc76C as an ITPa receptor in Drosophila using both in vitro and in vivo approaches. In vitro, the authors nicely confirmed that the inhibitory function of recombinant Drosophila ITPa on MT secretion is Gyc76C-dependent (knockdown Gyc76C specifically in two types of cells abolished the anti-diuretic action of Drosophila ITPa on renal tubules). They also used a combination of multiple approaches to investigate the roles of ITPa and Gyc76C on osmotic and metabolic homeostasis modulation in vivo. They revealed that ITPa signaling to renal tubules and fat body modulates osmotic and metabolic homeostasis via Gyc76C.

Furthermore, they tried to identify the upstream and downstream of ITP neurons in the nervous system by using connectomics and single-cell transcriptomic analysis. I found this interesting manuscript to be well-written and described. The findings in this study are valuable to help understand how ITP signals work on systemic homeostasis regulation. Both anatomical and single-cell transcriptome analysis here should be useful to many in the field.

Strengths:

- The question (what receptors of ITPa in Drosophila) that this study tries to address is important. The authors ruled out the Bombyx ITPa receptor orthologs as potential candidates. They identified a novel ITP receptor by using phylogenetic, anatomical analysis, and both in vitro and in vivo approaches.

- The authors exhibited detailed anatomical data of both ITP isoforms and Gyc76C (in the main and supplementary figures), which helped audiences understand the expression of the neurons studied in the manuscript.

- They also performed connectomes and single-cell transcriptomics analysis to study the synaptic and peptidergic connectivity of ITP-expressing neurons. This provided more information for better understanding and further study on systemic homeostasis modulation.

Weaknesses:

In the discussion section, the authors raised the limitations of the current study, which I mostly agree with, such as the lack of verification of direct binding between ITPa and Gyc76C, even though they provided different data to support that ITPa-Gyc76C signaling pathway regulates systemic homeostasis in adult flies.

Reviewer #2 (Public Review):

Summary:

The physiology and behaviour of animals are regulated by a huge variety of neuropeptide signalling systems. In this paper, the authors focus on the neuropeptide ion transport peptide (ITP), which was first identified and named on account of its effects on the locust hindgut (Audsley et al. 1992). Using Drosophila as an experimental model, the authors have mapped the expression of three different isoforms of ITP (Figures 1, S1, and S2), all of which are encoded by the same gene.

The authors then investigated candidate receptors for isoforms of ITP. Firstly, Drosophila orthologs of G-protein coupled receptors (GPCRs) that have been reported to act as receptors for ITPa or ITPL in the insect Bombyx mori were investigated. Importantly, the authors report that ITPa does not act as a ligand for the GPCRs TkR99D and PK2-R1 (Figure S3). Therefore, the authors investigated other putative receptors for ITPs. Informed by a previously reported finding that ITP-type peptides cause an increase in cGMP levels in cells/tissues (Dircksen, 2009, Nagai et al., 2014), the authors investigated guanylyl cyclases as candidate receptors for ITPs. In particular, the authors suggest that Gyc76C may act as an ITP receptor in Drosophila.

Evidence that Gyc76C may be involved in mediating effects of ITP in Bombyx was first reported by Nagai et al. (2014) and here the authors present further evidence, based on a proposed concordance in the phylogenetic distribution ITP-type neuropeptides and Gyc76C (Figure 2). Having performed detailed mapping of the expression of Gyc76C in Drosophila (Figures 3, S4, S5, S6), the authors then investigated if Gyc76C knockdown affects the bioactivity of ITPa in Drosophila. The inhibitory effect of ITPa on leucokinin- and diuretic hormone-31-stimulated fluid secretion from Malpighian tubules was found to be abolished when expression of Gyc76C was knocked down in stellate cells and principal cells, respectively (Figure 4). However, as discussed below, this does not provide proof that Gyc76C directly mediates the effect of ITPa by acting as its receptor. The effect of Gyc76C knockdown on the action of ITPa could be an indirect consequence of an alteration in cGMP signalling.

Having investigated the proposed mechanism of ITPa in Drosophila, the authors then investigated its physiological roles at a systemic level. In Figure 5 the authors present evidence that ITPa is released during desiccation and accordingly, overexpression of ITPa increases survival when animals are subjected to desiccation. Furthermore, knockdown of Gyc76C in stellate or principal cells of Malphigian tubules decreases survival when animals are subject to desiccation. However, whilst this is correlative, it does not prove that Gyc76C mediates the effects of ITPa. The authors investigated the effects of knockdown of Gyc76C in stellate or principal cells of Malphigian tubules on i). survival when animals are subject to salt stress and ii). time taken to recover from of chill coma. It is not clear, however, why animals over-expressing ITPa were also not tested for its effect on i). survival when animals are subject to salt stress and ii). time taken to recover from of chill coma. In Figures 6 and S8, the authors show the effects of Gyc76C knockdown in the female fat body on metabolism, feeding-associated behaviours and locomotor activity, which are interesting. Furthermore, the relevance of the phenotypes observed to potential in vivo actions of ITPa is explored in Figure 7. The authors conclude that "increased ITPa signaling results in phenotypes that largely mirror those seen following Gyc76C knockdown in the fat body, providing further support that ITPa mediates its effects via Gyc76C." Use of the term "largely mirror" seems inappropriate here because there are opposing effects- e.g. decreased starvation resistance in Figure 6A versus increased starvation resistance in Figure 7A. Furthermore, as discussed above, the results of these experiments do not prove that the effects of ITPa are mediated by Gyc76C because the effects reported here could be correlative, rather than causative.

Lastly, in Figures 8, S9, and S10 the authors analyse publicly available connectomic data and single-cell transcriptomic data to identify putative inputs and outputs of ITPa-expressing neurons. These data are a valuable addition to our knowledge ITPa expressing neurons; but they do not address the core hypothesis of this paper - namely that Gyc76C acts as an ITPa receptor.

Strengths:

(1) The main strengths of this paper are i) the detailed analysis of the expression and actions of ITP and the phenotypic consequences of over-expression of ITPa in Drosophila. ii). the detailed analysis of the expression of Gyc76C and the phenotypic consequences of knockdown of Gyc76C expression in Drosophila.

(2) Furthermore, the paper is generally well-written and the figures are of good quality.

Weaknesses:

(1) The main weakness of this paper is that the data obtained do not prove that Gyc76C acts as a receptor for ITPa. Therefore, the following statement in the abstract is premature: "Using a phylogenetic-driven approach and the ex vivo secretion assay, we identified and functionally characterized Gyc76C, a membrane guanylate cyclase, as an elusive Drosophila ITPa receptor." Further experimental studies are needed to determine if Gyc76C acts as a receptor for ITPa. In the section of the paper headed "Limitations of the study", the authors recognise this weakness. They state "While our phylogenetic analysis, anatomical mapping, and ex vivo and in vivo functional studies all indicate that Gyc76C functions as an ITPa receptor in Drosophila, we were unable to verify that ITPa directly binds to Gyc76C. This was largely due to the lack of a robust and sensitive reporter system to monitor mGC activation." It is not clear what the authors mean by "the lack of a robust and sensitive reporter system to monitor mGC activation". The discovery of mGCs as receptors for ANP in mammals was dependent on the use of assays that measure GC activity in cells (e.g. by measuring cGMP levels in cells). Furthermore, more recently cGMP reporters have been developed. The use of such assays is needed here to investigate directly whether Gyc76C acts as a receptor for ITPa. In summary, insufficient evidence has been obtained to conclude that Gyc76C acts as a receptor for ITPa. Therefore, I think there are two ways forward, either:<br /> (a) The authors obtain additional biochemical evidence that ITPa is a ligand for Gyc76C.<br /> or<br /> (b) The authors substantially revise the conclusions of the paper (in the title, abstract, and throughout the paper) to state that Gyc76C MAY act as a receptor for ITPa, but that additional experiments are needed to prove this.

(2) The authors state in the abstract that a phylogenetic-driven approach led to their identification of Gyc76C as a candidate receptor for ITPa. However, there are weaknesses in this claim. Firstly, because the hypothesis that Gyc76C may be involved in mediating effects of ITPa was first proposed ten years ago by Nagai et al. 2014, so this surely was the primary basis for investigating this protein. Nevertheless, investigating if there is correspondence in the phylogenetic distribution of ITP-type and Gyc76C-type genes/proteins is a valuable approach to addressing this issue. Unfortunately, the evidence presented is rather limited in scope. Essentially, the authors report that they only found ITP-type and Gyc76C-type genes/proteins in protostomes, but not in deuterostomes. What is needed is a more fine-grained analysis at the species level within the protostomes. Thus, are there protostome species in which both ITP-type and Gyc76C-type genes/proteins have been lost? Furthermore, are there any protostome species in which an ITP-type gene is present but an Gyc76C-type gene is absent, or vice versa? If there are protostome species in which an ITP-type gene is present but a Gyc76C-type gene is absent or vice versa, this would argue against Gyc76C being a receptor for ITPa. In this regard, it is noteworthy that in Figure 2A there are two ITP-type precursors in C. elegans, but there are no Gyc76C-type proteins shown in the tree in Figure 2B. Thus, what is needed is a more detailed analysis of protostomes to investigate if there really is correspondence in the phylogenetic distribution of Gyc76C-type and ITP-type genes at the species level.

(3) The manuscript would benefit from a more comprehensive overview and discussion of published literature on Gyc76C in Drosophila, both as a basis for this study and for interpretation of the findings of this study.

Reviewer #1 (Public Review):

Summary:

This work identified new NMD inhibitors and tested them for cancer treatment, based on the hypothesis that inhibiting NMD could lead to the production of cancer neoantigens from the stabilized mutant mRNAs, thereby enhancing the immune system's ability to recognize and kill cancer cells. Key points of the study include:

• Development of an RNA-seq based method for NMD analysis using mixed isogenic cells that express WT or mutant transcripts of STAG2 and TP53 with engineered truncation mutations.

• Application of this method for a drug screen and identified several potential NMD inhibitors.

• Demonstration that one of the identified compounds, LY3023414, inhibits NMD by targeting the SMG1 protein kinase in the NMD pathway in cultured cells and mouse xenografts.

• Due to the in vivo toxicity observed for LY3023414, the authors developed 11 new SMG1 inhibitors (KVS0001-KVS0011) based on the structures of the known SMG1 inhibitor SMG1i-11 and the SMG1 protein itself.

• Among these, KVS0001 stood out for its high potency, excellent bioavailability, and low toxicity in mice. Treatment with KVS0001 caused NMD inhibition and increased presentation of neoantigens on MHC-I molecules, resulting in the clearance of cancer cells in vitro by co-cultured T cells and cancer xenografts in mice by the immune system.

These findings support the strategy of targeting the NMD pathway for cancer treatment and provide new research tools and potential lead compounds for further exploration.

Strengths:

The RNA-seq-based NMD analysis, using isogenic cell lines with specific NMD-inducing mutations, represents a novel approach for the high-throughput identification of potential NMD modulators or genetic regulators. The effectiveness of this method is exemplified by the identification of a new activity of AKT1/mTOR inhibitor LY3023414 in inhibiting NMD.

The properties of KVS0001 described in the manuscript as a novel SMG1 inhibitor suggest its potential as a lead compound for further testing the NMD-targeting strategies in cancer treatment. Additionally, this compound may serve as a useful research tool.

The results of the in vitro cell killing assay and in vivo xenograft experiments in both immuno-proficient and immune-deficient mice indicate that inhibiting NMD could be a viable therapeutic strategy for certain cancers.

Weaknesses:

The authors did not address the potential effects of NMD/SMG1 inhibitors on RNA splicing. Given that the transcripts of many RNA-binding proteins are natural targets of NMD, inhibiting NMD could significantly alter splicing patterns. This, in turn, might influence the outcomes of the RNA-seq-based method for NMD analysis and result interpretation.

While the RNA-seq-based approach offers several advantages for analyzing NMD, the effects of NMD/SMG1 inhibitors observed through this method should be confirmed using established NMD reporters. This step is crucial to rule out the possibility that mutations in STAG2 or TP53 affect NMD in cells, as well as to address potential clonal variations between different engineered cell lines.

The results from the SMG1/UPF1 knockdown and SMG1i-11 experiments presented in Figure 3 correlate with the effects seen for LY3023414, but they do not conclusively establish SMG1 as the direct target of LY3023414 in NMD inhibition. An epistatic analysis with LY3023414 and SMG1-knockdown is needed.

Reviewer #2 (Public Review):

Summary:

Several publications during the past years provided evidence that NMD protects tumor cells from being recognized by the immune system by suppressing the display of neoantigens, and hence NMD inhibition is emerging as a promising anti-cancer approach. However, the lack of an efficacious and specific small-molecule NMD inhibitor with suitable pharmacological properties is currently a major bottleneck in the development of therapies that rely on NMD inhibition. In this manuscript, the authors describe their screen for identifying NMD inhibitors, which is based on isogenic cell lines that either express wild-type or NMD-sensitive transcript isoforms of p53 and STAG2. Using this setup, they screened a library of 2658 FDA-approved or late-phase clinical trial drugs and had 8 hits. Among them they further characterized LY3023414, showing that it inhibits NMD in cultured cells and in a mouse xenograft model, where it, however, was very toxic. Because LY3023414 was originally developed as a PI3K inhibitor, the authors claim that it inhibits NMD by inhibiting SMG1. While this is most likely true, the authors do not provide experimental evidence for this claim. Instead, they use this statement to switch their attention to another previously developed SMG1 inhibitor (SMG1i-11), of which they design and test several derivatives. Of these derivatives, KVS0001 showed the best pharmacological behavior. It upregulated NMD-sensitive transcripts in cultured cells and the xenograft mouse model and two predicted neoantigens could indeed be detected by mass spectrometry when the respective cells were treated with KVS0001. A bispecific antibody targeting T cells to a specific antigen-HLA complex led to increased IFN-gamma release and killing of cancer cells expressing this antigen-HLA complex when they were treated with KVS0001. Finally, the authors show that renal (RENCA) or lung cancer cells (LLC) were significantly inhibited in tumor growth in immunocompetent mice treated with KVS0001. Overall, this establishes KVS0001 as a novel and promising ant-cancer drug that by inhibiting SMG1 (and therewith NMD) increases the neoantigen production in the cancer cells and reveals them to the body's immune system as "foreign".

Strengths:

The novelty and significance of this work consists in the development of a novel and - judging from the presented data - very promising NMD inhibiting drug that is suitable for applications in animals. This is an important advance for the field, as previous NMD inhibitors were not specific, lacked efficacy, or were very toxic and hence not suitable for animal application. It will be still a long way with many challenges ahead towards an efficacious NMD inhibitor that is safe for use in humans, but KVS0001 appears to be a molecule that bears promise for follow-up studies. In addition, while the idea of inhibiting NMD to trigger neoantigen production in cancer cells and so reveal them to the immune system has been around for quite some time, this work provides ample and compelling support for the feasibility of this approach, at least for tumors with a high mutational burden.

Main weaknesses:

There is a disconnect between the screen and the KVS0001 compound, that they describe and test in the second part of the manuscript since KVS0001 is a derivative of the SMG1 inhibitors developed by Gopalsamy et al. in 2012 and not of the lead compound identified in the screen (LY3023414). Because of high toxicity in the mouse xenograft experiments, the authors did not follow up LY3023414 but instead switched to the published SMG1i-11 drug of Gopalsamy and colleagues, a molecule that is widely used among NMD researchers for NMD inhibition in cultured cells. Therefore, in my view, the description of the screen is obsolete, and the paper could just start with the optimization of the pharmacological properties of SMG1i-11 and the characterization of KVS0001. Even though the screen is based on an elegant setup and was executed successfully, it was ultimately a failure as it didn't reveal a useful lead compound that could be further optimized.

Additional points:

- Compared to SMG1i-11, KVS0001 seems less potent in inhibiting SMG1 (higher IC50). It would therefore be important to also compare the specificity of both drugs for SMG1 over other kinases at the applied concentrations (1 uM for SMG1i-11, 5 uM for KVS0001). The Kinativ Assay (Fig. S13) was performed with 100 nM KVS0001, which is 50-fold less than the concentration used for functional assays and hence not really meaningful. In addition, more information on the pharmacokinetic properties and toxicology of KVS0001 would allow a better judgment of the potential of this molecule as a future therapeutic agent.

- On many figures, the concentrations of the used drugs are missing. Please ensure that for every experiment that includes drugs, the drug concentration is indicated.

- Do the authors have an explanation for why LY3023414 has a much stronger effect on the p53 than on the STAG2 nonsense allele (Figure 1B, S8), whereas emetine upregulates the STAG2 nonsense alleles more than the p53 nonsense allele (Figure S5). I find this curious, but the authors do not comment on it.

- While it is a strength of the study that the NMD inhibitors were validated on many different truncation mutations in different cell lines, it would help readers if a table or graphic illustration was included that gives an overview of all mutant alleles tested in this study (which gene, type of mutation, in which cell type). In the current version, this information is scattered throughout the manuscript.

- Lines 194 and 302: That SMG1i-11 was highly insoluble in the hands of the authors is surprising. It is unclear why they used variant 11j, since variant 11e of this inhibitor is widely used among NMD researchers and readily dissolves in DMSO.

- Line 296: The authors claim that they were able to show that LY3023414 inhibited the SMG1 kinase, which is not true. To show this, they would have for example to show that LY3023414 prevents SMG1-mediated UPF1 phosphorylation, as they did for KVS0001 and SMG1i-11 in Fig. 3F. Unless the authors provide this data, the statement should be deleted or modified.

Reviewer #2 (Public Review):

Summary:<br /> The authors used four datasets spanning 30 countries to examine funding success and research quality score for various disciplines. They examined whether funding or research quality score were influenced by majority gender of the discipline and whether these affected men, women, or both within each discipline. They found that disciplines dominated by women have lower funding success and research quality score than disciplines dominated by men. These findings, are surprising because even the men in women-dominated fields experienced lower funding success and research quality score.

Strengths:<br /> - The authors utilized a comprehensive dataset covering 30 countries to explore the influence of the majority gender in academic disciplines on funding success and research quality scores.<br /> - Findings suggest a systemic issue where disciplines with a higher proportion of women have lower evaluations and funding success for all researchers, regardless of gender.<br /> - The manuscript is notable for its large sample size and the diverse international scope, enhancing the generalizability of the results.<br /> - The work accounts for various factors including age, number of research outputs, and bibliometric measures, strengthening the validity of the findings.<br /> - The manuscript raises important questions about unconscious bias in research evaluation and funding decisions, as evidenced by lower scores in women-dominated fields even for researchers that are men.<br /> - The study provides a nuanced view of gender bias, showing that it is not limited to individuals but extends to entire disciplines, impacting the perception and funding and quality or worth of research.<br /> - This work underscores the need to explore motivations behind gender distribution across fields, hinting at deep-rooted societal and institutional barriers.<br /> - The authors have opened a discussion on potential solutions to counter bias, like adjusting funding paylines or anonymizing applications, or other practical solutions.<br /> - While pointing out limitations such as the absence of data from major research-producing countries, the manuscript paves the way for future studies to examine whether its findings are universally applicable.

Weaknesses:<br /> - The study does not provide data on the gender of grant reviewers or stakeholders, which could be critical for understanding potential unconscious bias in funding decisions. These data are likely not available; however, this could be discussed. Are grant reviewers in fields dominated by women more likely to be women?<br /> - There could be more exploration into whether the research quality score is influenced by inherent biases towards disciplines themselves, rather than only being gender bias.<br /> - The manuscript should discuss how non-binary gender identities were addressed in the research. There is an opportunity to understand the impact on this group.<br /> - A significant limitation is absence of data from other major research-producing countries like China and the United States, raising questions about the generalizability of the findings. How comparable are the findings observed to these other countries?<br /> - The motivations and barriers that drive gender distribution in various fields could be expanded on. Are fields striving to reach gender parity through hiring or other mechanisms?<br /> - The authors could consider if the size of funding awards correlates with research scores, potentially overlooking a significant factor in the evaluation of research quality. Presumably there is less data on smaller 'pilot' funds and startup funds for disciplines where these are more common. Would funding success follow the same trend for these types of funds?<br /> - The language used in the manuscript at times may perpetuate bias, particularly when discussing "lower quality disciplines," which could influence the reader's perception of certain fields.<br /> - The manuscript does not clarify how many gender identities were represented in the datasets or how gender identity was determined, potentially conflating gender identity with biological sex.

Reviewer #3 (Public Review):

This study seeks to investigate one aspect of disparity in academia: how gender balance in a discipline is valued in terms of evaluated research quality score and funding success. This is important in understanding disparities within academia.<br /> This study uses publicly available data to investigate covariation between gender balance in an academic discipline and:<br /> i) Individual research quality scores of New Zealand academics as evaluated by one of 14 broader subject panels.<br /> ii) Funding success in Australia, Canada, Europe, UK.

The study would benefit from further discussion of it limitations, and from the clarification of some technical points (as described in the recommendations for the authors).

Reviewer #1 (Public Review):

Summary:

The authors provide very compelling evidence that the lateral septum (LS) engages in theta cycle skipping.

Strengths:

The data and analysis is highly compelling regarding the existence of cycle skipping.

Comments on the revised version:

All previous recommendations were addressed in this revision.

Reviewer #2 (Public Review):

Summary

Recent evidence indicates that cells of the navigation system representing different directions and whole spatial routes fire in a rhythmic alternation during 5-10 Hz (theta) network oscillation (Brandon et al., 2013, Kay et al., 2020). This phenomenon of theta cycle skipping was also reported in broader circuitry connecting the navigation system with the cognitive control regions (Jankowski et al., 2014, Tang et al., 2021). Yet nothing was known about the translation of these temporally separate representations to midbrain regions involved in reward processing as well as the hypothalamic regions, which integrate metabolic, visceral, and sensory signals with the descending signals from the forebrain to ensure adaptive control of innate behaviors (Carus-Cadavieco et al., 2017). The present work aimed to investigate theta cycle skipping and alternating representations of trajectories in the lateral septum, neurons of which receive inputs from large number of CA1 and nearly all CA3 pyramidal cells (Risold and Swanson, 1995). While spatial firing has been reported in the lateral septum before (Leutgeb and Mizumori, 2002, Wirtshafter and Wilson, 2019), its dynamic aspects have remained elusive. The present study replicates the previous findings of theta-rhythmic neuronal activity in the lateral septum and reports a temporal alternation of spatial representations in this region, thus filling an important knowledge gap and significantly extending the understanding of the processing of spatial information in the brain. The lateral septum thus propagates the representations of alternative spatial behaviors to its efferent regions. The results can instruct further research of neural mechanisms supporting learning during goal-oriented navigation and decision-making in the behaviourally crucial circuits entailing the lateral septum.

Strengths

To this end, cutting-edge approaches for high-density monitoring of neuronal activity in freely behaving rodents and neural decoding were applied. Strengths of this work include comparisons of different anatomically and probably functionally distinct compartments of the lateral septum, innervated by different hippocampal domains and projecting to different parts of the hypothalamus; large neuronal datasets including many sessions with simultaneously recorded neurons; consequently, the rhythmic aspects of the spatial code could be directly revealed from the analysis of multiple spike trains, which were also used for decoding of spatial trajectories; and comparisons of the spatial coding between the two differently reinforced tasks.

Weaknesses

Without using perturbation techniques, the present approach could not identify the aspects of the spatial code actually influencing the generation of behaviors by downstream regions.

Reviewer #1 (Public Review):

Summary:

The pituitary gonadotropins, FSH and LH, are critical regulators of reproduction. In mammals, synthesis and secretion of FSH and LH by gonadotrope cells are controlled by the hypothalamic peptide, GnRH. As FSH and LH are made in the same cells in mammals, variation in the nature of GnRH secretion is thought to contribute to the differential regulation of the two hormones. In contrast, in fish, FSH and LH are produced in distinct gonadotrope populations and may be less (or differently) dependent on GnRH than in mammals. In the present manuscript, the authors endeavored to determine whether FSH may be independently controlled by a distinct peptide, cholecystokinin (CCK), in zebrafish.

Strengths:

The authors demonstrated that the CCK receptor is enriched in FSH-producing relative to LH-producing gonadotropes, and that genetic deletion of the receptor leads to dramatic decreases in gonadotropin production and gonadal development in zebrafish. Also, using innovative in vivo and ex vivo calcium imaging approaches, they show that LH- and FSH-producing gonadotropes preferentially respond to GnRH and CCK, respectively. Exogenous CCK also preferentially stimulated FSH secretion ex vivo and in vivo.

Weaknesses:

The concept that there may be a distinct FSH-releasing hormone (FSHRH) has been debated for decades. As the authors suggest that CCK is the long-sought FSHRH (at least in fish), they must provide data that convincingly leads to such a conclusion. In my estimation, they have not yet met this burden. In particular, they show that CCK is sufficient to activate FSH-producing cells, but have not yet demonstrated its necessity. Their one attempt to do so was using fish in which they inactivated the CCK receptor using CRISPR-Cas9. While this manipulation led to a reduction in FSH, LH was affected to a similar extent. As a result, they have not shown that CCK is a selective regulator of FSH. Moreover, they do not yet demonstrate that the effects observed reflect the loss of the receptor's function in gonadotropes, as opposed to other cell types. It also is not clear whether the phenotypes of the fish reflect perturbations in pituitary development vs. a loss of CCK receptor function in the pituitary later in life. Ideally, the authors would attempt to block CCK signaling in adult fish that develop normally. For example, if CCK receptor antagonists are available, they could be used to treat fish and see whether and how this affects FSH vs. LH secretion.

In the Discussion, the authors suggest that CCK, as a satiety factor, may provide a link between metabolism and reproduction. This is an interesting idea, but it is not supported by the data presented. That is, none of the results shown link metabolic state to CCK regulation of FSH and fertility. Absent such data, the lengthy discussion of the link is speculative and not fully merited.

Also in the Discussion, the authors argue that "CCK directly controls FSH cells by innervating the pituitary gland and binding to specific receptors that are particularly abundant in FSH gonadotrophs." However, their imaging does not demonstrate innervation of FSH cells by CCK terminals (e.g., at the EM level). Moreover, they have not demonstrated the binding of CCK to these cells. Indeed, no CCK receptor protein data are shown. The calcium responses of FSH cells to exogenous CCK certainly suggest the presence of functional CCK receptors therein; but, the nature of the preparations (with all pituitary cell types present) does not demonstrate that CCK is acting directly in these cells. Indeed, the asynchrony in responses of individual FSH cells to CCK (Figure 4) suggests that not all cells may be activated in the same way. Contrast the response of LH cells to GnRH, where the onset of calcium signaling is similar across cells (Figure 3). Finally, as the authors note in the Discussion, the data presented do not enable them to conclude that the endogenous CCK regulating FSH (assuming it does) is from the brain as opposed to other sources (e.g., the gut).

Reviewer #2 (Public Review):

Summary:

This manuscript builds on previous work suggesting that the CCK peptide is the releasing hormone for FSH in fishes, which is different than that observed in mammals where both LH and FSH release are under the control of GnRH. Based on data using calcium imaging as a readout for stimulation of the gonadotrophs, the researchers present data supporting the hypothesis that CCK stimulates FSH-containing cells in the pituitary. In contrast, LH-containing cells show a weak and variable response to CCK but are highly responsive to GnRH. Data are presented that support the role of CCK in the release of FSH. Researchers also state that functional overlap exists in the potency of GnRH to activate FSH cells, thus the two signalling pathways are not separate.

The results are of interest to the field because for many years the assumption has been that fishes use the same signalling mechanism. These data present an intriguing variation where a hormone involved in satiation acts in the control of reproduction.

Strengths:

The strengths of the manuscript are that researchers have shed light on different pathways controlling reproduction in fishes.

Weaknesses:

Weaknesses are that it is not clear if multiple ligand/receptors are involved (more than one CCK and more than one receptor?). The imaging of the CCK terminals and CCK receptors needs to be reinforced.

Reviewer consultation summary:

- The data presented establish sufficiency, but not necessity of CCK in FSH regulation. The paper did not show that CCK endogenously regulates FSH in fish. This has not been established yet.

- The paper presents the pharmacological effects of CCK on ex vivo preparations but does not establish the in vivo physiological function of the peptide. The current evidence for a novel physiological regulatory mechanism is incomplete and would require further physiological experiments. These could include the use of a CCK receptor antagonist in adult fish to see the effects on FSH and LH release, the generation of a CCK knockout, or cell-specific genetic manipulations.

- Zebrafish have two CCK ligands: ccka, cckb and also multiple receptors: cckar, cckbra and cckbrb. There is ambiguity about which CCK receptor and ligand are expressed and which gene was knocked out.

- Blocking CCK action in fish (with receptor KO) affects FSH and LH. Therefore, the work did not demonstrate a selective role for CCK in FSH regulation in vivo and any claims to have discovered FSHRH need to be more conservative.

- The labelling of the terminals with anti-CCK looks a lot like the background and the authors did not show a specificity control (e.g. anti-CCK antibody pre-absorbed with the peptide or anti-CCK in morphant/KO animals).

Reviewer #1 (Public Review):

This is an interesting, informative, and well-designed study that combines theoretical and experimental methodologies to tackle the phenomenon of higher-resolution structures/substructures in model biomolecular condensates.

The authors have adequately addressed my previous concerns.

Reviewer #2 (Public Review):

Summary:

Latham A.P. et al. apply simulations and FLIM to analyse several di-block elastin-like polypetides and connect their sequence to the micro-structure of coacervates resulting from their phase-separation.

Strengths:

Understanding the molecular grammar of phase separating proteins and the connection with mesoscale properties of the coacervates is highly relevant. This work provides insights into micro-structures of coacervates resulting from di-block polypetides.

Weaknesses:

The results apply to a very specific architecture (di-block polypetides) with specific sequences.

Reviewer #1 (Public Review):

Summary:

Thakare et al propose a gravimetric method to evaluate feeding from solid food in Drosophila adults that can be used to evaluate the nutritional impact of high-fat food.

Strengths:

This method is new and fills a gap in the methods used in Drosophila research.

Weaknesses:

The data presented address a number of questions that are mainly interesting for people needing to reproduce such experiments. The work could be improved by being presented within a broader scope.

Reviewer #2 (Public Review):

Summary:

Thakare et al. present the DIETS assay for quantifying food consumption in adult Drosophila. DIETS measures food intake by weighing fly food before and after feeding. Technically, this is a well-designed, executed, and analyzed study. The interpretations are generally conservative and justified by the results. Although the results aren't always consistent with other published studies, which might reflect some of the unique conditions of the DIETS assay, the technique can clearly distinguish between some expected differences in food intake. Although lifespan is shortened in the DIETS chamber, the method seems robust for various time scales up to a week. DIETS adds another useful and versatile tool for fly researchers interested in studying feeding behavior.

Strengths:

The authors test various conditions, including food presentation, surface area, and humidity (by changing the food cup distance to an agar base) to demonstrate an optimized technique for quantifying consumption. Under these conditions, evaporation is generally limited to <10%.

The authors use DIETS to validate diverse feeding paradigms, including the published effects of temperature, food dilution, and intermittent fasting on food intake.

Weaknesses:

The studies to optimize and test the DIETS assay are technically rigorous and well-designed. However, the results reveal some weaknesses or potential caveats of the assay. As highlighted below, how much nutrition flies are actually obtaining may be misestimated due to vapor diffusion, and crowding/competition for food. This appears largely acceptable though, since the 'group' measurement can still clearly distinguish between expected feeding differences under different conditions, but it likely reduces accuracy, which may be important in some studies, and probably nullifies the effectiveness of using DIETS to restrict caloric intake.

It is my understanding that flies suck out nutrients from the medium, leaving behind the agar/cornmeal matrix. This seems consistent with the images in Figure S2B, where the spheroidal medium in the food cup maintains its shape as it shrinks, but there don't seem to be any pits or holes from fly consumption. Given that flies in DIETS consume a significant portion of the available food, it seems that the food concentration at the medium surface may be changing throughout the experiment. This may also make it challenging to use other common fly food ingredients, such as cornmeal, much of which is indigestible.

Similarly, vapor diffusion is expected between the agar bed and food cup (which the authors observed; in line 385), which may further affect assay accuracy, especially in comparisons between foods with different osmolarity.

In DIETS, increased feeding is observed with increased flies per chamber, but this is not observed in other techniques, such as EX-Q (Wu et al. 2020). It is unclear whether sensitivity to adult density is a DIETS-specific feature, or if adult density instead directly affects food intake estimates using DIETS (e.g., by affecting chamber humidity).

In another example, there is a ~300% difference in absolute feeding when the DIETS food cup is presented in different formats (Figure 3C). Again, it is unclear whether food presentation has an inherently greater effect in DIETS, or if the measurements themselves are highly sensitive to the environment.

Although the control of total food mass given to the animals is a novel feature of the assay, the likely differences in nutrient intake between individuals (and shortened lifespan) in a DIETS chamber makes this a challenging method to use to study caloric restriction. The shortened lifespan likely stems from the high adult density per vial, which has been explored in previous publications (e.g., Pearl in the 1920s; Mueller in the 1990s).

Reviewer #1 (Public Review):

Summary:

In the manuscript submission by Zhao et al. entitled, "Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila" the authors assert that cardiac arrhythmias in Drosophila on a high-fat diet are due in part to adipokinetic hormone (Akh) signaling activation. High-fat diet induces Akh secretion from activated endocrine neurons, which activate AkhR in posterior cardiac neurons. Silencing or deletion of Akh or AkhR blocks arrhythmia in Drosophila on a high-fat diet. Elimination of one of two AkhR-expressing cardiac neurons results in arrhythmia similar to a high-fat diet.

Strengths:

The authors propose a novel mechanism for high-fat diet-induced arrhythmia utilizing the Akh signaling pathway that signals to cardiac neurons.

Weaknesses:

Major comments:

(1) The authors state, "Arrhythmic pathology is rooted in the cardiac conduction system." This assertion is incorrect as a blanket statement on arrhythmias. There are certain arrhythmias that have been attributable to the conduction system, such as bradycardic rhythms, heart block, sinus node reentry, inappropriate sinus tachycardia, AV nodal reentrant tachycardia, bundle branch reentry, fascicular ventricular tachycardia, or idiopathic ventricular fibrillation to name a few. However the etiological mechanism of many atrial and ventricular arrhythmias, such as atrial fibrillation or substrate-based ventricular tachycardia, are not rooted in the conduction system. The introduction should be revised to reflect a clear focus on atrial fibrillation (AF). In addition, AF susceptibility is known to be modulated by autonomic tone, which is topically relevant to this manuscript.

(2) The authors state that "HFD led to increased heartbeat and an irregular rhythm." In representative examples shown, HFD resulted in pauses, slower heart rate, and increased irregularity in rhythm but not consistently increased heart rate (Figures 1B, 3A, and 4C). Based on the cited work by Ocorr et al (https://doi.org/10.1073/pnas.0609278104), Drosophila heart rate is highly variable with periods of fast and slow rates, which the authors attributed to neuronal and hormonal inputs. Ocorr et al then describe the use of "semi-intact" flies to remove autonomic input to normalize heart rate. Were semi-intact flies used? If not, how was heart rate variability controlled? And how was heart rate "increase" quantified in high-fat diet compared to normal-fat diet? Lastly, how does one measure "arrhythmia" when there is so much heart rate variability in normal intact flies?

(3) The authors state, "to test whether the HFD-induced increase in Akh in the APC affects APC neuron activity, we used CaLexA (https://doi.org/10.3109/01677063.2011.642910)." According to the reference, CaLexA is a tool to map active neurons and would not indicate, as the authors state, whether Akh affects APC neuron activity specifically. It is equally possible that APC neurons may be activated by HFD and produce more Akh. Please clarify this language.

(4) Are the AkhR+ neurons parasympathetic or sympathetic? Please provide additional experimentation that characterizes these neurons. The AkhR+ neurons appear to be anti-arrhythmic. Please expand the discussion to include a working hypothesis of the overall findings on Akh, AkhR, and AkhR+ neurons.

(5) The authors state, "Heart function is dependent on glucose as an energy source." However, the heart's main energy source is fatty acids with minimal use of glucose (doi: 10.1016/j.cbpa.2006.09.014). Glucose becomes more utilized by cardiomyocytes under heart failure conditions. Please amend/revise this statement.

Reviewer #2 (Public Review):

This manuscript explores mechanisms underlying heart contractility problems in metabolic disease using Drosophila as a model. They confirm, as others have demonstrated, that a high-fat diet (HFD) induces cardiac problems in flies. They showed that a high-fat diet increased Akh mRNA levels and calcium levels in the Akh-producing cells (APC), suggesting there is increased production and release of this hormone in a HFD context. When they knock down Akh production in the APCs using RNAi they see that cardiac contractility problems are abolished. They similarly show that levels of the Akh receptor (Akhr) are increased on a HFD and that loss of Akhr also rescues contractility problems on a HFD.

One highlight of the paper was the identification of a pair of neurons that express a receptor for the metabolic hormone Akh, and showing initial data that these neurons innervate the cardiac muscle. They then overexpress cell death gene reaper (rpr) in all Akhr-positive cells with Akhr-GAL4 and see that cardiac contractility becomes abnormal.

However, this paper contains several findings that have been reported elsewhere and it contains key flaws in both experimental design and data interpretation. There is some rationale for doing the experiments, and the data and images are of good quality. However, others have shown that HFD induces cardiac contractility problems (Birse 2010), that Akh mRNA levels are changed with HFD (Liao 2021) that Akh modulates cardiac rhythms (Noyes 1995), so Figures 1-4 are largely a confirmation of what is already known. This limits the overall magnitude of the advances presented in these figures. Overall, the stated concerns limit the impact of the manuscript in advancing our understanding of heart contractility.

Reviewer #3 (Public Review):

Zhao et al. provide new insights into the mechanism by which a high-fat diet (HFD) induces cardiac arrhythmia employing Drosophila as a model. HFD induces cardiac arrhythmia in both mammals and Drosophila. Both glucagon and its functional equivalent in Drosophila Akh are known to induce arrhythmia. The study demonstrates that Akh mRNA levels are increased by HFD and both Akh and its receptor are necessary for high-fat diet-induced cardiac arrhythmia, elucidating a novel link. Notably, Zhao et al. identify a pair of AKH receptor-expressing neurons located at the posterior of the heart tube. Interestingly, these neurons innervate the heart muscle and form synaptic connections, implying their roles in controlling the heart muscle. The study presented by Zhao et al. is intriguing, and the rigorous characterization of the AKH receptor-expressing neurons would significantly enhance our understanding of the molecular mechanism underlying HFD-induced cardiac arrhythmia.

Many experiments presented in the manuscript are appropriate for supporting the conclusions while additional controls and precise quantifications should help strengthen the authors' augments. The key results obtained by loss of Akh (or AkhR) and genetic elimination of the identified AkhR-expressing cardiac neurons do not reconcile, complicating the overall interpretation.

It is intriguing to see an increase in Akh mRNA levels in HFD-fed animals. This is a key result for linking HFD-induced arrhythmia to Akh. Thus, demonstrating that HFD also increases the Akh protein levels and Akh is secreted more should significantly strengthen the manuscript.

The experiments employing an AkhR null allele nicely demonstrate its requirement for HFD-induced cardiac arrhythmia. Depletion of Akh in Akh-expressing cells recapitulates the consequence of AkhR knockout, supporting that both Akh and its receptor are required for HFD-induced cardiac arrhythmia. Given that RNAi is associated with off-target effects and some RNAi reagents do not work, testing multiple independent RNAi lines is the standard procedure. It is also important to show the on-target effect of the RNAi reagents used in the study.

The most exciting result is the identification of AkhR-expressing neurons located at the posterior part of the heart tube (ACNs). The authors attempted to determine the function of ACNs by expressing rpr with AkhR-GAL4, which would induce cell death in all AkhR-expressing cells, including ACNs. The experiments presented in Figure 6 are not straightforward to interpret. Moreover, the conclusion contradicts the main hypothesis that elevated Akh is the basis of HFD-induced arrhythmia. The results suggest the importance of AkhR-expressing cells for normal heartbeat. However, elimination of Akh or AkhR restores normal rhythm in HFD-fed animals, suggesting that Akh and AkhR are not important for maintaining normal rhythms. If Akh signaling in ACNs is key for HFD-induced arrhythmia, genetic elimination of ACNs should unalter rhythm and rescue the HFD-induced arrhythmia. An important caveat is that the experiments do not test the specific role of ACNs. ACNs should be just a small part of the cells expressing AkhR. The experiments presented in Figure 6 cannot justify the authors' conclusion. Specific manipulation of ACNs will significantly improve the study. Moreover, the main hypothesis suggests that HFD may alter the activity of ACNs in a manner dependent on Akh and AkhR. Testing how HFD changes calcium, possibly by CaLexA (Figure 2) and/or GCaMP, in wild-type and AkhR mutants could be a way to connect ACNs to HFD-induced arrhythmia. Moreover, optogenetic manipulation of ACNs will allow for specific manipulation of ACNs, which is crucial for studying the specific role of ACNs in controlling cardiac rhythms.

Interestingly, expressing rpr with AkhR-GAL4 was insufficient to eliminate both ACNs. It is not clear why it didn't eliminate both ACNs. Given the incomplete penetrance, appropriate quantifications should be helpful. Additionally, the impact on other AhkR-expressing cells should be assessed. Adding more copies of UAS-rpr, AkhR-GAL4, or both may eliminate all ACNs and other AkhR-expressing cells. The authors could also try UAS-hid instead of UAS-rpr.

Reviewer #1 (Public Review):

Summary:

The manuscript by Jang et al. describes the application of new methods to measure the localization of GTP-binding signaling proteins (G proteins) on different membrane structures in a model mammalian cell line (HEK293). G proteins mediate signaling by receptors found at the cell surface (GPCRs), with evidence from the last 15 years suggesting that GPCRs can induce G-protein mediated signaling from different membrane structures within the cell, with variation in signal localization leading to different cellular outcomes. While it has been clearly shown that different GPCRs efficiently traffic to various intracellular compartments, it is less clear whether G proteins traffic in the same manner, and whether GPCR trafficking facilitates "passenger" G protein trafficking. This question was a blind spot in the burgeoning field of GPCR localized signaling in need of careful study, and the results obtained will serve as an important guidepost for further work in this field. The extent to which G proteins localize to different membranes within the cell is the main experimental question tested in this manuscript. This question is pursued through two distinct methods, both relying on genetic modification of the G-beta subunit with a tag. In one method, G-beta is modified with a small fragment of the fluorescent protein mNG, which combines with the larger mNG fragment to form a fully functional fluorescent protein to facilitate protein trafficking by fluorescent microscopy. This approach was combined with the expression of fluorescent proteins directed to various intracellular compartments (different types of endosomes, lysosome, endoplasmic reticulum, Golgi, mitochondria) to look for colocalization of G-beta with these markers. These experiments showed compelling evidence that G-beta co-localizes with markers at the plasma membrane and the lysosome, with weak or absent co-localization for other markers. A second method for measuring localization relied on fusing G-beta with a small fragment from a miniature luciferase (HiBit) that combines with a larger luciferase fragment (LgBit) to form an active luciferase enzyme. Localization of G-beta (and luciferase signal) was measured using a method known as bystander BRET, which relies on the expression of a fluorescent protein BRET acceptor in different cellular compartments. Results using bystander BRET supported findings from fluorescence microscopy experiments. These methods for tracking G protein localization were also used to probe other questions. The activation of GPCRs from different classes had virtually no impact on the localization of G-beta, suggesting that GPCR activation does not result in the shuttling of G proteins through the endosomal pathway with activated receptors.

Strengths:

The question probed in this study is quite important and, in my opinion, understudied by the pharmacology community. The results presented here are an important call to be cognizant of the localization of GPCR coupling partners in different cellular compartments. Abundant reports of endosomal GPCR signaling need to consider how the impact of lower G protein abundance on endosomal membranes will affect the signaling responses under study.

The work presented is carefully executed, with seemingly high levels of technical rigor. These studies benefit from probing the experimental questions at hand using two different methods of measurement (fluorescent microscopy and bystander BRET). The observation that both methods arrive at the same (or a very similar) answer inspires confidence about the validity of these findings.

Weaknesses:

The rationale for fusing G-beta with either mNG2(11) or SmBit could benefit from some expansion. I understand the speculation that using the smallest tag possible may have the smallest impact on protein performance and localization, but plenty of researchers have fused proteins with whole fluorescent proteins to provide conclusions that have been confirmed by other methods. Many studies even use G proteins fused with fluorescent proteins or luciferases. Is there an important advantage to tagging G-beta with small tags? Is there evidence that G proteins with full-size protein tags behave aberrantly? If the studies presented here would not have been possible without these CRISPR-based tagging approaches, it would be helpful to provide more context to make this clearer. Perhaps one factor would be interference from newly synthesized G proteins-fluorescent protein fusions en route to the plasma membrane (in the ER and Golgi).

As noted by the authors, they do not demonstrate that the tagged G-beta is predominantly found within heterotrimeric G protein complexes. If there is substantial free G-beta, then many of the conclusions need to be reconsidered. Perhaps a comparison of immunoprecipitated tagged G beta vs immunoprecipitated supernatant, with blotting for other G protein subunits would be informative.

Additional context and questions:

(1) There exists some evidence that certain GPCRs can form enduring complexes with G-beta-gamma (Pubmed: 23297229, 27499021). That would seem to offer a mechanism that would enable receptor-mediated transport of G protein subunits. It would be helpful for the authors to place the findings of this manuscript in the context of these previous findings since they seem somewhat contradictory.

(2) There is some evidence that GaS undergoes measurable dissociation from the plasma membrane upon activation (see the mechanism of the assay in Pubmed: 35302493). It seems possible that G-alpha (and in particular GaS) might behave differently than the G-beta subunit studied here. This is not entirely clear from the discussion as it now stands.

(3) The authors say "The presence of mNG-b1 on late endosomes suggested that some G proteins may be degraded by lysosomes". The mechanism of lysosomal degradation by proteins on the outside of the lysosome is not clear. It would be helpful for the authors to clarify.

(4) Although the authors do a good job of assessing G protein dilution in endosomal membranes, it is unclear how this behavior compares to the measurement of other lipid-anchored proteins using the same approach. Is the dilution of G proteins what we would expect for any lipid-anchored protein at the inner leaflet of the plasma membrane?

Reviewer #2 (Public Review):

This is an interesting method that addresses the important problem of assessing G protein localization at endogenous levels. The data are generally convincing.

Specific comments

Methods:<br /> The description of the gene editing method is unclear. There are two different CRISPR cell lines made in two different cell backgrounds. The methods should clearly state which CRISPR guides were used on which cell line. It is also not clear why HiBit is included in the mNG-β1 construct. Presumably, this is not critical but it would be helpful to explicitly note. In general, the Methods could be more complete.

Results:<br /> The explanation of validation experiments in Figures 1 C and D is incomplete and difficult to follow. The rationale and explanation of the experiments could be expanded. In addition, because this is an interesting method, it would be helpful to know if the endogenous editing affects normal GPCR signaling. For example, the authors could include data showing an Iso-induced cAMP response. This is not critical to the present interpretation but is relevant as a general point regarding the method. Also, it may be relevant to the interpretation of receptor effects on G protein localization.

Discussion:<br /> The conclusion that beta-gamma subunits do not redistribute after GPCR activation seems new and different from previous reports. Is this correct? Can the authors elaborate on how the results compare to previous literature?

Can the authors note that OpenCell has endogenously tagged Gβ1 and reports more obvious internal localization? Can the authors comment on this point?

Is this the first use of CRISPR / HiBit for BRET assay? It would be helpful to know this or cite previous work if not. Also, as this is submitted as a tools piece, the authors might say a little more about the potential application to other questions.

Reviewer #3 (Public Review):

Summary:

This article addresses an important and interesting question concerning intracellular localization and dynamics of endogenous G proteins. The fate and trafficking of G protein-coupled receptors (GPCRs) have been extensively studied but so far little is known about the trafficking routes of their partner G proteins that are known to dissociate from their respective receptors upon activation of the signaling pathway. The authors utilize modern cell biology tools including genome editing and bystander bioluminescence resonance energy transfer (BRET) to probe intracellular localization of G proteins in various membrane compartments in steady state and also upon receptor activation. Data presented in this manuscript shows that while G proteins are mostly present on the plasma membrane, they can be also detected in endosomal compartments, especially in late endosomes and lysosomes. This distribution, according to data presented in this study, seems not to be affected by receptor activation. These findings will have implications in further studies addressing GPCR signaling mechanisms from intracellular compartments.

Strengths:

The methods used in this study are adequate for the question asked. Especially, the use of genome-edited cells (for the addition of the tag on one of the G proteins) is a great choice to prevent the effects of overexpression. Moreover, the use of bystander BRET allowed authors to probe the intracellular localization of G proteins in a very high-throughput fashion. By combining imaging and BRET authors convincingly show that G proteins are very low abundant on early endosomes (also ER, mitochondria, and medial Golgi), however seem to accumulate on membranes of late endosomal compartments.

Weaknesses:

While the authors provide a novel dataset, many questions regarding G protein trafficking remain open. For example, it is not entirely clear which pathway is utilized to traffic G proteins from the plasma membrane to intracellular compartments. Additionally, future studies should also address the dynamics of G protein trafficking, for example by tracking them over multiple time points.

Reviewer #2 (Public Review):

Summary:

Kisspeptin neurons of the arcuate nucleus (ARC) are thought to be responsible for the pulsatile GnRH secretory pattern and to mediate feedback regulation of GnRH secretion by estradiol (E2). Evidence in the literature, including the work of the authors, indicates that ARC kisspeptin coordinate their activity through reciprocal synaptic interactions and the release of glutamate and of neuropeptide neurokinin B (NKB), which they co-express. The authors show here that E2 regulates the expression of genes encoding different voltage-dependent calcium channels, calcium-dependent potassium channels, and canonical transient receptor potential (TRPC5) channels and of the corresponding ionic currents in ARC kisspeptin neurons. Using computer simulations of the electrical activity of ARC kisspeptin neurons, the authors also provide evidence of what these changes translate into in terms of these cells' firing patterns. The experiments reveal that E2 upregulates various voltage-gated calcium currents as well as 2 subtypes of calcium-dependent potassium currents while decreasing TRPC5 expression (an ion channel downstream of NKB receptor activation), the slow excitatory synaptic potentials (slow EPSP) elicited in ARC kisspeptin neurons by NKB release and expression of the G protein-associated inward-rectifying potassium channel (GIRK). Based on these results, and on those of computer simulations, the authors propose that E2 promotes a functional transition of ARC kisspeptin neurons from neuropeptide-mediated sustained firing that supports coordinated activity for pulsatile GnRH secretion to a less intense firing in glutamatergic burst-like firing pattern that could favor glutamate release from ARC kisspeptin. The authors suggest that the latter might be important for the generation of the preovulatory surge in females.

Strengths:

The authors combined multiple approaches in vitro and in silico to gain insights into the impact of E2 on the electrical activity of ARC kisspeptin neurons. These include patch-clamp electrophysiology combined with selective optogenetic stimulation of ARC kisspeptin neurons, reverse transcriptase quantitative PCR, pharmacology, and CRIPR-Cas9-mediated knockdown of the Trpc5 gene. The addition of computer simulations for understanding the impact of E2 on the electrical activity of ARC kisspeptin cells is also a strength.

The authors add interesting information on the complement of ionic currents in ARC kisspeptin neurons and on their regulation by E2 to what was already known in the literature. Pharmacological and electrophysiological experiments appear of the highest standards. Robust statistical analyses are provided throughout, although some experiments (illustrated in Figures 7 and 8) do have rather low sample numbers.

The impact of E2 on calcium and potassium currents is compelling. Likewise, the results of Trpc5 gene knockdown do provide good evidence that the TRPC5 channel plays a key role in mediating the NKB-mediated slow EPSP. Surprisingly, this also revealed an unsuspected role for this channel in regulating the membrane potential and excitability of ARC kisspeptin neurons.

Weaknesses:

The manuscript also has weaknesses that obscure some of the conclusions drawn by the authors.

One has to do with the fact that "burst-like" firing that the authors postulate ARC kisspeptin neurons transition to after E2 replacement is only seen in computer simulations, and not in slice patch-clamp recordings. A more direct demonstration of the existence of this firing pattern, and of its prominence over neuropeptide-dependent sustained firing under conditions of high E2 would make a more convincing case for the authors' hypothesis.

In addition, and quite importantly, the authors compare here two conditions, OVX versus OVX replaced with high E2, that may not reflect the physiological conditions (the diestrous [low E2] and proestrous [high E2] stages of the estrous cycle) under which the proposed transition between neuropeptide-dependent sustained firing and less intense burst firing might take place. This is an important caveat to keep in mind when interpreting the authors' findings. Indeed, that E2 alters certain ionic currents when added back to OVX females, does not mean that the magnitude of these ionic currents will vary during the estrous cycle.

Lastly, the results of some of the pharmacological and genetic experiments may be difficult to interpret as presented. For example, in Figure 3, although it is possible that blockade of individual calcium channel subtypes suppresses the slow EPSP through decreased calcium entry at the somato-dendritic compartment to sustain TRPC5 activation and the slow depolarization (as the authors imply), a reasonable alternative interpretation would be that at least some of the effects on the amplitude of the slow EPSP result from suppression of presynaptic calcium influx and, thus, decreased neurotransmitter and neuropeptide secretion. Along the same lines, in Figure 12, one possible interpretation of the observed smaller slow EPSPs seen in mice with mutant TRPC5 could be that at least some of the effect is due to decreased neurotransmitter and neuropeptide release due to the decreased excitability associated with TRPC5 knockdown.

Reviewer #1 (Public Review):

Summary:

In this work, Qiu and colleagues examined the effects of preovulatory (i.e., proestrous or late follicular phase) levels of circulating estradiol on multiple calcium and potassium channel conductances in arcuate nucleus kisspeptin neurons. Although these cells are strongly linked to a role as the "GnRH pulse generator," the goal here was to examine the physiological properties of these cells in a hormonal milieu mimicking late proestrus, the time of the preovulatory GnRH-LH surge. Computational modeling is used to manipulate multiple conductances simultaneously and support a role for certain calcium channels in facilitating a switch in firing mode from tonic to bursting. CRISPR knockdown of the TRPC5 channel reduced overall excitability, but this was only examined in cells from ovariectomized mice without estradiol treatment. The patch clamp experiments are comprehensive and overall solid but a direct demonstration of the role of these conductances in being necessary for surge generation (or at least having a direct physiological consequence on surge properties) is lacking, substantially reducing the impact of the findings.

Strengths:

(1) Examination of multiple types of calcium and potassium currents, both through electrophysiology and molecular biology.

(2) Focus on arcuate kisspeptin neurons during the surge is relatively conceptually novel as the anteroventral periventricular nucleus (AVPV) kisspeptin neurons have received much more attention as the "surge generator" population.

(3) The modeling studies allow for direct examination of manipulation of single and multiple conductances, whereas the electrophysiology studies necessarily require examination of each current in isolation. The construction of an arcuate kisspeptin neuron model promises to be of value to the reproductive neuroendocrinology field.

Weaknesses:

(1) The novelty of some of the experiments needs to be clarified. This reviewer's understanding is that prior experiments largely used a different OVX+E2 treatment paradigm mimicking periods of low estradiol levels, whereas the present work used a "high E2" treatment model. However, Figures 10C and D are repeated from a previous publication by the same group, according to the figure legend. Findings from "high" vs. "low" E2 treatment regimens should be labeled and clearly separated in the text. It would also help to have direct comparisons between results from low E2 and high E2 treatment conditions.

(2) In multiple places, links are made between the changes in conductances and the transition from peptidergic to glutamatergic neurotransmission. However, this relationship is never directly assessed. The data that come closest are the qPCR results showing reduced Tac2 and increased Vglut2 mRNA, but in the figure legend, it appears that these results are from a prior publication using a different E2 treatment regimen.

(3) Similarly, no recordings of arcuate-AVPV glutamatergic transmission are made so the statements that Kiss1ARH neurons facilitate the GnRH surge via this connection are still only conjecture and not supported by the present experiments.

(4) Figure 1 is not described in the Results section, and is only tenuously connected to the statement in the introduction in which it is cited. The relevance of panels C and D is not clear. In this regard, much is made of the burst firing pattern that arises after E2 treatment in the model, but this burst firing pattern is not demonstrated directly in the slice electrophysiology examples.

(5) In Figure 3, it would be preferable to see the raw values for R1 and R2 in each cell, to confirm that all cells were starting from a similar baseline. In addition, it is unclear why the data for TTA-P2 is not shown, or how many cells were recorded to provide this finding.

(6) In Figure 5, panel C lists 11 cells in the E2 condition but panel E lists data from 37 cells. The reason for this discrepancy is not clear.

(7) In all histogram figures, it would be preferable to have the data for individual cells superimposed on the mean and SEM.

(8) The CRISPR experiments were only performed in OVX mice, substantially limiting interpretation with respect to potential roles for TRPC5 in shaping arcuate kisspeptin neuron function during the preovulatory surge.

(9) Furthermore, there are no demonstrations that the CRISPR manipulations impair or alter the LH surge.

(10) The time of day of slice preparation and recording needs to be specified in the Methods.

Reviewer #1 (Public Review):

Summary:

In this study, the authors show that a long-non coding RNA lncDACH1 inhibits sodium currents in cardiomyocytes by binding to and altering the localization of dystrophin. The authors use a number of methodologies to demonstrate that lncDACH1 binds to dystrophin and disrupt its localization to the membrane, which in turn downregulates NaV1.5 currents. Knockdown of lncDACH1 upregulates NaV1.5 currents. Furthermore, in heart failure, lncDACH1 is shown to be upregulated which suggests that this mechanism may have pathophysiological relevance.

Strengths:

(1) This study presents a novel mechanism of Na channel regulation which may be pathophysiologically important.

(2) The experiments are comprehensive and systematically evaluate the physiological importance of lncDACH1.

Reviewer #3 (Public Review):

Summary:

In this manuscript, the authors report the first evidence of Nav1.5 regulation by a long noncoding RNA, LncRNA-DACH1, and suggest its implication in the reduction in sodium current observed in heart failure. Since no direct interaction is observed between Nav1.5 and the LncRNA, they propose that the regulation is via dystrophin and targeting of Nav1.5 to the plasma membrane.

Strengths:

(1) First evidence of Nav1.5 regulation by a long noncoding RNA.<br /> (2) Implication of LncRNA-DACH1 in heart failure and mechanisms of arrhythmias.<br /> (3) Demonstration of LncRNA-DACH1 binding to dystrophin.<br /> (4) Potential rescuing of dystrophin and Nav1.5 strategy.

Weaknesses:

(1) The fact that the total Nav1.5 protein is reduced by 50% which is similar to the reduction in the membrane reduction questions the main conclusion of the authors implicating dystrophin in the reduced Nav1.5 targeting. The reduction in membrane Nav1.5 could simply be due to the reduction in total protein.

Reviewer #2 (Public Review):

This manuscript by Xue et al. describes the effects of a long noncoding RNA, lncDACH1, on the localization of Nav channel expression, the magnitude of INa, and arrhythmia susceptibility in the mouse heart. Because lncDACH1 was previously reported to bind and disrupt membrane expression of dystrophin, which in turn is required for proper Nav1.5 localization, much of the findings are inferred through the lens of dystrophin alterations.

The results report that cardiomyocyte-specific transgenic overexpression of lncDACH1 reduces INa in isolated cardiomyocytes; measurements in whole heart show a corresponding reduction in conduction velocity and enhanced susceptibility to arrhythmia. The effect on INa was confirmed in isolated WT mouse cardiomyocytes infected with a lncDACH1 adenoviral construct. Importantly, reducing lncDACH1 expression via either a cardiomyocyte-specific knockout or using shRNA had the opposite effect: INa was increased in isolated cells, as was conduction velocity in heart. Experiments were also conducted with a fragment of lnDACH1 identified by its conservation with other mammalian species. Overexpression of this fragment resulted in reduced INa and greater proarrhythmic behavior. Alteration of expression was confirmed by qPCR.

The mechanism by which lnDACH1 exerts its effects on INa was explored by measuring protein levels from cell fractions and immunofluorescence localization in cells. In general, overexpression was reported to reduce Nav1.5 and dystrophin levels and knockout or knockdown increased them.

The strengths of this manuscript include convincing evidence of a link between lncDACH1 and Na channel function. The identification of a lncDACH1 segment conserved among mammalian species is compelling. The observation that lncDACH1 is increased in a heart failure model and provides a plausible hypothesis for disease mechanism.

One limitation of the fractionation approach is the uncertain disposition of Na channel protein deemed "cytoplasmic." It seems likely that the membrane fraction includes ER membrane. The signal may reasonably be attributed to Na channel protein in stalled transport vesicles, or alternatively in stress granules, but this was not directly addressed.

Reviewer #1 (Public Review):

Wang, He et al have constructed comprehensive single nucleus atlas for the gills of the deep sea Bathymodioline mussels, which possess intracellular symbionts that provide a key source of carbon and allow them to live in these extreme environments. They provide annotations of the different cell states within the gills, shedding light on how multiple cell types cooperate to give rise to the emergent functions of the composite tissues and the gills as a whole. They pay special attention to characterizing the bacteriocyte cell populations and identifying sets of genes that may play a role in their interaction with the symbiotes.

Wang, He et al sample mussels from 3 different environments: animals from their native methane rich environment, animals transplanted to a methane-poor environment to induce starvation and animals that have been starved in the methane-poor environment and then moved back to the methane-rich environment. They demonstrated that starvation had the biggest impact on bacteriocyte transcriptomes. They hypothesize that the up-regulation of genes associated with lysosomal digestion leads to the digestion of the intracellular symbiont during starvation, while the non-starved and reacclimated groups more readily harvest the nutrients from symbiotes without destroying them. Further work exploring the differences in symbiote populations between ecological conditions will further elucidate the dynamic relationship between host and symbiote. This will help disentangle specific changes in transcriptomic state that are due to their changing interactions with the symbiotes from changes associated with other environmental factors.

This paper makes available a high quality dataset that is of interest to many disciplines of biology. The unique qualities of this non-model organism and collection of conditions sampled make it of special interest to those studying deep sea adaptation, the impact of environmental perturbation on Bathymodioline mussels populations, and intracellular symbiotes. The authors also use a diverse array of tools to explore and validate their data.

Reviewer #2 (Public Review):

Wang, He et al. shed insight into the molecular mechanisms of deep-sea chemosymbiosis at the single-cell level. They do so by producing a comprehensive cell atlas of the gill of Gigantidas platifrons, a chemosymbiotic mussel that dominates the deep-sea ecosystem. They uncover novel cell types and find that the gene expression of bacteriocytes, the symbiont-hosting cells, supports two hypotheses of host-symbiont interactions: the "farming" pathway, where symbionts are directly digested, and the "milking" pathway, where nutrients released by the symbionts are used by the host. They perform an in situ transplantation experiment in the deep sea and reveal transitional changes in gene expression that support a model where starvation stress induces bacteriocytes to "farm" their symbionts, while recovery leads to the restoration of the "farming" and "milking" pathways.

A major strength of this study includes the successful application of advanced single nucleus techniques to a non-model, deep sea organism that remains challenging to sample. I also applaud the authors for performing an in situ transplantation experiment in a deep sea environment. From gene expression profiles, the authors deftly provide a rich functional description of G. platifrons cell types that is well-contextualized within the unique biology of chemosymbiosis. These findings offer significant insight into the molecular mechanisms of deep-sea host-symbiont ecology, and will serve as a valuable resource for future studies into the striking biology of G. platifrons.

The authors' conclusions are generally well-supported by their results. However, I recognize that the difficulty of obtaining deep-sea specimens may have impacted experimental design and no replicates were sampled.

It is notable that the Fanmao cells were much more sparsely sampled. It appears that fewer cells were sequenced, resulting in the Starvation and Reconstitution conditions having 2-3x more cells after doublet filtering. These discrepancies also are reflected in the proportion of cells that survived QC, suggesting a distinction in quality or approach. However, the authors provide clear and sufficient evidence via bootstrapping that batch effects between the three samples are negligible. While batch effect does not appear to have affected gene expression profiles, the proportion of cell types may remain sensitive to sampling techniques, and thus interpretation of Fig. S12 must be approached with caution.

Reviewer #3 (Public Review):

Wang et al. explored the unique biology of the deep-sea mussel Gigantidas platifrons to understand fundamental principles of animal-symbiont relationships. They used single-nucleus RNA sequencing and validation and visualization of many of the important cellular and molecular players that allow these organisms to survive in the deep-sea. They demonstrate that a diversity of cell types that support the structure and function of the gill including bacteriocytes, specialized epithelial cells that host sulfur-oxidizing or methane-oxidizing symbionts as well as a suite of other cell types including supportive cells, ciliary, and smooth muscle cells. By performing experiments of transplanting mussels from one habitat which is rich in methane to methane-limited environments, the authors showed that starved mussels may consume endosymbionts versus in methane-rich environments upregulated genes involved in glutamate synthesis. These data add to the growing body of literature that organisms control their endosymbionts in response to environmental change.

The conclusions of the data are well supported. The authors adapted a technique that would have been technically impossible in their field environment by preserving the tissue and then performing nuclear isolation after the fact. The use of single-nucleus sequencing opens the possibility of new cellular and molecular biology that is not possible to study in the field. Additionally, the in-situ data (both WISH and FISH) are high-quality and easy to interpret. The use of cell-type-specific markers along with a symbiont-specific probe was effective. Finally, the SEM and TEM were used convincingly for specific purposes in the case of showing the cilia that may support water movement.

The one particular area for future exploration surrounds the concept of a proliferative progenitor population within the gills. The authors recover molecular markers for these putative populations and additional future work will uncover if these are indeed proliferative cells contribute to symbiont colonization.

Overall the significance of this work is identifying the relationship between symbionts and bacteriocytes and how these host bacteriocytes modulate their gene expression in response to environmental change. It will be interesting to see how similar or different these data are across animal phyla. For instance, the work of symbiosis in cnidarians may converge on similar principles of there may be independent ways in which organisms have been able to solve these problems.

Reviewer #1 (Public Review):

Summary:

Federer et al. tested AAVs designed to target GABAergic cells and parvalbumin-expressing cells in marmoset V1. Several new results were obtained. First, AAV-h56D targeted GABAergic cells with >90% specificity, and this varied with serotype and layer. Second, AAV-PHP.eB.S5E2 targeted parvalbumin-expressing neurons with up to 98% specificity. Third, the immunohistochemical detection of GABA and PV was attenuated near viral injection sites.

Strengths:

Vormstein-Schneider et al. (2020) tested their AAV-S5E2 vector in marmosets by intravenous injection. The data presented in this manuscript are valuable in part because they show the transduction pattern produced by intraparenchymal injections, which are more conventional and efficient.

Weaknesses:

The conclusions regarding the effects of serotype are based on data from single injection tracks in a single animal. I understand that ethical and financial constraints preclude high throughput testing, but these limitations do not change what can be inferred from the measurements. The text asserts that "...serotype 9 is a better choice when high specificity and coverage across all layers are required". The data presented are consistent with this idea but do not make a strong case for it.

A related criticism extends to the analysis of injection volume on viral specificity. Some replication was performed here, but reliability across injections was not reported. My understanding is that individual ROIs were treated as independent observations. These are not biological replicates (arguably, neither are multiple injection tracks in a single animal, but they are certainly closer). Idiosyncrasies between animals or injections (e.g. if one injection happened to hit one layer more than another) could have substantial impacts on the measurements. It remains unclear which results regarding injection volume or serotype would hold up had a large number of injections been made into a large number of marmosets.

Reviewer #2 (Public Review):

This is a straightforward manuscript assessing the specificity and efficiency of transgene expression in marmoset primary visual cortex (V1), for 4 different AAV vectors known to target transgene expression to either inhibitory cortical neurons (3 serotypes of AAV-h56D-tdTomato) or parvalbumin (PV)+ inhibitory cortical neurons in mice. Vectors are injected into the marmoset cortex and then postmortem tissue is analyzed following antibody labeling against GABA and PV. It is reported that: "in marmoset V1 AAV-h56D induces transgene expression in GABAergic cells with up to 91-94% specificity and 80% efficiency, depending on viral serotype and cortical layer. AAV-PHP.eB-S5E2 induces transgene expression in PV cells across all cortical layers with up to 98% specificity and 86-90% efficiency."

These claims are largely supported but slightly exaggerated relative to the actual values in the results presented. In particular, the overall efficiency for the best h56D vectors described in the results is: "Overall, across all layers, AAV9 and AAV1 showed significantly higher coverage (66.1{plus minus}3.9 and 64.9%{plus minus}3.7)". The highest coverage observed is just in middle layers and is also less than 80%: "(AAV9: 78.5%{plus minus}9.1; AAV1: 76.9%{plus minus}7.4)". For the AAV-PHP.eB-S5E2 the efficiency reported in the abstract ("86-90%) is also slightly exaggerated relative to the results: "Overall, across all layers coverage ranged from 78%{plus minus}1.9 for injection volumes >300nl to 81.6%{plus minus}1.8 for injection volumes of 100nl."

These data will be useful to others who might be interested in targeting transgene expression in these cell types in monkeys. Suggestions for improvement are to include more details about the vectors injected and to delete some comments about results that are not documented based on vectors that are not described (see below).

Major comments:

Details provided about the AAV vectors used with the h56D enhancer are not sufficient to allow assessment of their potential utility relative to the results presented. All that is provided is: "The fourth animal received 3 injections, each of a different AAV serotype (1, 7, and 9) of the AAV-h56D-tdTomato (Mehta et al., 2019), obtained from the Zemelman laboratory (UT Austin)." At a minimum, it is necessary to provide the titers of each of the vectors. It would also be helpful to provide more information about viral preparation for both these vectors and the AAVPHP.eB-S5E2.tdTomato. Notably, what purification methods were used, and what specific methods were used to measure the titers?

The first paragraph of the results includes brief anecdotal claims without any data to support them and without any details about the relevant vectors that would allow any data that might have been collected to be critically assessed. These statements should be deleted. Specifically, delete: "as well as 3 different kinds of PV-specific AAVs, specifically a mixture of AAV1-PaqR4-Flp and AAV1-h56D-mCherry-FRT (Mehta et al., 2019), an AAV1-PV1-ChR2-eYFP (donated by G. Horwitz, University of Washington)," and delete "Here we report results only from those vectors that were deemed to be most promising for use in primate cortex, based on infectivity and specificity. These were the 3 serotypes of the GABA-specific pAAV-h56D-tdTomato, and the PV-specific AAVPHP.eB-S5E2.tdTomato." These tools might in fact be just as useful or even better than what is actually tested and reported here, but maybe the viral titer was too low to expect any expression.

Based on the description in the Methods it seems that no antibody labeling against TdTomato was used to amplify the detection of the transgenes expressed from the AAV vectors. It should be verified that this is the case - a statement could be added to the Methods.

Reviewer #3 (Public Review):

Summary:

Federer et al. describe the laminar profiles of GABA+ and of PV+ neurons in marmoset V1. They also report on the selectivity and efficiency of expression of a PV-selective enhancer (S5E2). Three further viruses were tested, with a view to characterizing the expression profiles of a GABA-selective enhancer (h56d), but these results are preliminary.

Strengths:

The derivation of cell-type specific enhancers is key for translating the types of circuit analyses that can be performed in mice - which rely on germline modifications for access to cell-type specific manipulation - in higher-order mammals. Federer et al. further validate the utility of S5E2 as a PV-selective enhancer in NHPs.

Additionally, the authors characterize the laminar distribution pattern of GABA+ and PV+ cells in V1. This survey may prove valuable to researchers seeking to understand and manipulate the microcircuitry mediating the excitation-inhibition balance in this region of the marmoset brain.

Weaknesses:

Enhancer/promoter specificity and efficiency cannot be directly compared, because they were packaged in different serotypes of AAV.

The three different serotypes of AAV expressing reporter under the h56D promoter were only tested once each, and all in the same animal. There are many variables that can contribute to the success (or failure) of a viral injection, so observations with an n=1 cannot be considered reliable.

The language used throughout conflates the cell-type specificity conferred by the regulatory elements with that conferred by the serotype of the virus.

Reviewer #1 (Public Review):

The manuscript by Zhao et al describes the identification of RAPSYN, a NEDD8 E3 ligase previously studied for its role in acetylcholine receptor clustering and neuromuscular junction formation, as a factor promoting the stabilisation of the BCR-ABL oncogene in Chronic Myeloid Leukemia (CML) cells. The authors have identified that NEDDylation of BCR-ABL by RAPSYN antagonises its poly-ubiquitin and subsequent proteasome-based degradation. Knocking down RAPSYN with shRNA led to increased poly-ubiquitination and faster turnover of BCR-ABL. Furthermore, they describe that SRC-dependent phosphorylation of RAPSYN facilitates its NEDD8-ligase activity.

The authors' findings are primarily rooted in a series of well-conducted in vitro experiments using two CML cell lines, K562 and MEG-01. They have performed some further validations using primary CML samples, which have strengthened their claims.

The author's initial discoveries have come from interrogating a number of publicly available gene expression datasets, both microarray-based and RNA-seq, which revealed that RAPSYN is increased at the protein level but that RNA levels are not different between healthy and CML samples. This is a very interesting observation which warrants further future investigation.

The conclusions of this revised manuscript are broadly supported by the data and the analyses. It also describes novel findings that can spur future studies, both into the basic cellular biology of CML as well as into potential new therapeutic strategies.

Comments on revised version:

I thank the authors for addressing my concerns in the initial review. The revised manuscript with additional data is much stronger.

Reviewer #2 (Public Review):

In this study the authors aim to elucidate the role of RAPSYN in BCR-ABL-mediated leukemogenesis. RAPSYN is mainly known as a scaffolding protein for anchoring acetylcholine receptors (AChRs) to the cytoskeleton in muscle cells, facilitating AChR clustering through neddylation (Li et al., 2016). The authors demonstrate, through a broad and rigorous array of biochemical assays, that RAPSYN also plays a crucial role in the neddylation of BCR-ABL in leukemia cells. Their results indicate that this process shields BCR-ABL from ubiquitination and subsequent degradation, likely through a mechanism involving competition for binding with the BCR-ABL ubiquitin ligase c-CBL. In addition, the authors delve into the regulatory mechanisms underlying RAPSYN stability, demonstrating that it is enhanced through phosphorylation by SRC. This discovery further deepens our understanding of the complex dynamics of the molecular interactions that regulate BCR-ABL stability in leukemia.

To confirm the physiological significance of their findings, the authors effectively utilize cell viability assays and in vivo models. The integration of these approaches lends strength and validity to their conclusions.

The implications of the findings presented in this study are important, particularly in relation to our understanding of the pathogenesis and potential therapeutic strategies for Philadelphia chromosome-positive leukemias. By illuminating the role of RAPSYN in the regulation of BCR-ABL stability, this research potentially uncovers avenues for the development of targeted therapies, making a significant contribution to the field.

Two areas of the study could benefit from additional validation and exploration:

(1) The authors propose that targeting RAPSYN in Ph+ leukemia could have a high therapeutic index, suggesting that inhibition of RAPSYN may lead to cytotoxicity in Ph+ leukemia with high specificity and minimal side effects. The authors now include data showing RAPSYN knockdown in HS-5 cells does not affect cell growth (Figure 1C), supporting this assertion. This observation presents a contrast to DepMap data (https://depmap.org/), where RNAi and CRISPR-mediated RAPSYN depletion across hundreds of cell lines does not exhibit obvious differential effects on cell viability compared to Ph+ leukemia cell lines. Therefore, while the current results are promising, they call for additional validation by future studies to confirm RAPSYN as a viable therapeutic target in this context.

(2) A particularly notable yet underexplored aspect of this study is the observed disparity between RAPSYN protein and mRNA levels in Ph+ patient samples and cell lines. There is a marked enrichment of RAPSYN protein levels (Figure 1A, B) despite seemingly unchanged mRNA levels (Supplementary Figure 1 A-C). The authors convincingly demonstrate that RAPSYN stabilizes BCR-ABL, while SRC-mediated phosphorylation in turn stabilizes RAPSYN. This points to a specific, SRC-driven stabilization mechanism of RAPSYN in the Ph+ leukemia context. Consequently, the question arises whether BCR-ABL (through activation of SRC) reciprocally stabilize RAPSYN? Exploring the effects of BCR-ABL depletion on RAPSYN levels could shed light on this potential two-way stabilization mechanism, offering deeper insight into the complex molecular dynamics of RAPSYN and BCR-ABL in Ph+ leukemias.

In conclusion, this study represents a pivotal advancement in our understanding of Philadelphia chromosome-positive leukemias. It uniquely positions RAPSYN, a protein previously not associated with leukemogenesis, as a key regulator of BCR-ABL stability. Future research is essential to establish RAPSYN's potential as a therapeutic target and to more comprehensively understand its role in this context.

Comments on revised version:

I acknowledge and appreciate the author responses. Below are our comments on each reply:

Reply 1: Your response and the inclusion of data regarding RAPSYN knockdown in HS-5 cells adequately address the concerns.

Reply 2: The issue of the disparity between RAPSYN protein and mRNA levels in Ph+ leukemias has not sufficiently been resolved. Refer to point 2 in the revised review for more details. If conducting the proposed experiment is not feasible, I recommend a more thorough discussion in the manuscript to address and hypothesize about the causes of this discrepancy between protein and mRNA levels.

Reply 3: Your rationale for not performing additional assays with inactive mutants is satisfactory.

Reply 4: The clarification provided in your revision of the method section and the reorganization of Figure 6 successfully resolve the previously noted discrepancies. However, to ensure consistency and clarity across the paper, I recommend that you also specify the batches of constructs/viruses used in other relevant figures, such as Figure 1E.

Reply 5: The clarification provided on the immunoblots sufficiently addresses the concern raised.

Reviewer #1 (Public Review):

In this study, the researchers aimed to investigate the cellular landscape and cell-cell interactions in cavernous tissues under diabetic conditions, specifically focusing on erectile dysfunction (ED). They employed single-cell RNA sequencing to analyze gene expression patterns in various cell types within the cavernous tissues of diabetic individuals. The researchers identified decreased expression of genes associated with collagen or extracellular matrix organization and angiogenesis in several cell types, including fibroblasts, chondrocytes, myofibroblasts, valve-related lymphatic endothelial cells, and pericytes. They also discovered a newly identified marker, LBH, that distinguishes pericytes from smooth muscle cells in mouse and human cavernous tissues. Furthermore, the study revealed that pericytes play a role in angiogenesis, adhesion, and migration by communicating with other cell types within the corpus cavernosum. However, these interactions were found to be significantly reduced under diabetic conditions. The study also investigated the role of LBH and its interactions with other proteins (CRYAB and VIM) in maintaining pericyte function and highlighted their potential involvement in regulating neurovascular regeneration. Overall, the manuscript is well-written and the study provides novel insights into the pathogenesis of ED in patients with diabetes and identifies potential therapeutic targets for further investigation.

Comments on revised version:

All my concerns have been properly addressed.

Reviewer #3 (Public Review):

Bae and colleagues substantially improved the data quality and revised their manuscript "Single cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction". While these revisions clarify some of the concerns raised, others remain. In my view, the following question must be addressed:

In my prior question on #3, I completely disagree with the statement that "identified cells with pericyte-like characteristics in the walls of large blood vessels". The staining that authors provided for LBH, was clearly stained for SMCs, not pericytes. Per Fig 2E, the authors are correct that LBH is colocalized with SMA+ cells( SMCs). However, the red signal from LBH clearly stains endothelial cells. In the rest of 2E and 2D, LBH is CD31- and their location suggests LBH stained for SMCs in the Aorta, Kidney vasculature, Dorsal vein, and Dorsal Artery.

Reviewer #1 (Public Review):

Summary:

This paper by Watanabe et al described an expression system that can express the paired heavy and light chains of IgG antibodies from single cell B cells. In addition, they used FACS sorting for specific antigens to screen/select the specific populations for more targeted cloning of mAb genes. By staining with multiple antigens, they were able to zoom in to cross-reactive antibodies.

Strengths:

A highly efficient process that combines selection/screening with dua expression of both antibody chains. It is particularly suitable for the isolation of cross-reactive antibodies against conserved epitopes of different antigens, such as surface proteins of related viruses.

Weaknesses:

(1) The overall writing is very difficult to follow and the authors need to work on significant re-writing.

(2) The paper in its current form really lacks detail and it is NOT possible for readers to repeat or follow their methods. For example: a) It is not clear whether the authors checked the serum to see if the mice were producing antibodies before they sacrificed them to harvest spleen/blood i.e. using ELISA? b) How long after administration of the second dose were the mice sacrificed? c) What cell types are taken for single B cell sorting? Splenocytes or PBMC? These are just some of the questions which need to be addressed.

(3) According to the authors, 77 clones were sorted from the PR8+ and H2+ double positive quadrant. It is surprising that after transfection and re-analysing of bulk antibody presenting EXPI cells on FACS, only 13 clones (or 8 clones? - unclear) seemed to be truly cross-reactive. If that is the case, the approach is not as efficient as the authors claimed.

Reviewer #2 (Public Review):

Summary:

Watanabe, Takashi, et al. investigated the use of the Golden Gate dual-expression vector system to enhance the modern standard for rapid screening of recombinant monoclonal antibodies. The presented data builds upon modern techniques that currently use multiple expression vectors to express heavy and light chain pairs. In a single vector, they express the linked heavy and light chain variable genes with a membrane-bound Ig which allows for rapid and more affordable cell-based screening. The final validation of H1 and H2 strain influenza screening resulted in 81 "H1+", 48 "H2+", and 9 "cross" reactive clones. The kinetics of some of the soluble antibodies were tested via SPR and validated with a competitive inhibition with classical well-characterized neutralizing clones.

Strengths:

In this study, Watanabe, Takashi, et al. further develop and refine the methodologies for the discovery of monoclonal antibodies. They elegantly merge newer technologies to speed up turnaround time and reduce the cost of antibody discovery. Their data supports the feasibility of their technique.

This study will have an impact on pandemic preparedness and antibody-based therapies.

Weaknesses:

A His tagged antigen was used for immunization and H1-his was used in all assays. Either the removal of His specific clones needs to be done before selection, or a different tag needs to be used in the subsequent assays.

This assay doesn't directly test the neutralization of influenza but rather equates viral clearance to competitive inhibition. The results would be strengthened with the demonstration of a functional antibody in vivo with viral clearance.

Limitations of this new technique are as follows: there is a significant loss of cells during FACs, transfection and cloning efficiency are critical to success, and well-based systems limit the number of possible clones (as the author discussed in the conclusions). Early enrichment of the B cells could improve efficiency, such as selection for memory B cells.

Reviewer #1 (Public Review):

This is a very nice study of Belidae weevils using anchored phylogenomics that presents a new backbone for the family and explores, despite a limited taxon sampling, several evolutionary aspects of the group. The phylogeny is useful to understand the relationships between major lineages in this group and preliminary estimation of ancestral traits reveals interesting patterns linked to host-plant diet and geographic range evolution. I find that the methodology is appropriate, and all analytical steps are well presented. The paper is well-written and presents interesting aspects of Belidae systematics and evolution. The major weakness of the study is the very limited taxon sampling which has deep implications for the discussion of ancestral estimations.

Reviewer #2 (Public Review):

Summary:

The authors used a combination of anchored hybrid enrichment and Sanger sequencing to construct a phylogenomic data set for the weevil family Belidae. Using evidence from fossils and previous studies they can estimate a phylogenetic tree with a range of dates for each node - a time tree. They use this to reconstruct the history of the belids' geographic distributions and associations with their host plants. They infer that the belids' association with conifers pre-dates the rise of the angiosperms. They offer an interpretation of belid history in terms of the breakup of Gondwanaland but acknowledge that they cannot rule out alternative interpretations that invoke dispersal.

Strengths:

The strength of any molecular-phylogenetic study hinges on four things: the extent of the sampling of taxa; the extent of the sampling of loci (DNA sequences) per genome; the quality of the analysis; and - most subjectively - the importance and interest of the evolutionary questions the study allows the authors to address. The first two of these, sampling of taxa and loci, impose a tradeoff: with finite resources, do you add more taxa or more loci? The authors follow a reasonable compromise here, obtaining a solid anchored-enrichment phylogenomic data set (423 genes, >97 kpb) for 33 taxa, but also doing additional analyses that included 13 additional taxa from which only Sanger sequencing data from 4 genes was available. The taxon sampling was pretty solid, including all 7 tribes and a majority of genera in the group. The analyses also seemed to be solid - exemplary, even, given the data available.

This leaves the subjective question of how interesting the results are. The very scale of the task that faces systematists in general, and beetle systematists in particular, presents a daunting challenge to the reader's attention: there are so many taxa, and even a sophisticated reader may never have heard of any of them. Thus it's often the case that such studies are ignored by virtually everyone outside a tiny cadre of fellow specialists. The authors of the present study make an unusually strong case for the broader interest and importance of their investigation and its focal taxon, the belid weevils.

The belids are of special interest because - in a world churning with change and upheaval, geologically and evolutionarily - relatively little seems to have been going on with them, at least with some of them, for the last hundred million years or so. The authors make a good case that the Araucaria-feeding belid lineages found in present-day Australasia and South America have been feeding on Araucaria continuously since the days when it was a dominant tree taxon nearly worldwide before it was largely replaced by angiosperms. Thus these lineages plausibly offer a modern glimpse of an ancient ecological community.

Weaknesses:

I didn't find the biogeographical analysis particularly compelling. The promise of vicariance biogeography for understanding Gondwanan taxa seems to have peaked about 3 or 4 decades ago, and since then almost every classic case has been falsified by improved phylogenetic and fossil evidence. I was hopeful, early in my reading of this article, that it would be a counterexample, showing that yes, vicariance really does explain the history of *something*. But the authors don't make a particularly strong claim for their preferred minimum-dispersal scenario; also they don't deal with the fact that the range of Araucaria was vastly greater in the past and included places like North America. Were there belids in what is now Arizona's petrified forest? It seems likely. Ignoring all of that is methodologically reasonable but doesn't yield anything particularly persuasive.

Reviewer #1 (Public Review):

Summary:

Páramo et al. used 3D geometric morphometric analyses of the articulated femur, tibia, and fibula of 17 macronarian taxa (known to preserve these three skeletal elements) to investigate morphological changes that occurred in the hind limb through the evolutionary history of this sauropod clade. A principal components analysis was completed to understand the distribution of the morphological variation. A supertree was constructed to place evolutionary trends in morphological variation into phylogenetic context, and hind limb centroid size was used to investigate potential relationships between skeletal anatomy and gigantism. The majority of the results did not yield statistically significant differences, but they did identify interesting shape-change trends, especially within subclades of Titanosauria. Many previous studies have attempted to elucidate a link between wide-gauge posture and gigantism, which in this study Páramo et al. investigate among several titanosaurian subclades. They propose that morphologies associated with wide-gauge posture arose in parallel with increasing body size among basal members of Macronaria and that this connection became less significant once wide-gauge posture was acquired within Titanosauria. The authors also suggest that other biomechanical factors influenced the independent evolution of subclades within Titanosauria and that these influences resulted in instances of convergent evolution. Therefore, they infer that, overall, wide-gauge posture was not significantly correlated with gigantism, though some morphological aspects of hind limb skeletal anatomy appear to have been associated with gigantism. Their work also supports previous findings of a decrease in body size within Titanosauriformes (which they found to be not significant with shape variables but significant with Pagel's lambda). Collectively, their results support and build on previous work to elucidate more specifics on the evolution of this enigmatic clade. Further study will show if their hypotheses stand or if the inclusion of additional specimens and taxa yields alternative results.

Strengths:

Páramo et al. were diligent in their efforts to digitize and prepare specimens for this study while also minimizing user bias. Their previous work provided a strong platform for this study, specifically for their robust methodology. Between their supplemental files (which include details about specimen digitization and preparation) and the main body of the manuscript, the authors fully provide their results in detailed tables and figures. Their conclusions on evolutionary trends within Titanosauria are reasonably well supported (see weaknesses below) and they provide important details that enhance our understanding of the evolution of this clade and complement previous findings. Their discussion of links between morphology and various biomechanical adaptations is important, and future studies can use these results to investigate such biomechanical adaptations. The trends they identify within the subclades of Titanosauria are very interesting and highlight the diversity of this clade. It is possible that additional investigations of the evolution of these subclades could unite findings in sauropod myology and biomechanics, each of which has been suggested to vary among titanosaurian taxa without a clear phylogenetic or evolutionary distribution. The authors suggest that certain common morphologies arose via convergent evolution among titanosaurian subclades, such as members of Colossosauria exhibiting morphologies more similar to basal titanosaurians than derived saltasaurines. While this conclusion about convergent evolution is not well explained, only future testing will determine if this hypothesis remains supported. Additionally, the authors discuss the influence of uncertainty on the phylogenetic position of some taxa, and this reminds readers to view their findings as tentative trends that may be illuminated through further quantitative analyses. If one accepts the use of hind limb centroid size as a reliable approximation of body size (see concerns in Weaknesses below) then their data also support a hypothesis of decreasing body size through titanosaurian evolution (with PC 2 further differentiating small titanosaurian taxa from one another), providing an opportunity for future analyses to further investigate these interesting trends.

Weaknesses:

Several sentences throughout the manuscript could benefit from citations. For example, the discussion of using hind limb centroid size as a proxy for body mass has no citations attributed. This should be cited or described as a new method for estimating body mass with data from extant taxa presented in support of this relationship. This particular instance is a very important point to include supporting documentation because the authors' conclusions about evolutionary trends in body size are predicated on this relationship.

An additional area of concern is the lack of any discussion of taphonomic deformation in Section 3.3 Caveats of This Study, the results, or the methods. The authors provide a long and detailed discussion of taphonomic loss and how this study does a good job of addressing it; however, taphonomic deformation to specimens and its potential effects on the ensuing results were not addressed at all. Hedrick and Dodson (2013) highlight that, with fossils, a PCA typically includes the effects of taphonomic deformation in addition to differences in morphology, which results in morphometric graphs representing taphomorphospaces. For example, in this study, the extreme negative positioning of Dreadnoughtus on PC 2 (which the authors highlight as "remarkable") is almost certainly the result of taphonomic deformation to the distal end of the holotype femur, as noted by Ullmann and Lacovara (2016).

The authors investigated 17 taxa and divided them into 9 clades, with only Titanosauria and Lithostrotia including more than two taxa (and four clades are only represented by one taxon). While some of these clades represent the average of multiple individuals, the small number of plotted taxa can only weakly support trends within Titanosauria. If similar general trends could be found when the taxa are parsed into fewer, more inclusive clades, it would support and strengthen their claims. Of course, the authors can only study what is preserved in the fossil record, and titanosaurian remains are often highly fragmentary; these deficiencies should therefore not be held against the authors. They clearly put effort and thought into their choices of taxa to include in this study, but there are limitations arising from this low sample size that inherently limit the confidence that can be placed on their conclusions, and this caveat should be more clearly discussed. Specifically, the authors note that their dataset contains many lithostrotians, but they do not discuss unevenness in body size sampling. As neither their size-category boundaries nor the taxa which fall into each of them are clearly stated, the reader must parse the discussion to glean which taxa are in each size category. It should be noted that the authors include both Jainosaurus and Dreadnoughtus as 'large' taxa even though the latter is estimated to have been roughly five times the body mass of the former, making Dreadnoughtus the only taxon included in this extreme size category. The effects that this may have on body size trends are not discussed. Additionally, few taxa between the body masses of Jainosaurus and Dreadnoughtus have been included even though the hind limbs of several such macronarians have been digitized in prior studies (such as Diamantinasaurus and Giraffititan; Klinkhamer et al. 2018). Also, several members of Colossosauria are more similar in general body size to Dreadnoughtus than Jainosaurus, but unfortunately, they do not preserve a known femur, tibia, and fibula, so the authors could not include them in this study. Exclusion of these taxa may bias inferences about body size evolution, and this is a sampling caveat that could have been discussed more clearly. Future studies including these and other taxa will be important for further evaluating the hypotheses about macronarian evolution advanced by Páramo et al. in this study.

Reviewer #2 (Public Review):

The authors report a quantitative comparative study regarding hind limb evolution among titanosaurs. I find the conclusions and findings of the manuscript interesting and relevant. The strength of the paper would be increased if the authors were to improve their reporting of taxon sampling and their discussion of age estimation and the potential implications that uncertainty in these estimates would have for their conclusions regarding gigantism (vs. ontogenetic patterns).

Reviewer #1 (Public Review):

Summary:

In the paper entitled "PI3K/HSCB axis facilitates FOG1 nuclear translocation to promote erythropoiesis and megakaryopoiesis", the authors sought to determine the role of HSCB, a known regulator of Iron sulfur cluster transfer, in the generation of erythrocytes and megakaryocytes. They utilized a human primary cell model of hematopoietic differentiation to identify a novel mechanism whereby HSCB is necessary for activation of erythroid and megakaryocytic gene expression through regulation of the nuclear localization of FOG-1, a essential transcription co-regulator of the GATA transcription factors. Their work establishes this novel regulatory axis as a mechanism by which cytokine signaling through EPO-R and MPL drives the lineage-specification of hematopoietic progenitors to erythrocytes and megakaryocytes, respectively.

Impact:

The major impact of this work is in a greater understanding of how cytokine signaling through EPO/TPO function to promote lineage specification of hematopoietic stem/progenitor cells. While the major kinase cascades downstream of the EPO/TPO receptors have been elucidated, how those cascades effect gene expression to promote a specific differentiation program is poorly understood. For this work, we now understand that nuclear localization of FOG is a critical regulatory node by which EPO/TPO signaling is required to launch FOG-dependent gene expression. However, these cytokine receptors have many overlapping and redundant targets, so it still remains to be elucidated how signaling through the different receptors promotes divergent gene expression programs. Perhaps similar regulatory mechanisms exist for other lineage-specifying transcription factors.

Strengths:

The authors use two different cellular models of erythroid differentiation (K562 and human primary CD34+ cells) to elucidate the multi-factorial mechanism controlling FOG-1 nuclear localization. The studies are well-controlled and rigorously establish their mechanism through complementary approaches. The differentiation effects are established through cell surface marker expression, protein expression, and gene expression analyses. Novel protein interactions discovered by proteomics analyses were validated through bi-directional co-IP experiments in multiple experimental systems. Protein cellular localization findings are supported by both immunofluorescence and cell fractionation immunoblot analyses. The robustness of their experimental findings gives great confidence for the likelihood that the methods and findings can be reproduced in future work based on their conclusions.

Weaknesses:

The one unexplained step in this intricately described mechanism is how HSCB functions to promote TACC3 degradation. It appears that the proteasome is involved since MG-132 reverses the effect of HSCB deficiency, but no other details are provided. Does HSCB target TACC3 for ubiquitination somehow? Future studies will be required to understand this portion of the mechanism.

One weakness of the study design is that no in vivo experiments are conducted. The authors comment that the HSCB mouse phenotype is too dramatic to permit studies of erythropoiesis in vivo; however, a conditional approach could have been pursued.<br /> It should also be noted that a previous study had already shown that TACC3 regulates the nuclear localization of FOG-1, so this portion of the mechanism is not entirely novel. However, the role of HSCB and the proteasomal degradation of TACC3 is entirely novel to my knowledge.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Liu et al. identified an important pathway regulating the nuclear translocation of the key transcriptional factor FOG1 during human hematopoiesis. The authors show that heat shock cognate B (HSCB) can interact with and promote the proteasomal degradation of TACC3, and this function is independent of its role in iron-sulfur cluster biogenesis. TACC3 represses the activity of FOG1 by sequestering it in the cytoplasm. Therefore, HSCB can promote the nuclear translocation of FOG1 through down-regulating TACC3. The authors further show that the phosphorylation of HSCB by PI3K downstream of the EPO signaling pathway is important for its role in regulating the nuclear translocation of FOG1. The data are solid and the manuscript is overall well written. The findings of this manuscript provide important new knowledge to the fields of hematopoiesis and cell biology.

Strengths:

(1) This study uses a multi-pronged approach that combines techniques from a number of fields to convincingly demonstrate the pathway regulating the nuclear translocation of FOG1 during hematopoiesis. The proposed role of each component in the pathway is well supported by solid data.

(2) This work provides important new insights into the function of HSCB, which was known to be an iron-sulfur cluster assembly protein. This study identifies a new role of HSCB and shows that HSCB can regulate the stability of the TACC3 protein, and this cytoplasmic function of HSCB is regulated by protein phosphorylation by PI3K.

(3) The findings of this work open up new directions for research in hematopoiesis and related fields. For example, are there any other TACC3-binding proteins whose subcellular localization are regulated by the presence or absence of TACC3? What is the E3 ligase responsible for the degradation of TACC3? Does this identified mechanism contribute to the sideroblastic anemias observed in HSCB human patients and animal models?

Reviewer #1 (Public Review):

Summary:

This is an interesting study that performs scRNA-Seq on infected and uninfected wounds. The authors sought to understand how infection with E. faecalis influences the transcriptional profile of healing wounds. The analysis demonstrated that there is a unique transcriptional profile in infected wounds with specific changes in macrophages, keratinocytes, and fibroblasts. They also speculated on potential crosstalk between macrophages and neutrophils and macrophages and endothelial cells using NicheNet analysis and CellChat. Overall the data suggest that infection causes keratinocytes to not fully transition which may impede their function in wound healing and that the infection greatly influenced the transcriptional profile of macrophages and how they interact with other cells.

Strengths:

It is a useful dataset to help to understand the impact of wound infection on transcription of specific cell types. The analysis is very thorough in terms of transcriptional analysis and uses a variety of techniques and metrics.

Weaknesses:

Some drawbacks of the study are the following. First the fact that it only has two mice per group, and only looks at one time point after wounding decreases the impact of the study. Wound healing is a dynamic and variable process so understanding the full course of the wound healing response would be very important to understand the impact of infection on the healing wound. The analysis has been bolstered by applying a cross-entropy test on the integrated dataset and to ensure robustness of the datasets (Fig S1F). Including unwounded skin in the scRNA-Seq would also lend a lot more significance to this study. However, this was technically challenging due to constraints with the number of immune cells in unwounded skin as described in the limitations section. Another drawback of the study is that mouse punch biopsies are very different than human wounds as they heal primarily by contraction instead of re-epithelialization like human wounds. The authors mitigated this somewhat be extracting the incisional parts of the wound. So while the conclusions are generally supported the scope of the work is somewhat limited.

Reviewer #2 (Public Review):

Summary:

The authors have performed a detailed analysis of the complex transcriptional status of numerous cell types present in wounded tissue, including keratinocytes, fibroblasts, macrophages, neutrophils, and endothelial cells. The comparison between infected and uninfected wounds is interesting and the analysis suggests possible explanations for why infected wounds are delayed in their healing response.

Strengths:

The paper presents a thorough and detailed analysis of the scRNAseq data. The paper is clearly written and the conclusions drawn from the analysis are appropriately cautious. The results provide an important foundation for future work on the healing of infected and uninfected wounds.

Weaknesses:

The analysis is purely descriptive and no attempt is made to validate whether any of the factors identified are playing functional roles in wound healing. Such experiments would be appropriate for followup work. The experimental setup is analyzing a single time point and does not include a comparison to unwounded skin. Nevertheless, the present data do provide a useful point of comparison for the field.

Reviewer #1 (Public Review):

The current manuscript revisits previous reports in the literature. The human Pannexin 1 channel is regulated by phosphorylation at two residues by Src kinase. From this series of experiments, the authors conclude that PANX-1 is not phosphorylated at these residues.

The biggest strength of the manuscript is the comprehensiveness of the approach. The authors recapitulate prior experiments in the literature and also add a series of new, orthogonal experiments that all examine the claim of PANX-1 phosphorylation. The breadth of the reported experiments extends over multiple cell lines and protein constructs, in vitro purified proteins, mass spec, different phosphorylation detection reagents and antibodies, and functional electrophysiology assays that show that the addition of Src does not impact gating. The combined weight of all these data strongly suggests that the field should re-examine the claim that PANX-1 is regulated by phosphorylation at Y199 and Y309.

Another strength is that the authors go beyond simply showing that the antibodies do not recognize phosphorylated PANX-1. They also provide potential mechanisms for how the antibodies may be misleading. Both antibodies recognize phosphorylated Src-1. In the case of anti-PANX1-pY308, the authors provide solid mutagenesis evidence that the antibody also weakly recognizes a non-phosphorylated epitope of PANX1 in the same region as the tyrosine. This helps make a convincing case.

Such experiments, while not glamorous, have great practical importance for developing an accurate understanding of how Pannexin channels are regulated.

Reviewer #2 (Public Review):

The widely distributed pannexin 1 (PANX1) is an ATP-permeable channel that plays an important role in intercellular communication and has been implicated in various pathophysiological processes and diseases. Previous studies have demonstrated that PANX1 can be phosphorylated at two molecular sites via the non-receptor kinase Src, thereby leading to channel opening and ATP release. In this paper, the authors used a variety of methods to detect tyrosine phosphorylation modification of PANX1 channel protein, however, their results showed that commercially available antibodies against the two phosphorylation sites used in previous studies did not work well, in other words, phosphorylation changes in PANX1 could not be detected by those antibodies. Therefore, the authors call for the re-examination and evaluation of previous research results.

In general, this is a meticulous study, using different detection methods and different expression systems.

Reviewer #3 (Public Review):

The manuscript by Ruan et al. addresses an important issue in Panx1 research, i.e. the activation of the channel formed by Panx1 via protein phosphorylation. If the authors' conclusions are correct, the previous claims for Panx1 phosphorylation on the basis of the commercial anti-phospho-Panx1 antibodies would be in question.

This is a very detailed and comprehensive analysis making use of state-of-the-art techniques, including mass spectrometry and phos-tag gel electrophoresis.

In general, the study is well-controlled as relating to negative controls.

The value of this manuscript is, that it could spawn new, more function-oriented studies on the activation of Panx1 channels.

The weaknesses identified previously are reproduced below:

Weaknesses:

Although the manuscript addresses an important issue, the activation of the ATP-release channel Panx1 by protein phosphorylation, the data provided do not support the firm conclusion that such activation does not exist. The failure to reproduce published data obtained with commercial anti-phospho Panx1 antibodies can only be of limited interest for a subfield.

(1) The title claiming that "Panx1 is NOT phosphorylated..." is not justified by the failure to reproduce previously published data obtained with these antibodies. If, as claimed, the antibodies do not recognize Panx1, their failure cannot be used to exclude tyrosine phosphorylation of the Panx1 protein. There is no positive control for the antibodies.

(2) The authors claim that exogenous SRC expression does not phosphorylate Y198. DeLalio et al. 2019 show that Panx1 is constitutively phosphorylated at Y198, so an effect of exogenous SRC expression is not necessarily expected.

(3) The authors argue that the GFP tag of Panx1at the COOH terminus does not interfere with folding since the COOH modified (thrombin cleavage site) Panx1 folds properly, forming an amorphous glob in the cryo-EM structure. However, they do not show that the COOH-modified Panx1 folds properly. It may not, because functional data strongly suggest that the terminal cysteine dives deep into the pore. For example, the terminal cysteine, C426, can form a disulfide bond with an engineered cysteine at position F54 (Sandilos et al. 2012).

(4) The authors dismiss the additional arguments for tyrosine phosphorylation of Panx1 given by the various previous studies on Panx1 phosphorylation. These studies did not, as implied, solely rely on the commercial anti-phospho-Panx1 antibodies, but also presented a wealth of independent supporting data. Contrary to the authors' assertion, in the previous papers the pY198 and pY308 antibodies recognized two protein bands in the size range of glycosylated and partial glycosylated Panx1.

(5) A phosphorylation step triggering channel activity of Panx1 would be expected to occur exclusively on proteins embedded in the plasma membrane. The membrane-bound fraction is small in relation to the total protein, which is particularly true for exogenously expressed proteins. Thus, any phosphorylated protein may escape detection when total protein is analyzed. Furthermore, to be of functional consequence, only a small fraction of the channels present in the plasma membrane need to be in the open state. Consequently, only a fraction of the Panx1 protein in the plasma membrane may need to be phosphorylated. Even the high resolution of mass spectroscopy may not be sufficient to detect phosphorylated Panx1 in the absence of enrichment processes.

(6) In the electrophysiology experiments described in Figure 7, there is no evidence that the GFP-tagged Panx1 is in the plasma membrane. Instead, the image in Figure 7a shows prominent fluorescence in the cytoplasm. In addition, there is no evidence that the CBX-sensitive currents in 7b are mediated by Panx1-GFP and are not endogenous Panx1. Previous literature suggests that the hPanx1 protein needs to be cleaved (Chiu et al. 2014) or mutated at the amino terminus (Michalski et al 2018) to see voltage-activated currents, so it is not clear that the currents represent hPANX1 voltage-activated currents.

Note from the editors: The authors provided a rebuttal to the latest review, but no additional data, so we encourage readers to read the concerns and the author responses.

Reviewer #2 (Public Review):

In this revised manuscript Aguillon and collaborators convincingly demonstrating that CLK is required for free-running behavioral rhythms under constant conditions in the Cnidarian Nematostella. The results also convincingly show that CLK impacts rhythmic gene expression in this organism. This original work thus demonstrates that CLK was recruited very early during animal evolution in the circadian clock mechanism to optimize behavior and gene expression with the time-of-day.

Reviewer #1 (Public Review):

Summary:

The authors analyzed the bacterial colonization of human sperm using 16S rRNA profiling. Patterns of microbiota colonization were subsequently correlated with clinical data, such as spermiogram analysis, the presence of reactive oxygen species (ROS), and DNA fragmentation. The authors identified three main clusters dominated by Streptococcus, Prevotella, and Lactobacillus & Gardnerella, respectively, which aligns with previous observations. Specific associations were observed for certain bacterial genera, such as Flavobacterium and semen quality. Overall, it is a well-conducted study that further supports the importance of the seminal microbiota.

Strengths:

- The authors performed the analysis on 223 samples, which is the largest dataset in semen microbiota analysis so far.<br /> - Inclusion of negative controls to control contaminations.<br /> - Inclusion of a positive control group consisting of men with proven fertility.

Weaknesses:<br /> - The manuscript needs comprehensive proofreading for language and formatting. In many instances, spaces are missing or not required.<br /> - Could the authors explore correlation network analyses to get additional insights into the structure of different clusters?<br /> - The GitHub link is not correct.<br /> - It is not possible to access the dataset on ENA.<br /> - Add the graphs obtained with decontam analysis as a supplementary figure.<br /> - There is nothing about the RPL group in the results section, while the authors discuss this issue in the introduction. What about the controls with proven fertility?<br /> - While correctly stated in the title, the term microbiota should be used throughout the manuscript instead of "microbiome"