Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors established an in vitro triple co-culture BBB model and demonstrated its advantages compared with the mono or double co-culture BBB model. Further, the authors used their established in vitro BBB model and combined it with other methodologies to investigate the specific mechanism that co-culture with astrocytes but also neurons enhanced the integrity of endothelial cells.

Strengths:

The results persuasively showed the established triple co-culture BBB model well mimicked several important characteristics of BBB compared with the mono-culture BBB model, including better barrier function and in vivo/in vitro correlation. The human-derived immortalized cells used made the model construction process faster and more efficient, and have a better in vivo correlation without species differences. This model is expected to be a useful high-throughput evaluation tool in the development of CNS drugs.

Based on the previous experimental results, detailed studies investigated how co-culture with neurons and astrocytes promoted claudin-5 and VE-cadherin in endothelial cells, and the specific signaling mechanisms were also studied. Interestingly, the authors found that neurons also released GDNF to promote barrier properties of brain endothelial cells, as most current research has focused on the promoting effect of astrocytes-derived GDNF on BBB. Meanwhile, the author also validated the functions of GDNF for BBB integrity in vivo by silencing GDNF in mouse brains. Overall, the experiments and data presented support their claim that, in addition to astrocytes, neurons also have a promoting effect on the barrier function of endothelial cells through GDNF secretion.

Weaknesses:

Although the authors demonstrated a highly usable for predicting the BBB permeability, recorded TEER measurements are still far from the human BBB in vivo reported measurements of TEER, and expression of transporters was not promoted by co-culture, which may lead to the model being unsuitable for studying drug transport mediated by transporters on BBB.

Reviewer #2 (Public Review):

Summary:

Yang and colleagues developed a new in vitro blood-brain barrier model that is relatively simple yet outperforms previous models. By incorporating a neuroblastoma cell line, they demonstrated increased electrical resistance and decreased permeability to small molecules.

Strengths:

The authors initially elucidated the soluble mediator responsible for enhancing endothelial functionality, namely GDNF. Subsequently, they elucidated the mechanisms by which GDNF upregulates the expression of VE-cadherin and Claudin-5. They further validated these findings in vivo, and demonstrated predictive value for molecular permeability as well. The study is meticulously conducted and easily comprehensible. The conclusions are firmly supported by the data, and the objectives are successfully achieved. This research is poised to advance future investigations in BBB permeability, leakage, dysfunction, disease modeling, and drug delivery, particularly in high-throughput experiments. I anticipate an enthusiastic reception from the community interested in this area. While other studies have produced similar results with tri-cultures (PMID: 25630899), this study notably enhances electrical resistance compared to previous attempts.

Weaknesses:

Considerable effort has been directed towards developing in vitro models that more closely resemble their in vivo counterparts, utilizing stem cell-derived NVU cells. Although these examples are currently rudimentary, they offer better BBB mimicry than Yang's study.

Additionally, some instances might benefit from more robust statistical tests; nonetheless, I do not think this would significantly alter the experimental conclusions.

Similar experiments with tri-cultures yielding analogous results have been reported by other authors (PMID: 25630899). TEER values are a bit higher than the aforementioned experiments; however, this study has values at least one order of magnitude lower than physiological levels.

Reviewer #1 (Public Review):

Cheng et al explore the utility of analyte ratios instead of relative abundance alone for biological interpretation of tissue in a MALDI MSI workflow. Utilizing the ratio of metabolites and lipids that have complimentary value in metabolic pathways, they show the ratio as a heat map which enhances the understanding of how multiple analytes relate to each other spatially. Normally, this is done by projecting each analyte as a unique color but using a ratio can help clarify visualization and add to biological interpretability. However, existing tools to perform this task are available in open-source repositories, and fundamental limitations inherent to MALDI MSI need to be made clear to the reader. The study lacks rigor and controls, i.e. without quantitative data from a variety of standards (internal isotopic or tissue mimetic models for example), the potential delta in ionization efficiencies of different species subtracts from the utility of pathway analysis using metabolite ratios.

Reviewer #2 (Public Review):

Summary:

In the article, "Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging" the authors describe their software package in R for visualizing metabolite ratio pairs. I think the novelty of this manuscript is overstated and there are several notable issues with the figures that prevent detailed assessment but the work would be of interest to the mass spectrometry community.

Strengths:

The authors describe a software that would be of use to those performing MALDI MSI. This software would certainly add to the understanding of metabolomics data and enhance the identification of critical metabolites.

Weaknesses:

The authors are missing several references and discussion points, particularly about SIMS MSI, where ratio imaging has been previously performed.

There are several misleading sentences about the novelty of the approach and the limitations of metabolite imaging.

Several sentences lack rigor and are not quantitative enough.

The figures are difficult to interpret/ analyze in their current state and lack some critical components, including labels and scale bars.

Reviewer #2 (Public Review):

Liu et al., by focusing on the regulation of G protein-signaling 10 (RGS10), reported that RGS10 expression was significantly lower in patients with breast cancer, compared with normal adjacent tissue. Genetic inhibition of RGS10 caused epithelial-mesenchymal transition, and enhanced cell proliferation, migration, and invasion, respectively. These results suggest an inhibitory role of RGS10 in tumor metastasis. Furthermore, bioinformatic analyses determined signaling cascades for RGS10-mediated breast cancer distant metastasis. More importantly, both in vitro and in vivo studies evidenced that alteration of RGS10 expression by modulating its upstream regulator miR-539-5p affects breast cancer metastasis. Altogether, these findings provide insight into the pathogenesis of breast tumors and hence identify potential therapeutic targets in breast cancer.

The conclusions of this study are mostly well supported by data.

Reviewer #3 (Public Review):

Distant metastasis is the major cause of death in patients with breast cancer. In this manuscript, Liu et al. show that RGS10 deficiency elicits distant metastasis via epithelial-mesenchymal transition in breast cancer. As a prognostic indicator of breast cancer, RGS10 regulates the progress of breast cancer and affects tumor phenotypes such as epithelial-mesenchymal transformation, invasion, and migration. The conclusions of this paper are mostly well supported by data.

Reviewer #1 (Public Review):

The paper has shown the expression of RGS10 is related to the molecular subtype, distant metastasis, and survival status of breast cancer. The study utilizes bioinformatic analyses, human tissue samples, and in vitro and in vivo experiments which strengthen the data. RGS10 was validated to inhibit EMT through a novel mechanism dependent on LCN2 and miR-539-5p, thereby reducing cancer cell proliferation, colony formation, invasion, and migration. The study elaborated on the function of RGS10 in influencing the prognosis and biological behavior which could be considered as a potential drug target in breast cancer.

Reviewer #1 (Public Review):

Summary:

This paper is focused on the role of Cadherin Flamingo (Fmi) - also called Starry night (stan) - in cell competition in developing Drosophila tissues. A primary genetic tool is monitoring tissue overgrowths caused by making clones in the eye disc that express activated Ras (RasV12) and that are depleted for the polarity gene scribble (scrib). The main system that they use is ey-flp, which makes continuous clones in the developing eye-antennal disc beginning at the earliest stages of disc development. It should be noted that RasV12, scrib-i (or lgl-i) clones only lead to tumors/overgrowths when generated by continuous clones, which presumably creates a privileged environment that insulates them from competition. Discrete (hs-flp) RasV12, lgl-i clones are in fact out-competed (PMID: 20679206), which is something to bear in mind.

The authors show that clonal loss of Fmi by an allele or by RNAi in the RasV12, scrib-i tumors suppresses their growth in both the eye disc (continuous clones) and wing disc (discrete clones). The authors attributed this result to less killing of WT neighbors when Myc over-expressing clones lacking Fmi, but another interpretation (that Fmi regulates clonal growth) is equally as plausible with the current results. Next, the authors show that scrib-RNAi clones that are normally out-competed by WT cells prior to adult stages are present in higher numbers when WT cells are depleted for Fmi. They then examine death in RasV12, scrib-i ey-FLP clones, or in discrete hs-FLP UAS-Myc clones. They state that they see death in WT cells neighboring RasV12, scrib-i clones in the eye disc (Figures 4A-C). Next, they write that RasV12, scrib-I cells become losers (i.e., have apoptosis markers) when Fmi is removed. Neither of these results are quantified and thus are not compelling. They state that a similar result is observed for Myc over-expression clones that lack Fmi, but the image was not compelling, the results are not quantified and the controls are missing (Myc over-expressing clones alone and Fmi clones alone). They then want to test whether Myc over-expressing clones have more proliferation. They show an image of a wing disc that has many small Myc overexpressing clones with and without Fmi. The pHH3 results support their conclusion that Myc overexpressing clones have more pHH3, but I have reservations about the many clones in these panels (Figures 5L-N). They show that the cell competition roles of Fmi are not shared by another PCP component and are not due to the Cadherin domain of Fmi. The authors appear to interpret their results as Fmi is required for winner status. Overall, some of these results are potentially interesting and at least partially supported by the data, but others are not supported by the data.

Strengths:

Fmi has been studied for its role in planar cell polarity, and its potential role in competition is interesting.

Weaknesses:

(1) In the Myc over-expression experiments, the increased size of the Myc clones could be because they divide faster (but don't outcompete WT neighbors). If the authors want to conclude that the bigger size of the Myc clones is due to out-competition of WT neighbors, they should measure cell death across many discs of with these clones. They should also assess if reducing apoptosis (like using one copy of the H99 deficiency that removes hid, rpr, and grim) suppresses winner clone size. If cell death is not addressed experimentally and quantified rigorously, then their results could be explained by faster division of Myc over-expressing clones (and not death of neighbors). This could also apply to the RasV12, scrib-i results.

(2) This same comment about Fmi affecting clone growth should be considered in the scrib RNAi clones in Figure 3.

(3) I don't understand why the quantifications of clone areas in Figures 2D, 2H, 6D are log values. The simple ratio of GFP/RFP should be shown. Additionally, in some of the samples (e.g., fmiE59 >> Myc, only 5 discs and fmiE59 vs >Myc only 4 discs are quantified but other samples have more than 10 discs). I suggest that the authors increase the number of discs that they count in each genotype to at least 20 and then standardize this number.

(4) There is a typo when referring to Figures 3C-D. It should be Figure 2C-D.

(5) Figure 4 - shows examples of cell death. Cas3 is written on the figure but Dcp-1 is written in the results. Which antibody was used? The authors need to quantify these results. They also need to show that the death of cells is part of the phenotype, like an H99 deficiency, etc (see above).

(6) It is well established that clones overexpressing Myc have increased cell death. The authors should consider this when interpreting their results.

(7) A better characterization of discrete Fmi clones would also be helpful. I suggest inducing hs-flp clones in the eye or wing disc and then determining clone size vs twin spot size and also examining cell death etc. If such experiments have already been done and published, the authors should include a description of such work in the preprint.

(8) We need more information about the expression pattern of Fmi. Is it expressed in all cells in imaginal discs? Are there any patterns of expression during larval and pupal development?

(9) Overall, the paper is written for specialists who work in cell competition and is fairly difficult to follow, and I suggest re-writing the results to make it accessible to a broader audience.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Bosch et al. reveal Flamingo (Fmi), a planar cell polarity (PCP) protein, is essential for maintaining 'winner' cells in cell competition, using Drosophila imaginal epithelia as a model. They argue that tumor growth induced by scrib-RNAi and RasV12 competition is slowed by Fmi depletion. This effect is unique to Fmi, not seen with other PCP proteins. Additional cell competition models are applied to further confirm Fmi's role in 'winner' cells. The authors also show that Fmi's role in cell competition is separate from its function in PCP formation.

Strengths:

(1) The identification of Fmi as a potential regulator of cell competition under various conditions is interesting.

(2) The authors demonstrate that the involvement of Fmi in cell competition is distinct from its role in planar cell polarity (PCP) development.

Weaknesses:

(1) The authors provide a superficial description of the related phenotypes, lacking a comprehensive mechanistic understanding. Induction of apoptosis and JNK activation are general outcomes, but it is important to determine how they are specifically induced in Fmi-depleted clones. The authors should take advantage of the power of fly genetics and conduct a series of genetic epistasis analyses.

(2) The depletion of Fmi may not have had a significant impact on cell competition; instead, it is more likely to have solely facilitated the induction of apoptosis.

(3) To make a solid conclusion for Figure 1, the authors should investigate whether complete removal of Fmi by a mutant allele affects tumor growth induced by expressing RasV12 and scrib RNAi throughout the eye.

(4) The authors should test whether the expression level of Fmi (both mRNA and protein) changes during tumorigenesis and cell competition.

Reviewer #3 (Public Review):

Summary:

In this manuscript, Bosch and colleagues describe an unexpected function of Flamingo, a core component of the planar cell polarity pathway, in cell competition in the Drosophila wing and eye disc. While Flamingo depletion has no impact on tumour growth (upon induction of Ras and depletion of Scribble throughout the eye disc), and no impact when depleted in WT cells, it specifically tunes down winner clone expansion in various genetic contexts, including the overexpression of Myc, the combination of Scribble depletion with activation of Ras in clones or the early clonal depletion of Scribble in eye disc. Flamingo depletion reduces the proliferation rate and increases the rate of apoptosis in the winner clones, hence reducing their competitiveness up to forcing their full elimination (hence becoming now "loser"). This function of Flamingo in cell competition is specific to Flamingo as it cannot be recapitulated with other components of the PCP pathway, and does not rely on the interaction of Flamingo in trans, nor on the presence of its cadherin domain. Thus, this function is likely to rely on a non-canonical function of Flamingo which may rely on downstream GPCR signaling.

This unexpected function of Flamingo is by itself very interesting. In the framework of cell competition, these results are also important as they describe, to my knowledge, one of the only genetic conditions that specifically affect the winner cells without any impact when depleted in the loser cells. Moreover, Flamingo does not just suppress the competitive advantage of winner clones, but even turns them into putative losers. This specificity, while not clearly understood at this stage, opens a lot of exciting mechanistic questions, but also a very interesting long-term avenue for therapeutic purposes as targeting Flamingo should then affect very specifically the putative winner/oncogenic clones without any impact in WT cells.

The data and the demonstration are very clean and compelling, with all the appropriate controls, proper quantification, and backed-up by observations in various tissues and genetic backgrounds. I don't see any weakness in the demonstration and all the points raised and claimed by the authors are all very well substantiated by the data. As such, I don't have any suggestions to reinforce the demonstration.

While not necessary for the demonstration, documenting the subcellular localisation and levels of Flamingo in these different competition scenarios may have been relevant and provided some hints on the putative mechanism (specifically by comparing its localisation in winner and loser cells).

Also, on a more interpretative note, the absence of the impact of Flamingo depletion on JNK activation does not exclude some interesting genetic interactions. JNK output can be very contextual (for instance depending on Hippo pathway status), and it would be interesting in the future to check if Flamingo depletion could somehow alter the effect of JNK in the winner cells and promote downstream activation of apoptosis (which might normally be suppressed). It would be interesting to check if Flamingo depletion could have an impact in other contexts involving JNK activation or upon mild activation of JNK in clones.

Strengths:

- A clean and compelling demonstration of the function of Flamingo in winner cells during cell competition.

- One of the rare genetic conditions that affects very specifically winner cells without any impact on losers, and then can completely switch the outcome of competition (which opens an interesting therapeutic perspective in the long term)

Weaknesses:

- The mechanistic understanding obviously remains quite limited at this stage especially since the signaling does not go through the PCP pathway.

Reviewer #1 (Public Review):

Summary:

This study shows a new mechanism of GS regulation in the archaean Methanosarcina maze and clarifies the direct activation of GS activity by 2-oxoglutarate, thus featuring another way in which 2-oxoglutarate acts as a central status reporter of C/N sensing.

Mass photometry and single particle cryoEM structure analysis convincingly show the direct regulation of GS activity by 2-OG promoted formation of the dodecameric structure of GS. The previously recognized small proteins GlnK1 and Sp26 seem to play a subordinate role in GS regulation, which is in good agreement with previous data. Although these data are quite clear now, there remains one major open question: how does 2-OG further increase GS activity once the full dodecameric state is achieved (at 5 mM)? This point needs to be reconsidered.

Strengths:

Mass photometry reveals a dynamic mode of the effect of 2-OG on the oligomerization state of GS. Single particle Cryo-EM reveals the mechanism of 2-OG mediated dodecamer formation.

Weaknesses:

It is not entirely clear, how very high 2-OG concentrations activate GS beyond dodecamer formation.

The data presented in this work are in stark contrast to the previously reported structure of M. mazei GS by the Schumacher lab. This is very confusing for the scientific community and requires clarification. The discussion should consider possible reasons for the contradictory results.

Importantly, it is puzzling how Schumacher could achieve an apo-structire of dodecameeric GS? If 2-OG is necessary for dodecameric formation, this should be discussed. If GlnK1 doesn't form a complex with the dodecameric GS, how could such a complex be resolved there?

In addition, the text is in principle clear but could be improved by professional editing. Most obviously there is insufficient comma placement.

Reviewer #2 (Public Review):

Summary:

Herdering et al. introduced research on an archaeal glutamine synthetase (GS) from Methanosarcina mazei, which exhibits sensitivity to the environmental presence of 2-oxoglutarate (2-OG). While previous studies have indicated 2-OG's ability to enhance GS activity, the precise underlying mechanism remains unclear. Initially, the authors utilized biophysical characterization, primarily employing a nanomolar-scale detection method called mass photometry, to explore the molecular assembly of Methanosarcina mazei GS (M. mazei GS) in the absence or presence of 2-OG. Similar to other GS enzymes, the target M. mazei GS forms a stable dodecamer, with two hexameric rings stacked in tail-to-tail interactions. Despite approximately 40% of M. mazei GS existing as monomeric or dimeric entities in the detectable solution, the majority spontaneously assemble into a dodecameric state. Upon mixing 2-OG with M. mazei GS, the population of the dodecameric form increases proportionally with the concentration of 2-OG, indicating that 2-OG either promotes or stabilizes the assembly process. The cryo-electron microscopy (cryo-EM) structure reveals that 2-OG is positioned near the interface of two hexameric rings. At a resolution of 2.39 Å, the cryo-EM map vividly illustrates 2-OG forming hydrogen bonds with two individual GS subunits as well as with solvent water molecules. Moreover, local side-chain reorientation and conformational changes of loops in response to 2-OG further delineate the 2-OG-stabilized assembly of M. mazei GS.

Strengths & Weaknesses:

The investigation studies the impact of 2-oxoglutarate (2-OG) on the assembly of Methanosarcina mazei glutamine synthetase (M mazei GS). Utilizing cutting-edge mass photometry, the authors scrutinized the population dynamics of GS assembly in response to varying concentrations of 2-OG. Notably, the findings demonstrate a promising and straightforward correlation, revealing that dodecamer formation can be stimulated by 2-OG concentrations of up to 10 mM, although GS assembly never reaches 100% dodecamerization in this study. Furthermore, catalytic activities showed a remarkable enhancement, escalating from 0.0 U/mg to 7.8 U/mg with increasing concentrations of 2-OG, peaking at 12.5 mM. However, an intriguing gap arises between the incomplete dodecameric formation observed at 10 mM 2-OG, as revealed by mass photometry, and the continued increase in activity from 5 mM to 10 mM 2-OG for M mazei GS. This prompts questions regarding the inability of M mazei GS to achieve complete dodecamer formation and the underlying factors that further enhance GS activity within this concentration range of 2-OG.

Moreover, the cryo-electron microscopy (cryo-EM) analysis provides additional support for the biophysical and biochemical characterization, elucidating the precise localization of 2-OG at the interface of two GS subunits within two hexameric rings. The observed correlation between GS assembly facilitated by 2-OG and its catalytic activity is substantiated by structural reorientations at the GS-GS interface, confirming the previously reported phenomenon of "funnel activation" in GS. However, the authors did not present the cryo-EM structure of M. mazei GS in complex with ATP and glutamate in the presence of 2-OG, which could have shed light on the differences in glutamine biosynthesis between previously reported GS enzymes and the 2-OG-bound M. mazei GS.

Furthermore, besides revealing the cryo-EM structure of 2-OG-bound GS, the study also observed the filamentous form of GS, suggesting that filament formation may be a universal stacking mechanism across archaeal and bacterial species. However, efforts to enhance resolution to investigate whether the stacked polymer is induced by 2-OG or other factors such as ions or metabolites were not undertaken by the authors, leaving room for further exploration into the mechanisms underlying filament formation in GS.

Reviewer #3 (Public Review):

Summary:

The current manuscript investigates the effect of 2-oxoglutarate and the Glk1 protein as modulators of the enzymatic reactivity of glutamine synthetase. To do this, the authors rely on mass photometry, specific activity measurements, and single-particle cryo-EM data.

From the results obtained, the authors convey that glutamine synthetase from Methanosarcina mazei exists in a non-active monomeric/dimeric form under low concentrations of 2-oxoglutarate, and its oligomerization into a dodecameric complex is triggered by higher concentration of 2-oxoglutarate, also resulting in the enhancement of the enzyme activity.

Strengths:

Glutamine synthetase is a crucial enzyme in all domains of life. The dodecameric fold of GS is recurrent amongst prokaryotic and archaea organisms, while the enzyme activity can be regulated in distinct ways. This is a very interesting work combining protein biochemistry with structural biology.

The role of 2-OG is here highlighted as a crucial effector for enzyme oligomerization and full reactivity.

Weaknesses:

Various opportunities to enhance the current state-of-the-art were missed. In particular, omissions of the ligand-bound state of GnK1 leave unexplained the lack of its interaction with GS (in contradiction with previous results from the authors). A finer dissection of the effect and role of 2-oxoglurate are missing and important questions remain unanswered (e.g. are dimers relevant during early stages of the interaction or why previous GS dodecameric structures do not show 2-oxoglutarate).

Reviewer #1 (Public Review):

The paper meticulously explores various conformations and states of the ribosome-translocon complex. Employing advanced techniques such as cryoEM structural determination and AlphaFold modeling, the study delves into the dynamic nature of the ribosome-translocon complex. The findings from these analyses unveil crucial insights, significantly advancing our understanding of the co-translational translocation process in cellular mechanisms.

To begin with, the authors employed a construct comprising the first two transmembrane domains of rhodopsin as a model for studying protein translocation. They conducted in vitro translation, followed by the purification of the ribosome-translocon complex, and determined its cryoEM structures. An in-depth analysis of their ribosome-translocon complex structure revealed that the nascent chain can pass through the lateral gate of translocon Sec61, akin to the behavior of a Signaling Peptide. Additionally, Sec61 was found to interact with 28S rRNA helix 24 and the ribosomal protein uL24. In summary, their structural model aligns with the through-pore model of insertion, contradicting the sliding model.

Secondly, the authors successfully identified RAMP4 in their ribosome-translocon complex structure. Notably, the transmembrane domain of RAMP4 mimics the binding of a Signaling Peptide at the lateral gate of Sec61, albeit without unplugging. Intriguingly, RAMP4 is exclusively present in the non-multipass translocon ribosome-translocon complex, not in those containing multipass translocon. This observation suggests that co-translational translocation specifically occurs in the Sec61 channel that includes bound RAMP4. Additionally, the authors discovered an interaction between the C-tail of ribosomal proteins uL22 and the translocon Sec61, providing valuable insights into the nascent chain's behavior.

Moving on to the third point, the focused classification unveiled TRAP complex interactions with various components. The authors propose that the extra density observed in their novel ribosome-translocon complex can be attributed to calnexin, a major binder of TRAP according to previous studies. Furthermore, the new structure reveals a TRAP-OSTA interaction. This newly identified TRAP-OSTA interaction offers a potential explanation for why patients with TRAP delta defects exhibit congenital disorders of glycosylation.

In conclusion, this paper presents a robust contribution to the field with its thorough structural and modeling analyses. The significance of the findings is evident, providing valuable insights into the intricate mechanisms of protein co-translational translocation. The well-crafted writing, meticulous analyses, and clear figures collectively contribute to the overall strength of the paper.

Reviewer #2 (Public Review):

Summary:

In the manuscript Lewis and Hegde present a structural study of the ribosome-bound multipass translocon (MPT) based on re-analysis of cryo-EM single particle data of ribosome-MPTs processing the multipass transmembrane substrate RhoTM2 from a previous publication (Smalinskaité et al, Nature 2022) and AlphaFold2 multimer modeling. Detailed analysis of the laterally open Sec61 is obtained from PAT-less particles.

The following major claims are made:

- TMs can bind similarly to the Sec61 lateral gate as signal peptides.

- Ribosomal H59 is in immediate proximity to basic residues of TMs and signal peptides, suggesting it may contribute to the positive-inside rule.

- RAMP4/SERP1 binds to the Sec61 lateral gate and the ribosome near 28S rRNA's helices 47, 57, and 59 as well as eL19, eL22, and eL31.

- uL22 C-terminal tail binds H24/47 blocking a potential escape route for nascent peptides to the cytosol.

- TRAP and BOS compete for binding to Sec61 hinge.

- Calnexin TM binds to TRAPg.

- NOMO wedges between TRAP and MPT.

Strengths:

The manuscript contains numerous novel new structural analyses and their potential functional implications. While all findings are exciting, the highlight is the discovery of RAMP4/SERP1 near the Sec61 lateral gate. Overall, the strength is the thorough and extensive structural analysis of the different high-resolution RTC classes as well as the expert bioinformatic evolutionary analysis.

Reviewer #1 (Public Review):

Summary:

The authors have previously described a way to boost WNT/CTNNB1 signaling in a tissue-specific manner, by directing an RSPO2 mutant protein (RSPO2RA) to a liver-specific receptor (ASGR1/2). This is done by fusing the RSPO2RA to an antibody that binds ASGR1/2.

Here the authors describe two new antibodies, 8M24 and 8G8, with similar effects. 8M24 shows specificity for ASGR1, while 8G8 has broader affinity for mouse/human ASGR1/2.<br /> The authors resolve and describe the crystal structure of the hASGR1CRD:8M24 complex and the hASGR2CRD:8G8 complex in great detail, which help explain the specificities of the 8M24 and 8G8 antibodies. Their epitopes are non-overlapping.<br /> Upon fusion of the antibodies to an RSPO2RA (an RSPO mutant), these antibodies are able to enhance WNT signaling by promoting the ASGR1-mediated clearance of ZNRF3/RNF43, thereby increasing cell surface expression of FZD. This has previously also been shown to be the case for RSPO2RA fused to an anti-ASGR1 antibody 4F3 - and the paper also tests how the antibodies compare to the 4F3 fusion.

Strengths:

(1) One challenge in treating diseases, is the fact that one would like therapeutics to be highly specific - not just in terms of their target (e.g. aimed at a specific protein of interest) but also in terms of tissue specificity (i.e. affecting only tissue X but leaving all others unaffected). This study broadens the collection of antibodies that can be used for this purpose and thus expands a potential future clinical toolbox.

(2) The authors have addressed questions raised after a first round of review, e.g. by showing that ASGR1 is itself indeed ubiquitinated.

Weaknesses:

(1) Some questions remain as to how 8M24 and 8G8 compare to 4F3.

(2) Some questions remain as to the specificity of the approach: the initial goal was not to also downregulate ASGR1 per se, so this targeting to a specific receptor/membrane protein is not trivial and/or neutral.

Reviewer #1 (Public Review):

The manuscript presents novel results on the regulation of Drosophila wing growth by the protocadherins Ds and Fat. The manuscript performs a more careful analysis of disc volume, larval size, and the relationship between the two, in normal and mutant larvae, and after localized knockdown or overexpression of Fat and Ds. Not all of the results are equally surprising given the previous work on Fat, Ds, and their regulation of disc growth, pupariation, and the Hippo pathway, but the presentation and detail of the presented data is new. The most novel results concern the scaling of gradients of Fat and Ds protein during development, a largely unstudied gradient of Fat protein, and using overexpression of Ds to argue that changes in the Ds gradient do not underlie the slowing and halting of cell divisions during development.

Reviewer #2 (Public Review):

This manuscript from Liu et al. examines the role of Fat and Dachsous, two transmembrane proto-cadherins that function both in planar cell polarity and in tissue growth control mediated by the Hippo pathway. The authors developed a new method for measuring growth of the wing imaginal disc during late larval development and then used this approach to examine the effects of disruption of Fat/Dachsous function on disc growth. The authors show that during mid to late third instar the wing imaginal disc normally grows in a linear rather than exponential fashion and that this occurs due to slowing of the mitotic cell cycle as the disc grows during this period. Consistent with their known role in regulating Hippo pathway activity, this slowing of growth is disrupted by loss of Fat/Dachsous function. The authors also observed a previously unreported gradient of Fat protein across the wing blade. However, graded expression of Fat or Dachsous is not necessary for proper growth regulation in the late third instar because ectopic Dachsous expression, which affects gradients of both Dachsous and Fat, has no growth phenotype.

Reviewer #1 (Public Review):

Muscle models are important tools in the fields of biomechanics and physiology. Muscle models serve a wide variety of functions, including validating existing theories, testing new hypotheses, and predicting forces produced by humans and animals in health and disease. This paper attempts to provide an alternative to Hill-type muscle models that includes contributions of titin to force enhancement over multiple time scales. Due to the significant limitations of Hill-type models, alternative models are needed and therefore the work is important and timely.

The effort to include a role for titin in muscle models is a major strength of the methods and results. The results clearly demonstrate the weaknesses of Hill models and the advantages of incorporating titin into theoretical treatments of muscle mechanics. Another strength is to address muscle mechanics over a large range of time scales.

The authors succeed in demonstrating the need to incorporate titin in muscle models, and further show that the model accurately predicts in situ force of cat soleus (Kirsch et al. 1994; Herzog & Leonard, 2002) and rabbit posts myofibrils (Leonard et al. 2010). However, it remains unclear whether the model will be practical for use with data from different muscles or preparations. Several ad hoc modifications were described in the paper, and the degree to which the model requires parameter optimization for different muscles, preparations and experiment types remains unclear.

Reviewer #2 (Public Review):

This model of skeletal muscle includes springs and dampers which aim to capture the effect of crossbridge and titin stiffness during the stretch of active muscle. While both crossbridge and titin stiffness have previously been incorporated, in some form, into models, this model is the first to simultaneously include both. The authors suggest that this will allow for the prediction of muscle force in response to short-, mid- and long-range stretches. All these types of stretch are likely to be experienced by muscle during in vivo perturbations, and are known to elicit different muscle responses. Hence, it is valuable to have a single model which can predict muscle force under all these physiologically relevant conditions. In addition, this model dramatically simplifies sarcomere structure to enable this muscle model to be used in multi-muscle simulations of whole-body movement.

In order to test this model, its force predictions are compared to 3 sets of experimental data which focus on short-, mid- and long-range perturbations, and to the predictions of a Hill-type muscle model. The choice of data sets is excellent and provide a robust test of the model's ability to predict forces over a range of length perturbations. However, I find the comparison to a Hill-type muscle model to be somewhat limiting. It is well established that Hill-type models do not have any mechanism by which they can predict the effect of active muscle stretch. Hence, that the model proposed here represents an improvement over such a model is not a surprise. Many other models, some of which are also simple enough to be incorporated into whole-body simulations, have incorporated mechanistic elements which allow for the prediction of force responses to muscle stretch. And it is not clear from the results presented here that this model would outperform such models.

The paper begins by outlining the phenomenological vs mechanistic approaches taken to muscle modelling, historically. It appears, although is not directly specified, that this model combines these approaches. A somewhat mechanistic model of the response of the crossbridges and titin to active stretch is combined with a phenomenological implementation of force-length and force-velocity relationships. This combination of approaches may be useful improving the accuracy of predictions of muscle models and whole-body simulations, which is certainly a worthy goal. However, it also may limit the insight that can be gained. For example, it does not seem that this model could reflect any effect of active titin properties on muscle shortening. In addition, it is not clear to me, either physiologically or in the model, what drives the shift from the high stiffness in short-range perturbations to the somewhat lower stiffness in mid-range perturbations.

Reviewer #1 (Public Review):

Summary:<br /> In the paper by Choi et al., the authors aimed to develop base editing strategies to convert CAG repeats to CAA repeats in the huntingtin gene (HTT), which causes Huntington's disease (HD). They hypothesized that this conversion would delay disease onset by shortening the uninterrupted CAG repeat. Using HEK-293T cells as a model, the researchers employed cytosine base editors and guide RNAs (gRNAs) to efficiently convert CAG to CAA at various sites within the CAG repeat. No significant indels, off-target edits, transcriptome alterations, or changes in HTT protein levels were detected. Interestingly, somatic CAG repeat expansion was completely abolished in HD knock-in mice carrying CAA-interrupted repeats.

Strengths:<br /> This study represents the first proof-of-concept exploration of the cytosine base editing technique as a potential treatment for HD and other repeat expansion disorders with similar mechanisms.

Weaknesses:<br /> Given that HD is a neurodegenerative disorder, it is crucial to determine the efficiency of the base editing strategies tested in this manuscript and their feasibility in relevant cells affected by HD and the brain, which needed to be improved in this manuscript.

Reviewer #2 (Public Review):

Summary:<br /> In a proof-of-concept study with the aspiration of developing a treatment to delay HD onset, Choi et al. design and test an A>G DNA base editing strategy to exploit the recently established inverse relationship between the number of uninterrupted CAG repeats in polyglutamine repeat expansions and the age-of-onset of Huntington's Disease (HD). Most of the study is devoted to optimizing a base editing strategy typified by BE4max and gRNA2. The base editing is performed in human HEK293 cells engineered with a 51 CAG canonical repeat and in HD knock-in mice harboring 105+ CAG repeats.

Weaknesses:<br /> Genotypic data on DNA editing are not portrayed in a clear manner consistent with the study's goal, namely reducing the number of uninterrupted CAG repeats by a clinically relevant amount according to the authors' least square approximated mean age-at-onset. No phenotypic data are presented to show that editing performed in either model would lead to reduced hallmarks of HD onset.

More evidence is needed to support the central claims and therapeutic potential needs to be more adequate.

Reviewer #3 (Public Review):

Summary:<br /> In human patients with Huntington's disease (HD), caused by a CAG repeat expansion mutation, the number of uninterrupted CAG repeats at the genomic level influences age-at-onset of clinical signs independent of the number of polyglutamine repeats at the protein level. In most patients, the CAG repeat terminates with a CAA-CAG doublet. However, CAG repeat variants exist that either do not have that doublet or have two doublets. These variants consequently differ in their number of uninterrupted CAG repeats, while the number of glutamine repeats is the same as both CAA and CAG codes for glutamine. The authors first confirm that a shorter uninterrupted CAG repeat number in human HD patients is associated with developing the first clinical signs of HD later. They predict that introducing a further CAA-CAG doublet will result in years of delay of clinical onset. Based on this observation, the authors tested the hypothesis that turning CAG to CAA within a CAG repeat sequence using base editing techniques will benefit HD biology. They show that, indeed, in HD cell models (HEK293 cells expressing 16/17 CAG repeats; a single human stem cell line carrying a CAG repeat expansion in the fully penetrant range with 42 CAG repeats), their base editing strategies do induce the desired CAG-CAA conversion. The efficiency of conversion differed depending on the strategy used. In stem cells, delivery posed a problem, so to test allele specificity, the authors then used a HEK 293 cell line with 51 CAG repeats on the expanded allele. Conversion occurred in both alleles with huntingtin protein and mRNA levels; transcriptomics data was unchanged. In knock-in mice carrying 110 CAG repeats, however, base editing did not work as well for different, mainly technical, reasons.

Strengths:<br /> The authors use state-of-the-art methods and carefully and thoroughly designed experiments. The data support the conclusions drawn. This work is a very valuable translation from the insight gained from large GWAS studies into HD pathogenesis. It rightly emphasises the potential this has as a causal treatment in HD, while the authors also acknowledge important limitations.

Weaknesses:<br /> They could dedicate a little more to discussing several of the mentioned challenges. The reader will better understand where base editing is in HD currently and what needs to be done before it can be considered a treatment option. For instance,

-It is important to clarify what can be gained by examining again the relationship between uninterrupted CAG repeat length and age-at-onset. Could the authors clarify why they do this and what it adds to their already published GWAS findings? What is the n of datasets?<br /> -What do they think an ideal conversion rate would be, and how that could be achieved?<br /> -Is there a dose-effect relationship for base editing, and would it be realistic to achieve the ideal conversion rate in target cells, given the difficulties described by the authors in differentiated neurons from stem cells?<br /> - The liver is a good tool for in-vivo experiments examining repeat instability in mouse models. However, the authors could comment on why they did not examine the brain.<br /> - Is there a limit to judging the effects of base editing on somatic instability with longer repeats, given the difficulties in measuring long CAG repeat expansions?<br /> - Given the methodological challenges for assessing HTT fragments, are there other ways to measure the downstream effects of base editing rather than extrapolate what it will likely be?<br /> - Sequencing errors could mask low-level, but biologically still relevant, off-target effects (such as gRNA-dependent and gRNA-independent DNA, Off-targets, RNA off-targets, bystander editing). How likely is that?<br /> - How worried are the authors about immune responses following base editing? How could this be assessed?

Reviewer #1 (Public Review):

Summary:

In this study, the authors used a multi-alternative decision task and a multidimensional signal-detection model to gain further insight into the cause of perceptual impairments during the attentional blink. The model-based analyses of behavioural and EEG data show that such perceptual failures can be unpacked into distinct deficits in visual detection and discrimination, with visual detection being linked to the amplitude of late ERP components (N2P and P3) and discrimination being linked to the coherence of fronto-parietal brain activity.

Strengths:

The main strength of this paper lies in the fact that it presents a novel perspective on the cause of perceptual failures during the attentional blink. The multidimensional signal-detection modelling approach is explained clearly, and the results of the study show that this approach offers a powerful method to unpack behavioural and EEG data into distinct processes of detection and discrimination.

Weaknesses:

While the model-based analyses are compelling, the paper also features some analyses that seem misguided, or, at least, insufficiently motivated and explained. Specifically, in the introduction, the authors raise the suggestion that the attentional blink could be due to a reduction in sensitivity or a response bias. The suggestion that a response bias could play a role seems misguided, as any response bias would be expected to be constant across lags, while the attentional blink effect is only observed at short lags. Thus, it is difficult to understand why the authors would think that a response bias could explain the attentional blink.

A second point of concern regards the way in which the measures for detection and discrimination accuracy were computed. If I understand the paper correctly, a correct detection was defined as either correctly identifying T2 (i.e., reporting CW or CCW if T2 was CW or CCW, respectively, see Figure 2B), or correctly reporting T2's absence (a correct rejection). Here, it seems that one should also count a misidentification (i.e., incorrect choice of CW or CCW when T2 was present) as a correct detection, because participants apparently did detect T2, but failed to judge/remember its orientation properly in case of a misidentification. Conversely, the manner in which discrimination performance is computed also raises questions. Here, the authors appear to compute accuracy as the average proportion of T2-present trials on which participants selected the correct response option for T2, thus including trials in which participants missed T2 entirely. Thus, a failure to detect T2 is now counted as a failure to discriminate T2. Wouldn't a more proper measure of discrimination accuracy be to compute the proportion of correct discriminations for trials in which participants detected T2?

My last point of critique is that the paper offers little if any guidance on how the inferred distinction between detection and discrimination can be linked to existing theories of the attentional blink. The discussion mostly focuses on comparisons to previous EEG studies, but it would be interesting to know how the authors connect their findings to extant, mechanistic accounts of the attentional blink. A key question here is whether the finding of dissociable processes of detection and discrimination would also hold with more meaningful stimuli in an identification task (e.g., the canonical AB task of identifying two letters shown amongst digits). There is evidence to suggest that meaningful stimuli are categorized just as quickly as they are detected (Grill-Spector & Kanwisher, 2005; Grill-Spector K, Kanwisher N. Visual recognition: as soon as you know it is there, you know what it is. Psychol Sci. 2005 Feb;16(2):152-60. doi: 10.1111/j.0956-7976.2005.00796.x. PMID: 15686582.). Does that mean that the observed distinction between detection and discrimination would only apply to tasks in which the targets consist of otherwise meaningless visual elements, such as lines of different orientations?

Reviewer #2 (Public Review):

Summary:

The authors had two aims: First, to decompose the attentional blink (AB) deficit into the two components of signal detection theory; sensitivity and bias. Second, the authors aimed to assess the two subcomponents of sensitivity; detection and discrimination. They observed that the AB is only expressed in sensitivity. Furthermore, detection and discrimination were doubly dissociated. Detection modulated N2p and P3 ERP amplitude, but not frontoparietal beta-band coherence, whereas this pattern was reversed for discrimination.

Strengths:

The experiment is elegantly designed, and the data - both behavioral and electrophysiological - are aptly analyzed. The outcomes, in particular the dissociation between detection and discrimination blinks, are consistently and clearly supported by the results. The discussion of the results is also appropriately balanced.

Weaknesses:

The lack of an effect of stimulus contrast does not seem very surprising from what we know of the nature of AB already. Low-level perceptual factors are not thought to cause AB. This is fine, as there are also other, novel findings reported, but perhaps the authors could bolster the importance of these (null) findings by referring to AB-specific papers, if there are indeed any, that would have predicted different outcomes in this regard.

On an analytical note, the ERP analysis could be finetuned a little more. The task design does not allow measurement of the N2pc or N400 components, which are also relevant to the AB, but the N1 component could additionally be analyzed. In doing so, I would furthermore recommend selecting more lateral electrode sites for both the N1, as well as the P1. Both P1 and N1 are likely not maximal near the midline, where the authors currently focused their P1 analysis.

Impact & Context:

The results of this study will likely influence how we think about selective attention in the context of the AB phenomenon. However, I think its impact could be further improved by extending its theoretical framing. In particular, there has been some recent work on the nature of the AB deficit, showing that it can be discrete (all-or-none) and gradual (Sy et al., 2021; Karabay et al., 2022, both in JEP: General). These different faces of target awareness in the AB may be linked directly to the detection and discrimination subcomponents that are analyzed in the present paper. I would encourage the authors to discuss this potential link and comment on the bearing of the present work on these previous behavioral findings.

Reviewer #3 (Public Review):

Summary:

In the present study, the authors aimed to achieve a better understanding of the mechanisms underlying the attentional blink, that is, a deficit in processing the second of two target stimuli when they appear in rapid succession. Specifically, they used a concurrent detection and identification task in- and outside of the attentional blink and decoupled effects of perceptual sensitivity and response bias using a novel signal detection model. They conclude that the attentional blink selectively impairs perceptual sensitivity but not response bias, and link established EEG markers of the attentional blink to deficits in stimulus detection (N2p, P3) and discrimination (fronto-parietal high-beta coherence), respectively. Taken together, their study suggests distinct mechanisms mediating detection and discrimination deficits in the attentional blink.

Strengths:

Major strengths of the present study include its innovative approach to investigating the mechanisms underlying the attentional blink, an elegant, carefully calibrated experimental paradigm, a novel signal detection model, and multifaceted data analyses using state-of-the-art model comparisons and robust statistical tests. The study appears to have been carefully conducted and the overall conclusions seem warranted given the results. In my opinion, the manuscript is a valuable contribution to the current literature on the attentional blink. Moreover, the novel paradigm and signal detection model are likely to stimulate future research.

Weaknesses:

Weaknesses of the present manuscript mainly concern the negligence of some relevant literature, unclear hypotheses, potentially data-driven analyses, relatively low statistical power, potential flaws in the EEG methods, and the absence of a discussion of limitations. In the following, I will list some major and minor concerns in detail.

Major points

Hypotheses:<br /> I appreciate the multifaceted, in-depth analysis of the given dataset including its high amount of different statistical tests. However, neither the Introduction nor the Methods contain specific statistical hypotheses. Moreover, many of the tests (e.g., correlations) rely on selected results of previous tests. It is unclear how many of the tests were planned a priori, how many more were performed, and how exactly corrections for multiple tests were implemented. Thus, I find it difficult to assess the robustness of the results.

Power:<br /> Some important null findings may result from the rather small sample sizes of N = 24 for behavioral and N = 18 for ERP analyses. For example, the correlation between detection and discrimination d' deficits across participants (r=0.39, p=0.059) (p. 12, l. 263) and the attentional blink effect on the P1 component (p=0.050, no test statistic) (p. 14, 301) could each have been significant with one more participant. In my opinion, such results should not be interpreted as evidence for the absence of effects.

Neural basis of the attentional blink:<br /> The introduction (e.g., p. 4, l. 56-76) and discussion (e.g., p. 19, 427-447) do not incorporate the insights from the highly relevant recent review by Zivony & Lamy (2022), which is only cited once (p. 19, l. 428). Moreover, the sections do not mention some relevant ERP studies of the attentional blink (e.g., Batterink et al., 2012; Craston et al., 2009; Dell'Acqua et al., 2015; Dellert et al., 2022; Eiserbeck et al., 2022; Meijs et al., 2018).

Detection versus discrimination:<br /> Concerning the neural basis of detection versus discrimination (e.g., p. 6, l. 98-110; p. 18, l. 399-412), relevant existing literature (e.g., Broadbent & Broadbent, 1987; Hillis & Brainard, 2007; Koivisto et al., 2017; Straube & Fahle, 2011; Wiens et al., 2023) is not included.

Pooling of lags and lag 1 sparing:<br /> I wonder why the authors chose to include 5 different lags when they later pooled early (100, 300 ms) and late (700, 900 ms) lags, and whether this pooling is justified. This is important because T2 at lag 1 (100 ms) is typically "spared" (high accuracy) while T2 at lag 3 (300 ms) shows the maximum AB (for reviews, see, e.g., Dux & Marois, 2009; Martens & Wyble, 2010). Interestingly, this sparing was not observed here (p. 43, Figure 2). Nevertheless, considering the literature and the research questions at hand, it is questionable whether lag 1 and 3 should be pooled.

Discrimination in the attentional blink<br /> Concerning the claims that previous attentional blink studies conflated detection and discrimination (p. 6, l. 111-114; p. 18, l. 416), there is a recent ERP study (Dellert et al., 2022) in which participants did not perform a discrimination task for the T2 stimuli. Moreover, since the relevance of all stimuli except T1 was uncertain in this study, irrelevant distractors could not be filtered out (cf. p. 19, l. 437). Under these conditions, the attentional blink was still associated with reduced negativities in the N2 range (cf. p. 19, l. 427-437) but not with a reduced P3 (cf. p. 19, l 439-447).

General EEG methods:<br /> While most of the description of the EEG preprocessing and analysis (p. 31/32) is appropriate, it also lacks some important information (see, e.g., Keil et al., 2014). For example, it does not include the length of the segments, the type and proportion of artifacts rejected, the number of trials used for averaging in each condition, specific hypotheses, and the test statistics (in addition to p-values).

EEG filters:<br /> P. 31, l. 728: "The data were (...) bandpass filtered between 0.5 to 18 Hz (...). Next, a bandstop filter from 9-11 Hz was applied to remove the 10 Hz oscillations evoked by the RSVP presentation." These filter settings do not follow common recommendations and could potentially induce filter distortions (e.g., Luck, 2014; Zhang et al., 2024). For example, the 0.5 high-pass filter could distort the slow P3 wave. Mostly, I am concerned about the bandstop filter. Since the authors commendably corrected for RSVP-evoked responses by subtracting T2-absent from T2-present ERPs (p. 31, l. 746), I wonder why the additional filter was necessary, and whether it might have removed relevant peaks in the ERPs of interest.

Coherence analysis:<br /> P. 33, l. 786: "For subsequent, partial correlation analyses of coherence with behavioral metrics and neural distances (...), we focused on a 300 ms time period (0-300 ms following T2 onset) and high-beta frequency band (20-30 Hz) identified by the cluster-based permutation test (Fig. 5A-C)." I wonder whether there were any a priori criteria for the definition and selection of such successive analyses. Given the many factors (frequency bands, hemispheres) in the analyses and the particular shape of the cluster (p. 49, Fig 5C), this focus seems largely data-driven. It remains unclear how many such tests were performed and whether the results (e.g., the resulting weak correlation of r = 0.22 in one frequency band and one hemisphere in one part of a complexly shaped cluster; p. 15, l. 327) can be considered robust.

References<br /> Batterink, L., Karns, C. M., & Neville, H. (2012). Dissociable mechanisms supporting awareness: The P300 and gamma in a linguistic attentional blink task. Cerebral Cortex, 22(12), 2733-2744. https://doi.org/10.1093/cercor/bhr346<br /> Broadbent, D. E., & Broadbent, M. H. P. (1987). From detection to identification: Response to multiple targets in rapid serial visual presentation. Perception & Psychophysics, 42(2), 105-113. https://doi.org/10.3758/BF03210498<br /> Craston, P., Wyble, B., Chennu, S., & Bowman, H. (2009). The attentional blink reveals serial working memory encoding: Evidence from virtual and human event-related potentials. Journal of Cognitive Neuroscience, 21(3), 550-566. https://doi.org/10.1162/jocn.2009.21036<br /> Dell'Acqua, R., Dux, P. E., Wyble, B., Doro, M., Sessa, P., Meconi, F., & Jolicœur, P. (2015). The attentional blink impairs detection and delays encoding of visual information: Evidence from human electrophysiology. Journal of Cognitive Neuroscience, 27(4), 720-735. https://doi.org/10.1162/jocn_a_00752<br /> Dellert, T., Krebs, S., Bruchmann, M., Schindler, S., Peters, A., & Straube, T. (2022). Neural correlates of consciousness in an attentional blink paradigm with uncertain target relevance. NeuroImage, 264C, 119679. https://doi.org/10.1016/j.neuroimage.2022.119679<br /> Dux, P. E., & Marois, R. (2009). The attentional blink: A review of data and theory. Attention, Perception, & Psychophysics, 71(8), 1683-1700. https://doi.org/10.3758/APP.71.8.1683<br /> Hillis, J. M., & Brainard, D. H. (2007). Distinct mechanisms mediate visual detection and identification. Current Biology, 17(19), 1714-1719. https://doi.org/10.1016/j.cub.2007.09.012<br /> Keil, A., Debener, S., Gratton, G., Junghöfer, M., Kappenman, E. S., Luck, S. J., Luu, P., Miller, G. A., & Yee, C. M. (2014). Committee report: Publication guidelines and recommendations for studies using electroencephalography and magnetoencephalography. Psychophysiology, 51(1), 1-21. https://doi.org/10.1111/psyp.12147<br /> Koivisto, M., Grassini, S., Salminen-Vaparanta, N., & Revonsuo, A. (2017). Different electrophysiological correlates of visual awareness for detection and identification. Journal of Cognitive Neuroscience, 29(9), 1621-1631. https://doi.org/10.1162/jocn_a_01149<br /> Luck, S. J. (2014). An introduction to the event-related potential technique. MIT Press.<br /> Martens, S., & Wyble, B. (2010). The attentional blink: Past, present, and future of a blind spot in perceptual awareness. Neuroscience & Biobehavioral Reviews, 34(6), 947-957. https://doi.org/10.1016/j.neubiorev.2009.12.005<br /> Meijs, E. L., Slagter, H. A., de Lange, F. P., & Gaal, S. van. (2018). Dynamic interactions between top-down expectations and conscious awareness. Journal of Neuroscience, 38(9), 2318-2327. https://doi.org/10.1523/JNEUROSCI.1952-17.2017<br /> Straube, S., & Fahle, M. (2011). Visual detection and identification are not the same: Evidence from psychophysics and fMRI. Brain and Cognition, 75(1), 29-38. https://doi.org/10.1016/j.bandc.2010.10.004<br /> Wiens, S., Andersson, A., & Gravenfors, J. (2023). Neural electrophysiological correlates of detection and identification awareness. Cognitive, Affective, & Behavioral Neuroscience. https://doi.org/10.3758/s13415-023-01120-5<br /> Zhang, G., Garrett, D. R., & Luck, S. J. (2024). Optimal filters for ERP research II: Recommended settings for seven common ERP components. Psychophysiology, n/a(n/a), e14530. https://doi.org/10.1111/psyp.14530

Reviewer #1 (Public Review):

Summary:

This manuscript from So et al. describes what is suggested to be an improved protocol for single-nuclei RNA sequencing (snRNA-seq) of adipose tissue. The authors provide evidence that modifications to the existing protocols result in better RNA quality and nuclei integrity than previously observed, with ultimately greater coverage of the transcriptome upon sequencing. Using the modified protocol, the authors compare the cellular landscape of murine inguinal and perigonadal white adipose tissue (WAT) depots harvested from animals fed a standard chow diet (lean mice) or those fed a high-fat diet (mice with obesity).

Strengths:

Overall, the manuscript is well-written, and the data are clearly presented. The strengths of the manuscript rest in the description of an improved protocol for snRNA-seq analysis. This should be valuable for the growing number of investigators in the field of adipose tissue biology that are utilizing snRNA-seq technology, as well as those other fields attempting similar experiments with tissues possessing high levels of RNAse activity.

Moreover, the study makes some notable observations that provide the foundation for future investigation. One observation is the correlation between nuclei size and cell size, allowing for the transcriptomes of relatively hypertrophic adipocytes in perigonadal WAT to be examined. Another notable observation is the identification of an adipocyte subcluster (Ad6) that appears "stressed" or dysfunctional and likely localizes to crown-like inflammatory structures where pro-inflammatory immune cells reside.

Weaknesses:

Analogous studies have been reported in the literature, including a notable study from Savari et al. (Cell Metabolism). This somewhat diminishes the novelty of some of the biological findings presented here. Moreover, a direct comparison of the transcriptomic data derived from the new vs. existing protocols (i.e. fully executed side by side) was not presented. As such, the true benefit of the protocol modifications cannot be fully understood.

Reviewer #2 (Public Review):

Summary:

In the present manuscript So et al utilize single-nucleus RNA sequencing to characterize cell populations in lean and obese adipose tissues.

Strengths:

The authors utilize a modified nuclear isolation protocol incorporating VRC that results in higher-quality sequencing reads compared with previous studies.

Weaknesses:

The use of VRC to enhance snRNA-seq has been previously published in other tissues. The snRNA-seq snRNA-seq data sets presented in this manuscript, when compared with numerous previously published single-cell analyses of adipose tissue, do not represent a significant scientific advance.

Figure 1-3: The snRNA-seq data obtained by the authors using their enhanced protocol does not represent a significant improvement in cell profiling for the majority of the highlighted cell types including APCs, macrophages, and lymphocytes. These cell populations have been extensively characterized by cytoplasmic scRNA-seq which can achieve sufficient sequencing depth, and thus this study does not contribute meaningful additional insight into these cell types. The authors note an increase in the number of rare endothelial cell types recovered, however this is not translated into any kind of functional analysis of these populations.

Figure 4: The authors did not provide any evidence that the relative fluorescent brightness of GFP and mCherry is a direct measure of the nuclear size, and the nuclear size is only a moderate correlation with the cell size. Thus sorting the nuclei based on GFP/mCherry brightness is not a great proxy for adipocyte diameter. Furthermore, no meaningful insights are provided about the functional significance of the reported transcriptional differences between small and large adipocyte nuclei.

Figure 5-6: The Ad6 population is highly transcriptionally analogous to the mAd3 population from Emont et al, and is thus not a novel finding. Furthermore, in the present data set, the authors conclude that Ad6 are likely stressed/dying hypertrophic adipocytes with a global loss of gene expression, which is a well-documented finding in eWAT > iWAT, for which the snRNA-seq reported in the present manuscript does not provide any novel scientific insight.

Reviewer #3 (Public Review):

Summary:

The authors aimed to improve single-nucleus RNA sequencing (snRNA-seq) to address current limitations and challenges with nuclei and RNA isolation quality. They successfully developed a protocol that enhances RNA preservation and yields high-quality snRNA-seq data from multiple tissues, including a challenging model of adipose tissue. They then applied this method to eWAT and iWAT from mice fed either a normal or high-fat diet, exploring depot-specific cellular dynamics and gene expression changes during obesity. Their analysis included subclustering of SVF cells and revealed that obesity promotes a transition in APCs from an early to a committed state and induces a pro-inflammatory phenotype in immune cells, particularly in eWAT. In addition to SVF cells, they discovered six adipocyte subpopulations characterized by a gradient of unique gene expression signatures. Interestingly, a novel subpopulation, termed Ad6, comprised stressed and dying adipocytes with reduced transcriptional activity, primarily found in eWAT of mice on a high-fat diet. Overall, the methodology is sound, the writing is clear, and the conclusions drawn are supported by the data presented. Further research based on these findings could pave the way for potential novel interventions in obesity and metabolic disorders, or for similar studies in other tissues or conditions.

Strengths:

• The authors developed a robust snRNA-seq technique that preserves the integrity of the nucleus and RNA across various tissue types, overcoming the challenges of existing methods.

• They identified adipocyte subpopulations that follow adaptive or pathological trajectories during obesity.

• The study reveals depot-specific differences in adipose tissues, which could have implications for targeted therapies.

Weaknesses:

• The adipose tissues were collected after 10 weeks of high-fat diet treatment, lacking the intermediate time points for identifying early markers or cell populations during the transition from healthy to pathological adipose tissue.

• The expansion of the Ad6 subpopulation in obese iWAT and gWAT is interesting. The author claims that Ad6 exhibited a substantial increase in eWAT and a moderate rise in iWAT (Figure 4C). However, this adipocyte subpopulation remains the most altered in iWAT upon obesity. Could the authors elaborate on why there is a scarcity of adipocytes with ROS reporter and B2M in obese iWAT?

• While the study provides extensive data on mouse models, the potential translation of these findings to human obesity remains uncertain.

Reviewer #1 (Public Review):

Summary:

This paper by Beath et. al. identifies a potential regulatory role for proteins involved in cytoplasmic streaming and maintaining the grouping of paternal organelles: holding sperm contents in the fertilized embryos away from the oocyte meiotic spindle so that they don't get ejected into the polar body during meiotic chromosome segregation. The authors show that by time-lapse video, paternal mitochondria (used as a readout for sperm and its genome) is excluded from yolk granules and maternal mitochondria, even when moving long distances by cytoplasmic streaming. To understand how this exclusion is accomplished, they first show that it is independent of both internal packing and the engulfment of the paternal chromosomes by maternal endoplasmic reticulum creating an impermeable barrier. They then test whether the control of cytoplasmic steaming affects this exclusion by knocking down two microtubule motors, Katanin and kinesis I. They find that the ER ring, which is used as a proxy for paternal chromosomes, undergoes extensive displacement with these treatments during anaphase I and interacts with the meiotic spindle, supporting their hypothesis that the exclusion of paternal chromosomes is regulated by cytoplasmic streaming. Next, they test whether a regulator of maternal ER organization, ATX-2, disrupts sperm organization so that they can combine the double depletion of ATX-2 and KLP-7, presumably because klp-7 RNAi (unlike mei-1 RNAi) does not affect polar body extrusion and they can report on what happens to paternal chromosomes. They find that the knockdown of both ATX-2 and KLP-7 produces a higher incidence of what appears to be the capture of paternal chromosomes by the meiotic spindle (5/24 vs 1/25). However, this capture event appears to halt the cell cycle, preventing the authors from directly observing whether this would result in the paternal chromosomes being ejected into the polar body.

Strengths:

This is a useful, descriptive paper that highlights a potential challenge for embryos during fertilization: when fertilization results in the resumption of meiotic divisions, how are the paternal and maternal genomes kept apart so that the maternal genome can undergo chromosome segregation and polar body extrusion without endangering the paternal genome? In general, the experiments are well-executed and analyzed. In particular, the authors' use of multiple ways to knock down ATX-2 shows rigor.

Weaknesses:

The paper makes a case that this regulation may be important but the authors should do some additional work to make this case more convincing and accessible for those outside the field. In particular, some of the figures could include greater detail to support their conclusions, they could explain the rationale for some experiments better and they could perform some additional control experiments with their double depletion experiments to better support their interpretations. Also, the authors' inability to assess the functional biological consequences of the capture of the sperm genome by the oocyte spindle should be discussed, particularly in light of the cell cycle arrest that they observe.

Reviewer #2 (Public Review):

Summary

In this manuscript, Beath et al. use primarily C. elegans zygotes to test the overarching hypothesis that cytoplasmic mechanisms exit to prevent interaction between paternal chromosomes and the meiotic spindle, which are present in a shared zygotic cytoplasm after fertilization. Previous work, much of which by this group, had characterized cytoplasmic streaming in the zygote and the behavior of paternal components shortly after fertilization, primarily the clustering of paternal mitochondria and membranous organelles around the paternal chromosomes. This work set out to identify the molecular mechanisms responsible for that clustering and test the specific hypothesis that the "paternal cloud" helps prevent the association of paternal chromosomes with the meiotic spindle.

Strengths

This work is a collection of technical achievements. The data are primarily 3- and 4-channel time-lapse images of zygotes shortly after fertilization, which were performed inside intact animals. There are many instances in which the experiments show extreme technical skill, such as tracking the paternal chromosomes over large displacements throughout the volume of the embryo. The authors employ a wide variety of fluorescent reporters to provide a remarkably clear picture of what is going on in the zygote. These reagents and the novel characterization of these stages that they provide will be widely beneficial to the community.

The data provide direct visualization of what had previously been a mostly hypothetical structure, the "paternal cloud," using simultaneous labeling of paternal DNA and mitochondria in combination with a variety of maternal proteins including maternal mitochondria, yolk granules, tubulin, and plasma membrane. Together, these images provided convincing evidence of the existence of this specified cytoplasmic domain. They go on to show that the knockdown of the ataxin-2 homolog ALX-2, a protein previously shown to affect ER dynamics, disrupted the paternal cloud, identifying a role for ER organization in this structure.

The authors then used the system to test the functional consequences of perturbing the cytoplasmic organization. Consistent with the paternal cloud being a stable structure, it stayed intact during large movements the authors generated using previously published knockdowns (of mei-1/katanin and kinesin-13/kpl-7) that increased cytoplasmic streaming. They used this data to document instances in which the paternal chromosomes were likely to have been attached to the spindle. They concluded with direct evidence of spindle fibers connecting to the paternal chromatin upon knockdown of ATX-2 in combination with increased cytoplasmic streaming, providing strong, direct support for their overarching hypothesis.

Weaknesses

While the data is convincing, the narrative of the paper could be streamlined to highlight the novelty of the experiments and better articulate the aims. For example, the cloud of paternal mitochondria and membranous organelles was previously shown, but Figures 1-2 largely reiterate that observation. The innovation seems to be that the combination of ER, yolk, and maternal mitochondrial markers makes the existence of a specified domain more concrete. There are also some instances where more description is needed to make the conclusions from the images clear.

The manuscript intersperses what read like basic characterizations of fluorescent markers that, as written, can distract from the main story. The authors characterized the dynamics of ER organization throughout the substages of meiosis and the permeability of the envelope of ER that surrounds the paternal chromatin, but it could be more clearly established how the ability to visualize these structures allowed them to address their aims. More background on what was previously known about ER organization in M-phase and the role of ataxin proteins specifically may help provide more continuity.

Reviewer #3 (Public Review):

Summary:

This study by Beath et al. investigated the mechanisms by which sperm DNA is excluded from the meiotic spindle after fertilization. Time-lapse imaging revealed that sperm DNA is surrounded by paternal mitochondria and maternal ER that is permeable to proteins. By increasing cytoplasmic streaming using kinesin-13 or katanin RNAi, the authors demonstrated that limiting cytoplasmic streaming in the embryo is an important step that prevents the capture of sperm DNA by the oocyte meiotic spindle. Further experiments showed that the Ataxin-2 protein is required to hold paternal mitochondria together and close to the sperm DNA. Finally, double depletion of kinesin-13 and Ataxin-2 suggested an increased risk of meiotic spindle capture of sperm DNA.

Overall, this is an interesting finding that could provide a new understanding of how meiotic spindle capture of sperm DNA and its accidental expulsion into the polar body is prevented. However, some conceptual gaps need to be addressed and further experiments and improved data analyses would strengthen the paper.

• It would be helpful if the authors could discuss in good detail how they think maternal ER surrounds the sperm DNA and why is it not disrupted following Ataxin disruption.

• Since important phenotypes revealed in RNAi experiments (e.g. kinesin-13 and ataxin-2 double depletion) are not very robust, the authors should consider toning down their conclusions and revising some of their section headings. I appreciate that they are upfront about some limitations, but they do nonetheless make strong concluding sentences.

• The discussion section could be improved further to present the authors' findings in the larger context of current knowledge in the field.

• The authors previously demonstrated that F-actin prevents meiotic spindle capture of sperm DNA in this system. However, the current manuscript does not discuss how the katanin, kinesin-13 and Ataxin-2 mechanisms could work together with previously established functions of F-actin in this process.

• How can the authors exclude off-target effects in their RNAi depletion experiments? Can kinesin-13, katanin, and Ataxin phenotypes be rescued for instance?

• How are the authors able to determine if the paternal genome was actually captured by the spindle? Does lack of movement definitively suggest capture without using a spindle marker?

Joint Public Review:

Summary:

The study identified biallelic variants of DNAH3 in four unrelated Han Chinese infertile men through whole-exome sequencing, which contributes to abnormal sperm flagellar morphology and ultrastructure. To investigate the importance of DNAH3 in male infertility, the authors generated crispant DNAH3 knockout (KO) male mice. They observed that KO mice are also infertile, showing a severe reduction in sperm movement with abnormal IDA (inner dynein arms) and mitochondrion structure. Moreover, nonfunctional DNAH3 expression decreased the expression of IDA-associated proteins in the spermatozoa of patients and KO mice, which are involved in the disruption of sperm motility. Interestingly, the infertility of patients and KO mice was rescued by intracytoplasmic sperm injection (ICSI). Taken together, the authors propose that DNAH3 is a novel pathogenic gene for asthenoterozoospermia and male infertility.

Strengths:

This work investigates the role of DNAH3 in sperm mobility and male infertility and utilised gold-standard molecular biology techniques, showing strong evidence of its role in male infertility. All aspects of the study design and methods are well described and appropriate to address the main question of the manuscript. The conclusions drawn are consistent with the analyses conducted and supported by the data.

Weaknesses:

(1) The manuscript lacks a comparison with previous studies on DNAH3 in the Discussion section.

(2) The variants of DNAH3 in four infertile men were identified through whole-exome sequencing. Providing an overview of the WES data would be beneficial to offer additional insights into whether other variants may contribute the infertility. This could also help explain why ICSI only works for two out of four patients with DNAH3 variants.

(3) Quantification of images would help substantiate the conclusions, particularly in Figures 2, 3, 4, and 6. Improved images in Figures 3A, 4B, and 4C, would help increase confidence in the claims made.

Reviewer #1 (Public Review):

The goal of Knudsen-Palmer et al. was to define a biological set of rules that dictate the differential RNAi-mediated silencing of distinct target genes, motivated by facilitating the long-term development of effective RNAi-based drugs/therapeutics. To achieve this, the authors use a combination of computational modeling and RNAi function assays to reveal several criteria for effective RNAi-mediated silencing. This work provides insights into how (1) cis-regulatory elements influence the RNAi-mediated regulation of genes; (2) it is determined that genes can "recover" from RNAi-silencing signals in an animal; and 3) pUGylation occurs exclusively downstream of the dsRNA trigger sequence, suggesting 3º siRNAs are not produced. In addition, the authors show that the speed at which RNAi-silencing is triggered does not correlate with the longevity of the silencing. These insights are significant because they suggest that if we understand the rules by which RNAi pathways effectively silence genes with different transcription/processing levels then we can design more effective synthetic RNAi-based therapeutics targeting endogenous genes. The conclusions of this study are mostly supported by the data, but there are some aspects that need to be clarified.

(1) The methods do not describe the "aged RNAi plates feeding assay" in Figure 2E. The figure legend states that "aged RNAi plates" were used to trigger weaker RNAi, but the detail explaining the experiment is insufficient. How aged is aged? If the goal was to effectively reduce the dsRNA load available to the animals, why not quantitatively titrate the dsRNA provided? Were worms previously fed on the plates, or was simply a lawn of bacteria grown until presumably the IPTG on the plate was exhausted?

(2) Is the data presented in Figure 2F completed using the "aged RNAi plates" to achieve the partial silencing of dpy-7 observed? Clarification of this point would be helpful.

(3) Throughout the manuscript the authors refer to "non-dividing cells" when discussing animals' ability to recover from RNA silencing. It is not clear what the authors specifically mean with the phrase "non-dividing cells", but as this is referred to in one of their major findings, it should be clarified. Do they mean the cells are somatic cells in aged animals, thus if they are "non-dividing" the siRNA pools within the cells cannot be diluted by cell division? Based on the methods, the animals of RNAi assays were L4/Young adults that were scored over 8 days after the initial pulse of dsRNA feeding. If this is the case, wouldn't these animals be growing into gravid adults after the feeding, and thus have dividing cells as they grew?

(4) What are the typical expression levels/turnover of unc-22 and bli-1? Based on the results from the altered cis-regulatory regions of bli-1 and unc-22 in Figure 5, it seems like the transcription/turnover rates of each of these genes could also be used as a proof of principle for testing the model proposed in Figure 4. The strength of the model would be further increased if the RNAi sensitivity of unc-22 reflects differences in its transcription/turnover rates compared to bli-1.

Reviewer #2 (Public Review):

Summary:

This manuscript by Knudsen-Palmer et al. describes and models the contribution of MUT-16 and RDE-10 in the silencing through RNAi by the Argonaute protein NRDE-3 or others. The authors show that MUT-16 and RDE-10 constitute an intersecting network that can be redundant or not depending on the gene being targeted by RNAi. In addition, the authors provide evidence that increasing dsRNA processing can compensate for NRDE-3 mutants. Overall, the authors provide convincing evidence to understand the factors involved in RNAi in C. elegans by using a genetic approach.

Major Strengths:

The author's work presents a compelling case for understanding the intricacies of RNA interference (RNAi) within the model organism Caenorhabditis elegans through a meticulous genetic approach. By harnessing genetic manipulation, they delve into the role of MUT-16 and RDE-10 in RNAi, offering a nuanced understanding of the molecular mechanisms at play in two independent case study targets (unc-22 and bli-1).

Major Weaknesses:

(1) It is unclear how the molecular mechanisms of amplification are different under the MUT-16 and RDE-10 branches of the regulatory pathway, since they are clearly distinct proteins structurally. It would be interesting to do some small-RNA-seq of products generated from unc-22 and bli-1, on wild-type conditions and some of the mutants studied (eg. mut-16, rde-10 and mut-16 + rde-10). That would provide some insights into whether the products of the 2 amplifications are the same in all conditions, just changing in abundance, or whether they are distinct in sequence patterns.

(2) In the same line, Figure 5 aims to provide insights into the sequence determinants that influence the RNAi of bli-1. It is unclear whether the changes in transcript stability dictated by the 3'UTR are the sole factor governing the preference for the MUT-16 and RDE-10 branches of the regulatory pathway. In line with the mutant jam297, it might be interesting to test whether factors like codon optimality, splicing, ... of the ORF region upstream from bli-1-dsRNA can affect its sensitivity to the MUT-16 and RDE-10 branches of the regulatory pathway.

Reviewer #1 (Public Review):

Summary:

Clostridium thermocellum serves as a model for consolidated bioprocess (CBP) in lignocellulosic ethanol production, but yet faces limitations in solid contents and ethanol titers achieved by engineered strains thus far. The primary ethanol production pathway involves the enzyme aldehyde-alcohol dehydrogenase (AdhE), which forms long oligomeric structures known as spirosomes, previously characterized via the 3.5 Å resolution E. coli AdhE structure using single-particle cryo-EM. The present study describes the cryo-EM structure of the C. thermocellum ortholog, sharing 62% sequence identity with E. coli AdhE, resolved at 3.28 Å resolution. Detailed comparative structural analysis, including the Vibrio cholerae AdhE structure, was conducted. Integrating cryo-EM data with molecular dynamics simulations indicated that the aldehyde intermediate resides longer in the channel of the extended form, supporting the hypothesis that the extended spirosome represents the active form of AdhE.

Strengths:

The study conducts a comprehensive structural comparative analysis of oligomerization interfaces and the acetaldehyde channel across compact and extended conformations. Structural and computational results suggest the extended spirosome as the most likely active state of AdhE.

Weaknesses:

The overall resolution of the C. thermocellum structure is similar to the E. coli ortholog, which shares 62% sequence identity, and the oligomerization interfaces and the acetaldehyde channel were previously described.

Reviewer #2 (Public Review):

Summary:

The manuscript by Ziegler et al, entitled 'Structural characterization and dynamics of AdhE ultrastructure from Clostridium thermocellum: A containment strategy for toxic intermediates?" presents the atomic resolution cryo-EM structure of C. thermocellum AdhE showing that it show dominantly an extended form while E.coli AdhE shows dominantly a compact form. With comparative analysis of their C. thermocellum structure and the previous E.coli AdhE structure, they tried to reveal the mechanism by which C.thermocellum and E.coli show different dominant conformations. In addition, they also analyzed the substrate channel by comparative and computational approaches. Lastly, their computational analysis using CryoDRGN reveals conformational heterogeneity in the sample. Although this manuscript suggests a potential mechanism of the different features of AdhEs, this manuscript is very descriptive and does not provide sufficient data to support the authors' conclusions, which may be due to the lack of experimental data to support their findings from the computational analysis.

Strengths:

This manuscript provides the first C. thermocellum (Ct) AdhE structure and comparatively analyzed this structure with E.coli AdhE.

Weaknesses:

Their main conclusions obtained mostly by computational and comparative analysis are not supported by experimental data.

Reviewer #3 (Public Review):

This study describes the first structure of Gram-positive bacterial AdhE spirosomes that are in a native extended conformation. All the previous structures of AdhE spirosomes obtained come from Gram-negative bacterial species with native compact spirosomes (E. coli, V. cholerae). In E. coli, AdhE spirosomes can be found in two different conformational states, compact and extended, depending on the substrates and cofactors they are bound to.

The high-resolution cryoEM structure of the extended C. thermocellum AdhE spirosomes produced in E. coli in an apo state (without any substrate or cofactors) is compared to the E. coli extended and compact AdhE spirosomes structures previously published. The authors have modeled (in Swiss-Model) the structure of compact C. thermocellum AdhE spirosomes, using E. coli compact AdhE spirosome conformation as a template, and performed molecular dynamics simulations. They have identified a channel in which the toxic reaction intermediate aldehyde could transit from the aldehyde dehydrogenase active site to the alcohol dehydrogenase active site, in an analogous manner to E. coli spirosomes. These findings are in line with the hypothesis that the extended spirosomes could correspond to the active form of the enzyme.

In this work, the authors speculate that the C. thermocellum AdhE spirosomes could switch from the native extended conformation to a compact conformation, in a way that is inverse of E. coli spirosomes. Although attractive, this hypothesis is not supported by the literature. Amazingly, in some Gram-positive bacterial species (S. pneumoniae, S. sanguinis or C. difficile...), AdhE spirosomes are natively extended and have never been observed in a compact conformation. On the opposite, E. coli (and other Gram-negative bacteria) native AdhE spirosomes are compact and are able to switch to an extended conformation in the presence of the cofactors (NAD+, coA, and iron). The data presented as they are now are not convincing to confirm the existence of C. thermocellum AdhE spirosomes in a compact conformation.

Reviewer #1 (Public Review):

In their paper, Kang et al. investigate rigidity sensing in amoeboid cells, showing that, despite their lack of proper focal adhesions, amoeboid migration of single cells is impacted by substrate rigidity. In fact, many different amoeboid cell types can durotax, meaning that they preferentially move towards the stiffer side of a rigidity gradient.

The authors observed that NMIIA is required for durotaxis and, building on this observation, they generated a model to explain how durotaxis could be achieved in the absence of strong adhesions. According to the model, substrate stiffness alters the diffusion rate of NMAII, with softer substrates allowing for faster diffusion. This allows for NMAII accumulation at the back, which, in turn, results in durotaxis.

The experiments support the main message of the paper regarding durotaxis by amoeboid cells. In my opinion, a few clarifications on the mechanism proposed to explain this phenomenon could strengthen this research:

(1) According to your model, the rear end of the cell, which is in contact with softer substrates, will have slower diffusion rates of MNIIA. Does this mean that bigger cells will durotax better than smaller cells because the stiffness difference between front and rear is higher? Is it conceivable to attenuate the slope of the durotactic gradient to a degree where smaller cells lose their ability to durotact, while longer cells retain their capacity for directional movement?

(2) Where did you place the threshold for soft, middle, and stiff regions (Figure 6)? Is it possible that you only have a linear rigidity gradient in the center of your gel and the more you approach the borders, the flatter the gradient gets? In this case, cells would migrate randomly on uniform substrates. Did you perform AFM over the whole length of the gel or just in the central part?

(3) In which region (soft, middle, stiff) did you perform all the cell tracking of the previous figures?

(4) What is the level of confinement experienced by the cells? Is it possible that cells on the soft side of the gels experience less confinement due to a "spring effect" whereby the coverslips descending onto the cells might exert diminished pressure because the soft hydrogels act as buffers, akin to springs? If this were the case, cells could migrate following a confinement gradient.

Reviewer #2 (Public Review):

Summary:<br /> The authors developed an imaging-based device that provides both spatial confinement and stiffness gradient to investigate if and how amoeboid cells, including T cells, neutrophils, and Dictyostelium, can durotax. Furthermore, the authors showed that the mechanism for the directional migration of T cells and neutrophils depends on non-muscle myosin IIA (NMIIA) polarized towards the soft-matrix-side. Finally, they developed a mathematical model of an active gel that captures the behavior of the cells described in vitro.

Strengths:

The topic is intriguing as durotaxis is essentially thought to be a direct consequence of mechanosensing at focal adhesions. To the best of my knowledge, this is the first report on amoeboid cells that do not depend on FAs to exert durotaxis. The authors developed an imaging-based durotaxis device that provides both spatial confinement and stiffness gradient and they also utilized several techniques such as quantitative fluorescent speckle microscopy and expansion microscopy. The results of this study have well-designed control experiments and are therefore convincing.

Weaknesses:

Overall this study is well performed but there are still some minor issues I recommend the authors address:

(1) When using NMIIA/NMIIB knockdown cell lines to distinguish the role of NMIIA and NMIIB in amoeboid durotaxis, it would be better if the authors took compensatory effects into account.<br /> (2) The expansion microscopy assay is not clearly described and some details are missed such as how the assay is performed on cells under confinement.<br /> (3) In this study, an active gel model was employed to capture experimental observations. Previously, some active nematic models were also considered to describe cell migration, which is controlled by filament contraction. I suggest the authors provide a short discussion on the comparison between the present theory and those prior models.<br /> (4) In the present model, actin flow contributes to cell migration while myosin distribution determines cell polarity. How does this model couple actin and myosin together?

Reviewer #1 (Public Review):

Summary:

The authors address cellular mechanisms underlying the early stages of Sjogren's syndrome, using a mouse model in which 5,6-Dimethyl-9-oxo-9H-xanthene-4-acetic acid (DMXAA) is applied to stimulate the interferon gene (STING) pathway. They show that, in this model, salivary secretion in response to neural stimulation is greatly reduced, even though individual secretory cell calcium responses were enhanced. They attribute the secretion defect to reduced activation of Ca2+ -activated Cl- channels (TMEM16a), due to an increased distance between Ca2+ release channels (IP3 receptors) and TMEM16a which is expected to reduce the [Ca2+] sensed by TMEM16a. A variety of disruptions in mitochondria were also observed after DMXAA treatment, including reduced abundance, altered morphology, depolarization, and reduced oxygen consumption rate. The results of this study shed new light on some of the early events leading to the loss of secretory function in Sjogren's syndrome, at a time before inflammatory responses cause the death of secretory cells.

Strengths:

Two-photon microscopy enabled Ca2+ measurements in the salivary glands of intact animals in response to physiological stimuli (nerve stimulation). This approach has been shown previously by the authors as necessary to preserve the normal spatiotemporal organization of calcium signals that lead to secretion under physiological conditions.

Superresolution (STED) microscopy allowed precise measurements of the spacing of IP3R and TMEM16a and the cell membranes that would otherwise be prevented by the diffraction limit. The measured increase of distance (from 84 to 155 nm) would be expected to reduce [Ca2+] at the TMEM16a channel.

The authors effectively ruled out a variety of alternative explanations for reduced secretion, including changes in AQP5 expression, TMEM16a expression, localization, and Ca2+ sensitivity as indicated by Cl- current in response to defined levels of Ca2+.

Weaknesses:

While the Ca2+ distribution in the cells was less restricted to the apical region in DMXAA-treated cells, it is not clear that this is relevant to the reduced activation of TMEM16a. The way in which the change in Ca2+ distribution is quantified (apical/basal ratio) is not informative, as this is not what activates TMEM16a, but rather the local [Ca2+] at the channel.

Despite the decreased level of secretion, Ca2+ signal amplitudes were higher in the treated cells, raising the question of how much this might compensate for the increased distance between IP3R and TMEM16a. The authors assume that the increased separation of IP3R and TMEM16a (and the resulting decrease in local [Ca2+]) outweighed the effect of higher global [Ca2+], but this important point was not addressed.

The description of mitochondrial changes in abundance, morphology, membrane potential, and oxygen consumption rate were not well integrated into the rest of the paper. While they may be a facet of the multiple effects of STING activation and may occur during Sjogren's syndrome, their possible role in reducing secretion was not examined. As it stands, the mitochondrial results are largely descriptive and there is no evidence here that they contribute to the secretory phenotype.

Reviewer #2 (Public Review):

Summary:

This manuscript describes a very eloquent study of disrupted stimulus-secretion coupling in salivary acinar cells in the early stages of an animal model (DMXAA) of Sjogren's syndrome (SS). The study utilizes a range of technically innovative in vivo imaging of Ca signaling, in vivo salivary secretion, patch clamp electrophysiology to assess TMEM16a activity, immunofluorescence and electron microscopy, and a range of morphological and functional assays of mitochondrial function. Results show that in mice with DMXAA-induced Sjogren's syndrome, there was a reduced nerve-stimulation-induced salivary secretion, yet surprisingly the nerve-stimulation-induced Ca signaling was enhanced. There was also a reduced carbachol (CCh)-induced activation of TMEM16a currents in acinar cells from DMXAA-induced SS mice, whereas the intrinsic Ca-activated TMEM16a currents were unaltered, further supporting that stimulus-secretion coupling was impaired. Consistent with this, high-resolution STED microscopy revealed that there was a loss of close physical spatial coupling between IP3Rs and TMEM16a, which may contribute to the impaired stimulus-secretion coupling. Furthermore, the authors show that the mitochondria were both morphologically and functionally impaired, suggesting that bioenergetics may be impaired in salivary acinar cells of DMXAA-induced SS mice.

Strengths:

Overall, this is an outstanding manuscript, that will have a huge impact on the field. The manuscript is beautifully well-written with a very clear narrative. The experiments are technically innovative, very well executed, and with a logical design The data are very well presented and appropriately analyzed and interpreted.

Reviewer #3 (Public Review):

Summary:

The pathomechanism underlying Sjögren's syndrome (SS) remains elusive. The authors have studied if altered calcium signaling might be a factor in SS development in a commonly used mouse model. They provide a thorough and straightforward characterization of the salivary gland fluid secretion, cytoplasmic calcium signaling, mitochondrial morphology, and respiration. A special strength of the study is the spectacular in vivo imaging, very few if any groups could have succeeded with the studies. The authors show that the cytoplasmic calcium signaling is upregulated in the SS model and the Ca2+ regulated Cl- channels are normally localized and function, but still fluid secretion is suppressed. They also find altered localization of the IP3R and speculate about lesser exposure of Cl- channels to high local [Ca2+]. In addition, they describe changes in mitochondrial morphology and function that might also contribute to the attenuated secretory response. Although the exact contribution of calcium and mitochondria to secretory dysfunction remains to be determined, the results seem to be useful for a range of scientists.

Specific points to consider:

(1) Are all the effects of DMXAA mediated through STING? DMXAA has been reported to inhibit NAD(P)H quinone oxidoreductase (NQO1) PMID: 10423172, which might be relevant both for the calcium and mitochondrial phenotypes. I would recommend that the authors either test the dependency of the DMXAA effects on STING or avoid attributing all effects of DMXAA to STING.

(2) "mitochondrial membrane potential (ΔΨm), the driving force of ATP production" the driving force is the electrochemical H+ gradient.

(3) ΔΨm is assessed as decreased in the DMXAA model without a change in TMRE steady state. Higher post-uncoupler fluorescence caused a lesser uncoupler-sensitive pool. This is not a very common observation. Was the autofluorescence of the DMXAA-treated cells higher in the red channel?

(4) The EM study indicated ER structure disruption. Are there any clues to the contribution of this to the augmented agonist/electrical stimulation-induced calcium signaling and decreased fluid secretion?

Reviewer #1 (Public Review):

Summary:

The current manuscript provides an extensive in vivo analysis of two guidance pathways identifying multiple mechanisms that shape the bifurcation of DRG axons when forming the dorsal funiculus in the DREZ.

Strengths:

Multiple mouse mutant lines were used, together with complementary techniques; the results are very clear and compelling.<br /> The findings are very significant and clearly move forward our understanding of the regulation of axonal development at the DREZ.

Weaknesses:

No major weaknesses were found. As it is I have no recommendations that would increase the clarity or quality of the manuscript.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors conduct a detailed analysis of the molecular cues that control guidance of bifurcated dorsal root ganglion axons in a key region of the spinal cord called the dorsal funiculus. This is a specific case of axon guidance that occurs in a precise way. The authors knew that Slit was important but many axons still target correctly in Slit knockouts, suggesting a role for other guidance factors. Netrin1 is also expressed in this region, so they looked at netrin mutants. The authors found axons outside the DREZ in the Ntn1 mutants, and they show by single neuron genetic labeling that many of these come from DRG neurons. Quantified axonal tracing studies in Slit1/2, Ntn1, or triple mutant embryos supports the idea that Slit and Ntr1 have distinct functions in guidance and that the effect of their loss is additive. Interestingly none of these knockouts affect bifurcation itself but rather the guidance of one or both of the bifurcated axon terminals. Knockout of the Slit receptors (Robo1/2) or the Netrin 1 receptor (DCC) in embryos causes similar guidance defects to loss of the ligands, providing an additional confirmation of the requirement for both guidance pathways. This study expands understanding of the role of the axon guidance factors Ntr1/DCC and Slit/Robo in a specific axon guidance decision. The strength of the study is the careful axonal labeling and quantification, which allows the authors to establish precise consequences of the loss of each guidance factor or receptor.

Reviewer #3 (Public Review):

Summary:

In this paper, Curran et al investigate the role of Ntn, Slit1 and Slit 2 in axon patterning of DRG neurons. The paper uses mouse genetics to perturb each guidance molecule and its corresponding receptor. Cre-based approaches and immunostaining of DRG neurons are used to assess the phenotypes. Overall, the study uses the strength of mouse genetics and imaging to reveal new genetic modifiers of DRG axons. The conclusions of the experiments match the presented results. The paper is an important contribution to the field, as evidence that dorsal funiculus formation is impacted by Ntn and Slit signaling. The paper clearly demonstrates molecules that impact the patterning of the dorsal funiculus formation, which can provide a foundation for future studies on the specific steps in that patterning that require the studied molecules.

Strengths:

The manuscript uses the advantage of mouse genetics to investigate axon patterning of DRG neurons. The work does a great job of assessing individual phenotypes in single and double mutants. This reveals an intriguing cooperative and independent function of Ntn, Slit1 and Slit2 in DRG axon patterning. The sophisticated triple mutant analysis is lauded and provides important insight.

Weaknesses:

Overall, the manuscript is sound in technique and analysis. While not a weakness, the paper provides the foundation for future studies that investigate the specific molecular mechanisms of each step in the patterning of the dorsal funiculus.

Reviewer #2 (Public Review):

The authors sought to establish the role played by N343 glycosylation on the SARS-CoV-2 S receptor binding domain structure and binding affinity to the human host receptor ACE2 across several variants of concern. The work includes both computational analysis in the form of molecular dynamics simulations and experimental binding assays between the RBD and ganglioside receptors.

The work extensively samples the conformational space of the RBD beginning with atomic coordinates representing both the bound and unbound states and computes molecular dynamics trajectories until equilibrium is achieved with and without removing N343 glycosylation. Through comparison of these simulated structures, the authors are able to demonstrate that N343 glycosylation stabilizes the RBD. Prior work had demonstrated that glycosylation at this site plays an important role in shielding the RBD core and in this work the authors demonstrate that removal of this glycan can trigger a conformational change to reduce water access to the core without it. This response is variant dependent and variants containing interface substitutions which increase RBD stability, including Delta substitution L452R, do not experience the same conformational change when the glycan is removed. The authors also explore structures corresponding to Alpha and Beta in which no structure-reinforcing substitutions were identified and two Omicron variants in which other substitutions with an analogous effect to L452R are present.

The authors experimentally assessed these inferred structural changes by measuring the binding affinity of the RBD for the oligosaccharides of the monosialylated gangliosides GM1os and GM2os with and without the glycan at N343. While GM1os and GM2os binding is influenced by additional factors in the Beta and Omicron variants, the comparison between Delta and Wuhan-hu-1 is clear: removal of the glycan abrogated binding for Wuhan-hu-1 and minimally affected Delta as predicted by structural simulations.

In summary, these findings suggest, in the words of the authors, that SARS-CoV-2 has evolved to render the N-glycosylation site at N343 "structurally dispensable". This study emphasizes how glycosylation impacts both viral immune evasion and structural stability which may in turn impact receptor binding affinity and infectivity. Mutations which stabilize the antigen may relax the structural constraints on glycosylation opening up avenues for subsequent mutations which remove glycans and improve immune evasion. This interplay between immune evasion and receptor stability may support complex epistatic interactions which may in turn substantially expand the predicted mutational repertoire of the virus relative to expectations which do not take into account glycosylation.

Reviewer #3 (Public Review):

Summary:

The receptor binding domain of SARS-Cov-2 spike protein contains two N-glycans which have been conserved the variants observed in these last 4 years. Through the use of extensive molecular dynamics, the authors demonstrate that even if glycosylation is conserved, the stabilization role of glycans at N343 differs among the strains. They also investigate the effect of this glycosylation on the binding of RBD towards sialylated gangliosides, also as a function of evolution

Strengths:

The molecular dynamics characterization is well performed and demonstrates differences on the effect of glycosylation as a factor of evolution. The binding of different strains to human gangliosides shows variations of strong interest. Analyzing structure function of glycans on SARS-Cov-2 surface as a function of evolution is important for the surveillance of novel variants, since it can influence their virulence.

Weaknesses:

The revised article does not hold significant weaknesses

Reviewer #1 (Public Review):

Summary:

The study by Seo et al highlights knowledge gaps regarding the role of cerebellar complex spike (CS) activity during different phases of learning related to optokinetic reflex (OKR) in mice. The novelty of the approach is twofold: first, specifically perturbing the activity of climbing fibers (CFs) in the flocculus (as opposed to disrupting communication between the inferior olive (IO) and its cerebellar targets globally); and second, examining whether disruption of the CS activity during the putative "consolidation phase" following training affects OKR performance.

The first part of the results provides adequate evidence supporting the notion that optogenetic disruption of normal CF-Purkinje neuron (PN) signaling results in the degradation of OKR performance. As no effects are seen in OKR performance in animals subjected to optogenetic irradiation during the memory consolidation or retrieval phases, the authors conclude that CF function is not essential beyond memory acquisition. However, the manuscript does not provide a sufficiently solid demonstration that their long-term activity manipulation of CF activity is effective, thus undermining the confidence of the conclusions.

Strengths:

The main strength of the work is the aim to examine the specific involvement of the CF activity in the flocculus during distinct phases of learning. This is a challenging goal, due to the technical challenges related to the anatomical location of the flocculus as well as the IO. These obstacles are counterbalanced by the use of a well-established and easy-to-analyse behavioral model (OKR), that can lead to fundamental insights regarding the long-term cerebellar learning process.

Weaknesses:

The impact of the work is diminshed by several methodological shortcomings.

Most importantly, the key finding that prolonged optogenetic inhibition of CFs (for 30 min to 6 hours after the training period) must be complemented by the demonstration that the manipulation maintains its efficacy. In its current form, the authors only show inhibition by short-term optogenetic irradiation in the context of electrical-stimulation-evoked CSs in an ex vivo preparation. As the inhibitory effect of even the eNpHR3.0 is greatly diminished during seconds-long stimulations (especially when using the yellow laser as is done in this work (see Zhang, Chuanqiang, et al. "Optimized photo-stimulation of halorhodopsin for long-term neuronal inhibition." BMC biology 17.1 (2019): 1-17. ), we remain skeptical of the extent of inhibition during the long manipulations. In short, without a demonstration of effective inhibition throughout the putative consolidation phase (for example by showing a significant decrease in CS frequency throughout the irradiation period), the main claim of the manuscript of phase-specific involvement of CF activity in OKR learning can not be considered to be based on evidence.

Second, the choice of viral targeting strategy leaves gaps in the argument for CF-specific mechanisms. CaMKII promoters are not selective for the IO neurons, and even the most precise viral injections always lead to the transfection of neurons in the surrounding brainstem, many of which project to the cerebellar cortex in the form of mossy fibers (MF). Figure 1Bii shows sparsely-labelled CFs in the flocculus, but possibly also MFs. While obtaining homogenous and strong labeling in all floccular CFs might be impossible, at the very least the authors should demonstrate that their optogenetic manipulation does not affect simple spiking in PNs.

Finally, while the paper explicitly focuses on the effects of CF-evoked complex spikes in the PNs and not, for example, on those mediated by molecular layer interneurons or via direct interaction of the CF with vestibular nuclear neurons, it would be best if these other dimensions of CF involvement in cerebellar learning were candidly discussed.

Reviewer #2 (Public Review):

Summary:

The authors aimed to explore the role of climbing fibers (CFs) in cerebellar learning, with a focus on optokinetic reflex (OKR) adaptation. Their goal was to understand how CF activity influences memory acquisition, memory consolidation, and memory retrieval by optogenetically suppressing CF inputs at various stages of the learning process.

Strengths:

The study addresses a significant question in the cerebellar field by focusing on the specific role of CFs in adaptive learning. The authors use optogenetic tools to manipulate CF activity. This provides a direct method to test the causal relationship between CF activity and learning outcomes.

Weaknesses:

Despite shedding light on the potential role of CFs in cerebellar learning, the study is hampered by significant methodological issues that question the validity of its conclusions. The absence of detailed evidence on the effectiveness of CF suppression and concerns over tissue damage from optogenetic stimulation weakens the argument that CFs are not essential for memory consolidation. These challenges make it difficult to confirm whether the study's objectives were fully met or if the findings conclusively support the authors' claims. The research commendably attempts to unravel the temporal involvement of CFs in learning but also underscores the difficulties in pinpointing specific neural mechanisms that underlie the phases of learning. Addressing these methodological issues, investigating other signals that might instruct consolidation, and understanding CFs' broader impact on various learning behaviors are crucial steps for future studies.

Reviewer #1 (Public Review):

Summary:

In this paper, the authors used target agnostic MBC sorting and activation methods to identify B cells and antibodies against sexual stages of Plasmodium falciparum. While they isolated some Mabs against PFs48/45 and PFs230, two well-known candidates for "transmission blocking" vaccines, these antibodies' efficacies, as measured by TRA, did not perform as well as other known antibodies. They also isolated one cross-reactive mAb to proteins containing glutamic acid-rich repetitive elements, that express at different stages of the parasite life cycle. They then determined the structure of the Fab with the highest protein binder they could determine through protein microarray, RESA, and observed homotypic interactions.

Strengths:

- Target agnostic B cell isolation (although not a novel methodology).<br /> - New cross-reactive antibody and mechanism (homotypic interactions) as demonstrated by structural data and other biophysical data.

Weaknesses:

The paper lacks clarity at times and could benefit from more transparency (showing all the data) and explanations.<br /> In particular:<br /> -define SIFA<br /> -define TRAbs<br /> -it is not possible to read the Supplementary Figure 6B and C panels.

Reviewer #2 (Public Review):

This manuscript by Amen, Yoo, Fabra-Garcia et al describes a human monoclonal antibody B1E11K, targeting EENV repeats which are present in parasite antigens such as Pfs230, RESAs, and 11.1. The authors isolated B1E11K using an initial target agnostic approach for antibodies that would bind gamete/gametocyte lysate which they made 14 mAbs. Following a suite of highly appropriate characterization methods from Western blotting of recombinant proteins to native parasite material, use of knockout lines to validate specificity, ITC, peptide mapping, SEC-MALS, negative stain EM, and crystallography, the authors have built a compelling case that B1E11K does indeed bind EENV repeats. In addition, using X-ray crystallography they show that two B1E11K Fabs bind to a 16 aa RESA repeat in a head-to-head conformation using homotypic interactions and provide a separate example from CSP, of affinity-matured homotypic interactions.

There are some minor comments and considerations identified by this reviewer, These include that one of the main conclusions in the paper is the binding of B1E11K to RESAs which are blood stage antigens that are exported to the infected parasite surface. It would have been interesting if immunofluorescence assays with B1E11K mAb were performed with blood-stage parasites to understand its cellular localization in those stages.

Reviewer #3 (Public Review):

The manuscript from Amen et al reports the isolation and characterization of human antibodies that recognize proteins expressed at different sexual stages of Plasmodium falciparum. The isolation approach was antigen agnostic and based on the sorting, activation, and screening of memory B cells from a donor whose serum displays high transmission-reducing activity. From this effort, 14 antibodies were produced and further characterized. The antibodies displayed a range of transmission-reducing activities and recognized different Pf sexual stage proteins. However, none of these antibodies had higher TRA than previously described antibodies.

The authors then performed further characterization of antibody B1E11K, which was unique in that it recognized multiple proteins expressed during sexual and asexual stages. Using protein microarrays, B1E11K was shown to recognize glutamate-rich repeats, following an EE-XX-EE pattern. An impressive set of biophysical experiments was performed to extensively characterize the interactions of B1E11K with various repeat motifs and lengths. Ultimately, the authors succeeded in determining a 2.6 A resolution crystal structure of B1E11K bound to a 16AA repeat-containing peptide. Excitingly, the structure revealed that two Fabs bound simultaneously to the peptide and made homotypic antibody-antibody contacts. This had only previously been observed with antibodies directed against CSP repeats.

Overall I found the manuscript to be very well written, although there are some sections that are heavy on field-specific jargon and abbreviations that make reading unnecessarily difficult. For instance, 'SIFA' is never defined. Strengths of the manuscript include the target-agnostic screening approach and the thorough characterization of antibodies. The demonstration that B1E11K is cross-reactive to multiple proteins containing glutamate-rich repeats, and that the antibody recognizes the repeats via homotypic interactions, similar to what has been observed for CSP repeat-directed antibodies, should be of interest to many in the field.

Reviewer #1 (Public Review):

Throughout the paper, the authors do a fantastic job of highlighting caveats in their approach, from image acquisition to analysis. Despite this, some conclusions and viewpoints portrayed in this study do not appear well-supported by the provided data. Furthermore, there are a few technical points regarding the analysis that should be addressed.

(1) Analysis of signaling traces

- Relevance of "modeled signaling level": It is not clear whether this added complexity and potential for error (below) provides benefits over a more simple analysis such as taking the derivative (shown in Figure 3C). Could the authors provide evidence for the benefits? For example, does the "maximal response" given a simpler metric correlate less well with cell fate than that calculated from the fitted response?

- Assumptions for "modeled signaling level": According to equation (1) Kaede levels are monotonically increasing. This is assumed given the stability of the fluorescent protein. However, this only holds for the "totally produced Kaede/fluorescence". Other metrics such as mean fluorescence can very well decrease over time due to growth and division. Does "intensity" mean total fluorescence? Visual inspection of the traces shown in Figure 2 suggests that "fluorescence intensity" can decrease. What does this mean for the inferred traces?

- Estimation of Kaede reporter half-live: It is not clear how the mRNA stability of Kaede is estimated. It sounds like it was just assessed visually, which seems not entirely appropriate given the quantitative aspects of the rest of the study. Also, given that Shh signaling was inhibited on the level of Smoothened, it is not obvious how the dynamics of signaling shutdown affect the estimate. Most results in Figure 7 seem to be quite robust to the estimate of the half-live. That they are, might suggest that the whole analysis is unnecessary in the first place. However, not all are. Thus, it would be important to make this estimate more quantitative.

(2) Assignment of fates and correlations

- Error estimate for cell-type assignment: Trying to correlate signaling traces to cell fate decisions requires accurate cell fate assignment post-tracking. The provided protocol suggests a rather manual, expert-directed process of making those decisions. Can the authors provide any error-bound on those decisions, for example comparing the results obtained by two experts or something comparable? I am particularly concerned about the results regarding the higher degree of variability in the correlation between signaling dynamics and cell fate in the posterior neural tube. Here, the expression of Olig2 does not seem to segregate between different assigned fates, while it does so nicely in the anterior neural tube. This would suggest to me that cells in the posterior neural tube might not yet be fully committed to a fate or that there could be a relatively high error rate in assigning fates. Thus, the results could emerge from technical errors or differences in pure timing. Could the authors please comment on these possibilities?

- Clustering and fates: One approach the authors use to analyze the correlation between signaling and fate is clustering of cell traces and comparison of the fate distributions in those clusters. There is a large number of clusters with only single traces, suggesting that the data (number of traces) might not be sufficient for this analysis. Furthermore, I am skeptical about clustering cells of different anterior-posterior identities together, given potential differences in the timing of signal reception and signaling. I am not convinced that this analysis reveals enough about how signaling maps to fate given the heterogeneity in traces in large clusters and the prevalence of extremely small clusters.

- Signaling vector and hand-picked metrics: As an alternative approach, that might be better suited for their data, the authors then pick three metrics (based on their model-predicted signaling dynamics) and show that the maximal response is a very good predictor of fate for different anterior-posterior identities. Previous information-theoretic analysis of signaling dynamics has found that a whole time-vector of signaling can carry much more information than individual metrics (Selimkhanov et al, 2014, PMID: 25504722). Have the authors tried to use approaches that make use of the whole trace (such as simple classifiers (Granados et al, 2018, PMID: 29784812), or can comment on why this is not feasible for their data? The authors should at least make clear that their results present a lower bound to how accurately cells can make cell-fate decisions based on signaling dynamics.

(3) Consequences of signaling heterogeneity

The authors focus heavily on portraying that signaling dynamics are highly variable, which seems visually true at first glance. However, there is no metric used or a description given of what this actually means. Mainly, the variability seems to relate to the correlation between signaling and fate. However, given the data and analysis, I would argue that the decoding of signaling dynamics into fate is surprisingly accurate. So signaling dynamics that seem quite noisy and variable by visual inspection can actually be very well discriminated by cells, which to me appears very exciting.

Indeed, simple features of signaling traces can predict cell fate as well as position (for anterior progenitors). Given that signaling should be a function of position, it naively seems as if signaling read-out could be almost perfect. It might be interesting to plot dorsal-ventral position vs the signaling metrics, to also investigate how Shh concentration/position maps to signaling dynamics, this would give an even more comprehensive view of signal transmission.

There remains the discrepancy between signaling traces and fate in the posterior neural tube. The authors point towards differences in tissue architecture and difficulties in interpreting a "small" Shh gradient. However, the data seems consistent with differences in timing of cell-fate decisions between anterior and posterior cells. The authors show that fate does initially not correlate well with position in the posterior neural tube. So, signaling dynamics should likely also not, as they should rather be a function of position, given they are downstream of the Shh gradient. As mentioned above, not even Olig2 expression does segregate the assigned fates well. All this points towards a difference in the time of fate assignment between the anterior and posterior. Given likely delays in reporter protein production and maturation, it can thus not be expected that signaling dynamics correlate better with cell fate than the reporter "83%". Can the authors please discuss this possibility in the paper?

Thus, while this paper represents an example of what the community needs to do to gain a better understanding of robust patterning under variability, the provided data is not always sufficient to make clear conclusions regarding the functional consequences of signaling dynamics.

Reviewer #2 (Public Review):

Summary:

In this work, Xiong and colleagues examine the relationship between the profile of the morphogen Shh and the resulting cell fate decisions in the zebrafish neural tube. For this, the authors combine high-resolution live imaging of an established Shh reporter with reporter lines for the different progenitor types arising in the forming neural tube. One of the key observations in this manuscript is that, while, on average, cells respond to differences in Shh activity to adopt distinct progenitor fates, at the single cell level there is strong heterogeneity between Shh response and fate choices. Further, the authors showed that this heterogeneity was particularly prominent for the pMN fate, with similar Shh response dynamics to those observed in neighboring LFP progenitors.

Strengths:

It is important to directly correlate Shh activity with the downstream TFs marking distinct progenitor types in vivo and with single cell resolution. This additional analysis is in line with previous observations from these authors, namely in Xiong, 2013. Further, the authors show that cells in different anterior-posterior positions within the neural tube show distinct levels of heterogeneity in their response to Shh, which is a very interesting observation and merits further investigation.

Weaknesses:

This is a convincing work, however, adding a few more analyses and clarifications would, in my view, strengthen the key finding of heterogeneity between Shh response and the resulting cell fate choices.

Reviewer #1 (Public Review):

Summary:

There is a long-standing idea that choices influence evaluation: options we choose are re-evaluated to be better than they were before the choice. There has been some debate about this finding, and the authors developed several novel methods for detecting these re-evaluations in task designs where options are repeatedly presented against several alternatives. Using these novel methods the authors clearly demonstrate this re-evaluation phenomenon in several existing datasets.

Strengths:

The paper is well-written and the figures are clear. The authors provided evidence for the behaviour effect using several techniques and generated surrogate data (where the ground truth is known) to demonstrate the robustness of their methods.

Weaknesses:

The description of the results of the fMRI analysis in the text is not complete: weakening the claim that their re-evaluation algorithm better reveals neural valuation processes.

Reviewer #2 (Public Review):

Summary:

Zylberberg and colleagues show that food choice outcomes and BOLD signal in the vmPFC are better explained by algorithms that update subjective values during the sequence of choices compared to algorithms based on static values acquired before the decision phase. This study presents a valuable means of reducing the apparent stochasticity of choices in common laboratory experiment designs. The evidence supporting the claims of the authors is solid, although currently limited to choices between food items because no other goods were examined. The work will be of interest to researchers examining decision-making across various social and biological sciences.

Strengths:

The paper analyses multiple food choice datasets to check the robustness of its findings in that domain.

The paper presents simulations and robustness checks to back up its core claims.

Weaknesses:

To avoid potential misunderstandings of their work, I think it would be useful for the authors to clarify their statements and implications regarding the utility of item ratings/bids (e-values) in explaining choice behavior. Currently, the paper emphasizes that e-values have limited power to predict choices without explicitly stating the likely reason for this limitation given its own results or pointing out that this limitation is not unique to e-values and would apply to choice outcomes or any other preference elicitation measure too. The core of the paper rests on the argument that the subjective values of the food items are not stored as a relatively constant value, but instead are constructed at the time of choice based on the individual's current state. That is, a food's subjective value is a dynamic creation, and any measure of subjective value will become less accurate with time or new inputs (see Figure 3 regarding choice outcomes, for example). The e-values will change with time, choice deliberation, or other experiences to reflect the change in subjective value. Indeed, most previous studies of choice-induced preference change, including those cited in this manuscript, use multiple elicitations of e-values to detect these changes. It is important to clearly state that this paper provides no data on whether e-values are more or less limited than any other measure of eliciting subjective value. Rather, the paper shows that a static estimate of a food's subjective value at a single point in time has limited power to predict future choices. Thus, a more accurate label for the e-values would be static values because stationarity is the key assumption rather than the means by which the values are elicited or inferred.

There is a puzzling discrepancy between the fits of a DDM using e-values in Figure 1 versus Figure 5. In Figure 1, the DDM using e-values provides a rather good fit to the empirical data, while in Figure 5 its match to the same empirical data appears to be substantially worse. I suspect that this is because the value difference on the x-axis in Figure 1 is based on the e-values, while in Figure 5 it is based on the r-values from the Reval algorithm. However, the computation of the value difference measure on the two x-axes is not explicitly described in the figures or methods section and these details should be added to the manuscript. If my guess is correct, then I think it is misleading to plot the DDM fit to e-values against choice and RT curves derived from r-values. Comparing Figures 1 and 5, it seems that changing the axes creates an artificial impression that the DDM using e-values is much worse than the one fit using r-values.

Relatedly, do model comparison metrics favor a DDM using r-values over one using e-values in any of the datasets tested? Such tests, which use the full distribution of response times without dividing the continuum of decision difficulty into arbitrary hard and easy bins, would be more convincing than the tests of RT differences between the categorical divisions of hard versus easy.

Revaluation and reduction in the imprecision of subjective value representations during (or after) a choice are not mutually exclusive. The fact that applying Reval in the forward trial order leads to lower deviance than applying it in the backwards order (Figure 7) suggests that revaluation does occur. It doesn't tell us if there is also a reduction in imprecision. A comparison of backwards Reval versus no Reval would indicate whether there is a reduction in imprecision in addition to revaluation. Model comparison metrics and plots of the deviance from the logistic regression fit using e-values against backward and forward Reval models would be useful to show the relative improvement for both forms of Reval.

Did the analyses of BOLD activity shown in Figure 9 orthogonalize between the various e-value- and r-value-based regressors? I assume they were not because the idea was to let the two types of regressors compete for variance, but orthogonalization is common in fMRI analyses so it would be good to clarify that this was not used in this case. Assuming no orthogonalization, the unique variance for the r-value of the chosen option in a model that also includes the e-value of the chosen option is the delta term that distinguishes the r and e-values. The delta term is a scaled count of how often the food item was chosen and rejected in previous trials. It would be useful to know if the vmPFC BOLD activity correlates directly with this count or the entire r-value (e-value + delta). That is easily tested using two additional models that include only the r-value or only the delta term for each trial.

Please confirm that the correlation coefficients shown in Figure 11 B are autocorrelations in the MCMC chains at various lags. If this interpretation is incorrect, please give more detail on how these coefficients were computed and what they represent.

The paper presents the ceDDM as a proof-of-principle type model that can reproduce certain features of the empirical data. There are other plausible modifications to bounded evidence accumulation (BEA) models that may also reproduce these features as well or better than the ceDDM. For example, a DDM in which the starting point bias is a function of how often the two items were chosen or rejected in previous trials. My point is not that I think other BEA models would be better than the ceDDM, but rather that we don't know because the tests have not been run. Naturally, no paper can test all potential models and I am not suggesting that this paper should compare the ceDDM to other BEA processes. However, it should clearly state what we can and cannot conclude from the results it presents.

This work has important practical implications for many studies in the decision sciences that seek to understand how various factors influence choice outcomes. By better accounting for the context-specific nature of value construction, studies can gain more precise estimates of the effects of treatments of interest on decision processes. That said, there are limitations to the generalizability of these findings that should be noted.

These limitations stem from the fact that the paper only analyzes choices between food items and the outcomes of the choices are not realized until the end of the study (i.e., participants do not eat the chosen item before making the next choice). This creates at least two important limitations. First, preferences over food items may be particularly sensitive to mindsets/bodily states. We don't yet know how large the choice deltas may be for other types of goods whose value is less sensitive to satiety and other dynamic bodily states. Second, the somewhat artificial situation of making numerous choices between different pairs of items without receiving or consuming anything may eliminate potential decreases in the preference for the chosen item that would occur in the wild outside the lab setting. It seems quite probable that in many real-world decisions, the value of a chosen good is reduced in future choices because the individual does not need or want multiples of that item. Naturally, this depends on the durability of the good and the time between choices. A decrease in the value of chosen goods is still an example of dynamic value construction, but I don't see how such a decrease could be produced by the ceDDM.

Reviewer #1 (Public Review):

Summary:

Drosophila is one of the most studied model organisms to understand how neural circuits form and function to control intricate animal behaviors. The ventral nerve cord (VNC) part of the fly's CNS serves as a sensory processing and motor output center just like our spinal cord. Over the last decade, the VNC has become a fruitful platform to understand neural circuits responsible for motor behavior such as walking and flying. The missing resource was the complete connectome of the VNC neurons. This study provides this needed resource. The authors documented their approaches on how to generate the data from tissue preparation to computer-assisted reconstruction in a simple manner and left the in-depth analysis of the network features of the connecting neurons to two other well-written companion articles.

Strengths:<br /> Unlike many other previously published EM datasets, the authors presented a ready-to-view connectome dataset of the adult fly VNC. Readers, without needing permission, can access the dataset to find their neurons of interest and determine their synaptic partners with a few clicks. The authors also share their novel approaches in a detailed manner for others to reproduce similar EM volumes for other tissues.

Weaknesses:

The reconstruction completion, around 50%, might be considered a weakness. However, the data appear to have ~ %50 completion across all different neuropils suggesting that sampling is homogenous and does not induce bias. Nevertheless, a higher percentage will give a more complete picture.

Reviewer #2 (Public Review):

Summary:

Takemura et al. achieved a milestone in connectomics with their dense reconstruction of the Male Adult Nerve Cord (MANC) in Drosophila, revealing the neural circuitry of the primary premotor and motor domains in the CNS of the fruit fly. The team meticulously reconstructed neuron morphologies and synaptic connections and registered these data with light microscopy datasets (of driver lines for example), made neuronal lineage annotations and neurotransmitter predictions, providing the basis for new hypotheses about motor control. A description of the dataset and methods are presented here, while cell type annotations and characterisation of connectivity between brain descending neurons and motor neurons are provided in two companion papers, Marin et al. and Cheong, Eichler, Stürner et al., respectively. This dataset and analysis will provide a rich resource for future neuroscientific exploration.

Strengths:

The authors fully utilise a wealth of tools and techniques developed over the course of over a decade to produce a new publicly available dataset with an impressive number of reconstructed neurons and synapses. The precision and recall of connections are as high or higher than past datasets (e.g. the Hemibrain), pointing to the reliability of any downstream analyses performed on this connectome. These data are augmented with neurotransmitter identities, providing essential information for modelling and computational analysis. The MANC connectome can also be linked to genetic tools through registration to pre-existing light microscopy datasets, allowing experimentalists to test hypotheses made based on the connectome.

Weaknesses:

This dataset presents the nerve cord connectome of just a single animal, so connectivity variability and validity will be hard to assess. However, it is bilaterally reconstructed, which does allow comparison between bilaterally symmetrical neurons on the left and right sides of the nerve cord, increasing confidence in connections observed on both sides. Damage occurred to the nerves during sample preparation, which will have to be considered when analysing sensory connectivity.

Erschienen: 2024-05-08 Genre: Studien-Report Die Autor:innen des neuen Global Electricity Reports des Thinktanks Ember gehen davon aus, dass 2023 der Höhepunkt der Treibhausgas-Emissionen durch die Stromerzeugunng erreicht wurde. Erstmals stammten 30% des weltweit erzeugten Stroms aus erneuerbaren Energien. Hinzu kommen fast 10% Strom aus Kernkraft. Die Kohlendioxidemissionen aus der Stromerzeugung erreichten allerdings ebenfalls einen Rekord, weil der Strombedarf stieg.<br /> https://www.zeit.de/wissen/umwelt/2024-05/gruener-strom-klimapolitik-energiewende-klimaschutz

Reviewer #1 (Public Review):

This is an important and very well conducted study providing novel evidence on the role of zinc homeostasis for the control of infection with the intracellular bacterium S. typhimurium also disentangling the underlying mechanisms and providing clear evidence on the importance of spatio-temporal distribution of (free) zinc within the cell.

Comments:

It would be important to provide more information on the genotype of mice. It is rather unlikely that C57Bl6 mice survive up to two weeks after i.p. injection of 1x10E5 bacteria.

To be sure that macrophages Slc30A1 fl/fl LysMcre mice really have an impaired clearance of bacteria it would be important to rule out an effect of Slc30A1 deletion of bacterial phagocytosis and containment (f.e. evaluation of bacterial numbers after 30 min of infection).

Does the addition of zinc to macrophages negatively affect iNOS transcription as previously observed for the divalent metal iron and is a similar mechanism also employed (CEBPß/NF-IL6 modulation) (Dlaska M et al. J Immunol 1999)?

How does Zinc or TPEN supplementation to bacteria in LB medium affect the log growth of Salmonella?

Reviewer #2 (Public Review):

This paper explores the importance of zinc metabolism in host defense against the intracellular pathogen Salmonella Typhimurium. Using conditional mice with a deletion of the Slc30a1 zinc exporter, the authors show a critical role for zinc homeostasis in the pathogenesis of Salmonella. Specifically, mice deficient in Slc30a1 gene in LysM+ myeloid cells are hypersusceptible to Salmonella infection, and their macrophages show alter phenotypes in response to Salmonella. The study adds important new information on the role metal homeostasis plays in microbe host interactions. Despite the strengths, the manuscript has some weaknesses. The authors conclude that lack of slc30a1 in macrophages impairs nos2-dependent anti-Salmonella activity. However, this idea is not tested experimentally. In addition, the research presented on Mt1 is preliminary. The text related to Figure 7 could be deleted without affecting the overall impact of the findings.

Reviewer #3 (Public Review):

Na-Phatthalung et al observed that transcripts of the zinc transporter Slc30a1 was upregulated in Salmonella-infected murine macrophages and in human primary macrophages therefore they sought to determine if, and how, Slc30a1 could contribute to the control of bacterial pathogens. Using a reporter mouse the authors show that Slc30a1 expression increases in a subset of peritoneal and splenic macrophages of Salmonella-infected animals. Specific deletion of Slc30a1 in LysM+ cells resulted in a significantly higher susceptibility of mice to Salmonella infection which, counter to the authors conclusions, is not explained by the small differences in the bacterial burden observed in vivo and in vitro. Although loss of Slc30a1 resulted in reduced iNOS levels in activated macrophages, the study lacks experiments that mechanistically link loss of NO-mediated bactericidal activity to Salmonella survival in Slc30a1 deficient cells. The additional deletion of Mt1, another zinc binding protein, resulted in even lower nitrite levels of activated macrophages but only modest effects on Salmonella survival. By combining genetic approaches with molecular techniques that measure variables in macrophage activation and the labile zinc pool, Na-Phattalung et al successfully demonstrate that Slc30a1 and metallothionein 1 regulate zinc homeostasis in order to modulate effective immune responses to Salmonella infection. The authors have done a lot of work and the information that Slc30a1 expression in macrophages contributes to control of Salmonella infection in mice is a new finding that will be of interest to the field. Whether the mechanism by which SLC30A1 controls bacterial replication and/or lethality of infection involves nitric oxide production by macrophages remains to be shown.

Reviewer #1 (Public Review):

Sertonin is an important neurotransmitter and it synaptic concentration is controlled by re-uptake by the sodium-coupled serotonin transporter SERT. In this paper, some 6000 mutations of SERT were made and tested for surface expression and uptake of a serotonin analogue APP+. The SERT mutants were analysed and compared to the SERT structure and dynamics based on MD simulations. The authors have concluded that mutations located on surface exposed regions are tolerated whilst those involved in packing and structural integrity are not. Gain-of-function mutations map onto regions that in most cases favour opening of a solvent-exposed intracellular vestibule. Closure of the intracellular gate is thought to be rate-limiting to the transport cycle, and thus the evolutionary-based screen is consistent with the clustering of gain-of-function mutations.

Strengths:<br /> This paper using a large unbiased data-set to probe the evolution of the serotonin transporter SERT for the substrate APP+. They have been able to compare both localisation and transport data, which is an interesting data-set. Using MD simulations they are further able to provide some rationale basis for the gain-of-function mutants.

Weaknesses:<br /> They can only detect surface expression of myc-tagged SERT based on conjugation with a fluorescent anti-myc antibody. As such, they cannot distinguish between SERT mutants that abolish expression vs. those that are no longer trafficking to the plasma membrane. This is a downside, as it would have been interesting to know the fraction of SERT mutations disrupt trafficking. Indeed, the relationship between misfolding and targeting is poorly understood beyond the calnexin- calreticulin cycle. Furthermore, there seems to be a gap between the large-scale mutagenesis data and the MD simulations in which the main mechanistic conclusions seem to be based on (carried out in a separate publication). Thus, overall while the mutation data-set is impressive its not clear how this aids to our mechanistic understanding of SERT.

Reviewer #2 (Public Review):

The manuscript by Chan et al reports results of a systematic mutagenesis approach to study the surface expression and APP+ transport mechanism of serotonin transporter. They complement this experimental evidence with large-scale molecular simulations of the transporter in the presence of APP+. The use of deep mutagenesis and large-scale adaptive sampling simulations is impressive and could be very exciting contributions to the field.

On the whole, the results appear to provide a fascinating insight into the effects of mutations on transport mechanisms, and how those interrelate with the structural fold and biophysical properties of a dynamic protein and its substrate pathways. A weakness of the conclusions based on the molecular simulation is that it relies on comparison with previously-published work involving non-identical simulation systems (i.e. different protonation states).

Conclusions in this work about the origins of the sodium:serotonin 1:1 stoichiometry should also be considered in the context of the fact that there are two sodium ions bound in the structures of SERT, and more work is needed to explain why this ion is not also released/co-transported.

Some of the methods require additional information to be provided to be reproducible, for example, for the Transition Path Theory results, and so it is not possible to assess these conclusions with the manuscript in its current form.

Reviewer #3 (Public Review):

The results of the deep mutagenesis screen represent a wealth of information on the expression and function of SERT that everyone studying this protein will appreciate. However, as the authors explain, the screen identified mutations that increased APP+ transport but inhibited transport of the cognate substrate, 5-HT. Because of the methods used, 5-HT could not be used as a substrate, somewhat limiting the usefulness of the screen.

However, the authors have taken advantage of this limitation to address the mechanistic features of SERT that discriminate between 5-HT and APP+. From the position of mutations that augment APP+ transport, they have identified the aqueous pathway created in inward facing SERT conformations as a region of importance. Based on the MD simulations, transition to inward facing conformations is facilitated by 5-HT but less so by APP+. The authors conclude, quite reasonably, that mutations interfering with the stability of inward-closed SERT states could overcome the reduced ability of APP+ to open the pathway.

Another reasonable conclusion based on the mutant screen, is that mutations detrimental to surface expression were found in packed hydrophobic regions of the protein, but similar mutations in the permeation pathways were less likely to decrease expression. The authors postulate that this provides an evolutionary advantage by maintaining the structural fold while allowing modification of ion and substrate binding and coupling sites, a reasonable but speculative conclusion.

Not all gain-of-function mutations have to be specific to APP+. The authors point out that Ala173Gly converts SERT to the residue found in NET and DAT at this position. It would have been interesting to know how this mutation and others affect 5-HT transport. Indeed, the lack of any 5-HT transport measurements with the mutants is a glaring weakness of the manuscript.

Reviewer #1 (Public Review):

The authors report a high-quality genome assembly for a member of Xenacoelomorpha, a taxon that is at the center of the last remaining great controversies in animal evolution. The taxon and the species in question have "jumped around" the animal tree of life over the past 25 years, and seemed to have found their place as a sister-group to all remaining bilaterians. This hypothesis posits that the earliest split within Bilateria includes Xenacoelomorpha on the one hand and a clade known as Nephrozoa (Protostomia + Deuterostomia) on the other, and is thus referred to as the Nephrozoa hypothesis. Nephrozoa is supported by phylogenomic evidence, by a number of synapomorphic morphological characters in the Nephrozoa (namely, the presence of nephridia) and lack of some key bilaterian characters in Xenacoelomorpha, and by the presence of unique miRNAs in Nephrozoa.

The Nephrozoa hypothesis has been challenged several times by the authors' groups who alternatively suggest placing Xenacoelomorpha within Deuterostomia as a sister group to a clade known as Ambulacraria. This hypothesis (the Xenambulacraria hypothesis) is supported by alternative phylogenomic datasets and by the shared presence of a number of unique molecular signatures. In this contribution, the authors aim to strengthen their case by providing full genome data for Xenoturbella bocki.<br /> The actual sequencing and analysis are technically and methodologically excellent. Some of the analyses were done several years ago using approaches that may now seem obsolete, but there is no reason not to include them. As a detailed report of a newly sequenced genome, the manuscript meets the highest standards.

The authors emphasize a number of key findings. One is the fact that the genome is not as simple as one might expect from a "basal" taxon, and is on par with other bilaterian genomes and even more complex than the genome of secondarily simplified bilaterians. There is an implicit expectation here that the sister group to all Bilateria would represent the primitive state. This is of course not true, and the authors are aware of this, but it sometimes feels as though they are using this implicit assumption as a straw dog argument to say that since the genome is not as simple as expected, X. bocki must be nested within Bilateria. The authors get around this by acknowledging that their finding is consistent with a "weak version of the Nephrozoa hypothesis", which is essentially the Nephrozoa phylogenetic hypothesis without implicit assumptions of simplicity.

Another finding is a refutation of the miRNA data supporting Nephrozoa. This is an important finding although it is somewhat flogging a dead horse, since there is already a fair amount of skepticism about the validity of the miRNA data (now over 20 years old) for higher-level phylogenetics.

The finding that the authors feel is most important is gene presence-absence data that recovers a topology in which X. bocki is sister to Abulacraria. The problem is that the same tree does not support the monophyly of Xenacoelomorpha. This may be an artifact of fast evolving acoel genomes, as the authors suggest, but it still raises questions about the robustness of the data.

In sum, the authors' results and analyses leave an open window for the Xenambulacraria hypothesis, but do not refute the Nephrozoa hypothesis. The manuscript is a valuable contribution to the debate but does not go a significant way towards its resolution.<br /> The manuscript has gone through several rounds of review and revision on a preprint server and is thus fairly clear of typos, inconsistencies and lack of clarity. The authors are honest and open in their interpretation of the results and their strengths.

Reviewer #2 (Public Review):

The manuscript describes the genome assembly and analysis of Xenoturbella bocki, a worm that bears many morphological features ascribed to basal bilateria. The authors aim to analyse this genome in an attempt to determine the phylogenetic position of X. bocki as a representative of Xenacoelomorpha and its associated acoelomorphs. In doing so, they want to inform the debate as to whether xenacoelomorph belong among, or is in fact paraphyletic to all bilaterians.

This paper presents a high-quality assembly of the X. bocki genome. By virtue of the phylogenetic position of this species, this genome has considerable scientific interest. This assembly appears to be highly complete and is a strength of the paper. The further characterisation of the genome is well executed and presented. Solid results from this paper include a comprehensive description of the Hox genes, miRNA and neruopeptide repertoire, as well as a description of the linkage group and how they relate to the ancestral linkage groups.

Where this paper is weaker is that for the central claims and questions of this paper, i.e,. the question of the phylogenetic position of xenacoelomorph and whether X. bocki is a slowly evolving, but otherwise representative member of this clade, remains insufficiently resolved.

The authors have achieved the goal of describing the X. bocki genome very well. By contrast, it is unclear, based on the presented evidence, whether xenacoelomorph is truly a monophyletic group. The balance of the evidence seems to suggest that the X. bocki genome belongs within the bilateria group. However, it is unclear as to what is driving the position of the other acoels. Assumign that X. bocki and the other two species in that group are monophyletic, then the evidence will favour the authors' conclusion (but without clearly rejecting the alternatives).

This paper will likely further animate the debate regarding this basal species, and also questions related to the ancestral characters of bilateria as a whole. In particular the results from the HOX and paraHOX clusters, may provide an interesting counterpoint to the previous results based on the acoels.

Reviewer #1 (Public Review):

Rubin et al. study chondrocyte columns in the prenatal and postnatal growth plate in 3D for the first time, using a novel analysis pipeline in which Confetti clones in the murine growth plate are analysed morphometrically. Prenatal chondrocytes were found not to be organised in columns parallel to the main orientation of the long bone, but rather, prenatal chondrocytes were commonly organised perpendicular to the main direction of growth. In the postnatal (P40) growth plate there was a diverse arrangement of columns, but more of the columns were vertically aligned

I enjoyed reading the work and the analysis is rigorous. However, I think that it is not valid to state that columns do not form in the embryo. The data only supports the finding that strictly vertical columns do not form in the embryo, as the cells are still organised into columns, albeit with a range of orientations. I do not like the term "typically" aligned, as how can we know what is "typical" when orientation has never before been assessed in 3D... And the authors' data demonstrates that it is certainly not "typical" for chondrocyte to organise into vertical columns prenatally.

It would be very interesting to delve deeper into the reason for the change in orientation of columns between pre- and post-natal. For example, does more circumferential growth happen prenatally as compared to postnatally? Is the rate of circumferential vs longitudinal growth different between prenatal and postnatal, and could the change in column orientation be responsible for a (possible) shift in the balance between longitudinal vs circumferential growth before vs after birth? The first sentence of the Discussion refers to the role of chondrocyte columns in driving bone elongation, but aren't they also involved in driving bone morphology?

I feel describing the activity of the cells as "mis-rotations" which implies the orientations are not intentional. It is likely not accidental or mistaken that the chondrocytes align in the ways they do- the diaphysis is largely for longitudinal growth while the epiphyses, and lateral expansion of the joint is also important. I find the data in Figure 4 fascinating, especially the variation in orientations between the regions of the growth plate (from proximal to distal), with the most lateral orientation at the most proximal and distal ends- it would be nice to see more discussion of these variations and what they may be contributing to.

The abstract focuses solely on the analysis of columns prenatally and would benefit from the inclusion of the data from the postnatal growth plate and from the chondrocyte rotations.

Reviewer #2 (Public Review):

The origin and function of proliferative chondrocyte columns in the growth plate that are generally aligned with predicted longitudinal growth vectors have been robustly debated since the implementation of clonal analysis and live cell imaging techniques more than a decade ago. In particular, live cell imaging demonstrated that in the proliferative zone, most daughter pairs rotate fully or partially after division to form columns of stacked cells and a minority of pairs fail to rotate. These observations and others led to a mechanistic model of column formation, but limitations in the live cell imaging methods that only visualize a single round of division and rotation left open an important question - what is the effect of different rotation profiles on column formation, bone growth, and morphology?

This manuscript describes the use of an inducible lineage tracing system in the mouse combined with a novel image analysis pipeline to analyze column formation over multiple cell divisions. The main conclusion is that many clones generate single columns in postnatal mice (as expected), but clones in embryonic growth plate cartilage form clusters distributed laterally, not aligned with longitudinal growth. These findings are interpreted to suggest that column formation is not required for long bone growth in the embryo and that lateral expansion of proliferative chondrocyte clusters may drive an increase in bone width.

Although these findings are intriguing and potentially impactful, there are important caveats to the approach that generate significant uncertainty in both the measurements and the conclusions. (1) The claim that embryonic growth plate chondrocytes do not form columns conflicts with the observation of columnar stacks in the clusters. (2) Interpretation of nuclear elevation data is based on the unproven assumption that nuclei should be stacked in cell columns. (3) Clonal analysis of proliferative chondrocyte cell division and stacking behaviors is only valid if clone labeling is initiated in a proliferative chondrocyte, not when the founder cell is a resting chondrocyte. The data are insufficient to validate this absolute requirement.

Reviewer #3 (Public Review):

The manuscript by Rubin and Agrawal et al presents a very nice imaging analysis of clonal cell organization in the fetal and late juvenile mouse growth cartilages. The authors have performed a thorough quantification of the orientations of clusters and of clones of cells with respect to the growth axis. They conclude that growth cartilage is not as strictly 'columnar' as has been commonly described, especially at the fetal stage. There is value to having such quantifications in the literature as a reminder that interpretations of phenotypes need to be rooted in the cell biology of the stage at hand, as emphasized by the authors. However, although the approach is comprehensive, aspects of the quantification methods are not described adequately to determine if they are correct for the questions. There are also some inequivalent comparisons to prior literature and an oversight of important published observations showing that some of these conclusions have been known for decades, though not as thoroughly quantitative. There have long been observations that some growth cartilages do not have proliferative columns oriented in the axis of growth and that not all columns of a growth cartilage are perfectly organized; these facts do not negate the observations that columnar organization does exist, as re-confirmed here, and that it correlates with and contributes to rapid growth rates. Each of these points is further elaborated below.

Reviewer #1 (Public Review):

This manuscript presents, for the first time, the utilization of PRV viral transneuronal tracing to elucidate the central coding and control mechanisms governing sympathetic nervous system (SNS) efferent signals to bone. This groundbreaking work not only holds promising research prospects but also establishes a robust foundation for understanding the neural regulation of bone metabolism.

Reviewer #2 (Public Review):

Summary:<br /> In this study, the authors have used virtual transneuronal tracing technology to identify for the first time the central sympathetic nervous system outflow sites that innervate bone.

Strengths:<br /> The study provides a comprehensive atlas of the brain regions that potentially play a role in coding and decoding sympathetic nervous system signals to bone.

Weaknesses:<br /> While the study provides compelling evidence for the brain-bone sympathetic nervous system neuroaxis, it is unclear if diseases that affect bone (e.g. diabetes, osteoporosis, kidney failure) disrupt brain-bone sympathetic neural circuits.

Reviewer #3 (Public Review):

It has been reported that the sympathetic nervous system (SNS) mediates bone metabolism and nociceptive functions. However, the exact localization and organization of the central SNS circuitry innervating bone and the brain sites have not been mapped and efferent SNS outflow to bone has not yet been characterized yet. Authors used pseudorabies (PRV) viral transneuronal tracing approach to identify central SNS outflow sites that innervate bone. The authors found that the central SNS outflow to bone originates from brain nuclei, sub-nuclei and regions of six brain divisions (midbrain and pons, hypothalamus, hindbrain medulla, forebrain, cerebral cortex, and thalamus). The authors provided compelling evidence for a brain-bone SNS neuroaxis that may regulate bone metabolism and nociceptive functions, which provided a greater understanding of the neural regulation of bone metabolism and would stimulate further research into bone pain and the neural regulation of bone metabolism. Authors may discuss and summarize their results in detail for a better understanding of their findings and enhancing the manuscript's utility for readers.

Reviewer #1 (Public Review):

Garcia-Saldivar and colleagues present a manuscript investigating connections between diffusion-weighted imaging (DWI) parameters and paced finger tapping measures. A cohort of human participants (n=32) performed a paced finger tapping task with a synchronization-continuation paradigm, in which they were required to listen to a paced metronome, begin tapping in synchrony with it, and then continue tapping at the same rate without it. Both auditory and visual metronomes were used, at a range of intervals. All subjects received structural scans measuring DWI, with an emphasis on superficial and deep white matter structures. This latter analysis was the most innovative, as it allowed the authors to examine microstructural effects in short-range cortical connections.

Behaviorally, the authors replicated some well-known effects in paced finger tapping, with better performance for auditory over visual rhythms, negative lag-1 autocorrelations, and best performance at a range of ~1.5Hz. For the DWI analyses, a large number of correlations were observed across a wide variety of connections with various brain regions. The most salient effects observed were a connection between asynchrony, only for the auditory condition, and connections between the right auditory and motor systems, around the duration of peak performance, as well as a "chronotopic" organization across parts of the corpus callosum, most notably in areas linking motor regions between hemispheres.

Overall, this paper provides a critical missing link between measures of structural connectivity and rhythmic tapping abilities, pointing to some interesting possibilities for how tapping synchronization (at least for auditory intervals) is carried out. Negative aspects of the paper come from the largely exploratory aspects of the analysis, as well as potential biases from the low sample size.

Reviewer #2 (Public Review):

This is a valuable study of the relationships between aspects of white matter structure in the brain and the accuracy of tapping performance on auditory and visual versions of a synchronization-continuation task. The authors find brain-behaviour relationships between absolute asynchrony (precision of phase alignment between taps and stimulus events), but only for certain temporal rates (650 and 750 ms ISI, not 550, 850, or 950 ms ISI). Other behavioural metrics do not significantly correlate with white matter measures, and no visual condition behavioural metrics correlate either. The methodology and findings are solid, and of interest to those studying the neural mechanisms of timing.

The question is interesting, as the neural mechanisms of timing, and the nature of how modality differences in timing arise, are important, given that certain modality differences in timing accuracy (e.g., auditory benefits relative to visual) are less striking in our closest evolutionary relatives. Overall, the methods are well-presented and both behavioural and neural measures are appropriate.

The results are generally well-reported, although there is a lack of clarity about multiple comparison corrections for the number of separate behavioural metrics, different interval lengths examined, and the two sensory modalities.

Some weaknesses:<br /> The use of absolute (unsigned) asynchrony as a measure of 'predictive' ability is not fully justified. Signed asynchrony may be a more informative measure of predictive ability, as (small) negative asynchronies (taps prior to event onset) are often interpreted as indicating prediction, whereas positive asynchronies (taps after the event onset) are not.<br /> The work may benefit from considering the 'phase' and 'period' nature of the different behavioural measures, as they may tap different aspects of timing. Separating the behavioural metrics into those reflecting phase synchrony versus period matching may be a useful distinction, as the period-related metrics are the ones that do not have evidence of correlation with brain metrics.<br /> The manuscript does not present a very clear framework for why certain measures might be predicted to correlate with white matter structure and others not, and the pattern of results is also not easily interpretable. This may just be the nature of the data, but it would help clarify if more justification for the selection of task and stimulus rates was presented, along with an idea of the predictions made by different theoretical approaches for what relationships between this particular set of behavioural and brain data might exist. Similarly, a more nuanced discussion might further explore the potential reasons for the lack of evidence for a relationship at shorter and longer auditory interval lengths, as well as for any of the visual condition measures.

Overall, the authors find white-matter structure relationships with absolute asynchrony measures during auditory (but not visual) synchronization-continuation at certain rates. These findings appear reasonably justified.

Reviewer #1 (Public Review):

The manuscript demonstrates an analysis of the synaptic organization within the motor thalamus, emphasizing the interplay between the ventrolateral (VL) and ventroanterior (VA) nuclei and their respective inputs. The primary aim is to unravel the complexities of synaptic interactions among the motor cortex's layer 5 (M1L5), the cerebellum (Cb), and the basal ganglia output nuclei (GPi and SNr), which converge upon the VA/VL nuclei of the motor thalamus. This examination is executed using a combination of anatomical tracing, optogenetics, and electrophysiological recordings in mouse brain slices, which together yield novel insights into the motor control circuitry.

The study uncovers that contrary to traditional models that presumed segregation, some motor thalamic neurons simultaneously integrate inputs from the cerebellum and basal ganglia. Furthermore, a subset of these neurons also receive convergent inputs from M1L5 and basal ganglia, underscoring the complexity of these synaptic networks. Notably, the study reveals that both M1L5 and Cb inputs exhibit driver-type synaptic properties, suggesting a significant impact on thalamic relay neurons.

The functional implications of this synaptic convergence suggest a complex gating mechanism by the inhibitory outputs of the basal ganglia, which could modulate information flow within the motor thalamus. This modulation is significant not only for transthalamic information processing but also for the integration of cerebellar inputs to the motor cortex. The study also highlights direct projections from M1L5 to the motor thalamus, indicating a potential direct influence on thalamic activity, in addition to the known indirect influence through the cortico-basal ganglia-thalamo-cortical loop.

The manuscript suggests that the traditional understanding of motor thalamic connectivity requires reconsideration, and it emphasizes the necessity of further investigation to understand fully the functional implications of this synaptic convergence. Future research may focus on more direct demonstrations of triple-input convergence and its behavioral consequences, as well as cross-species comparative studies to enhance the findings' applicability.

While the study provides valuable contributions to our knowledge of the motor thalamus, illuminating the intricate synaptic architecture of the motor thalamus and setting the stage for future explorations that will deepen our comprehension of motor control and thalamic function.

Reviewer #2 (Public Review):

This study assesses how inputs from primary motor cortex layer 5 (M1L5), basal ganglia output nuclei (GPi and SNr), and cerebellum (Cb) converge onto motor thalamus nuclei (VA/VL).

Methodology includes anatomical tracing, optogenetics and electrophysiological recordings in mouse brain slices.

The major findings are:<br /> - Some motor thalamic neurons receive input from both cerebellar and basal ganglia. This is contrary to the common belief that assumes these two inputs are segregated in the motor thalamus.

- Some motor thalamus neurons receive converging input from both motor cortex (M1L5) and basal ganglia.

- Both M1L5 and Cb inputs to the motor thalamus have driver-type synaptic properties, indicating a strong influence on thalamic relay neurons.

Functional implications are:<br /> - Given the inhibitory nature of basal ganglia output neurons, the converging inputs can allow for basal ganglia to gate information flow through the motor thalamus. This applies to transthalamic information, ie information conveyed through the thalamus across cortical regions, as well as cerebellar information flow to motor cortex.

- The direct projection from M1L5 to motor thalamus suggests that motor cortex can affect motor thalamic activity not only indirectly, through the traditional cortico-basal ganglia-thalamo-cortical loop, but also through direct projections.

The study is convincing and has important implications for the field. Methodology involves elegant viral techniques.

The main weakness is that there is no direct functional demonstration of all the 3 inputs from motor cortex, cerebellum, and basal ganglia, converging onto the same cells in motor thalamus. All the recordings concern dual area stimulations, and the anatomical studies show a very small overlap of all the 3 inputs onto motor thalamus.

Reviewer #1 (Public Review):

This manuscript presents an exciting new method for separating insulin secretory granules using insulator-based dielectrophoresis (iDEP) of immunolabeled vesicles. The method has the advantage of being able to separate vesicles by subtle biophysical differences that do not need to be known by the experimenter, and hence could in principle be used to separate any type of organelle in an unbiased way. Any individual organelle ("particle") will have a characteristic ratio of electrokinetic to dielectrophoretic mobilities (EKMr) that will determine where it migrates in the presence of an electric field. Particles with different EKMr will migrate differently and thus can be separated. The present manuscript is primarily a methods paper to show the feasibility of the iDEP technique applied to insulin vesicles. Experiments are performed on cultured cells in low or high glucose, with the conclusion that there are several distinct subpopulations of insulin vesicles in both conditions, but that the distributions in the two conditions are different. As it is already known that glucose induces release of mature insulin vesicles and stimulates new vesicle biosynthesis and maturation, this finding is not necessarily new, but is intended as a proof of principle experiment to show that the technique works. This is a promising new technology based on solid theory that has the possibility to transform the study of insulin vesicle subpopulations, itself an emerging field. The technique development is a major strength of the paper. Also, cellular fractionation and iDEP experiments are performed well, and it is clear that the distribution of vesicle populations is different in the low and high glucose conditions. However, more work is needed to characterize the vesicle populations being separated, leaving open the possibility that the separated populations are not only insulin vesicles, but might consist of other compartments as well. It is also unclear whether the populations might represent immature and mature vesicles, distinct pools of mature vesicles such as the readily releasable pool and the reserve pool, or vesicles of different age. Without a better characterization of these populations, it is not possible to assess how well the iDEP technique is doing what is claimed.

Major comments:

(1) There is no attempt to relate the separated populations of vesicles to known subpopulations of insulin vesicles such as immature and mature vesicles, or the more recently characterized Syt9 and Syt7 vesicle subpopulations that differ in protein and lipid composition (Kreutzberger et al. 2020). Given that it is unclear exactly what populations of vesicles will be immunolabeled (see point #2 below), it is also possible that some of the "subpopulations" are other compartments being separated in addition to insulin vesicles. It will be important to examine other markers on these separated populations or to perform EM to show that they look like insulin vesicles.

(2) An antibody to synaptotagmin V is used to immunolabel vesicles, but there has been confusion between synaptotagmins V and IX in the literature and it isn't clear what exactly is being recognized by this antibody (this reviewer actually thinks it is Syt 9). If it is indeed recognizing Syt 9, it might already be labeling a restricted population of insulin vesicles (Kreutzberger et al. 2020). The specificity of this antibody should be clarified. Furthermore, Figure 2 is not convincing at showing that this synaptotagmin antibody specifically labels insulin vesicles nor is there convincing colocalization of this synaptotagmin antibody with insulin vesicles. In the image shown, several cells show very weak or no staining of both insulin and the synaptotagmin. The highlighted cell appears to show insulin mainly in a perinuclear structure (probably the Golgi) rather than in mature vesicles (which should be punctate), and insulin is not particularly well-colocalized with the synaptotagmin. Other cells in the image appear to have even less colocalization of insulin and synaptotagmin, and there is no quantification of colocalization. It seems possible that this antibody is recognizing other compartments in the cell, which would change the interpretation of the populations measured in the iDEP experiments. It would also be good to perform synaptotagmin staining under glucose-stimulating conditions, in case this alters the localization.

(3) The EKMr values of the vesicle populations between the low and high glucose conditions don't seem to precisely match. It is unclear if this just a technical limitation in comparing between experiments or instead suggests that glucose stimulation does not just change the proportion of vesicles in the subpopulations (i.e. the relative fluorescent intensities measured), but rather the nature of the subpopulations (i.e. they have distinct biophysical characteristics). This again gets to the issue of what these vesicle subpopulations represent. If glucose stimulation is simply converting immature to mature vesicles, one might expect it to change the proportion of vesicles, but not the biophysical properties of each subpopulation.

(4) The title of the paper promises "isolation" of insulin vesicles, but the manuscript only presents separation and no isolation of the separated populations. Isolation of the separated populations is important to be able to better define what these populations are (see point #1 above). Isolation is also critical if this is to be a valuable technique in the future. Yet the paper is unclear on whether it is actually technically feasible to isolate the populations separated by iDEP. In line 367, it states "this method provides a mechanism for the isolation and concentration of fractions which show the largest difference between the two population patterns for further bioanalysis (imaging, proteomics, lipidomics, etc.)." However, in line 361 it says "developing the capability to port the collected individual boluses will enable downstream analyses such as mass spectrometry or electron microscopy," suggesting that true isolation of these populations is not yet feasible. This should be clarified.

Reviewer #2 (Public Review):

This manuscript used DC-iDEP, a technology previously used on other organelle preparations to isolate insulin secretory granules from INS1 cells based on differences in dielectrophoretic and electrokinetic properties of synaptotagmin V positive insulin granules.

The major motivation presented for this work is to provide a methodology to allow for more sensitive isolation of subpopulations of granules allowing better understanding of the biochemical composition of these populations. This manuscript clearly demonstrates the ability of this technology to separate these subpopulations which will allow for future biochemical characterizations of insulin granules in future studies.

After proving these subpopulations can be observed, this method was then utilized to show there are shifts in these subpopulations when granules are isolated from glucose stimulated cells. Overall the method of isolation is novel and could provide a tool for further characterization of purified secretory granules.

The observation of glucose stimulation causing shifts in subpopulations is unsurprising. Glucose stimulation could cause a depletion of insulin and other secretory content from a subset of granules. It would be expected that this loss of content would cause a shift in electrochemical properties of the granules, but this is a nice confirmation that the isolation method has the sensitivity to delineate these changes.

Major comments:

(1) It is unclear what Synaptotagmin isoform is being looked at. Synaptotagmin V and IX have been repetitively interchanged in the literature. See note in syt IX section of "Moghadam and Jackson 2013 Front. Endocrinology" or read "Fukuda and Sagi-Eisenberg Calcium Bind Proteins 2008".

The 386 aa. isoform that is abundant in PC12 cells has been robustly observed in INS1 cells in multiple studies and has been frequently referred to as syt IX. The sequence the antibody was raised against should be determined from the company where this was purchased and then this should be mapped to to which isoform of Synaptotagmin by sequence and clarified in the text.

(2) Immunofluorescence of insulin and syt V is confusing. The example images do not appear to show robust punctate structures that are characteristic of secretory granules (in both the insulin and syt V stain).

(3) In the discussion it says, "Finally, this method provides a mechanism for the isolation and concentration of fractions which show the largest difference between the two population patterns for further bioanalysis (imaging, proteomics, lipidomics, etc.) that otherwise would not be possible given the low-abundance components of these subpopulations."

It would help to elaborate more on the yield and concentrations of isolated granules. This would give a better sense of what level of biochemical characterization could be performed on sub-populations of granules.

Reviewer #3 (Public Review):

The manuscript from Barekatain et al. is investigating heterogeneity within the population of insulin vesicles from an insulinoma cell line (INS-1E) in response to glucose stimulation. Prevailing dogma in the beta-cell field suggests that there are distinct pools of mature insulin granules, such as ready-releasable and a reserve pool, which contribute to distinct phases of insulin release in response to glucose stimulation. Whether these pools (and others) are distinct in protein/lipid composition or other aspects is not known, but has been suggested. In this manuscript, the authors use density gradient sedimentation to enrich for insulin vesicles, noting the existence of a number of co-purifying contaminants (ER and mitochondrial markers). Following immunolabeling with synaptotagmin V and fluorescent-conjugated secondary antibodies, insulin vesicles were applied to a microfluidic device and separated by dielectrophoretic and electrokinetic forces following an applied voltage. The equilibrium between these opposing forces was used to physically separate insulin granules. Here some differences were observed in the insulin (Syt V positive) granule populations, when isolated from cells that were either non-stimulated or stimulated with glucose, which has been suggested previously by other studies as noted by the authors; however in the current manuscript, the inclusion of a number of control experiments may provide a better context for what the data reveal about these changes.

The major strength of the paper is in the use of the novel, highly sophisticated methodology to examine physical attributes of insulin granules and thus begin to provide some insight into the existence of distinct insulin granule populations within a beta-cell -these include insulin granules that are maturing, membrane-docked (i.e. readily releasable), in reserve, newly-synthesized, aged, etc. Whether physical differences exist between these various granule pools is not known. In this capacity, the technical abilities of the current manuscript may begin to offer some insight into whether these perceived distinctions are physical.

The major weakness of the manuscript is that the study falls short in terms of linking the biology to the sophisticated changes observed and primarily focuses on differences in response to glucose. Without knowing what the various populations of granules are, it is challenging to understand what the changes in response to glucose mean.

Specific concerns are as follows:

(1) There is confusion on what the DC-iDEP separation between stimulated and stimulated cells reveals. Do these changes reflect maturation state of granules, nascent vs. old granules? Ready-releasable vs. reserve pool? The comments in the text seem to offer all possibilities.

(2) It is unclear what we can infer regarding the physical changes of granules between the stimulated states of the cells. Without an understanding of the magnitude of the effect, it is unclear how biologically significant these changes are. For example, what degree of lipid or protein remodeling would be necessary to give a similar change?

(3) The reliance on a single vesicle marker, Syt V, is concerning given that granule remodeling is the focus.

(4) Additional confirmation that the isolated vesicles are in fact insulin granules would be helpful. As noted, granules were gradient enriched, but did carry contaminants. Note that the microscopy image provided does not provide any real validation for this marker.

Further confirmation that the immune-isolated vesicles are in fact insulin granules should be included. EM with immunogold labeling post-SytV enrichment would be a potential methodology to confirm.

(5) It would be useful to understand if the observed effects are specific to the INS-1E cell line or are a more universal effect of glucose on beta-cells.

Reviewer #1 (Public Review):

Summary:

The manuscript describes a model based on 5-state cellular automata of development of an infection. The model is motivated and qualitatively justified by time-resolved measurements of expression levels of viral, interferon-producing, and antiviral genes. The model is set up in such a way that the crucial difference in outcomes (infection spreading vs. confinement) depends on the initial fraction of special virus-sensing cells. Those cells (denoted as 'type a') cannot be infected and do not support the propagation of infection, but rather inhibit it in a somewhat autocatalytic way. Presumably, such feedback makes the transition between two outcomes very sharp: a minor variation in concentration of 'a' cells results in qualitative change from one outcome to another. As in any percolation-like system, the transition between propagation and inhibition of infection goes through a critical state with all its attributes, including a power-law distribution of the cluster size (corresponding to the fraction of infected cells) with a fairly universal exponent and a cutoff at the upper limit of this distribution.

Strengths:

The proposed model suggests a well-justified explanation for the frequently observed yet puzzling diversity of outcomes of viral infections such as COVID.

Weaknesses:

None.

Reviewer #2 (Public Review):

Xu et al. introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection. In this study, the author first analyzes the single-cell RNA sequencing data from experiments and identifies four clusters of cells at 48 hours post-viral infection, including susceptible cells (O), infected cells (V), IFN-secreting cells (N), and antiviral cells (A). Next, a cellular automaton model (NOVAa model) is introduced by assuming the existence of a transient pre-antiviral state (a). The model consists of an LxL lattice; each site represents one cell. The cells change their state following the rules depending on the interaction of neighboring cells. The model introduces a key parameter, p_a, representing the fraction of pre-antiviral state cells. Cell apoptosis is omitted in the model. Model simulations show a threshold-like behavior of the final attack rate of the virus when p_a changes continuously. There is a critical value p_c, so that when p_a < p_c, infections typically spread to the entire system, while at a higher p_a > p_c, the propagation of the infected state is inhibited. Moreover, the radius R that quantifies the diffusion range of N cells may affect the critical value p_c; a larger R yields a smaller value of the critical value p_c. The authors further examine the result with stochastic version dynamics, and the main findings are unchanged upon stochastic dynamics. The structure of clusters is different for different values of R; greater R leads to a different microscopic structure with fewer A and N cells in the final state. Compared with the single-cell RNA seq data, which implies a low fraction of IFN-positive cells of around 1.7%, the model simulation suggests R=5. The authors also explored a simplified version of the model, the OVA model, with only three states. The OVA model also has an outbreak size. The OVA model shows dynamics similar to the NOVAa model. However, the change in microstructure as a function of the IFN range R observed in the NOVAa model is not observed in the OVA model.

Reviewer #3 (Public Review):

Summary:

This study considers how to model distinct host cell states that correspond to different stages of a viral infection: from naïve and susceptible cells to infected cells and a minority of important interferon-secreting cells that are the first line of defense against viral spread. The study first considers the distinct host cell states by analyzing previously published single-cell RNAseq data. Then an agent-based model on a square lattice is used to probe the dependence of the system on various parameters. Finally, a simplified version of the model is explored, and shown to have some similarity with the more complex model, yet lacks the dependence on the interferon range. By exploring these models one gains an intuitive understanding of the system, and the model may be used to generate hypotheses that could be tested experimentally, telling us "when to be surprised" if the biological system deviates from the model predictions.

Strengths:

- Clear presentation of the experimental findings and a clear logical progression from these experimental findings to the modeling.<br /> - The modeling results are easy to understand, revealing interesting behavior and percolation-like features.<br /> - The scaling results presented span several decades and are therefore compelling.<br /> - The results presented suggest several interesting directions for theoretical follow-up work, as well as possible experiments to probe the system (e.g. by stimulating or blocking IFN secretion).

Weaknesses:

- The fixed time-step of the agent-based modeling may introduce biases. I would consider simulating the system with Gillespie dynamics where the reaction rates depend on the ambient system parameters.<br /> - Single-cell RNAseq data requires careful handling or it may generate false leads. The strength of the RNAseq evidence presented is not clear.

Two places where the manuscript could be extended:

- Since the "range" of IFN is an important parameter, it makes sense to consider other lattice geometries other than the square lattice, which is somewhat pathological. Perhaps a hexagonal lattice would generalize better.<br /> - Tissues are typically three-dimensional, not two-dimensional. (Epithelium is an exception). It would be interesting to see how the modeling translates to the three-dimensional case. Percolations transitions are known to be very sensitive to the dimensionality of the system.

Justification of claims and conclusions:

The claims and conclusions are well justified.

Reviewer #1 (Public Review):

This paper can be seen as an extension of a recent study by two of the same authors [1]. In the previous paper, the authors considered two variants of the Moran process, labelled Model A and Model B, and examined differences between the evolutionary dynamics of these two models. They further described the site frequency spectra, expected allele counts, and expected singleton counts of these models, building on analytical results from prior studies, and used numerical simulations to investigate the models' evolutionary dynamics. Finally, they compared the site frequency spectra of the two models (using numerical simulations) to spectra derived from a small breast cancer data set (two sets of three samples).

In the new paper, the authors consider the same two Moran process variants (Model A and Model B) and some related branching processes. As before, they compare the site frequency spectra and various summary statistics of these models, but here they present only numerical simulations (except that some prior analytical results are summarized in Appendix A, which are never referred to in the main text and seem unconnected to the study). They then compare the site frequency spectra of these models (again using numerical simulations) to those derived from the same breast cancer samples as before and thus infer some evolutionary parameters.

The first main conclusion is that the critical branching process and the Moran process models behave similarly and generate similar site frequency spectra. This finding is unsurprising (indeed, the authors acknowledge that the result "has been expected"). For a reasonably large population size, the population size in the critical branching process has been shown to vary relatively little over time and the model is thus essentially a continuous time Moran process (see, for example, Equation 8.55 in ref 2). Nor is it surprising that the authors see stronger similarities when they select only the subset of branching process replicates in which the final population size is particularly close to the initial population size (this is because, in these replicates, the population size likely varies even less than usual).

The second main conclusion is that, although "the mutational SFS alone is not adequate" to quantify the strength of selection, "All fitted values for the selective disadvantage of passenger mutations are nonzero, supporting the view that they exert deleterious selection during tumorigenesis". Although the question of whether mildly deleterious mutations play an important role in cancer evolution is of considerable interest, it's debatable whether the results presented here help resolve the issue.

Many prominent researchers have called into question whether cancer evolutionary parameters can be reliably inferred from site frequency spectra (e.g., [3-7]), even using sophisticated statistical methods. The statistical approach used here (though not named as such in the paper) is a crude kind of approximate Bayesian computation. To improve the accuracy of the results, it would have been better to have set reasonably vague priors for the uncertain mutation rates, rather than fixing them arbitrarily. It would also have been better to have chosen a likelihood function explicitly based on an analysis of the sampling and error distributions, rather than just summing the absolute logged deviations. It is well known that "Checking the model is crucial to statistical analysis" and "A good Bayesian analysis, therefore, should include at least some check of the adequacy of the fit of the model to the data and the plausibility of the model for the purposes for which the model will be used" [8]. The authors' failure to describe any attempt to validate or check their model, using simulated data or otherwise, casts doubt on the reliability of their inferences.

Putting aside the potential biassing effects of sampling error, measurement error, and the limitations of the authors' statistical method, it is well established that both population growth and spatial structure profoundly alter the shape of site frequency spectra in ways that can mimic the effects of selection (e.g. [9-11]). Indeed, Figures 3, 4 and 5 show that the critical and super-critical branching processes generate markedly different site frequency spectra. It follows that if the population dynamics and spatial structure of the mathematical model used for inference don't match those of the biological process that produced the data then any inferred evolutionary parameter values will be unreliable. Breast cancer has two indisputable ecological features that shape its evolutionary dynamics: the cell population expands by many orders of magnitude from a single cell, and the population is spatially structured. In the authors' mathematical model, the population size is initially 100 cells and either remains constant or varies little, and there is no spatial structure. These profound mismatches between model and data cast further doubt on what is supposed to be the paper's most important biological finding.

In this paper the authors offer no justification for their decision to model breast cancer as a non-growing, non-spatial cell population. Nor do they engage with the extensive recent literature on the challenges of inferring evolutionary parameters from cancer site frequency spectra (they cite none of the many relevant papers listed at https://www.sottorivalab.org/neutral-evolution.html). Their 2022 paper [1] claims that, "it sometimes makes sense to consider cancer growth in the framework of constant-population models. Our models correspond to the situation in which a constant population of N "healthy" stem cells is gradually replaced by a growing clone of transformed cells with increasing fitness." No evidence was presented to support this hypothesis regarding breast cancer progression. On the other hand, a wealth of evidence supports the consensus view that, in breast cancer and other human solid tumours, the number of cells with unlimited proliferative potential is several orders of magnitude greater than 100 and grows over time (e.g. [12]).

Analytic expressions for the site frequency spectra with neutral mutations are already known. It is well known that the site frequency spectrum of an exponentially growing population has a tail following a power law S_k ~ k^(-2) [13, 14]. Similarly, it is known that for the critical branching process or the Moran process, the site frequency spectrum at equilibrium is S_k ~ k^(-1) [13, 15]. Especially noteworthy yet uncited studies that use those results about site frequency spectra to make inferences based on sequencing data include ref 16, in which selection is inferred, and ref 17, in which evolutionary parameters of constant populations (healthy cell populations) are inferred.

Although the paper is well written, the figures are ineffective in communicating the results. As others have put it, "A figure is meant to express an idea or introduce some facts or a result that would be too long (or nearly impossible) to explain only with words" and "If your figure is able to convey a striking message at first glance, chances are increased that your article will draw more attention from the community" [18]. On the contrary, Figures 3, 4, 5 and 6 are bewilderingly complicated, crowded, and repetitive. These figures comprise no fewer than fifty-six plots, each containing numerous curves or histograms, spread across four pages. To compare the results of different scenarios, the reader is presumably expected to put these figures side by side and try to spot the differences, hampered by inconsistent axis ranges, absence of axis labels, absence of titles, absence of legends, and unreliable captions ("cyan" seems to refer to pale blue, and "orange" to something closer to red). For example, the only notable difference between Figures 3 and 4 is in the shape of a single green curve in panel I. In the main text of a published paper, one would expect fewer, more carefully curated figures drawing attention to salient features, so that the reader can infer the main results with minimal effort. The rest can be put in supplementary figures.

In summary, this paper adds somewhat to our understanding of some standard mathematical models; whether it tells us anything new about cancer is open to debate.

References<br /> (1) Kurpas, Monika K., and Marek Kimmel. "Modes of selection in tumors as reflected by two mathematical models and site frequency spectra." Frontiers in Ecology and Evolution 10 (2022): 889438.<br /> (2) Bailey, Norman TJ. The elements of stochastic processes with applications to the natural sciences. John Wiley & Sons, 1964.<br /> (3) Tarabichi, Maxime, et al. "Neutral tumor evolution?." Nature Genetics 50.12 (2018): 1630-1633.<br /> (4) McDonald, Thomas O., Shaon Chakrabarti, and Franziska Michor. "Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution." Nature Genetics 50.12 (2018): 1620-1623.<br /> (5) Balaparya, Abdul, and Subhajyoti De. "Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data." Nature Genetics 50.12 (2018): 1626-1628.<br /> (6) Noorbakhsh, Javad, and Jeffrey H. Chuang. "Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures." Nature Genetics 49.9 (2017): 1288-1289.<br /> (7) Bozic, Ivana, Chay Paterson, and Bartlomiej Waclaw. "On measuring selection in cancer from subclonal mutation frequencies." PLoS Computational Biology 15.9 (2019): e1007368.<br /> (8) Neher, Richard A., and Oskar Hallatschek. "Genealogies of rapidly adapting populations." Proceedings of the National Academy of Sciences 110.2 (2013): 437-442.<br /> (9) Gelman, Andrew, et al. Bayesian data analysis (Third Edition). Chapman and Hall/CRC, 2014.<br /> (10) Fusco, Diana, et al. "Excess of mutational jackpot events in expanding populations revealed by spatial Luria-Delbrück experiments." Nature Communications 7.1 (2016): 12760.<br /> (11) Noble, Robert, et al. "Spatial structure governs the mode of tumour evolution." Nature Ecology & Evolution 6.2 (2022): 207-217.<br /> (12) Lawson, Devon A., et al. "Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells." Nature 526.7571 (2015): 131-135.<br /> (13) Gunnarsson, Einar B., Leder, Kevin, and Foo Jasmine. "Exact site frequency spectra of neutrally evolving tumors: A transition between power laws reveals a signature of cell viability" Theoretical Population Biology 142 (2021) 67-90<br /> (14) Durrett, Richard "Branching Process Models of Cancer" Springer (2015)<br /> (15) Durrett, Richard "Probability Models for DNA Sequence Evolution" Springer Science & Business media (2008)<br /> (16) Williams, Mark J. et al. "Quantification of subclonal selection in cancer from bulk sequencing data." Nature Genetics 50 (6). 895-903 (2018)<br /> (17) Moeller, Marius E. et al. "Measures of genetic diversification in somatic tissues at bulk and single-cell resolution" eLife (2024) 12:RP89780<br /> (18) Rougier, Nicolas P., Michael Droettboom, and Philip E. Bourne. "Ten simple rules for better figures." PLoS Computational Biology 10.9 (2014): e1003833.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors present a comparison of two models of cancer evolution with advantageous drivers and deleterious passengers: a fixed-population "Moran" model, and a "Branching Process" (BP) model with dynamic population size. The Moran model is more mathematically-tractable, but since cancer is a disease of uncontrolled growth, it is unclear to me how clinically-relevant it is to consider a model with constant population size. Intriguingly, both models can explain observed Site Frequency Spectrums (SFSs) in three breast cancers, which suggests that the Moran model may have some value. This distinction between the two models is addressed well.

Strengths:

The comparisons of the various BP models (extinction/non-extinction, and balanced/supercritical) are very interesting. The survivability of rare, fitness-disadvantaged clones has huge implications for treatment resistance in general - drug resistant clones are very often disadvantaged in the absence of drug. Clinical sequencing is, most decidedly, investigating population dynamics conditioned on non-extinction, however most published models do not condition on non-extinction - an unfortunate community oversight that this publication rectifies.

Site Frequency Spectrums in three breast cancers are measured with unprecedented resolution to my knowledge (allele abundances below one in a thousand).

Detailed description of the behavior of the various models.

Weaknesses:

I do not believe Moran B is a useful theoretical distinction between Moran A. Incorporating fitness effects into the birth process, instead of the death process, is generally mathematically equivalent when time is measured in generations (or cell divisions). Visible differences in the two models in Figures 2-6 by all accounts seem to be due to the fact that Moran B experiences more evolution in the balanced/driver-dominated case, and less evolution in the passenger dominated case. We generally do not use arbitrary time steps for this reason - we quantify time in 'generations'.

Reviewer #1 (Public Review):

Summary:

This study offers a new perspective. ACTL7A and ACTL7B play roles in epigenetic regulation in spermiogenesis. Actin-like 7 A (ACTL7A) is essential for acrosome formation, fertilization, and early embryo development. ACTL7A variants cause acrosome detachment responsible for male infertility and early embryonic arrest. It has been reported that ACTL7A is localized on the acrosome in mouse sperms (Boëda et al., 2011). Previous studies have identified ACTL7A mutations (c.1118G>A:p.R373H; c.1204G>A:p.G402S, c.1117C>T:p.R373C), All these variants were located in the actin domain and were predicted to be pathogenic, affecting the number of hydrogen bonds or the arrangement of nearby protein structures (Wang et al., 2023; Xin et al., 2020; Zhao et al., 2023; Zhou et al., 2023). This work used AI to model the role of ACTL7A/B in the nucleosome remodeling complex and proposed a testis-specific conformation of SCRAP complex. This is different from previous studies.

Strengths:

This study provides a new perspective to reveal the additional roles of these proteins.

Weaknesses:

The results section contains a substantial background description. However, the results and discussion sections require streamlining. There is a lack of mutual support for data between the sections, and direct data to support the authors' conclusions are missing.

Reviewer #2 (Public Review):

Summary:

How dynamics of gene expression accompany cell fate and cellular morphological changes is important for our understanding of molecular mechanisms that govern development and diseases. The phenomenon is particularly prominent during spermatogenesis, the process which spermatogonia stem cells develop into sperm through a series of steps of cell division, differentiation, meiosis, and cellular morphogenesis. The intricacy of various aspects of cellular processes and gene expression during spermatogenesis remains to be fully understood. In this study, the authors found that testis-specific actin-related proteins (which usually participate in modifying cells' cytoskeletal systems) ACTL7A and ACTL7B were expressed and localized in the nuclei of mouse spermatocytes and spermatids. Based on this observation, the authors analyzed protein sequence conservations of ACTL7B across dozens of species and identified a putative nuclear localization sequence (NLS) that is often responsible for the nuclear import of proteins that carry them. Using molecular biology experiments in a heterologous cell system, the authors verified the potential role of this internal NLS and found it indeed could facilitate the nuclear localization of marker proteins when expressed in cells. Using gene-deleted mouse models they generated previously, the authors showed that deletion of Actl7b caused changes in gene expression and mis-localization of nucleosomal histone H3 and chromatin regulator histone deacetylase HDAC1 and 2, supporting their proposed roles of ACTL7B in regulating gene expression. The authors further used alpha-Fold 2 to model the potential protein complexes that could be formed between the ARPs (ACTL7A and ACTL7B) and known chromatin modifiers, such as INO80 and SWI/SNF complexes and found that consistent with previous findings, it is likely that ACTL7A and ACTL7B interact with the chromatin-modifying complexes through binding to their alpha-helical HSA domain cooperatively. These results suggest that ACTL7B possesses novel functions in regulating chromatin structure and thus gene expression beyond conventional roles of cytoskeleton regulation, providing alternative pathways for understanding how gene expression is regulated during spermatogenesis and the etiology of relevant infertility diseases.

Strengths:

The authors provided sufficient background to the study and discussions of the results. Based on their previous research, this study utilized numerous methods, including protein complex structural modeling method alpha-fold 2 Multimers, to further investigate the functional roles of ACTL7B. The results presented here are in general of good quality. The identification of a potential internal NLS in ACTL7B is mostly convincing, in line with the phenotypes presented in the gene deletion model.

Weaknesses:

While the study offered an interesting new look at the functions of ARP proteins during spermatogenesis, some of the study is mainly theoretical speculations, including the protein complex formation. Some of the results may need further experimental verifications, for example, differentially expressed genes that were found in potentially spermatogenic cells at different developmental stages, in order to support the conclusions and avoid undermining the significance of the study.

Reviewer #3 (Public Review):

In this manuscript, Pierre Ferrer and colleagues explore the exciting possibility that, in the male germ line, the composition and function of deeply conserved chromatin remodeling complexes is fine-tuned by the addition of testis-specific actin-related proteins (ARPs). In this regard, the Authors aim to extend previously reported non-canonical (transcriptional) roles of ARPs in somatic cells to the unique developmental context of the germ line. The manuscript is focused on the potential regulatory role in post-meiotic transcription of two ARPs: ACTL7A and ACTL7B (particularly the latter). The canonical function of both testis-specific ARPs in spermatogenesis is well established, as they have been previously shown to be required for the extensive cellular morphogenesis program driving post-meiotic development (spermiogenesis). Disentangling the actual functions of ACTL7A and ACTL7B as transcriptional regulators from their canonical role in the profound morphological reshaping of post-meiotic cells (a process that also deeply impacts nuclear architecture and regulation) represents a key challenge in terms of interpreting the reported findings (see below).

The authors begin by documenting, via fluorescence microscopy, the intranuclear localization of ACTL7B. This ARP is convincingly shown to accumulate in the nucleus of spermatocytes and spermatids. Using a series of elegant reporter-based experiments in a somatic cell line, the authors map the driver of this nuclear accumulation to a potential NLS sequence in the ACTL7B actin-like body domain. Ferrer and colleagues then performed a testicular RNA-seq analysis in ACTL7B KO mice to define the putative role of ACTL7B in male germ cell transcription. They report substantial changes to the testicular transcriptome - particularly the upregulation of several classes of genes - in ACTL7B KO mice. However, wild-type testes were used as controls for this experiment, thus introducing a clear confounding effect to the analysis (ACTL7B KO testes have extensive post-meiotic defects due to the canonical role of ACTL7B in spermatid development). Then, the authors employ cutting-edge AI-driven approaches to predict that both ACTL7A and ACTL7B are likely to bind to four key chromatin remodeling complexes. Although these predictions are based on a robust methodology, they would certainly benefit from experimental validation. Finally, the authors associate the loss of ACTL7B with decreased lysine acetylation and lower levels of the HDAC1 and HDAC3 chromatin remodelers in the nucleus of developing spermatids.

Globally, these data may provide important insight into the unique processes male germ cells employ to sustain their extraordinarily complex transcriptional program. Furthermore, the concept that (comparably younger) testis-specific proteins can be incorporated into ancient chromatin remodeling complexes to modulate their function in the germ line is timely and exciting.

It is my opinion that the manuscript would benefit from additional experimental validation to better support the authors' conclusions. In particular, I believe that addressing two critical points would substantially strengthen the message of the manuscript:

(1) The proposed role of ACTL7B in post-meiotic transcriptional regulation temporally overlaps with the protein's previously reported canonical functions in spermiogenesis (PMID: 36617158 and 37800308). Indeed, the canonical functions of ACTL7B have been shown to have a profound effect at the level of spermatid morphology and to impact nuclear organization. This potentially renders the observed transcriptional deregulation in ACTL7B KO testes an indirect consequence of spermatid morphology defects. I acknowledge that it is experimentally difficult to disentangle the proposed intranuclear roles of ACTL7B from the protein's well-documented cytoplasmic function. Perhaps the generation of a NLS-scrambled ACTL7B variant could offer some insight. In light of the substantial investment this approach would represent, I would suggest, as an alternative, that instead of using wild-type testes as controls for the transcriptome and chromatin localization assays, the authors consider the possibility of using testicular tissue from a mutant with similarly abnormal spermiogenesis but due to transcription-independent defects. This would, in my opinion, offer a more suitable baseline to compare ACTL7B KO testes with.

(2) The manuscript would greatly benefit if experimental validation of the AI-driven predictions were to be provided (in terms of the binding capacity of ACTL7A and ACTL7B to key chromatin remodeling complexes). More so it seems that the authors have the technical expertise / available mass spectrometry data required for this purpose (lines 664-665). Still on this topic, given the predicted interactions of ACTL7A and ACTL7B with the SRCAP, EP400, SMARCA2 and SMARCA4 complexes (Figure 7), it is rather counter-intuitive that the Authors chose for their immunofluorescence assays, in ACTL7B KO testes, to determine the chromatin localization of HDAC1 and HDAC3, rather than that of any of above four complexes.

Reviewer #2 (Public Review):

Summary:

The goals of this study were to develop a genetic approach that would specifically and comprehensively target axo-axonic cells (AACs) throughout the brain and then to describe the patterns and characteristics of the targeted AACs in multiple, selected brain regions. The investigators have been successful in providing the most complete description of the regional distribution of putative (pAACs) throughout the brain to date. The supporting evidence is convincing, and the findings should serve as a guide for more detailed studies of AACs within each brain region and lead to new insights into their connectivity and functional organization of this important group of GABAergic interneurons.

Strengths:

The study has numerous strengths. A major strength is the development of a unique intersectional genetic strategy that uses cell lineage (Nkx2.1) and molecular (Unc5b or Pthlh) markers to identify AACs specifically and, apparently, nearly completely throughout the mouse brain. While AACs have been described previously in the cerebral cortex, hippocampus and amygdala, there has been no specific genetic marker that selectively identifies all AACs in these regions.

Importantly, the current genetic strategy labels pAACs in additional brain regions, including the claustrum-insular complex, extended amygdala, and several olfactory centers in which AACs have not been previously recognized. In general, the findings provide support for the specificity of the methods for targeting AACs and include several examples of labeling near markers of axon initial segments, providing validation of their AAC identity.

The descriptions and numerous low magnification images of the brain provide a roadmap for subsequent, detailed studies of AACs in numerous brain regions. The overview and summaries of the findings in the Abstract, Introduction and Discussion are particularly clear and helpful in placing the extensive regional descriptions of AACs in context.

Weaknesses:

Considering the unique and striking characteristics of AACs, it would have been ideal to include a clear, high resolution confocal image of an AAC from the Unc5b;Nkx2.1 mouse that would display the beauty of these cells with their numerous cartridges of axon terminals, emanating from a single AAC. While several cells are illustrated, the processes are often obscured by other labeling or the background created by the blue Dapi labeling. A high-resolution image of an isolated cell would not only support the identity of the cells as AACs but also demonstrate the potential advantages of their labeling for more detailed anatomical and neurophysiological studies. High magnification views of the axon terminals adjacent to AnkG-labeled axon initial segments are included and provide strong support for the identity of the cells. However, they cannot convey the extensiveness and patterns of the axonal arborizations of these cells.

The intersectional genetic methods included use of the lineage marker Nkx2.1 with either Unc5b or Pthlh as the molecular marker. As described, the mice with intersectional targeting of Nkx2.1 and Unc5b appear to show the most specific brain-wide labeling for AACs, and the majority of the descriptions are from these mice. The targeting with Nkx2.1 and Pthlh is less convincing and there appears to be a disconnect between the descriptions and the images. While the descriptions emphasize that the labeling is very similar in the two types of mice, the images suggest distinct differences, including labeling of non AACs in striatum and layer 4 of the cortex in the Pthlh;Nkx2.1 mouse, as described in the manuscript. In addition, the Pthlh;Nkx2.1 mouse has higher cell targeting in some regions and fewer labeled cells in others. Perhaps it would be more accurate to present the Pthlh;Nkx2.1 mouse as differing from the Unc5b;Nkx2.1 mouse, but useful for AAC labeling in select regions and under some conditions, such as following tamoxifen administration at specific ages. As currently presented, the inclusion of the Pthlh;Nkx2.1 detracts from the otherwise convincing argument that the Unc5b;Nkx2.1 mouse provides a specific and comprehensive way to identify AACs.

Reviewer #3 (Public Review):

Summary:

Raudales et al. aimed at providing an insight into the brain-wide distribution and synaptic connectivity of bona fide GABAergic inhibitory interneuron subtypes focusing on the axo-axonic cell (AAC), one of the most distinctive interneuron subtypes, which innervates the axon initial segments of glutamatergic projection neurons. They establish intersectional genetic strategies that enable them to specifically and comprehensively capture AACs based on their lineage (Nkx2.1) and marker expression (Unc5b, Pthlh). They find that AACs are deployed across essentially all the pallium-derived brain structures as well as anterior olfactory nucleus, taenia tecta, and lateral septum. They show that AACs in distinct areas and layers of the neocortex as well as different subregions of the hippocampal formation display unique soma and synaptic density and morphological variations. Rabies virus-based retrograde monosynaptic input tracing reveals that AACs in the neocortex, the hippocampus, and the basolateral amygdala receive synaptic inputs from common as well as specific brain regions and supports the utility of this novel genetic approach. This study elucidates brain-wide neuroanatomical features and morphological variations of AACs with solid techniques and analysis. Their novel AAC-targeting strategies will facilitate the study of their development and function in different brain regions. The conclusions in this paper are well supported by the data. However, there are a few minor comments.

(1) The authors added a description about validation of ChCs in the method section: "Validation was conducted with high-magnification confocal microscopy and defined by a cell exhibiting at least two RFP-labelled axons colocalized with AIS labelled by AnkryinG or Phospho-IκBα". However, this does not clearly define pAACs themselves. If they follow this criteria, an RFP-labeled cell exhibiting only one synaptic cartridge that is colocalized with an AIS should be a pAAC. Is this what the authors are triying to say?

On the other hand, in the response to reviewers, the authors apparently define pAACs in a different way, in which they more focus on the number of cells exhibiting cartridges that are associated with AISs in a certain anatomical region rather than the number of cartridges per cell.

"For BNST we did not positively identify more than a few exhibiting overlap with AnkryinG/IκBα, so we currently leave them as pAACs"<br /> "Putative AAC (pAACs) refers to populations in which relatively few single cell examples of AACs exhibiting co-localized cartridges were found"

The authors need to directly define pAACs.

(2) In the response to reviewers, the authors claimed that both Pthlh and Unc5b mice are useful for studying developing AACs. It would be nice if they include this content in the text (e.g. Discussion).

Reviewer #1 (Public Review):

Summary:

In this study, Rosenblum et al introduce a novel and automatic way of calculating sleep cycles from human EEG. Previous results have shown that the slope of the non-oscillatory component of the power spectrum (called the aperiodic or fractal component) changes with the sleep stage. Building on this, the authors present an algorithm that extracts the continuous-time fluctuations in the fractal slope and propose that peaks in this variable can be used to identify sleep cycle limits. Cycles defined in this way are termed "fractal cycles". The main focus of the article is a comparison of fractal and classical, manually defined sleep cycles in numerous datasets.

Strengths:

The manuscript amply illustrates through examples the strong overlap between fractal and classical cycle identification. Accordingly, a high percentage (81%) can be matched one-to-one between methods and sleep cycle duration is well correlated (around R = 0.5). Moreover, the methods track certain global changes in sleep structure in different populations: shorter cycles in children and longer cycles in patients medicated with REM-suppressing anti-depressants. Finally, a major strength of the results is that they show similar agreement between fractal and classical sleep cycle length in 5 different data sets, showing that it is robust to changes in recording settings and methods.

These results suggest that the fractal cycle methodology could provide a valuable new method to study sleep architecture and avoid the time-consuming steps of manual cycle identification. Moreover, it has the potential to be applied to animal studies which rarely deal with sleep cycle structure.

Weaknesses:

The match between fractal and classical cycles is not one-to-one. For example, the fractal method identifies a correlation between age and cycle duration in adults that is not apparent with the classical method. This raises the question as to whether differences are due to one method being more reliable than another or whether they are also identifying different underlying biological differences. It is not clear for example whether the agreement between the two methods is better or worse than between two human scorers, which generally serve as a gold standard to validate novel methods. The authors provide some insight into differences between the methods that could account for differences in results. However, given that the fractal method is automatic it would be important to clearly identify criteria for recordings in which it will produce similar results to the classical method.

Reviewer #2 (Public Review):

Summary:

This study focused on using strictly the slope of the power spectral density (PSD) to perform automated sleep scoring and evaluation of the durations of sleep cycles. The method appears to work well because the slope of the PSD is highest during slow-wave sleep, and lowest during waking and REM sleep. Therefore, when smoothed and analyzed across time, there are cyclical variations in the slope of the PSD, fit using an IRASA (Irregularly resampled auto-spectral analysis) algorithm proposed by Wen & Liu (2016).

Strengths:

The main novelty of the study is that the non-fractal (oscillatory) components of the PSD that are more typically used during sleep scoring can be essentially ignored because the key information is already contained within the fractal (slope) component. The authors show that for the most part, results are fairly consistent between this and conventional sleep scoring, but in some cases show disagreements that may be scientifically interesting.

Weaknesses:

One weakness of the study, from my perspective, was that the IRASA fits to the data (e.g. the PSD, such as in Figure 1B), were not illustrated. One cannot get a sense of whether or not the algorithm is based entirely on the fractal component or whether the oscillatory component of the PSD also influences the slope calculations. This should be better illustrated, but I assume the fits are quite good.

The cycles detected using IRASA are called fractal cycles. I appreciate the use of a simple term for this, but I am also concerned whether it could be potentially misleading? The term suggests there is something fractal about the cycle, whereas it's really just that the fractal component of the PSD is used to detect the cycle. A more appropriate term could be "fractal-detected cycles" or "fractal-based cycle" perhaps?

The study performs various comparisons of the durations of sleep cycles evaluated by the IRASA-based algorithm vs. conventional sleep scoring. One concern I had was that it appears cycles were simply identified by their order (first, second, etc.) but were not otherwise matched. This is problematic because, as evident from examples such as Figure 3B, sometimes one cycle conventionally scored is matched onto two fractal-based cycles. In the case of the Figure 3B example, it would be more appropriate to compare the duration of conventional cycle 5 vs. fractal cycle 7, rather than 5 vs. 5, as it appears is currently being performed.

There are a few statements in the discussion that I felt were either not well-supported. L629: about the "little biological foundation" of categorical definitions, e.g. for REM sleep or wake? I cannot agree with this statement as written. Also about "the gradual nature of typical biological processes". Surely the action potential is not gradual and there are many other examples of all-or-none biological events.

The authors appear to acknowledge a key point, which is that their methods do not discriminate between awake and REM periods. Thus their algorithm essentially detected cycles of slow-wave sleep alternating with wake/REM. Judging by the examples provided this appears to account for both the correspondence between fractal-based and conventional cycles, as well as their disagreements during the early part of the sleep cycle. While this point is acknowledged in the discussion section around L686. I am surprised that the authors then argue against this correspondence on L695. I did not find the "not-a-number" controls to be convincing. No examples were provided of such cycles, and it's hard to understand how positive z-values of the slopes are possible without the presence of some wake unless N1 stages are sufficient to provide a detected cycle (in which case, then the argument still holds except that its alterations between slow-wave sleep and N1 that could be what drives the detection).

To me, it seems important to make clear whether the paper is proposing a different definition of cycles that could be easily detected without considering fractals or spectral slopes, but simply adjusting what one calls the onset/offset of a cycle, or whether there is something fundamentally important about measuring the PSD slope. The paper seems to be suggesting the latter but my sense from the results is that it's rather the former.

Reviewer #1 (Public Review):

Summary:

This paper shows that E. coli exhibits a chemotactic response to potassium by measuring both the motor response (using a bead assay) and the intracellular signaling response (CheY phosporylation level via FRET) to step changes in potassium concentration. They find increase in potassium concentration induces a considerable attractant response, with amplitude comparable to aspartate, and cells can quickly adapt (and generally over-adapt). The authors propose that the mechanism for potassium response is through modifying intracellular pH; they find both that potassium modifies pH and other pH modifiers induce similar attractant responses. It is also shown, using Tar- and Tsr-only mutants, that these two chemoreceptors respond to potassium differently. Tsr has a standard attractant response, while Tar has a biphasic response (repellent-like then attractant-like). Finally, the authors use computer simulations to study the swimming response of cells to a periodic potassium signal secreted from a biofilm and find a phase delay that depends on the period of oscillation.

Strengths:

The finding that E. coli can sense and adapt to potassium signals and the connection to intracellular pH is quite interesting and this work should stimulate future experimental and theoretical studies regarding the microscopic mechanisms governing this response. The evidence (from both the bead assay and FRET) that potassium induces an attractant response is convincing, as is the proposed mechanism involving modification of intracellular pH. The updated manuscript controls for the impact of pH on the fluorescent protein brightness that can bias the measured FRET signal. After correction the response amplitude and sharpness (hill coefficient) are comparable to conventional chemoattractants (e.g. aspartate), indicating the general mechanisms underlying the response may be similar. The authors suggest that the biphasic response of Tar mutants may be due to pH influencing the activity of other enzymes (CheA, CheR or CheB), which will be an interesting direction for future study.

Weaknesses:

The measured response may be biased by adaptation, especially for weak potassium signals. For other attractant stimuli, the response typically shows a low plateau before it recovers (adapts). In the case of potassium, the FRET signal does not have an obvious plateau following the stimuli of small potassium concentrations, perhaps due to the faster adaptation compared to other chemoattractants. It is possible cells have already partially adapted when the response reaches its minimum, so the measured response may be a slight underestimate of the true response. Mutants without adaptation enzymes appear to be sensitive to potassium only at much larger concentrations, where the pH significantly disrupts the FRET signal; more accurate measurements would require the development of new mutants and/or measurement techniques.

Note added after the second revision: The authors made a reasonable argument regarding the effects of adaptation, which were estimated to be small.

Reviewer #1 (Public Review):

In this paper, the authors evaluate the utility of brain-age derived metrics for predicting cognitive decline by performing a 'commonality' analysis in a downstream regression that enables the different contribution of different predictors to be assessed. The main conclusion is that brain-age derived metrics do not explain much additional variation in cognition over and above what is already explained by age. The authors propose to use a regression model trained to predict cognition ('brain cognition') as an alternative suited to applications of cognitive decline. While this is less accurate overall than brain age, it explains more unique variance in the downstream regression.

Comments on revised version:

I thank the authors for the revision of the manuscript and for being more explicit about the inherent conceptual limitations of Brain Age / Brain Cognition. I have no further comments.

Reviewer #1 (Public Review):

In this work the authors propose a new regulatory role for one the most abundant circRNAs, circHIPK3. They demonstrate that circHIPK3 interacts with an RNA binding protein (IGF2BP2), sequestering it away from its target mRNAs. This interaction is shown to regulates the expression of hundreds of genes that share a specific sequence motif (11-mer motif) in their untranslated regions (3'-UTR), identical to one present in circHIPK3 where IGF2BP2 binds. The study further focuses on the specific case of STAT3 gene, whose mRNA product is found to be downregulated upon circHIPK3 depletion. This suggests that circHIPK3 sequesters IGF2BP2, preventing it from binding to and destabilizing STAT3 mRNA. The study presents evidence supporting this mechanism and discusses its potential role in tumor cell progression. These findings contribute to the growing complexity of understanding cancer regulation and highlight the intricate interplay between circRNAs and protein-coding genes in tumorigenesis.

Strengths:

The authors show mechanistic insight into a proposed novel "sponging" function of circHIPK3 which is not mediated by sequestering miRNAs but rather a specific RNA binding protein (IGF2BP2). They address the stoichiometry of the molecules involved in the interaction, which is a critical aspect that is frequently overlooked in this type of studies. They provide both genome-wide analysis and a specific case (STAT3) which is relevant for cancer progression. Overall, the authors have significantly improved their manuscript in their revised version.

Weaknesses:

There are seemingly contradictory effects of circHIPK3 and STAT3 depletion in cancer progression. However, the authors have addressed these issues in their revised manuscript, incorporating potential reasons that might explain such complexity.

Reviewer #2 (Public Review):

The manuscript by Okholm and colleagues identified an interesting new instance of ceRNA involving a circular RNA. The data are clearly presented and support the conclusions. Quantification of the copy number of circRNA and quantification of the protein were performed, and this is important to support the ceRNA mechanism.

This is the second rebuttal and the authors further improved the manuscript. The data are of interest for the large spectrum of readers of the journal.

Reviewer #3 (Public Review):

Summary:

In Okholm et al., the authors evaluate the functional impact of circHIPK3 in bladder cancer cells. By knocking it down and performing an RNA-seq analysis, the authors found thousand deregulated genes which look unaffected by miRNAs sponging function and that are, instead, enriched for a 11-mer motif. Further investigations showed that the 11-mer motif is shared with the circHIPK3 and able to bind the IGF2BP2 protein. The authors validated the binding of IGF2BP2 and demonstrated that IGF2BP2 KD antagonizes the effect of circHIPK3 KD and leads to the upregulation of genes containing the 11-mer. Among the genes affected by circHIPK3 KD and IGF2BP2 KD, resulting in downregulation and upregulation respectively, the authors found STAT3 gene which also consistently leads to the concomitant upregulation of one of its targets TP53. The authors propose a mechanism of competition between circHIPK3 and IGF2BP2 triggered by IGF2BP2 nucleation, potentially via phase separation.

Strengths:

The number of circRNAs continues to drastically grow however the field lacks detailed molecular investigations. The presented work critically addresses some of the major pitfalls in the field of circRNAs and there has been a careful analysis of aspects frequently poorly investigated. The time-point KD followed by RNA-seq, investigation of miRNAs-sponge function of circHIPK3, identification of 11-mer motif, identification and validation of IGF2BP2, and the analysis of copy number ratio between circHIPK3 and IGF2BP2 in assessing the potential ceRNA mode of action have been extensively explored and, comprehensively convincing.

Weaknesses:

The authors addressed the majority of the weak points raised initially. However the role played by the circHIPK3 in cancer remains elusive and not elucidated in full in this study.

Overall, the presented study surely adds some further knowledge in describing circHIPK3 function, its capability to regulate some downstream genes, and its interaction and competition for IGF2BP2. However, whereas the experimental part sounds technically logical, it remains unclear the overall goal of this study and the achieved final conclusions.

This study is a promising step forward in the comprehension of the functional role of circHIPK3. These data could possibly help to better understand the circHIPK3 role in cancer

Reviewer #1 (Public Review):

This paper describes RNA-sensing guide RNAs for controlled activation of CRISPR modification. This works by having an extended guide RNA with a sequence that folds back onto the targeting sequence such that the guide RNA cannot hybridise to its genomic target. The CRISPR is "activated" by the introduction of another RNA, referred to as a trigger, that competes with this "back folding" to make the guide RNA available for genome targeting. The authors first confirm the efficacy of the approach using several RNA triggers and a GFP reporter that is activated by dCas9 fused to transcriptional activators. A major potential application of this technique is the activation of CRISPR in response to endogenous biomarkers. As these will typically be longer than the first generation triggers employed by the authors they test some extended triggers, which also work though not always to the same extent. They then introduce MODesign which may enable the design of bespoke or improved triggers. After that, they determine that the mode of activation by the RNA trigger involves cleavage of the RNA complexes. Finally, they test the potential for their system to work in a developmental setting - specifically zebrafish embryos. There is some encouraging evidence, though the effects appear more subtle than those originally obtained in cell culture.

Overall, the potential of a CRISPR system that can be activated upon sensing an RNA is high and there are a myriad of opportunities and applications for it. This paper represents a reasonable starting point having developed such a system in principle.<br /> The weakness of the study is that it does not demonstrate that the system can be used in a completely natural setting. This would require an endogenous transcript as the RNA trigger with a clear readout. The authors now acknowledge this limitation in their revised manuscript. Future studies and experiments should focus on these aspects in order for the system to be employed to its full and intended potential.

Reviewer #1 (Public Review):

In the presence of predators, animals display attenuated foraging responses and increased defensive behaviors that serve to protect them from potential predatory attacks. Previous studies have shown that the basolateral nucleus of the amygdala (BLA) and the periaqueductal gray matter (PAG) are necessary for the acquisition and expression of conditioned fear responses. However, it remains unclear how BLA and PAG neurons respond to predatory threats when animals are foraging for food. To address this question, Kim and colleagues conducted in vivo electrophysiological recordings from BLA and PAG neurons and assessed approach-avoidance responses while rats search for food in the presence of a robotic predator.

The authors observed that rats exhibited a significant increase in the latency to obtain the food pellets and a reduction in the pellet success rate when the predator robot was activated. A subpopulation of PAG neurons showing increased firing rate in response to the robot activation didn't change their activity in response to food pellet retrieval during the pre- or post-robot sessions. Optogenetic stimulation of PAG neurons increased the latency to procure the food pellet in a frequency- and intensity-dependent manner, similar to what was observed during the robot test. Combining optogenetics with single-unit recordings, the authors demonstrated that photoactivation of PAG neurons increased the firing rate of 10% of BLA cells. A subsequent behavioral test in 3 of these same rats demonstrated that BLA neurons responsive to PAG stimulation displayed higher firing rates to the robot than BLA neurons nonresponsive to PAG stimulation. Next, because the PAG does not project monosynaptically to the BLA, the authors used a combination of retrograde and anterograde neural tracing to identify possible regions that could convey robot-related information from PAG to the BLA. They observed that neurons in specific areas of the paraventricular nucleus of the thalamus (PVT) that are innervated by PAG fibers contained neurons that were retrogradely labeled by the injection of CTB in the BLA. In addition, PVT neurons showed increased expression of the neural activity marker cFos after the robot test, suggesting that PVT may be a mediator of PAG signals to the BLA.

Overall, the idea that the PAG interacts with the BLA via the midline thalamus during a predator vs. foraging test is new and quite interesting. The authors have used appropriated tools to address their questions.

In this revised version of the manuscript, the authors have made important modifications in the text, inserted new data analyses, and incorporated additional references, as recommended by the reviewers. These modifications have significantly improved the quality of the manuscript.

Reviewer #2 (Public Review):

The authors characterized activity of the dorsal periaqueductal gray (dPAG) - basolateral amygdala (BLA) circuit. They show that BLA cells that are activated by dPAG stimulation are also more likely to be activated by a robot predator. These same cells are also more likely to display synchronous firing.

The authors also replicate prior results showing that dPAG stimulation evokes fear and the dPAG is activated by a predator.

Lastly, the report performs anatomical tracing to show that the dPAG may act on the BLA via the paraventricular thalamus (PVT). Indeed, the PVT receives dPAG projections and also projects to the BLA. However, the authors do not show if the PVT mediates dPAG to BLA communication with any functional behavioral assay. Furthermore, the authors also do not thoroughly characterize the activity of BLA cells during the predatory assay.

The major impact in the field would be to add evidence to their prior work, strengthening the view that the BLA can be downstream of the dPAG.

Reviewer #3 (Public Review):

In the present study, the authors examined how dPAG neurons respond to predatory threats and how dPAG and BLA communicate threat signals. The authors employed single-unit recording and optogenetics tools to address these issues in an 'approach food-avoid predator' paradigm. They characterized dPAG and BLA neurons responsive to a looming robot predator and found that dPAG opto-stimulation elicited fleeing and increased BLA activity. Importantly, they found that dPAG stimulation produces activity changes in subpopulations of BLA neurons related to predator detection, thus supporting the idea that dPAG conveys innate fear signals to the amygdala. In addition, injections of anterograde and retrograde tracers into the dPAG and BLA, respectively, along with the examination of c-FOS activity in midline thalamic relay stations, suggest that the paraventricular nucleus of the thalamus (PVT) may serve as a mediator of dPAG to BLA neurotransmission. Of relevance, the study helps to validate an important concept that dPAG mediates primal fear emotion and may engage upstream amygdalar targets to evoke defensive responses. The series of experiments provide a compelling case for supporting their conclusions. The study brings important concepts revealing dynamics of fear-related circuits particularly attractive to a broad audience, from basic scientists interested in neural circuits to psychiatrists.

Reviewer #1 (Public Review):

Summary:

This work describes a new protein factor required for filamentous phage assembly. The protein PSB15 binds to the packaging signal of the ssDNA, Trx and cardiolipin. A mechanism how the phage DNA is targeted to the assembly site in the bacterial inner membrane is discussed.

Strengths:

The work describes a clever way to detect factors required for phage propagation by looking at the plaque size of pseudorevertants that arise after infection of a phage with a directed mutation in the packaging signal. This led to the detection of a phage protein expressed from ORF9, the PSB15.

The authors convincingly show that PSB15 is expressed in infected cells and can complement a phage with a mutated orf9.

Weaknesses:

Given the fact that the phage LF-UK is not well explored, many open questions should be mentioned in the introduction. For the study, it is important to know if the phageLF-UK has a mimick or homolog of gV and gXI, and if not, whether PSB15 could take their role.

I am not convinced of the proposition of their term "checkpoint". The truth is that the authors do not know the real purpose of PSB15. I do not see an advantage for a checkpoint that only adds an additional step to enter the phage assembly site. There must be a biochemical reason for the action of PSB15. Looking at Figure 7, the step from "Release" to "Loading" is just adding many unknowns, e.g. how to transfer the DNA, how to dispose of PSB15 and Trx? Also, in the previous step are three question marks that do not add any solid information.

The in vivo study of subcellular localization is very questionable. Why is there a single fluorescent dot if there are thousands of PSB15 molecules expressed in the cell? I have my doubts that the conclusions the authors make here are correct and meaningful. The movies do not add anything significant.

Reviewer #2 (Public Review):

Secretion of the prototypical F-associated filamentous phage (Ff) of E. coli depends on the selective binding of a hairpin (the packaging signal, PS) by two phage encoded protein, pVII and pIX. PVII and pIX target the PS to IM channels formed by pI and pIV. However, integrative filamentous phages lack a homologue of pIX and pIV, and many of them also lack a homologue of pVII, raising questions on the assembly and secretion of new phages. In the manuscript, Yueh et al. present the identification of a phage-encoded protein, PSB15, which binds to the PS signal of a Xanthomonas integrative filamentous phage, ΦLf-UK. They showed that PSB15 is required for viral assembly and is conserved in several other integrative filamentous phages. They further analyzed how PSB15 binds to PS and demonstrated that it associates to the IM, which targets phage DNA to it. Finally, they show that thioredoxin, the only host protein that was found to be essential for Ff secretion, interacts with PSB15 and releases the PSB15-PS complex from the IM. These results are important because they elucidate a major step in the secretion of integrative filamentous phage, and the role of thioredoxin on filamentous phage secretion in general.

I found the data and interpretation convincing. However, the presentation and description are confusing in places because the reader has to juggle between figures. A scheme depicting what is known and unknown in the integration of Ff phages and interactive filamentous phages in the introduction would be useful to the general reader.

Joint Public Review:

Summary

This manuscript explores the transcriptomic identities of olfactory ensheathing cells (OECs), glial cells that support life-long axonal growth in olfactory neurons, as they relate to spinal cord injury repair. The authors show that transplantation of cultured, immunopurified rodent OECs at a spinal cord injury site can promote injury-bridging axonal regrowth. They then characterize these OECs using single-cell RNA sequencing, identifying five subtypes and proposing functional roles that include regeneration, wound healing, and cell-cell communication. They identify one progenitor OEC subpopulation and also report several other functionally relevant findings, notably, that OEC marker genes contain mixtures of other glial cell type markers (such as for Schwann cells and astrocytes), and that these cultured OECs produce and secrete Reelin, a regrowth-promoting protein that has been disputed as a gene product of OECs.

This manuscript offers an extensive, cell-level characterization of OECs, supporting their potential therapeutic value for spinal cord injury and suggesting potential underlying repair mechanisms. The authors use various approaches to validate their findings, providing interesting images that show the overlap between sprouting axons and transplanted OECs, and showing that OEC marker genes identified using single-cell RNA sequencing are present in vivo, in both olfactory bulb tissue and spinal cord after OEC transplantation.

Despite the breadth of information presented, however, further quantification of results and explanation of experimental approaches would be needed to support some of the authors' claims. Additionally, a more thorough discussion is needed to contextualize their findings relative to previous work.

(1) Important quantification is lacking for the data presented. For example, multiple figures include immunohistochemistry or immunocytochemistry data (Figures 1, 5, 6), but they are presented without accompanying measures like fractions of cells labeled or comparisons against controls. As a result, for axons projecting via OEC bridges in Figure 1, it is unclear how common these bridges are in the presence or absence of OECs. For Figure 6., it is unclear whether cells having an alternative OEC morphology coincide with progenitor OEC subtype marker genes to a statistically significant degree. Similar quantification is missing in other types of data such as Western blot images (Fig. 9) and OEC marker gene data (for which p-values are not reported; Table S2).

The addition of quantitative measures and, where appropriate, statistical comparisons with p-values or other significance measures, would be important for supporting the authors' claims and more rigorously conveying the results.

(2) Some aspects of the experimental design that are relevant to the interpretation of the results are not explained. For example, OECs appear to be collected from only female rats, but the potential implications of this factor are not discussed.

Additionally, it is unclear from the manuscript to what degree immunopurified cells are OECs as opposed to other cell types. The antibody used to retain OECs, nerve growth factor receptor p75 (Ngfr-p75), can also be expressed by non-OEC olfactory bulb cell types including astrocytes [1-3]. The possible inclusion of Ngfr-p75-positive but non-OEC cell types in the OEC culture is not sufficiently addressed. Such non-OEC cell types are also not distinguished in the analysis of single-cell RNA sequencing data (only microglia, fibroblasts, and OECs are identified; Figure 2). Thus, it is currently unclear whether results related to the OEC subtype may have been impacted by these experimental factors.

(3) The introduction, while well written, does not discuss studies showing no significant effect of OEC implantation after spinal cord injury. The discussion also fails to sufficiently acknowledge this variability in the efficacy of OEC implantation. This omission amplifies bias in the text, suggesting that OECs have significant effects that are not fully reflected in the literature. The introduction would need to be expanded to properly address the nuance suggested by the literature regarding the benefits of OECs after spinal cord injury. Additionally, in the discussion, relating the current study to previous work would help clarify how varying observations may relate to experimental or biological factors.

(a) Cragnolini, A.B. et al., Glia, (2009), doi: 10.1002/glia.20857.<br /> (b) Vickland H. et al., Brain Res., (1991), doi: 10.1016/0006-8993(91)91659-O.<br /> (c) Ung K. et al., Nat Commun., (2021), doi: 10.1038/s41467-021-25444-3.

Reviewer #1 (Public Review):

Summary:

It seems as if the main point of the paper is about the new data related to rat fish although your title is describing it as extant cartilaginous fishes and you bounce around between the little skate and ratfish. So here's an opportunity for you to adjust the title to emphasize ratfish is given the fact that leader you describe how this is your significant new data contribution. Either way, the organization of the paper can be adjusted so that the reader can follow along the same order for all sections so that it's very clear for comparative purposes of new data and what they mean. My opinion is that I want to read, for each subheading in the results, about the the ratfish first because this is your most interesting novel data. Then I want to know any confirmation about morphology in little skate. And then I want to know about any gaps you fill with the cat shark. (It is ok if you keep the order of "skate, ratfish, then shark, but I think it undersells the new data).

Strengths:

The imagery and new data availability for ratfish are valuable and may help to determine new phylogenetically informative characters for understanding the evolution of cartilaginous fishes. You also allude to the fossil record.

Opportunities:

I am concerned about the statement of ratfish paedomorphism because stage 32 and 33 were not statistically significantly different from one another (figure and prior sentences). So, these ratfish TMDs overlap the range of both 32 and 33. I think you need more specimens and stages to state this definitely based on TMD. What else leads you to think these are paedomorphic? Right now they are different, but it's unclear why. You need more outgroups.

Your headings for the results subsection and figures are nice snapshots of your interpretations of the results and I think they would be better repurposed in your abstract, which needs more depth.

Historical literature is more abundant than what you've listed. Your first sentence describes a long fascination and only goes back to 1990. But there are authors that have had this fascination for centuries and so I think you'll benefit from looking back. Especially because several of them have looked into histology and development of these fishes.

I agree that in the past 15 years or so a lot more work has been done because it can be done using newer technologies and I don't think your list is exhaustive. You need to expand this list and history which will help with your ultimate comparative analysis without you needed to sample too many new data yourself.

I'd like to see modifications to figure 7 so that you can add more continuity between the characters, illustrated in figure 7 and the body of the text. Generally Holocephalans are the outgroup to elasmobranchs - right now they are presented as sister taxa with no ability to indicate derivation. Why isn't the catshark included in this diagram?

In the last paragraph of the introduction, you say that "the data argue" and I admit, I am confused. Whose data? Is this a prediction or results or summary of other people's work? Either way, could be clarified to emphasize the contribution you are about to present.

Reviewer #2 (Public Review):

General comment:

This is a very valuable and unique comparative study. An excellent combination of scanning and histological data from three different species is presented. Obtaining the material for such a comparative study is never trivial. The study presents new data and thus provides the basis for an in-depth discussion about chondrichthyan mineralised skeletal tissues. I have, however, some comments. Some information is lacking and should be added to the manuscript text. I also suggest changes in the result and the discussion section of the manuscript.

Introduction:

The reader gets the impression almost no research on chondrichthyan skeletal tissues was done before the 2010 ("last 15 years", L45). I suggest to correct that and to cite also previous studies on chondrichthyan skeletal tissues, this includes studies from before 1900.

Material and Methods:

Please complete L473-492: Three different Micro-CT scanners were used for three different species? ScyScan 117 for the skate samples. Catshark different scanner, please provide full details. Chimera Scncrotron Scan? Please provide full details for all scanning protocols.

TMD is established in the same way in all three scanners? Actually not possible. Or, all specimens were scanned with the same scanner to establish TMD? If so please provide the protocol.

Please complete L494 ff: Tissue embedding medium and embedding protocol is missing. Specimens have been decalcified, if yes how? Have specimens been sectioned non-decalcified or decalcified?

Please complete L506 ff: Tissue embedding medium and embedding protocol is missing. Description of controls are missing.

Results:

L147: It is valuable and interesting to compare the degree of mineralisation in individuals from the three different species. It appears, however, not possible to provide numerical data for Tissue Mineral Density (TMD). First requirement, all specimens must be scanned with the same scanner and the same calibration values. This in not stated in the M&M section. But even if this was the case, all specimens derive from different sample locations and have, been preserved differently. Type of fixation, extension of fixation time in formalin, frozen, unfrozen, conditions of sample storage, age of the samples, and many more parameters, all influence TMD values. Likewise the relative age of the animals (adult is not the same as adult) influences TMD. One must assume different sampling and storage conditions and different types of progression into adulthood. Thus, the observation of different degrees of mineralisation is very interesting but I suggest not to link this observation to numerical values.

Parts of the results are mixed with discussion. Sometimes, a result chapter also needs a few references but this result chapter is full of references.

Based on different protocols, the staining characteristics of the tissue are analysed. This is very good and provides valuable additional data. The authors should inform the not only about the staining (positive of negative) abut also about the histochemical characters of the staining. L218: "fast green positive" means what? L234: "marked by Trichrome acid fuchsin" means what? And so on, see also L237, L289, L291<br /> Discussion

Please completely remove figure 7, please adjust and severely downsize the discussion related to figure 7. It is very interesting and valuable to compare three species from three different groups of elasmobranchs. Results of this comparison also validate an interesting discussion about possible phylogenetic aspects. This is, however, not the basis for claims about the skeletal tissue organisation of all extinct and extant members of the groups to which the three species belong. The discussion refers to "selected representatives" (L364), but how representative are the selected species? Can there be a extant species that represents the entire large group, all sharks, rays or chimeras? Are the three selected species basal representatives with a generalist life style?

Please completely remove the discussion about paedomorphosis in chimeras (already in the result section). This discussion is based on a wrong idea about the definition of paedomorphosis. Paedomorphosis can occur in members of the same group. Humans have paedormorphic characters within the primates, Ambystoma mexicanum is paedormorphic within the urodeals. Paedomorphosis does not extend to members of different vertebrate branches. That elasmobranchs have a developmental stage that resembles chimera vertebra mineralisation does not define chimera vertebra centra as paedomorphic. Teleost have a herocercal caudal fin anlage during development, that does not mean the heterocercal fins in sturgeons or elasmobranchs are paedomorphic characters.

L432-435: In times of Gadow & Abott (1895) science had completely wrong ideas bout the phylogenic position of chondrichthyans within the gnathostomes. It is curious that Gadow & Abott (1895) are being cited in support of the paedomorphosis claim.

The SCPP part of the discussion is unrelated to the data obtained by this study. Kawaki & WEISS (2003) describe a gene family (called SCPP) that control Ca-binding extracellular phosphoproteins in enamel, in bone and dentine, in saliva and in milk. It evolved by gene duplication and differentiation. They date it back to a first enamel matrix protein in conodonts (Reif 2006). Conodonts, a group of enigmatic invertebrates have mineralised structures but these structure are neither bone nor mineralised cartilage. Cat fish (6 % of all vertebrate species) on the other hand, have bone but do not have SCPP genes (Lui et al. 206). Other calcium binding proteins, such as osteocalcin, were initially believed to be required for mineralisation. It turned out that osteocalcin is rather a mineralisation inhibitor, at best it regulates the arrangement collagen fiber bundles. The osteocalcin -/- mouse has fully mineralised bone. As the function of the SCPP gene product for bone formation is unknown, there is no need to discuss SCPP genes. It would perhaps be better to finish the manuscript with summery that focuses on the subject and the methodology of this nice study.

Reviewer #1 (Public Review):

Summary:

The main observation that the sperm from CRISP proteins 1 and 3 KO lines are post-fertilization less developmentally competent is convincing. However, the molecular characterization of the mechanism that leads to these defects and the temporal appearance of the defects requires additional studies.

Strengths:

The generation of these double mutant mice is valuable for the field. Moreover, the fact that the double mutant line of Crisp 1 and 3 is phenotypically different from the Crisp 1 and 4 line suggests different functions of these epididymis proteins. The methods used to demonstrate that developmental defects are largely due to post-fertilization defects are also a considerable strength. The initial characterization of these sperm has altered intracellular Ca2+ levels, and increased rates of DNA fragmentation are valuable.

Weaknesses:

The study is mechanistically incomplete because there is no direct demonstration that the absence of these proteins alters the epididymal environment and fluid, wherein during the passage through the epididymis the sperm become affected. Also, a direct demonstration of how the proteins in question cause or lead to DNA damage and increased Ca2+ requires further characterization.

Reviewer #2 (Public Review):

The authors showed that CRISP1 and CRISP3, secreted proteins in the epididymis, are required for early embryogenesis after fertilization through DNA integrity in cauda epididymal sperm. This paper is the first report showing that the epididymal proteins are required for embryogenesis after fertilization. However, some data in this paper (Table 1 and Figure 2A) are overlapped in a published paper (Curci et al., FASEB J, 34,15718-15733, 2020; PMID: 33037689). Furthermore, the authors did not address why the disruption of CRISP1/3 leads to these phenomena (the increased level of the intracellular Ca2+ level and impaired DNA integrity in sperm) with direct evidence. Therefore, if the authors can address the following comments to improve the paper's novelty and clarification, this paper may be worthwhile to readers.

Reviewer #1 (Public Review):

Summary:

Using a cross-modal sensory selection task in head-fixed mice, the authors attempted to characterize how different rules reconfigured representations of sensory stimuli and behavioral reports in sensory (S1, S2) and premotor cortical areas (medial motor cortex or MM, and ALM). They used silicon probe recordings during behavior, a combination of single-cell and population-level analyses of neural data, and optogenetic inhibition during the task.

Strengths:

A major strength of the manuscript was the clarity of the writing and motivation for experiments and analyses. The behavioral paradigm is somewhat simple but well-designed and well-controlled. The neural analyses were sophisticated, clearly presented, and generally supported the authors' interpretations. The statistics are clearly reported and easy to interpret. In general, my view is that the authors achieved their aims. They found that different rules affected preparatory activity in premotor areas, but not sensory areas, consistent with dynamical systems perspectives in the field that hold that initial conditions are important for determining trial-based dynamics.

I think this is a well-performed, well-written and interesting study that shows differences in rule representations in sensory and premotor areas, and finds that rules reconfigure preparatory activity in motor cortex to support flexible behavior.

Reviewer #2 (Public Review):

Summary:

Chang et al. investigated neuronal activity firing patterns across various cortical regions in an interesting context-dependent tactile vs visual detection task, developed previously by the authors (Chevee et al., 2021; doi: 10.1016/j.neuron.2021.11.013). The authors report the important involvement of a medial frontal cortical region (MM, probably a similar location to wM2 as described in Esmaeili et al., 2021 & 2022; doi: 10.1016/j.neuron.2021.05.005; doi: 10.1371/journal.pbio.3001667) in mice for determining task rules.

Strengths:

The experiments appear to have been well carried out and the data well analysed. The manuscript clearly describes the motivation for the analyses and reaches clear and well-justified conclusions. I find the manuscript interesting and exciting!

Weaknesses:

I did not find any major weaknesses.

Reviewer #3 (Public Review):

Summary:

This study examines context-dependent stimulus selection by recording neural activity from several sensory and motor cortical areas along a sensorimotor pathway, including S1, S2, MM, and ALM. Mice are trained to either withhold licking or perform directional licking in response to visual or tactile stimulus. Depending on the task rule, the mice must respond to one stimulus modality while ignoring the other. Neural activity to the same tactile stimulus is modulated by task in all the areas recorded, with significant activity changes in a subset of neurons and population activity occupying distinct activity subspaces. Recordings further reveal a contextual signal in the pre-stimulus baseline activity that differentiates task context. This signal is correlated with subsequent task modulation of neural activity. Comparison across brain areas shows that this contextual signal is stronger in frontal cortical regions than sensory regions. Analyses link this signal to behavior by showing that it tracks the behavioral performance switch during task rule transitions. Silencing activity in frontal cortical regions during the baseline period impairs behavioral performance.

Strengths:

This is a carefully done study with solid results and thorough controls. The authors identify a contextual signal in baseline neural activity that predicts rule-dependent decision-related activity. The comprehensive characterization across a sensorimotor pathway is another strength. Analyses and perturbation experiments link this contextual signal to animals' behavior. The results provide a neural substrate that will surely inspire follow-up mechanistic investigations.

Weaknesses:

None. The authors have further improved the manuscript during the revision with additional analyses.

Impact:

This study reports an important neural signature for context-dependent decision-making that has important implications for mechanisms of context-dependent neural computation in general.

Reviewer #1 (Public Review):

Summary:

The classical pro/antisaccade task has become a valuable diagnostic tool in neurology and psychiatry (Antoniades et al., 2013, Vision Res). Although it is well-established that antisaccades require substantially longer latencies than prosaccades, the exact attentional mechanisms underlying these differences are not yet fully elucidated. This study investigates the separate influences of exogenous and endogenous attention on saccade generation. These two mechanisms are often confounded in classical pro/antisaccade tasks. In the current study, the authors build on their previous work using an urgent choice task (Salinas et al., 2019, eLife) to time-resolve the influences of exogenous and endogenous factors on saccade execution. The key contribution of the current study is to show that, when controlling for exogenous capture, antisaccades continue to require longer processing times. This longer processing time may be explained by a coupling between endogenous attention and saccade motor plans.

Strengths:

In the classical pro/antisaccade task the direction of exogenous capture (caused by the presentation of the cue) is typically congruent with the direction of prosaccades and incongruent with antisaccades. A key strength of the current study is the introduction of different experimental conditions that control for the effects of exogenous capture on saccade generation. In particular, Experiments 3 and 4 provide strong evidence for two independent (exogenous and endogenous) mechanisms that guide saccadic choices, acting at different times. Differences in timing for pro and antisaccades during the endogenous phase were consistent and independent of whether the exogenous capture biased early saccades toward the correct prosaccade direction or toward the correct antisaccade directions.

As in previous studies by the same group (Salinas et al., 2019, eLife; Goldstein et al., 2023, eLife), the detailed analysis of the time course of goal-directed saccades allowed the authors to determine the exact, additional time of 30 ms that is necessary to generate a correct antisaccade versus prosaccade.

Overall, the manuscript is very well written, and the data are presented clearly.

Weaknesses:

The main research question could be defined more clearly. In the abstract and at some points throughout the manuscript, the authors indicate that the main purpose of the study was to assess whether the allocation of endogenous attention requires saccade planning [e.g., ll.3-5 or ll.247-248]. While the data show a coupling between endogenous attention and saccades, they do not point to a specific direction of this coupling (i.e., whether endogenous attention is necessary to successfully execute a saccade plan or whether a saccade plan necessarily accompanies endogenous attention).

Some of the analyses were performed only on subgroups of the participants. The reporting of these subgroup analyses is transparent and data from all participants are reported in the supplementary figures. Still, these subgroup analyses may make the data appear more consistent, compared to when data is considered across all participants. For instance, the exogenous capture in Experiments 1 and 2 appears much weaker in Figure 2 (subgroup) than Figure S3 (all participants). Moreover, because different subgroups were used for different analyses, it is often difficult to follow and evaluate the results. For instance, the tachometric curves in Figure 2 (see also Figure 3 and 4) show no motor bias towards the cue (i.e., performance was at ~50% for rPTs <75 ms). I assume that the subsequent analyses of the motor bias were based on a very different subgroup. In fact, based on Figure S2, it seems that the motor bias was predominantly seen in the unreliable participants. Therefore, I often found the figures that were based on data across all participants (Figures 7 and S3) more informative to evaluate the overall pattern of results.

Reviewer #2 (Public Review):

Goldstein et al. provide a thorough characterization of the interaction of attention and eye movement planning. These processes have been thought to be intertwined since at least the development of the Premotor Theory of Attention in 1987, and their relationship has been a continual source of debate and research for decades. Here, Goldstein et al. capitalize on their novel urgent saccade task to dissociate the effects of endogenous and exogenous attention on saccades towards and away from the cue. They find that attention and eye movements are, to some extent, linked to one another but that this link is transient and depends on the nature of the task. A primary strength of the work is that the researchers are able to carefully measure the timecourse of the interaction between attention and eye movements in various well-controlled experimental conditions. As a result, the behavioral interplay of two forms of attention (endogenous and exogenous) is illustrated at the level of tens of milliseconds as they interact with the planning and execution of saccades towards and away from the cued location. Overall, the results allow the authors to make meaningful claims about the time course of visual behavior, attention, and the potential neural mechanisms at a timescale relevant to everyday human behavior.

Reviewer #3 (Public Review):

Summary and overall evaluation:

Human vision is inherently limited so that only a small part of a visual scene can be perceived at a given moment. To address this limitation, the visual system has evolved a number of strategies and mechanisms that work in concert. First, humans move their eyes using saccadic eye movements. This allows us to place the high-resolution region in the center of the eye's retina (the fovea centralis) on objects of interest so that these are sampled with high acuity. Second, salient, conspicuous stimuli that appear abruptly and/or differ strongly from the other stimuli in the scene, seem to automatically attract ("exogenous") attention, so that a large share of the neuronal "resources" for visual processing is devoted to the stimuli, which improves the perception of the stimuli. Third, stimuli that are important for the current task and the current behavioral goals can be prioritized by attention mechanisms ("endogenous" attention), which also secures their allocated share of processing resources and helps them be perceived. It is well-established that eye movements are closely linked to the mechanisms of attention (for a review, see Carrasco, 2011, cited in the manuscript). However, it is still unclear what role voluntary, endogenous attention plays in the control of saccadic eye movements.

The present study used an experimental procedure involving time-pressure for responding, in order to uncover how the control of saccades by exogenous and endogenous attention unfolds over time. The findings of the study indicate that saccade planning was indeed influenced by the locus of endogenous attention, but that this influence was short-lasting and could be overcome quickly. Taken together, the present findings reveal new dynamics between endogenous attention and eye movement control, and lead the way for studying them using experiments under time pressure.

The results provided by the present study advance our understanding of vision, eye movements, and their control by brain mechanisms for attention. In addition, they demonstrate how tasks involving time pressure can be used to study the dynamics of cognitive processes. Therefore, the present study seems highly important not only for vision science, but also for psychology, (cognitive) neuroscience, and related research fields more generally.

Strengths:

The experiments of the study are performed with great care and rigor and the data is analyzed thoroughly and comprehensively. Overall, the results support the authors' conclusions, so I have only minor comments (see below). Taken together, the findings seem important for a wide community of researchers in vision science, psychology, and neuroscience.

Weaknesses (minor points):

(1) In this experimental paradigm, participants must decide where to saccade based on the color of the cue in the visual periphery (they should have made a prosaccade toward a green cue and an antisaccade away from a magenta cue). Thus, irrespective of whether the cue signaled that a prosaccade or an antisaccade was to be made, the identity of the cue was always essential for the task (as the authors explain on p. 5, lines 129-138). Also, the location where the cue appeared was blocked, and thus known to the participants in advance, so that endogenous attention could be directed to the cue at the beginning of a trial (e.g., p. 5, lines 129-132). These aspects of the experimental paradigm differ from the classic prosaccade/antisaccade paradigm (e.g. Antoniades et al., 2013, Vision Research). In the classic paradigm, the identity of the cues does not have to be distinguished to solve the task, since there is only one stimulus that should be looked at (prosaccade) or away from (antisaccade), and whether a prosaccade or antisaccade was required is constant across a block of trials. Thus, in contrast to the present paradigm, in the classic paradigm, the participants do not know where the cue is about to appear, but they know whether to perform a prosaccade or an antisaccade based on the location of the cue.

The present paradigm keeps the location of the cue constant in a block of trials by intention, because this ensures that endogenous attention is allocated to its location and is not overpowered by the exogenous capture of attention that would happen when a single stimulus appeared abruptly in the visual field. Thus, the reason for keeping the location of the cue constant seems convincing. However, I wondered what consequences the constant location would have for the task representations that persist across the task and govern how attention is allocated. In the classic paradigm, there is always a single stimulus that captures attention exogenously (as it appears abruptly). In a prosaccade block, participants can prioritize the visual transient caused by the stimulus, and follow it with a saccade to its coordinates. In an antisaccade block, following the transient with a saccade would always be wrong, so that participants could try to suppress the attention capture by the transient, and base their saccade on the coordinates of the opposite location. Thus, in prosaccade and antisaccade blocks, the task representations controlling how visual transients are processed to perform the task differ. In the present task, prosaccades and antisaccades cannot be distinguished by the visual transients. Thus, such a situation could favor endogenous attention and increase its influence on saccade planning, even though saccade planning under more naturalistic conditions would be dominated by visual transients. I suggest discussing how this (and vice versa the emphasis on visual transients in the classic paradigm) could affect the generality of the presented findings (e.g., how does this relate to the interpretation that saccade plans are obligatorily coupled to endogenous attention? See, Results, p. 10, lines 306-308, see also Deubel & Schneider, 1996, Vision Research).

(2) Discussion (p. 16, lines 472-475): The authors suppose that "It is as if the exogenous response was automatically followed by a motor bias in the opposite direction. Perhaps the oculomotor circuitry is such that an exogenous signal can rapidly trigger a saccade, but if it does not, then the corresponding motor plan is rapidly suppressed regardless of anything else.". I think this interesting point should be discussed in more detail. Could it also be that instead of suppression, other currently active motor plans were enhanced? Would this involve attention? Some attention models assume that attention works by distributing available (neuronal) processing resources (e.g., Desimone & Duncan, 1995, Annual Review of Neuroscience; Bundesen, 1990, Psychological Review; Bundesen et al., 2005, Psychological Review) so that the information receiving the largest share of resources results in perception and is used for action, but this happens without the active suppression of information.

(3) Methods, p. 19, lines 593-596: It is reported that saccades were scored based on their direction. I think more information should be provided to understand which eye movements entered the analysis. Was there a criterion for saccade amplitude? I think it would be very helpful to provide data on the distributions of saccade amplitudes or on their accuracy (e.g. average distance from target) or reliability (e.g. standard deviation of landing points). Also, it is reported that some data was excluded from the analysis, and I suggest reporting how much of the data was excluded. Was the exclusion of the data related to whether participants were "reliable" or "unreliable" performers?

(4) Results, p. 9, lines 262-266: Some data analyses are performed on a subset of participants that met certain performance criteria. The reasons for this data selection seem convincing (e.g. to ensure empirical curves were not flat, line 264). Nevertheless, I suggest to explain and justify this step in more detail. In addition, if not all participants achieved an acceptable performance and data quality, this could also speak to the experimental task and its difficulty. Thus, I suggest discussing the potential implications of this, in particular, how this could affect the studied mechanisms, and whether it could limit the presented findings to a special group within the studied population.

Reviewer #2 (Public Review):

This manuscript illustrates the power of "combined" research, incorporating a range of tools, both old and new to answer a question. This thorough approach identifies a novel target in a well-established signalling pathway and characterises a new player in Drosophila CNS development.

Largely, the experiments are carried out with precision, meeting the aims of the project, and setting new targets for future research in the field. It was particularly refreshing to see the use of multi-omics data integration and Targeted DamID (TaDa) findings to triage scRNA-seq data. Some of the TaDa methodology was unorthodox, however, this does not affect the main finding of the study. The authors (in the revised manuscript) have appropriately justified their TaDa approaches and mentioned the caveats in the main text.

Their discovery of Spar as a neuropeptide precursor downstream of Alk is novel, as well as its ability to regulate activity and circadian clock function in the fly. Spar was just one of the downstream factors identified from this study, therefore, the potential impact goes beyond this one Alk downstream effector.

Reviewer #3 (Public Review):

Summary:

The receptor tyrosine kinase Anaplastic Lymphoma Kinase (ALK) in humans is nervous system expressed and plays an important role as an oncogene. A number of groups have been studying ALK signalling in flies to gain mechanistic insight into its various roles. In flies, ALK plays a critical role in development, particularly embryonic development and axon targeting. In addition, ALK was also shown to regulate adult functions including sleep and memory. In this manuscript, Sukumar et al., used a suite of molecular techniques to identify downstream targets of ALK signalling. They first used targeted DamID, a technique that involves a DNA methylase to RNA polymerase II, so that GATC sites in close proximity to PolII binding sites are marked. They performed these experiments in wild type and ALK loss of function mutants (using an Alk dominant negative ALkDN), to identify Alk responsive loci. Comparing these loci with a larval single cell RNAseq dataset identified neuroendocrine cells as an important site of Alk action. They further combined these TaDa hits with data from RNA seq in Alk Loss and Gain of Function manipulations to identify a single novel target of Alk signalling - a neuropeptide precursor they named Sparkly (Spar) for its expression pattern. They generated a mutant allele of Spar, raised an antibody against Spar, and characterised its expression pattern and mutant behavioural phenotypes including defects in sleep and circadian function.

Strengths:

The molecular biology experiments using TaDa and RNAseq were elegant and very convincing. The authors identified a novel gene they named Spar. They also generated a mutant allele of Spar (using CrisprCas technology) and raised an antibody against Spar. These experiments are lovely, and the reagents will be useful to the community. The paper is also well written, and the figures are very nicely laid out making the manuscript a pleasure to read.

Weaknesses:

The manuscript has improved very substantially in revision. The authors have clearly taken the comments on board in good faith.

Editors' note: The authors have satisfactorily addressed the concerns raised in the previous rounds of review. These were related to the unconventional analysis of the TaDa data, the addition of other means of down regulated gene function, and the nature of analyses of behavioural data.

Reviewer #1 (Public Review):

Olszyński and colleagues present data showing variability from canonical "aversive calls", typically described as long 22 kHz calls rodents emit in aversive situations. Similarly long but higher-frequency (44 kHz) calls are presented as a distinct call type, including analyses both of their acoustic properties and animals' responses to hearing playback of these calls. While this work adds an intriguing and important reminder, namely that animal behavior is often more variable and complex than perhaps we would like it to be, there is some caution warranted in the interpretation of these data.

The exclusive use of males is a major concern lacking adequate justification and should be disclosed in the title and abstract to ensure readers are aware of this limitation. With several reported sex differences in rat vocal behaviors this means caution should be exercised when generalizing from these findings. The occurrence of an estrus cycle in typical female rats is not justification for their exclusion. Note also that male rodents experience great variability in hormonal states as well, distinguishing between individuals and within individuals across time. The study of endocrinological influences on behavior can be separated from the study of said behavior itself, across all sexes. Similarly, concerns about needing to increase the number of animals when including all sexes are usually unwarranted (see Shansky [2019] and Phillips et al. [2023]).

Regarding the analysis where calls were sorted using DBSCAN based on peak frequency and duration, my comment on the originally reviewed version stands. It seems that the calls are sorted by an (unbiased) algorithm into categories based on their frequency and duration, and because 44kHz calls differ by definition on frequency and duration the fact that the algorithm sorts them as a distinct category is not evidence that they are "new calls [that] form a separate, distinct group". I appreciate that the authors have softened their language regarding the novelty and distinctness of these calls, but the manuscript contains several instances where claims of novelty and specificity (e.g. the subtitle on line 193) is emphasized beyond what the data justifies.

The behavioral response to call playback is intriguing, although again more in line with the hypothesis that these are not a distinct type of call but merely represent expected variation in vocalization parameters. Across the board animals respond rather similarly to hearing 22 kHz calls as they do to hearing 44 kHz calls, with occasional shifts of 44 kHz call responses to an intermediate between appetitive and aversive calls. This does raise interesting questions about how, ethologically, animals may interpret such variation and integrate this interpretation in their responses. However, the categorical approach employed here does not address these questions fully.

I appreciate the amendment in discussing the idea of arousal being the key determinant for the increased emission of 44kHz, and the addition of other factors. Some of the items in this list, such as annoyance/anger and disgust/boredom, don't really seem to fit the data. I'm not sure I find the idea that rats become annoyed or disgusted during fear conditioning to be a particularly compelling argument. As such the list appears to be a collection of emotion-related words, with unclear potential associations with the 44kHz calls.

Later in the Discussion the authors argue that the 44kHz aversive calls signal an increased intensity of a negative valence emotional state. It is not clear how the presented arguments actually support this. For example, what does the elongation of fear conditioning to 10 trials have to do with increased negative emotionality? Is there data supporting this relationship between duration and emotion, outside anthropomorphism? Each of the 6 arguments presented seems quite distant from being able to support this conclusion.

In sum, rather than describing the 44kHz long calls as a new call type, it may be more accurate to say that sometimes aversive calls can occur at frequencies above 22 kHz. Individual and situational variability in vocalization parameters seems to be expected, much more so than all members of a species strictly adhering to extremely non-variable behavioral outputs.

[Editors' note: The reviewer agrees that the additional analysis has ruled out the possibility that the calls are due to fatigue.]

Reviewer #1 (Public Review):

Summary:

The authors assess the accuracy of short variant calling (SNPs and indels) in bacterial genomes using Oxford Nanopore reads generated on R10.4 flow cells from a very similar genome (99.5% ANI), examining the impact of variant caller choice (three traditional variant callers: bcftools, freebayes, and longshot, and three deep learning based variant callers: clair3, deep variant, and nano caller), base calling model (fast, hac and sup) and read depth (using both simplex and duplex reads).

Strengths:

Given the stated goal (analysis of variant calling for reads drawn from genomes very similar to the reference), the analysis is largely complete and results are compelling. The authors make the code and data used in their analysis available for re-use using current best practices (a computational workflow and data archived in INSDC databases or Zenodo as appropriate).

Weaknesses:

While the medaka variant caller is now deprecated for diploid calling, it is still widely used for haploid variant calling and should at least be mentioned (even if the mention is only to explain its exclusion from the analysis).

Appraisal:

The experiments the authors engaged in are well structured and the results are convincing. I expect that these results will be incorporated into "best practice" bacterial variant calling workflows in the future.

Reviewer #2 (Public Review):

Summary:

Hall et al describe the superiority of ONT sequencing and deep learning-based variant callers to deliver higher SNP and Indel accuracy compared to previous gold-standard Illumina short-read sequencing. Furthermore, they provide recommendations for read sequencing depth and computational requirements when performing variant calling.

Strengths:

The study describes compelling data showing ONT superiority when using deep learning-based variant callers, such as Clair3, compared to Illumina sequencing. This challenges the paradigm that Illumina sequencing is the gold standard for variant calling in bacterial genomes. The authors provide evidence that homopolymeric regions, a systematic and problematic issue with ONT data, are no longer a concern in ONT sequencing.

Weaknesses:

(1) The inclusion of a larger number of reference genomes would have strengthened the study to accommodate larger variability (a limitation mentioned by the authors).

(2) In Figure 2, there are clearly one or two samples that perform worse than others in all combinations (are always below the box plots). No information about species-specific variant calls is provided by the authors but one would like to know if those are recurrently associated with one or two species. Species-specific recommendations could also help the scientific community to choose the best sequencing/variant calling approaches.

(3) The authors support that a read depth of 10x is sufficient to achieve variant calls that match or exceed Illumina sequencing. However, the standard here should be the optimal discriminatory power for clinical and public health utility (namely outbreak analysis). In such scenarios, the highest discriminatory power is always desirable and as such an F1 score, Recall and Precision that is as close to 100% as possible should be maintained (which changes the minimum read sequencing depth to at least 25x, which is the inflection point).

(4) The sequencing of the samples was not performed with the same Illumina and ONT method/equipment, which could have introduced specific equipment/preparation artefacts that were not considered in the study. See for example https://academic.oup.com/nargab/article/3/1/lqab019/6193612.

Reviewer #3 (Public Review):

Hall et al. benchmarked different variant calling methods on Nanopore reads of bacterial samples and compared the performance of Nanopore to short reads produced with Illumina sequencing. To establish a common ground for comparison, the authors first generated a variant truth set for each sample and then projected this set to the reference sequence of the sample to obtain a mutated reference. Subsequently, Hall et al. called SNPs and small indels using commonly used deep learning and conventional variant callers and compared the precision and accuracy from reads produced with simplex and duplex Nanopore sequencing to Illumina data. The authors did not investigate large structural variation, which is a major limitation of the current manuscript. It will be very interesting to see a follow-up study covering this much more challenging type of variation.

In their comprehensive comparison of SNPs and small indels, the authors observed superior performance of deep learning over conventional variant callers when Nanopore reads were basecalled with the most accurate (but also computationally very expensive) model, even exceeding Illumina in some cases. Not surprisingly, Nanopore underperformed compared to Illumina when basecalled with the fastest (but computationally much less demanding) method with the lowest accuracy. The authors then investigated the surprisingly higher performance of Nanopore data in some cases and identified lower recall with Illumina short read data, particularly from repetitive regions and regions with high variant density, as the driver. Combining the most accurate Nanopore basecalling method with a deep learning variant caller resulted in low error rates in homopolymer regions, similar to Illumina data. This is remarkable, as homopolymer regions are (or, were) traditionally challenging for Nanopore sequencing.

Lastly, Hall et al. provided useful information on the required Nanopore read depth, which is surprisingly low, and the computational resources for variant calling with deep learning callers. With that, the authors established a new state-of-the-art for Nanopore-only variant, calling on bacterial sequencing data. Most likely these findings will be transferred to other organisms as well or at least provide a proof-of-concept that can be built upon.

As the authors mention multiple times throughout the manuscript, Nanopore can provide sequencing data in nearly real-time and in remote regions, therefore opening up a ton of new possibilities, for example for infectious disease surveillance.

However, the high-performing variant calling method as established in this study requires the computationally very expensive sup and/or duplex Nanopore basecalling, whereas the least computationally demanding method underperforms. Here, the manuscript would greatly benefit from extending the last section on computational requirements, as the authors determine the resources for the variant calling but do not cover the entire picture. This could even be misleading for less experienced researchers who want to perform bacterial sequencing at high performance but with low resources. The authors mention it in the discussion but do not make clear enough that the described computational resources are probably largely insufficient to perform the high-accuracy basecalling required.

Reviewer #1 (Public Review):

Summary:

Winged seeds or ovules from the Devonian are crucial to understanding the origin and early evolutionary history of wind dispersal strategy. Based on exceptionally well-preserved fossil specimens, the present manuscript documented a new fossil plant taxon (new genus and new species) from the Famennian Series of Upper Devonian in eastern China and demonstrated that three-winged seeds are more adapted to wind dispersal than one-, two- and four-winged seeds by using mathematical analysis.

Strengths:

The manuscript is well organised and well presented, with superb illustrations. The methods used in the manuscript are appropriate.

Weaknesses:

I would only like to suggest moving the "Mathematical analysis of wind dispersal of ovules with 1-4 wings" section from the supplementary information to the main text, leaving the supplementary figures as supplementary materials.

Reviewer #2 (Public Review):

Summary:

This manuscript described the second earliest known winged ovule without a capule in the Famennian of Late Devonian. Using Mathematical analysis, the authors suggest that the integuments of the earliest ovules without a cupule, as in the new taxon and Guazia, evolved functions in wind dispersal.

Strengths:

The new ovule taxon's morphological part is convincing. It provides additional evidence for the earliest winged ovules, and the mathematical analysis helps to understand their function.

Weaknesses:

The discussion should be enhanced to clarify the significance of this finding. What is the new advance compared with the Guazia finding? The authors can illustrate the character transformations using a simplified cladogram. The present version of the main text looks flat.

Reviewer #1 (Public Review):

Summary:

By combining an analysis of the evolutionary age of the genes expressed in male germ cells, a study of genes associated with spermatocyte protein-protein interaction networks and functional experiments in Drosophila, Brattig-Correia and colleagues provide evidence for an ancient origin of the genetic program underlying metazoan spermatogenesis. This leads to identifying a relatively small core set of functional interactions between deeply conserved gene expression regulators, whose impairment is then shown to be associated with cases of human male infertility.

Strengths:

In my opinion, the work is important for three different reasons. First, it shows that, even though reproductive genes can evolve rapidly and male germ cells display a significant level of transcriptional noise, it is still possible to obtain convincing evidence that a conserved core of functionally interacting genes lies at the basis of the male germ transcriptome. Second, it reports an experimental strategy that could also be applied to gene networks involved in different biological problems. Third, the authors make a compelling case that, due to its effects on human spermatogenesis, disruption of the male germ cell orthoBackbone can be exploited to identify new genetic causes of infertility.

Weaknesses:

The main strength of the general approach followed by the authors is, inevitably, also a weakness. This is because a study rooted in comparative biology is unlikely to identify newly emerged genes that may adopt key roles in processes such as species-specific gamete recognition. Additionally, using a TPM >1 threshold for protein-coding transcripts may exclude genes, such as those encoding proteins required for gamete fusion, which are thought to be expressed at a very low level. Although these considerations raise the possibility that the chosen approach may miss information that, depending on the species, could be potentially highly functionally important, this by no means reduces its value in identifying genes belonging to the conserved genetic program of spermatogenesis.

Reviewer #2 (Public Review):

Summary:

This is a tour de force study that aims to understand the genetic basis of male germ cell development across three animal species (human, mouse, and flies) by performing a genetic program conservation analysis (using phylostratigraphy and network science) with a special emphasis on genes that peak or decline during mitosis-to-meiosis. This analysis, in agreement with previous findings, reveals that several genes active during and before meiosis are deeply conserved across species, suggesting ancient regulatory mechanisms. To identify critical genes in germ cell development, the investigators integrated clinical genetics data, performing gene knockdown and knockout experiments in both mice and flies. Specifically, over 900 conserved genes were investigated in flies, with three of these genes further studied in mice. Of the 900 genes in flies, ~250 RNAi knockdowns had fertility phenotypes. The fertility phenotypes for the fly data can be viewed using the following browser link: https://pages.igc.pt/meionav. The scope of target gene validation is impressive. Below are a few minor comments.

(1) In Supplemental Figure 2, it is notable that enterocyte transcriptomes are predominantly composed of younger genes, contrasting with the genetic age profile observed in brain and muscle cells. This difference is an intriguing observation and it would be curious to hear the author's comments.

(2) Regarding the document, the figures provided only include supplemental data; none of the main text figures are in the full PDF.

(3) Lastly, it would be great to section and stain mouse testis to classify the different stages of arrest during meiosis for each of the mouse mutants in order to compare more precisely to flies.

This paper serves as a vital resource, emphasizing that only through the analysis of hundreds of genes can we prioritize essential genes for germ cell development. its remarkable that about 60% of conserved genes have no apparent phenotype during germ cell development.

Strengths:

The high-throughput screening was conducted on a conserved network of 920 genes expressed during the mitosis-to-meiosis transition. Approximately 250 of these genes were associated with fertility phenotypes. Notably, mutations in 5 of the 250 genes have been identified in human male infertility patients. Furthermore, 3 of these genes were modeled in mice, where they were also linked to infertility. This study establishes a crucial groundwork for future investigations into germ cell development genes, aiming to delineate their essential roles and functions.

Weaknesses:

The fertility phenotyping in this study is limited, yet dissecting the mechanistic roles of these proteins falls beyond its scope. Nevertheless, this work serves as an invaluable resource for further exploration of specific genes of interest.

Reviewer #1 (Public Review):

Summary:

The manuscript by Anbarcia et al. re-evaluates the function of the enigmatic Rete Ovarii (RO), a structure that forms in close association with the mammalian ovary. The RO has generally been considered a functionless structure in the adult ovary. This manuscript follows up on a previous study from the lab that analyzed ovarian morphogenesis using high-resolution microscopy (McKey et al., 2022). The present study adds finer details to RO development and possible function by (1) identifying new markers for OR sub-regions (e.g. GFR1a labels the connecting rete) suggesting that the sub-regions are functionally distinct, (2) showing that the OR sub-regions are connected by a luminal system that allows transport of material from the extra-ovarian rete (EOR) to the inter-ovarian rete (IOG), (3) identifies proteins that are secreted into the OR lumen and that may regulate ovarian homeostasis, and finally, (4) better defines how the vasculature, nervous, and immune system integrates with the OR.

Strengths:

The data is beautifully presented and convincing. They show that the RO is composed of three distinct domains that have unique gene expression signatures and thus likely are functionally distinct.

Weaknesses:

It is not always clear what the novel findings are that this manuscript is presenting. It appears to be largely similar to the analysis done by McKey et al. (2022) but with more time points and molecular markers. The novelty of the present study's findings needs to be better articulated.

Reviewer #2 (Public Review):

A large number of ovarian experiments have been conducted - especially in morphological and molecular biology studies - specifically removing the ovarian membrane. This experiment is a good supplement to existing knowledge and plays an important role in early ovarian development and the regulation of ovarian homeostasis during the estrous cycle. There are also innovations in research ideas and methods, which will meet the requirements of experimental design and provide inspiration for other researchers.

This reviewer did not identify any major issues with the article. However, the following points could be further clarified:

(1) Is there any comparative data on the proteomics of RO and rete testis in early development? With some molecular markers also derived from rete testis, it would be better to provide the data or references.

(2) Although the size of RO and its components is quite small and difficult to operate, the researchers in this article had already been able to perform intracavitary injection of EOR and extract EOR or CR for mass spectrometry analysis. Therefore, can EOR, CR, or IOR be damaged or removed, providing further strong evidence of ovarian development function?

(3) Although IOR is shown on the schematic diagram, it cannot be observed in the immunohistochemistry pictures in Figure 1 and Figure 3. The authors should provide a detailed explanation.

Reviewer #3 (Public Review):

Summary:

The rete ovarii (RO) has long been disregarded as a non-functional structure within the ovary. In their study, Anbarci and colleagues have delineated the markers and developmental dynamics of three distinct regions of the RO - the intraovarian rete (IOR), the extraovarian rete (EOR), and the connecting rete (CR). Notably focusing on the EOR, the authors presented evidence illustrating that the EOR forms a convoluted tubular structure culminating in a dilated tip. Intriguingly, microinjections into this tip revealed luminal flow towards the ovary containing potentially secreted functional proteins. Additionally, the EOR cells exhibit associations with vasculature, macrophages, and neuronal projections, proposing the notion that the RO may play a functional role in ovarian development during critical ovariogenesis stages. By identifying marker genes within the RO, the authors have also suggested that the RO could serve as a potential structure linking the ovary with the neuronal system.

Strengths:

Overall, the reviewer commends the authors for their systematic research on the RO, shedding light on this overlooked structure in developing ovaries. Furthermore, the authors have proposed a series of hypotheses that are both captivating and scientifically significant, with the potential to reshape our understanding of ovarian development through future investigations.

Weaknesses:

There is a lack of conclusive data supporting many conclusions in the manuscript. Therefore, the paper's overall conclusions should be moderated until functional validations are conducted.

Joint Public Review:

Summary:

Idiopathic scoliosis (IS) is a common spinal deformity. Various studies have linked genes to IS, but underlying mechanisms are unclear such that we still lack understanding of the causes of IS. The current manuscript analyzes IS patient populations and identifies EPHA4 as a novel associated gene, finding three rare variants in EPHA4 from three patients (one disrupting splicing and two missense variants) as well as a large deletion (encompassing EPHA4) in a Waardenburg syndrome patient with scoliosis. EPHA4 is a member of the Eph receptor family. Drawing on data from zebrafish experiments, the authors argue that EPHA4 loss of function disrupts the central pattern generator (CPG) function necessary for motor coordination.

Strengths:

The main strength of this manuscript is the human genetic data, which provides convincing evidence linking EPHA4 variants to IS. The loss of function experiments in zebrafish strongly support the conclusion that EPHA4 variants that reduce function lead to IS.

Weaknesses:

The conclusion that disruption of CPG function causes spinal curves in the zebrafish model is not well supported. The authors' final model is that a disrupted CPG leads to asymmetric mechanical loading on the spine and, over time, the development of curves. This is a reasonable idea, but currently not strongly backed up by data in the manuscript. Potentially, the impaired larval movements simply coincide with, but do not cause, juvenile-onset scoliosis. Support for the authors' conclusion would require independent methods of disrupting CPG function and determining if this is accompanied by spine curvature. At a minimum, the language of the manuscript could be toned down, with the CPG defects put forward as a potential explanation for scoliosis in the discussion rather than as something this manuscript has "shown". An additional weakness of the manuscript is that the zebrafish genetic tools are not sufficiently validated to provide full confidence in the data and conclusions.

Reviewer #1 (Public Review):

Summary:

It is evident that studying leukocyte extravasation in vitro is a challenge. One needs to include physiological flow, culture cells and isolate primary immune cells. Timing is of utmost importance and a reproducible setup essential. Extra challenges are met when extravasation kinetics in different vascular beds is required, e.g., across the blood-brain barrier. In this study, the authors describe a reliable and reproducible method to analyze leukocyte TEM under physiological flow conditions, including this analysis. That the software can also detect reverse TEM is a plus.

Strengths:

It is quite a challenge to get this assay reproducible and stable, in particular as there is flow included. Also for the analysis, there is currently no clear software analysis program, and many labs have their own methods. This paper gives the opportunity to unify the data and results obtained with this assay under label-free conditions. This should eventually lead to more solid and reproducible results.

Also, the comparison between manual and software analysis is appreciated.

Weaknesses:

The authors stress that it can be done in BBB models, but I would argue that it is much more broadly applicable. This is not necessarily a weakness of the study but more an opportunity to strengthen the method. So I would encourage the authors to rewrite some parts and make it more broadly applicable.

Reviewer #2 (Public Review):

Summary:

This paper develops an under-flow migration tracker to evaluate all the steps of the extravasation cascade of immune cells across the BBB. The algorithm is useful and has important applications.

Strengths:

Algorithm is almost as accurate as manual tracking and importantly saves time for researchers.

Weaknesses:

Applicability can be questioned because the device used is 2D and physiological biology is in 3D. Comparisons to other automated tools was not performed by the authors.

Reviewer #3 (Public Review):

Summary:

The authors aimed to establish a faster and more efficient method of tracking steps of T-cell extravasation across the blood brain barrier. The authors developed a framework to visualize, recognize and track the movement of different immune cells across primary human and mouse brain microvascular endothelial cells without the need for fluorescence-based imaging. The authors succinctly describe the basic requirements for tracking in the introduction followed by an in-depth account of the execution.

Weaknesses and Strengths:

Materials & methods and results:

(1) The methods section also lacks details of the microfluidic device that the authors talk about in the paper. Under physiological sheer stress, the T-cells detach from the pMBMEC monolayer, and are hence unable to be detected; however, this observation requires an explanation pertaining to the reason of occurrence and potential solutions to circumvent it to ensure physiologically relevant experimental parameters.

(2) The author describes a method for debris exclusion using UFMTrack that eliminates objects of <30 pixels in size from analysis based on a mean pixel size of 400 for T lymphocytes. However, this mean pixel size appears to stem from in-vitro activated CD8 T cells, which rapidly grow and proliferate upon stimulation. In line with this, activated lymphocytes exhibit increased cytoplasmic area, making them appear less dense or "brighter" by phase microscopy compared to naïve lymphocytes, which are relatively compact and subsequently appear dimmer. Given this, it is not clear whether UFMTrack is sufficiently trained to identify naïve human lymphocytes in circulating blood, nor smaller, murine lymphocytes. Analysis of each lymphocyte subtype in terms of pixel size and intensity would be beneficial to strengthen the claim that UFMTrack can identify each of these populations. Additionally, demonstrating that UFMTrack can correctly characterize the behavior of naïve versus activated lymphocytes isolated from murine and human sources would strengthen the claim that UFMTrack can be broadly applied to study lymphocyte dynamics in diverse models without additional training

(3) Average precision was compared to the analysis of UFMTrack but it is unclear how average precision was calculated. This information should have been included in the methods section

(4) CD4 and CD8 T cells exhibit distinct biology and interaction kinetics driven in part by their MHC molecule affinity and distinct receptor expression profiles. Thus, it is unclear why two distinct mechanisms of endothelial cell activation are needed to see differences between the populations.

(5) The BMECs are barrier tissues but were cultured on µdishes in this study. To study the transmigration of T-cells across the endothelium, the model would have been more relevant on a semi-permeable membrane instead of a closed surface.

(6) Methods are provided for the isolation and expansion of human effector and memory CD4+ T cells. However, there is no mention of specific CD4+ T cell populations used for analysis with UFMTrack, nor a clear breakdown of tracking efficiency for each subpopulation. Further, there is no similar method for the isolation of CD8+ T cell compartments. A clear breakdown of the performance efficiency of UFMTrack with each cell population investigated in this study would provide greater insight into the software's performance with regard to tracking the behavior and movement of distinct immune populations.

(7) The results section is quite extensive and discusses details of establishment of the framework while highlighting both the pros and cons of the different aspects of the process, for example the limitation of the two models, 2D and 2D+T were highlighted well. However, the results section includes details which may be more fitting in the methods section.

(8) A few statements in the results section lacked literary support, which was not provided in the discussion either, such as support for increased variance of T-cell instantaneous speed on stimulated vs non-stimulated pMBMECs. Another example is the enhancement of cytokine stimulation directed T-cell movement on the pMBMECs that the authors observed but failed to relay the physiological relevance of it. The authors don't provide enough references for developments in the field prior to their work which form the basis and need for this technology.

(9) The rationale for use of OT-1 and 2D2-derived murine lymphocytes is unclear here. The OT-1 model has been generated to study antigen-specific CD8+ T cell responses, while the 2D2 model has been generated to recapitulate CD4 T cell-specific myelin oligodendrocyte glycoprotein (MOG) responses.

Figures and text:

(1) There are certain discrepancies and misarrangement of figures and text. For example, discussion of the effect of sheer flow on T cell attachment as part of the introduction in figure 1 and then mentioning it in the text again in the results section as part of figure 4 is repetitive.

(2) Section IV, subsection 1 of the results section, refers to 'data acquisition section above' in line 279, however the said section is part of materials and methods which is provided towards the end of the manuscript.

(3) There are figures in the manuscript that have not been referenced in the results section, for example, figure 3A and B. Figure 1 hasn't been addressed until subsection 7 of materials and methods

(4) A lack of significance but an observed trend of increased variance of T cell instantaneous speed is reported in line 296-298; however, the graph (figure 4G) shows a significant change in instantaneous speed between non-stimulated and TNFα-stimulated systems. This is misleading to the readers.

(5) The authors talk about three beginner experimentors testing the manual T cell tracking process but figure 5 only showcases data from two experimentors without stating the reason for excluding experimentor 1.

Discussion:

(1) While the discussion captures the major takeaways from the paper, it lacks relevant supporting references to relate the observation to physiological conditions and applicability.

(2) The discussion lacks connection to the results since the figures were not referenced while discussing an observed trend

(3) The authors briefly looked into mouse and human BMECs and their individual interaction with T-cells, but don't discuss the differences between the two, if any, that challenged their framework.

(4) Even though though the imaging tool relies on difference in appearance for detection, the authors talk about lack of feasibility in detecting transmigration of BMDMs due to their significantly different appearance. The statement lacks a problem solving approach to discuss how and why this was the case.

Relevance to the field:

Utilizing the framework provided by the authors, the application can be adapted and/or utilized for visualizing a range of different cell types, provided they are different in appearance. However, this would require extensive changes to the script and won't be adaptable in its current form.

Reviewer #1 (Public Review):

Summary:

The study seeks to establish accurate computational models to explore the role of hydrodynamic interactions on energy savings and spatial patterns in fish schools. Specifically, the authors consider a system of (one degree-of-freedom) flapping airfoils that passively position themselves with respect to the streamwise direction, while oscillating at the same frequency and amplitude, with a given phase lag and at a constant cross-stream distance. By parametrically varying the phase lag and the cross-stream distance, they systematically explore the stability and energy costs of emergent configurations. Computational findings are leveraged to distill insights into universal relationships and clarify the role of the wake of the leading foil.

Strengths:

(1) The use of multiple computational models (computational fluid dynamics, CFD, for full Navier-Stokes equations and computationally efficient inviscid vortex sheet, VS, model) offers an extra degree of reliability of the observed findings and backing to the use of simplified models for future research in more complex settings.

(2) The systematic assessment of the stability and energy savings in multiple configurations of pairs and larger ensembles of flapping foils is an important addition to the literature.

(3) The discovery of a linear phase-distance relationship in the formation attained by pairs of flapping foils is a significant contribution, which helps compare different experimental observations in the literature.

(4) The observation of a critical size effect for in-line formations of larger, above which cohesion and energetic benefits are lost at once, is a new discovery in the field.

Weaknesses:

(1) The extent to which observations on one-degree-of-freedom flapping foils could translate to real fish schools is presently unclear so some of the conclusions on live fish schools are likely to be overstated and would benefit from some more biological framing.

(2) The analysis of non-reciprocal coupling is not as novel as the rest of the study and potentially not as convincing due to the chosen linear metric of interaction (that is, the flow agreement).

Overall, this is a rigorous effort on a critical topic: findings of the research can offer important insight into the hydrodynamics of fish schooling, stimulating interdisciplinary research at the interface of computational fluid mechanics and biology.

Reviewer #2 (Public Review):

The document "Mapping spatial patterns to energetic benefits in groups of flow-coupled swimmers" by Heydari et al. uses several types of simulations and models to address aspects of stability of position and power consumption in few-body groups of pitching foils. I think the work has the potential to be a valuable and timely contribution to an important subject area. The supporting evidence is largely quite convincing, though some details could raise questions, and there is room for improvement in the presentation. My recommendations are focused on clarifying the presentation and perhaps spurring the authors to assess additional aspects:

(1) Why do the authors choose to set the swimmers free only in the propulsion direction? I can understand constraining all the positions/orientations for investigating the resulting forces and power, and I can also understand the value of allowing the bodies to be fully free in x, y, and their orientation angle to see if possible configurations spontaneously emerge from the flow interactions. But why constrain some degrees of freedom and not others? What's the motivation, and what's the relevance to animals, which are fully free?

(2) The model description in Eq. (1) and the surrounding text is confusing. Aren't the authors computing forces via CFD or the VS method and then simply driving the propulsive dynamics according to the net horizontal force? It seems then irrelevant to decompose things into thrust and drag, and it seems irrelevant to claim that the thrust comes from pressure and the drag from viscous effects. The latter claim may in fact be incorrect since the body has a shape and the normal and tangential components of the surface stress along the body may be complex.

(3) The parameter taudiss in the VS simulations takes on unusual values such as 2.45T, making it seem like this value is somehow very special, and perhaps 2.44 or 2.46 would lead to significantly different results. If the value is special, the authors should discuss and assess it. Otherwise, I recommend picking a round value, like 2 or 3, which would avoid distraction.

(4) Some of the COT plots/information were difficult to interpret because the correspondence of beneficial with the mathematical sign was changing. For example, DeltaCOT as introduced on p. 5 is such that negative indicates bad energetics as compared to a solo swimmer. But elsewhere, lower or more negative COT is good in terms of savings. Given the many plots, large amounts of data, and many quantities being assessed, the paper needs a highly uniform presentation to aid the reader.

(5) I didn't understand the value of the "flow agreement parameter," and I didn't understand the authors' interpretation of its significance. Firstly, it would help if this and all other quantities were given explicit definitions as complete equations (including normalization). As I understand it, the quantity indicates the match of the flow velocity at some location with the flapping velocity of a "ghost swimmer" at that location. This does not seem to be exactly relevant to the equilibrium locations. In particular, if the match were perfect, then the swimmer would generate no relative flow and thus no thrust, meaning such a location could not be an equilibrium. So, some degree of mismatch seems necessary. I believe such a mismatch is indeed present, but the plots such as those in Figure 4 may disguise the effect. The color bar is saturated to the point of essentially being three tones (blue, white, red), so we cannot see that the observed equilibria are likely between the max and min values of this parameter.

(6) More generally, and related to the above, I am favorable towards the authors' attempts to find approximate flow metrics that could be used to predict the equilibrium positions and their stability, but I think the reasoning needs to be more solid. It seems the authors are seeking a parameter that can indicate equilibrium and another that can indicate stability. Can they clearly lay out the motivation behind any proposed metrics, and clearly present complete equations for their definitions? Further, is there a related power metric that can be appropriately defined and which proves to be useful?

(7) Why do the authors not carry out CFD simulations on the larger groups? Some explanations should be given, or some corresponding CFD simulations should be carried out. It would be interesting if CFD simulations were done and included, especially for the in-line case of many swimmers. This is because the results seem to be quite nuanced and dependent on many-body effects beyond nearest-neighbor interactions. It would certainly be comforting to see something similar happen in CFD.

(8) Related to the above, the authors should discuss seemingly significant differences in their results for long in-line formations as compared to the CFD work of Peng et al. [48]. That work showed apparently stable groups for numbers of swimmers quite larger than that studied here. Why such a qualitatively different result, and how should we interpret these differences regarding the more general issue of the stability of tandem groups?

(9) The authors seem to have all the tools needed to address the general question about how dynamically stable configurations relate to those that are energetically optimal. Are stable solutions optimal, or not? This would seem to have very important implications for animal groups, and the work addresses closely related topics but seems to miss the opportunity to give a definitive answer to this big question.

(10) Time-delay particle model: This model seems to construct a simplified wake flow. But does the constructed flow satisfy basic properties that we demand of any flow, such as being divergence-free? If not, then the formulation may be troublesome.

Reviewer #1 (Public Review):

Summary:

This is an interesting study by Xu et al showing the effects of infection with the Treponema pallidum virus (which causes syphilis disease) on neuronal development using iPSC-derived human brain organoids as a model and single-cell RNA sequencing. This work provides an important insight into the impact of the virus on human development, bridging the gap between the phenomena observed in studies using animal models as well as non-invasive human studies showing developmental abnormalities in fetuses infected with the virus in utero through maternal vertical transmission.

Using single-cell RNAseq in combination with qPCR and immunofluorescence techniques, the authors show that T. pallidum infected organoids are smaller in size, in particular during later growth stages, contain a larger number of undifferentiated neuronal lineage cells, and exhibit decreased numbers of specific neuronal subcluster, which the authors have identified as undifferentiated hindbrain neurons.

The study is an important first step in understanding how T. pallidum affects human neuronal development and provides important insight into the potential mechanisms that underlie the neurodevelopmental abnormalities observed in infected human fetuses.

Strengths:

(1) The study is well written, and the data quality is good for the most part.

(2) The study provides an important first step in utilizing human brain organoids to study the impact of T. pallidum infection on neuronal development.

(3) The study's conclusions may provide important insight to other researchers focused on studying how viral infections impact neuronal development.

Reviewer #3 (Public Review):

This article is the first report to study the effects of T. pallidum on the neural development of an iSPC-derived brain organoid model. The study indicates that T. pallidum inhibits the differentiation of subNPC1B neurons into hindbrain neurons, hence affecting brain organoid neurodevelopment. Additionally, the TCF3 and notch signaling pathways may be involved in the inhibition of the subNPC1B-hindbrain neuron differentiation axis. While the majority of the data in this study support the conclusions, there are still some questions that need to be addressed and data quality needs to be improved. The study provides valuable insights for future investigations into the mechanisms underlying congenital neurodevelopment disability.

Reviewer #1 (Public Review):

Summary:

The study presented by Atsumi et al. is about using smartphone-driven, community-sourced data to enhance biodiversity monitoring. The idea is to leverage the widespread use of smartphones to gather data from the community quickly, contributing to a more comprehensive understanding of biodiversity. The authors discuss the importance of ecosystem services linked to biodiversity and the threats posed by human activities. It emphasizes the need for comprehensive biodiversity data to implement the Kunming-Montreal Global Biodiversity Framework. The 'Biome' mobile app, launched in Japan, uses species identification algorithms and gamification to gather over 6 million observations since 2019. While community-sourced data may have biases, incorporating it into Species Distribution Models (SDMs) improves accuracy, especially for endangered species. The app covers urban-natural gradients uniformly, enhancing traditional survey data biased towards natural areas. Combining these sources provides valuable insights into species distributions for conservation, protected area designation, and ecosystem service assessment.

Strengths:

The use of a smartphone app ('Biome') for community-driven species occurrence data collection represents an innovative and inclusive approach to biodiversity monitoring, leveraging the widespread use of smartphones. The app has successfully accumulated a large volume of species occurrence data since its launch in 2019, showcasing its effectiveness in rapidly gathering information from diverse locations. Despite challenges with certain taxa, the study highlights high species identification accuracy, especially for birds, reptiles, mammals, and amphibians, making the 'Biome' app a reliable tool for species observation. The integration of community-sourced data into Species Distribution Models (SDMs) improves the accuracy of predicting species distributions. This has implications for conservation planning, including the designation of protected areas and assessment of ecosystem services. The rapid accumulation of data and advancements in machine learning methods open up opportunities for conducting time-series analyses, contributing to the understanding of ecosystem stability and interaction strength over time. The study emphasizes the collaborative nature of the platform, fostering collaboration among diverse stakeholders, including local communities, private companies, and government agencies. This inclusive approach is essential for effective biodiversity assessment and decision-making. The platform's engagement with various stakeholders, including local communities, supports biodiversity assessment, management planning, and informed decision-making. Additionally, the app's role in fostering nature-positive awareness in society is highlighted as a significant contribution to creating a sustainable society.

Weaknesses:

While the studies make significant contributions to biodiversity monitoring, they also have some weaknesses. Firstly, relying on smartphone-driven, community-sourced data may introduce spatial and taxonomic biases. The 'Biome' app, for example, showed lower accuracy for certain taxa like seed plants, molluscs, and fishes, potentially impacting the reliability of the gathered data. Furthermore, the effectiveness of Species Distribution Models (SDMs) relies on the assumption that biases in community-sourced data can be adequately accounted for. The unique distribution patterns of the 'Biome' data, covering urban-natural gradients uniformly, might not fully represent the diversity of certain ecosystems, potentially leading to inaccuracies in the models. Moreover, the divergence in data distribution patterns along environmental gradients between 'Biome' data and traditional survey data raises concerns. The app data shows a more uniform distribution across natural-urban gradients, while traditional data is biased towards natural areas. This discrepancy may impact the representation of certain ecosystems and influence the accuracy of Species Distribution Models (SDMs). While the integration of 'Biome' data into SDMs improves accuracy, the study notes that controlling the sampling efforts is crucial. Spatially-biased sampling efforts in community-sourced data need careful consideration, and efforts to control biases are essential for reliable predictions.

Reviewer #1 (Public Review):

The revised manuscript "Diffusive lensing as a mechanism of intracellular transport and compartmentalization" is very similar to the original manuscript. The main difference between the revised and the original manuscript is that the authors have removed the reference to viscosity gradient and instead talk of diffusivity gradient. With this change the manuscript the analysis and claims in the manuscript are much more aligned. The manuscript, as the original version, explores the role of spatially varying diffusion constant in three scenarios:

(i) Spatial localization of non-particles<br /> (ii) Clustering in presence of inter-particle interactions<br /> (iii) Moment analysis for non-interacting particles in space with discrete patches of inhomogeneous diffusivity.

Since the manuscript has not changed much the strengths and weaknesses, in my opinion, remain similar to that of the original manuscript.

Strengths: The implications of a heterogeneous environment on phase separation and reaction kinetics in cells are under-explored. This makes the general theme of this manuscript relevant and interesting.

Weaknesses: The central part of the paper "diffusive lensing", i.e., particles localizing in the region of low diffusion constant is not new. Some of the papers authors cite already show that. The parts on phase separation and frap analysis that could provide new results are not rigorous enough for a theory paper.

I reiterate some of my comments from the original version that are valid for the revised version as well.

My main criticism was not to say that some convention should be used or some not. But instead, the main point was to say that just because there is spatial diffusion constant that does not mean there will be a spatial gradient of particles. From the authors response to my comments, it is clear that they understand the subtilties around it and are aware of the relevant papers. However, a reader not familiar with this discussion may work under the impression that if there if there is a spatialy varying diffusion constant in cell there will be an accumulation of particles in the region of low diffusivity but that may not always be the case. Moreover, localisation of particles in the region of low diffusivity has been reported in many different context. Some of the papers that the author cite already show that. For example, in Rupprecht et al. 2018 non-isothermal interpretation is applied to the dynamics of objects inside cells.

Given that the central result is not new. The paper could still be of general interest to the biophysics community if the follow up sections (ii) Clustering in presence of inter-particle interactions and (iii) Moment analysis for non-interacting particles in space with discrete patches of inhomogeneous diffusivity were analysed rigorously.

Reviewer #2 (Public Review):

Summary:

The authors study through theory and simulations the diffusion of microscopic particles, and aim to account for the effects of inhomogeneous viscosity and diffusion - in particular regarding the intracellular environment. They propose a mechanism, termed "Diffusive lensing", by which particles are attracted towards low-diffusivity regions where they remain trapped. To obtain these results, the authors rely on agent-based simulations using custom rules performed within the Ito stochastic calculus convention, without drift. They acknowledge the fact that this convention does not describe equilibrium systems, and that their results would not hold at equilibrium - and discard these facts by invoking the facts that cells are out-of-equilibrium. Finally, they show some applications of their findings, in particular enhanced clustering in the low-diffusivity regions. The authors conclude that as inhomogeneous diffusion is ubiquitous in life, so must their mechanism be, and hence it must be important.

Strengths:

The article is well-written, clearly intelligible, its hypotheses are stated relatively clearly and the models and mathematical derivations are compatible with these hypotheses. In the appendices, the authors connect their findings to known results for classic stochastic differential equation formalisms.

Weaknesses:

This study is, in my opinion, deeply flawed. The main problem lies in the hypotheses, in particular the choice of considering drift-less dynamics in the Ito convention. It is regrettable that the authors choose to use agent-based custom simulations with little physical motivation, rather than a well-established stochastic differential equations framework.

Indeed, stochastic conventions are a notoriously tricky business, but they are both mathematically and physically well-understood and do not result in any "dilemma" [some citations in the article, such as (Lau and Lubensky) and (Volpe and Wehr), make an unambiguous resolution of these]. In the continuous-time limit, conventions are not an intrinsic, fixed property of a system, but a choice of writing; however, whenever going from one to another, one must include a corresponding "spurious drift" that compensates the effect of this change - a mathematical subtlety that is omitted in the article (except in a quick note in the appendix): in the presence of diffusive gradients, if the drift is zero in one convention, it will thus be non-zero in another. It is well established that for equilibrium systems obeying fluctuation-dissipation, the spurious drift vanishes in the anti-Ito stochastic convention; more precisely one can write in the anti-Ito convention

dx/dt = - D(x)/kT grad U(x) + sqrt(2D(x)) dW

with D(x) the diffusion, kT the thermal energy (which is space-independent at equilibrium), and dW a d-dimensional Wiener process. Equivalently one can write in the Ito convention:

dx/dt = - D(x)/kT grad U(x) + sqrt(2D(x)) dW + div D(x) (*)

where the latter term is the spurious drift arising from convention change. This ensures that the diffusion gradients do not induce currents and probability gradients, and thus that the steady-state PDF is the Gibbs measure (this form has been confirmed experimentally, for instance, for colloidal particles near walls, that have strong diffusivity gradients despite not having significant forces). It generalizes to near-equilibrium systems with non-conservative forces and/or temperature gradient in the form:

dx/dt = F(x) + sqrt(2D(x)) dW + div D(x) (**)

where the drift field F(x) encodes these forces. In some cases, it has been shown through careful microscopic analysis that one can have effectively a different form for the last term, namely

dx/dt = F(x) + sqrt(2D(x)) dW + alpha div D(x)

where alpha is a "convention parameter" that would be =1 at equilibrium. For instance, in the Volpe and Wehr review this can occur through memory effects in robotic dynamics, or through strong fluctuation-dissipation breakdown. In a near-equilibrium system, this should be strongly justified, as the continuous-time dynamics with alpha \neq 1 and drift F would be indistinguishable from one with alpha = 1 and drift F + (1-alpha) div D: the authors would have the burden of proving that the observed (absence of) drift is indeed due to alpha\neq 1, rather than to much more common force fields F(x).

Here, without further motivation than the statement that cells are out-of-equilibrium, drifts are arbitrarily set to zero in the Ito convention, which is in (**) the equivalent to adding a force with drift $-div D$ exactly compensating the spurious drift. It is the effects of this arbitrary force that are studied in the article. The fact that it results in probability gradients is trivial once formulated this way (and in no way is this new - many of the references, for instance Volpe and Wehr, mention this). Enhanced clustering is also a trivial effect of this probability gradient (the local concentration is increased by this force field, so phase separation can occur). As a side note the "neighbor sensing" scheme to describe interactions is itself very peculiar and not physically motivated - it violates stochastic thermodynamics laws too, as detailed balance is apparently not respected. There again, the authors have chosen to disregard a century of stochastic thermodynamics in favor of a non-justified unphysical custom rule.

The authors make no further justification of their choice of driftless Ito simulations than the fact that cells are out-of-equilibrium, leaving the feeling that this is a detail. They make mentions of systems (eg glycogen, prebiotic environment) for which (near-)equilibrium physics should mostly prevail, and of fluctuation dissipation ("Diffusivity varies inversely with viscosity", in the introduction). Yet the "phenomenon" they discuss is entirely reliant on an undiscussed mechanism by which these assumptions would be completely violated (the citations they make for this - Gnesotto '18 and Phillips '12 - are simply discussions of the fact that cells are out-of-equilibrium, not on any consequences on the convention).

Finally, while inhomogeneous diffusion is ubiquitous, the strength of this effect in realistic conditions is not discussed. Even in the most "optimistic" case where alpha=0 would make sense (knowing that in the cellular context we are discussing thermal systems immersed in water and if energy consumption and metabolism were stopped alpha would relax back to 1), the equation (*) above shows that having zero ito drift is equivalent to having a potential countering the spurious drift, with value

U(x) = kT log(D(x) / D0 )

[I have assumed isotropic diffusion for simplicity here, so the div is replaced by a grad]. This means that the diffusion contrasts logarithmically compare to the chemical potential ones -- for instance a major diffusion difference of 100x is equivalent to 4.6kT in potential energy, a relatively modest effect. To prove that the authors' effect of "diffusive lensing" is involved in such a system, one would thus have to<br /> 1) observe strong spatial variations of the diffusion coefficient (this is doable, and was done before), AND<br /> 2) show that there is an enrichment of the diffusing species in the low-diffusion region inversely proportional to the diffusion, AND<br /> 3) show that this enrichment cannot be attributed to mild differences in potential energy, for instance by showing that if nonequilibrium energy consumption stops, the concentration fully homogenizes while the diffusion gradients remain.

If the authors were to successfully show all that in an experimental system, or design a theoretical framework where these effects convincingly emerge from physically realistic microscopic dynamical rules, they would have indeed discovered a new phenomenon. In contrast, the current article only demonstrates the well-known fact that when using arbitrary dynamical rules in heterogeneous diffusion simulations, one can get concentration gradients.

Joint Public Review:

This manuscript by Yue et al. aims to understand the molecular mechanisms underlying the better reproductive outcomes of Tibetans at high altitude by characterizing the transcriptome and histology of full-term placenta of Tibetans and compare them to those Han Chinese at high elevations.

The approach is innovative, and the data collected are valuable for testing hypotheses regarding the contribution of the placenta to better reproductive success of populations that adapted to hypoxia. The authors identified hundreds of differentially expressed genes (DEGs) between Tibetans and Han, including the EPAS1 gene that harbors the strongest signals of genetic adaptation. The authors also found that such differential expression is more prevalent and pronounced in the placentas of male fetuses than those of female fetuses, which is particularly interesting, as it echoes with the more severe reduction in birth weight of male neonates at high elevation observed by the same group of researchers (He et al., 2022).

Comments on latest version:

The revised manuscript has incorporated the suggested changes and weakened conclusions regarding natural selection. Limitations of the study are also clearly stated in the Discussion section.

Reviewer #1 (Public Review):

This study is one in a series of excellent papers by the Forstmann group focusing on the ability of fMRI to reliably detect activity in small subcortical nuclei - in this case, specifically those purportedly involved in the hyper- and indirect inhibitory basal ganglia pathways. I have been very fond of this work for a long time, beginning with the demonstration of De Hollander, Forstmann et al. (HBM 2017) of the fact that 3T fMRI imaging (as well as many 7T imaging sequences) do not afford sufficient signal to noise ratio to reliably image these small subcortical nuclei. This work has done a lot to reshape my view of seminal past studies of subcortical activity during inhibitory control, including some that have several thousand citations.

Comments on revised version:

This is my second review of this article, now entitled "Multi-study fMRI outlooks on subcortical BOLD responses in the stop-signal paradigm" by Isherwood and colleagues.

The authors have been very responsive to the initial round of reviews.

I still think it would be helpful to see a combined investigation of the available 7T data, just to really drive the point home that even with the best parameters and a multi-study sample size, fMRI cannot detect any increases in BOLD activity on successful stop compared to go trials. However, I agree with the authors that these "sub samples still lack the temporal resolution seemingly required for looking at the processes in the SST."

As such, I don't have any more feedback.

Reviewer #2 (Public Review):

This work aggregates data across 5 openly available stopping studies (3 at 7 tesla and 2 at 3 tesla) to evaluate activity patterns across the common contrasts of Failed Stop (FS) > Go, FS > stop success (SS), and SS > Go. Previous work has implicated a set of regions that tend to be positively active in one or more of these contrasts, including the bilateral inferior frontal gyrus, preSMA, and multiple basal ganglia structures. However, the authors argue that upon closer examination, many previous papers have not found subcortical structures to be more active on SS than FS trials, bringing into question whether they play an essential role in (successful) inhibition. In order to evaluate this with more data and power, the authors aggregate across five datasets and find many areas that are *more* active for FS than SS, including bilateral preSMA, GPE, thalamus, and VTA. They argue that this brings into question the role of these areas in inhibition, based upon the assumption that areas involved in inhibition should be more active on successful stop than failed stop trials, not the opposite as they observed.

Since the initial submission, the authors have improved their theoretical synthesis and changed their SSRT calculation method to the more appropriate integration method with replacement for go omissions. They have also done a better job of explaining how these fMRI results situate within the broader response inhibition literature including work using other neuroscience methods.

They have also included a new Bayes Factor analysis. In the process of evaluating this new analysis, I recognized the following comments that I believe justify additional analyses and discussion:

First, if I understand the author's pipeline, for the ROI analyses it is not appropriate to run FSL's FILM method on the data that were generated by repeating the same time series across all voxels of an ROI. FSL's FILM uses neighboring voxels in parts of the estimation to stabilize temporal correlation and variance estimates and was intended and evaluated for use on voxelwise data. Instead, I believe it would be more appropriate to average the level 1 contrast estimates over the voxels of each ROI to serve as the dependent variables in the ROI analysis.

Second, for the group-level ROI analyses there seems to be inconsistencies when comparing the z-statistics (Figure 3) to the Bayes Factors (Figure 4) in that very similar z-statistics have very different Bayes Factors within the same contrast across different brain areas, which seemed surprising (e.g., a z of 6.64 has a BF of .858 while another with a z of 6.76 has a BF of 3.18). The authors do briefly discuss some instances in the frequentist and Bayesian results differ, but they do not ever explain by similar z-stats yield very different bayes factors for a given contrast across different brain areas. I believe a discussion of this would be useful.

Third, since the Bayes Factor analysis appears to be based on repeated measures ANOVA and the z-statistics are from Flame1+2, the BayesFactor analysis model does not pair with the frequentist analysis model very cleanly. To facilitate comparison, I would recommend that the same repeated measures ANOVA model should be used in both cases. My reading of the literature is that there is no need to be concerned about any benefits of using Flame being lost, since heteroscedasticity does not impact type I errors and will only potentially impact power (Mumford & Nichols, 2009 NeuroImage).

Fourth, though frequentist statistics suggest that many basal ganglia structures are significantly more active in the FS > SS contrast (see 2nd row of Figure 3), the Bayesian analyses are much more equivocal, with no basal ganglia areas showing Log10BF > 1 (which would be indicative of strong evidence). The authors suggest that "the frequentist and Bayesian analyses are monst in line with one another", but in my view, this frequentist vs. Bayesian analysis for the FS > SS contrast seems to suggest substantially different conclusions. More specifically, the frequentist analyses suggest greater activity in FS than SS in most basal ganglia ROIs (all but 2), but the Bayesian analysis did not find *any* basal ganglia ROIs with strong evidence for the alternative hypothesis (or a difference), and several with more evidence for the null than the alternative hypothesis. This difference between the frequentist and Bayesian analyses seems to warrant discussion, but unless I overlooked it, the Bayesian analyses are not mentioned in the Discussion at all. In my view, the frequentist analyses are treated as the results, and the Bayesian analyses were largely ignored.

Overall, I think this paper makes a useful and mostly solid contribution to the literature. I have made some suggestions for adjustments and clarification of the neuroimaging pipeline and Bayesian analyses that I believe would strengthen the work further.

Reviewer #1 (Public Review):

In this work, the authors investigate an important question - under what circumstances should a recurrent neural network optimised to produce motor control signals receive preparatory input before the initiation of a movement, even though it is possible to use inputs to drive activity just-in-time for movement?

This question is important because many studies across animal models have show that preparatory activity is widespread in neural populations close to motor output (e.g. motor cortex / M1), but it isn't clear under what circumstances this preparation is advantageous for performance, especially since preparation could cause unwanted motor output during a delay.

They show that networks optimised under reasonable constraints (speed, accuracy, lack of pre-movement) will use input to seed the state of the network before movement, and that these inputs reduce the need for ongoing input during the movement. By examining many different parameters in simplified models they identify a strong connection between the structure of the network and the amount of preparation that is optimal for control - namely, that preparation has the most value when nullspaces are highly observable relative to the readout dimension and when the controllability of readout dimensions is low. They conclude by showing that their model predictions are consistent with the observation in monkey motor cortex that even when a sequence of two movements is known in advance, preparatory activity only arises shortly before movement initiation.

Overall, this study provides valuable theoretical insight into the role of preparation in neural populations that generate motor output, and by treating input to motor cortex as a signal that is optimised directly this work is able to sidestep many of the problematic questions relating to estimating the potential inputs to motor cortex.

Reviewer #2 (Public Review):

This work clarifies neural mechanisms that can lead to a phenomenology consistent with motor preparation in its broader sense. In this context, motor preparation refers to activity that occurs before the corresponding movement. Another property often associated with preparatory activity is a correlation with global movement characteristics such as reach speed (Churchland et al., Neuron 2006), reach angle (Sun et al., Nature 2022), or grasp type (Meirhaeghe et al., Cell Reports 2023). Such activity has notably been observed in premotor and primary motor cortices, and it has been hypothesized to serve as an input to a motor execution circuit. The timing and mechanisms by which such 'preparatory' inputs are made available to motor execution circuits remain however unclear in general, especially in light of the presence of a 'trigger-like' signal that appears to relate to the transition from preparatory dynamics to execution activity (Kaufman et al. eNeuron 2016, Iganaki et al., Cell 2022, Zimnik and Churchland, Nature Neuroscience 2021).

The preparatory inputs have been hypothesized to fulfill one or several (non-mutually-exclusive) possible objectives. Two notable hypotheses are that these inputs could be shaped to maximize output accuracy under regularization of the input magnitude; or that they may help the flexible re-use of the neural machinery involved in the control of movements in different contexts.

Here, the authors investigate in detail how the former hypothesis may be compatible with the presence of early inputs in recurrent network models driving arm movements, and compare models to data.

Strengths:

The authors are able to deploy an in-depth evaluation of inputs that are optimized for producing an accurate output at a pre-defined time while using a regularization term on the input magnitude, in the case of movements that are thought to be controlled in a quasi-open loop fashion such as reaches.

First, the authors have identified that optimal control theory is a great framework to study this question as it provides methods to find and analyze exact solutions to this cost function in the case of models with linear dynamics. The authors not only use this framework to get an exact assessment of how much pre-movement input arises in large recurrent networks, but also give insight into the mechanisms by which it happens by dissecting in detail low-dimensional networks. The authors find that two key network properties - observability of the readout's nullspace and limited controllability - give rise to optimal inputs that are large before the start of the movement (while the corresponding network activity lies in the nullspace of the readout). Further, the authors numerically investigate the timing of optimized inputs in models with nonlinear dynamics, and find that pre-movement inputs can also arise in these more general networks. The authors also explore how some variations on their model's constraints - such as penalizing the input roughness or changing task contingencies about the go cue timing - affect their results. Finally, the authors point out some coarse-grained similarities between the pre-movement activity driven by the optimized inputs in some of the models they studied, and the phenomenology of preparation observed in the brain during single reaches and reach sequences. Overall, the authors deploy an impressive arsenal of tools and a very in-depth analysis of their models.

Limitations:

(1) Though the optimal control theory framework is ideal to determine inputs that minimize output error while regularizing the input norm or other simple input features, it cannot easily account for some other varied types of objectives - especially those that may lead to a complex optimization landscape. For instance, the reusability of parts of the circuit, sparse use of additional neurons when learning many movements, and ease of planning (especially under uncertainty about when to start the movement), may be alternative or additional reasons that could help explain the preparatory activity observed in the brain. It is interesting to note that inputs that optimize the objective chosen by the authors arguably lead to a trade-off in terms of other desirable objectives. Specifically, the inputs the authors derive are time-dependent, so a recurrent network would be needed to produce them and it may not be easy to interpolate between them to drive new movement variants. In addition, these inputs depend on the desired time of output and therefore make it difficult to plan, e.g. in circumstances when timing should be decided depending on sensory signals. Finally, these inputs are specific to the full movement chain that will unfold, so they do not permit reuse of the inputs e.g. in movement sequences of different orders. Of note, the authors have pointed out in the discussion how their framework may be extended in future work to account for some additional objectives, such as inputs' temporal smoothness or some strategies for dealing with go cue timing uncertainty.

(2) Relatedly, if the motor circuits were to balance different types of objectives, the activity and inputs occurring before each movement may be broken down into different categories that may each specialize into their own objective. For instance, previous work (Kaufman et al. eNeuron 2016, Iganaki et al., Cell 2022, Zimnik and Churchland, Nature Neuroscience 2021) has suggested that inputs occurring before the movement could be broken down into preparatory inputs 'stricto sensu' - relating to the planned characteristics of the movement - and a trigger signal, relating to the transition from planning to execution - irrespective of whether the movement is internally timed or triggered by an external event. The current work does not address which type(s) of early input may be labeled as 'preparatory' or may be thought of as a part of 'planning' computations, or whether these inputs may come from several different source circuits.

(3) While the authors rightly point out some similarities between the inputs that they derive and observed preparatory activity in the brain, notably during motor sequences, there are also some differences. For instance, while both the derived inputs and the data show two peaks during sequences, the data reproduced from Zimnik and Churchland show preparatory inputs that have a very asymmetric shape that really plummets before the start of the next movement, whereas the derived inputs have larger amplitude during the movement period - especially for the second movement of the sequence. In addition, the data show trigger-like signals before each of the two reaches. Finally, while the data show a very high correlation between the pattern of preparatory activity of the second reach in the double reach and compound reach conditions, the derived inputs appear to be more different between the two conditions. Note that the data would be consistent with separate planning of the two reaches even in the compound reach condition, as well as the re-use of the preparatory input between the compound and double reach conditions. Therefore, different motor sequence datasets - notably, those that would show even more coarticulation between submovements - may be more promising to find a tight match between the data and the author's inputs. Further analyses in these datasets could help determine whether the coarticulation could be due to simple filtering by the circuits and muscles downstream of M1, planning of movements with adjusted curvature to mitigate the work performed by the muscles while permitting some amount of re-use across different sequences, or - as suggested by the authors - inputs fully tailored to one specific movement sequence that maximize accuracy and minimize the M1 input magnitude.

(4) Though iLQR is a powerful optimization method to find inputs optimizing the author's cost function, it also has some limitations. First, given that it relies on a linearization of the dynamics at each timestep, it has a limited ability to leverage potential advantages of nonlinearities in the dynamics. Second, the iLQR algorithm is not a biologically plausible learning rule and therefore it might be difficult for the brain to learn to produce the inputs that it finds. Therefore, when observing differences between model and data, this can confound the question of whether it comes from a difference of assumed objective or a difference of optimization procedure. It remains unclear whether using alternative algorithms with different limitations - for instance, using variants of BPTT to train a separate RNN to produce the inputs in question - could impact some of the results.

(5) Under the objective considered by the authors, the amount of input occurring before the movement might be impacted by the presence of online sensory signals for closed-loop control. Even if considering that the inputs could include some sensory activity and/or that the RNN activity could represent general variables whose states can be decoded from M1, the model would not include mechanisms that process imperfect (delayed, noisy) sensory feedback to adapt the output in a trial-specific manner. It is therefore an open question whether the objective and network characteristics suggested by the authors could also explain the presence of preparatory activity before e.g. grasping movements that are thought to be more sensory-driven (Meirhaeghe et al., Cell Reports 2023).

Reviewer #3 (Public Review):

I remain enthusiastic about this study. The manuscript is well-written, logical, and conceptually clear. To my knowledge, no prior modeling study has tackled the question of 'why prepare before executing, why not just execute?' Prior studies have simply assumed, to emulate empirical findings, that preparatory inputs precede execution. They never asked why. The authors show that, when there are constraints on inputs, preparation becomes a natural strategy. In contrast, with no constraint on inputs, there is no need for preparation as one could get anything one liked just via the inputs during movement. For the sake of tractability, the authors use a simple magnitude constraint: the cost function punishes the integral of the squared inputs. Thus, if small inputs before movement can reduce the size of the inputs needed during movement, preparation is a good strategy. This occurs if (and only if) the network has strong dynamics (otherwise feeding it preparatory activity would not produce anything interesting). All of this is sensible and clarifying.

As discussed in the prior round of reviews, the central constraint that the authors use is a mathematically tractable stand-in for a range of plausible (but often trickier to define and evaluate) constraints, such as simplicity of inputs (or inputs being things that other areas could provide). The manuscript now embraces this fact more explicitly, and also gives some results showing that other constraints (such as on the derivative of activity, which is one component of complexity) can have the same effect. The manuscript also now discusses and addresses a modest weakness of the previous manuscript: the preparatory activity in their simulations is often overly complex temporally, lacking the (rough) plateau typically seen for data. Depending on your point of view, this is simply 'window dressing', but from my perspective it was important to know that their approach could yield more realistic-looking preparatory activity. Both these additions (the new constraint, and the more realistic temporal profile of preparatory activity) are added simply as supplementary figures rather than in the main text, and are brought up only in the Discussion. At first this struck me as slightly odd, but in the end I think this is appropriate. These are really Discussion-type issues, and dealing with them there makes sense. The 'different constraints' issue in particular is deep, tricky to explore for technical reasons, and could thus support a small research program. I think it is fair to talk about it thoughtfully (as the Discussion now does) and then just mention some simple results.

My remaining comments largely pertain to some subtle (but to me important) nuances at a few locations in the text. These should be easy for the authors to address, in whatever way they see fit.

Specific comments:

(1) The authors state the following on line 56: "For preparatory processes to avoid triggering premature movement, any pre-movement activity in the motor and dorsal pre-motor (PMd) cortices must carefully exclude those pyramidal tract neurons."<br /> This constraint is overly restrictive. PT neurons absolutely can change their activity during preparation in principle (and appear to do so in practice). The key constraint is looser: those changes should have no net effect on the muscles. E.g., if d is the vector of changes in PT neuron firing rates, and b is the vector of weights, then the constraint is that b'd = 0. d = 0 is one good way of doing this, but only one. Half the d's could go up and half could go down. Or they all go up, but half the b's are negative. Put differently, there is no reason the null space has to be upstream of the PT neurons. It could be partly, or entirely, downstream.<br /> In the end, this doesn't change the point the authors are making. It is still the case that d has to be structured to avoid causing muscle activity, which raises exactly the point the authors care about: why risk this unless preparation brings benefits? However, this point can be made with a more accurate motivation. This matters, because people often think that a null-space is a tricky thing to engineer, when really it is quite natural. With enough neurons, preparing in the null space is quite simple.

(2) Line 167: 'near-autonomous internal dynamics in M1'.<br /> It would be good if such statements, early in the paper, could be modified to reflect the fact that the dynamics observed in M1 may depend on recurrence that is NOT purely internal to M1. A better phrase might be 'near-autonomous dynamics that can be observed in M1'. A similar point applies on line 13. This issue is handled very thoughtfully in the Discussion, starting on line 713. Obviously it is not sensible to also add multiple sentences making the same point early on. However, it is still worth phrasing things carefully, otherwise the reader may have the wrong impression up until the Discussion (i.e. they may think that both the authors, and prior studies, believe that all the relevant dynamics are internal to M1). If possible, it might also be worth adding one sentence, somewhere early, to keep readers from falling into this hole (and then being stuck there till the Discussion digs them out).

(3) The authors make the point, starting on line 815, that transient (but strong) preparatory activity empirically occurs without a delay. They note that their model will do this but only if 'no delay' means 'no external delay'. For their model to prepare, there still needs to be an internal delay between when the first inputs arrive and when movement generating inputs arrive.

This is not only a reasonable assumption, but is something that does indeed occur empirically. This can be seen in Figure 8c of Lara et al. Similarly, Kaufman et al. 2016 noted that "the sudden change in the CIS [the movement triggering event] occurred well after (~150 ms) the visual go cue... (~60 ms latency)" Behavioral experiments have also argued that internal movement-triggering events tend to be quite sluggish relative to the earliest they could be, causing RTs to be longer than they should be (Haith et al. Independence of Movement Preparation and Movement Initiation). Given this empirical support, the authors might wish to add a sentence indicating that the data tend to justify their assumption that the internal delay (separating the earliest response to sensory events from the events that actually cause movement to begin) never shrinks to zero.

While on this topic, the Haith and Krakauer paper mentioned above good to cite because it does ponder the question of whether preparation is really necessary. By showing that they could get RTs to shrink considerably before behavior became inaccurate, they showed that people normally (when not pressured) use more preparation time than they really need. Given Lara et al, we know that preparation does always occur, but Haith and Krakauer were quite right that it can be very brief. This helped -- along with neural results -- change our view of preparation from something more cognitive that had to occur, so something more mechanical that was simply a good network strategy, which is indeed the authors current point. Working a discussion of this into the current paper may or may not make sense, but if there is a place where it is easy to cite, it would be appropriate.

Reviewer #1 (Public Review):

Dasguta et al. have dissected the role of Sema7a in fine tuning of a sensory microcircuit in the posterior lateral line organ of zebrafish. They attempt to also outline the different roles of a secreted verses membrane-bound form of Sema7a in this process. Using genetic perturbations and axonal network analysis, the authors show that loss of both Sema7a isoforms causes abnormal axon terminal structure with more bare terminals and fewer loops in contact with presynaptic sensory hair cells. Further, they show that loss of Sema7a causes decreased number and size of both the pre- and post-synapse. Finally, they show that overexpression of the secreted form of Sema7a specifically can elicit axon terminal outgrowth to an ectopic Sema7a expressing cell. Together, the analysis of Sema7a loss of function and overexpression on axon arbor structure is fairly thorough and revealed a novel role for Sema7a in axon terminal structure.

Reviewer #2 (Public Review):

In this work, Dasgupta et al. investigate the role of Sema7a in the formation of peripheral sensory circuit in the lateral line system of zebrafish. They show that Sema7a protein is present during neuromast maturation and localized, in part, to the base of hair cells (HCs). This would be consistent with pre-synaptic Sema7a mediating formation and/or stabilization of the synapse. They use sema7a loss-of-function strain to show that lateral line sensory terminals display abnormal arborization. They provide highly quantitative analysis of the lateral line terminal arborization to show that a number of specific topological parameters are affected in mutants. Next, they ectopically express a secreted form of Sema7a to show that lateral line terminals can be ectopically attracted to the source. Finally, they also demonstrate that the synaptic assembly is impaired in the sema7a mutant. Overall, the data are of high quality and properly controlled. The availability of Sema7a antibody is a big plus, as it allows to address the endogenous protein localization as well to show the signal absence in the sema7a mutant. The quantification of the arbor topology should be useful to people in the field who are looking at the lateral line as well as other axonal terminals.

Reviewer #3 (Public Review):

The data reported here demonstrate that Sema7a defines the local behavior of growing axons in the developing zebrafish lateral line. The analysis is sophisticated and convincingly demonstrates effects on axon growth and synapse architecture. Collectively, the findings point to the idea that the diffusible form of sema7a may influence how axons grow within the neuromast and that the GPI-linked form of sema7a may subsequently impact how synapses form, though additional work is needed to strongly link each form to its' proposed effect on circuit assembly.

Comments on latest version:

The authors comprehensively and appropriately addressed most of the reviewers' concerns. In particular, they added evidence that hair cells express both Sema7A isoforms, showed that membrane bound Sema7A does not have long range effects on guidance, demonstrated how axons behave close to ectopic Sema7A, and analyzed other features of the hair cells that revealed no strong phenotypes. The authors also softened the language in many, but not all places. Overall, I am satisfied with the study as a whole.

Reviewer #4 (Public Review):<br /> <br /> This study provides direct evidence showing that Sema7a plays a role in the axon growth during the formation of peripheral sensory circuits in the lateral-line system of zebrafish. This is a valuable finding because the molecules for axon growth in hair-cell sensory systems are not well understood. The majority of the experimental evidence is convincing, and the analysis is rigorous. The evidence supporting Sema7a's juxtracrine vs. secreted role and involvement in synapse formation in hair cells is less conclusive. The study will be of interest to cell, molecular and developmental biologists, and sensory neuroscientists.

Reviewer #1 (Public Review):

Summary:

People with Parkinson's disease often experience a variety of nonmotor symptoms, the biological bases of which remain poorly understood. Johansson et al began to study potential roles of the dorsal raphe nucleus (DRN) degeneration in the pathophysiology of neuropsychiatric symptoms in PD.

Strengths:

Boi et al validated a transgenic reporter mouse line that can reliably label dopaminergic neurons in the DRN. This brain region shows severe neurodegeneration and has been proposed to contribute to the manifestation of neuropsychiatric symptoms in PD. Using this mouse line (and others), Boi and colleagues characterized electrophysiological and morphological phenotypes of dopaminergic and serotoninergic neurons in the raphe nucleus. This study involved very careful topographical registration of recorded neurons to brain slices for post hoc immunohistochemical validation of cell identity, making it an elegant and thorough piece of work.

Of relevance to PD pathophysiology, the authors evaluated the physiological and morphological changes of DRN serotoninergic and dopaminergic neurons after a partial loss of nigrostriatal dopamine neurons, which serves as a mouse model of early parkinsonian pathology. Moreover, the authors identified a series of physiological and morphological changes of subtypes of DRN neurons that depend on nigral dopaminergic neurodegeneration, LC noradrenergic neurodegeneration, or both. Indeed this work highlights the importance of LC noradrenergic degeneration in PD pathophysiology.

Overall, this is a well-designed study with high significance to the Parkinson's research field.

Reviewer #2 (Public Review):

In this paper, Boi et al. thoroughly classified the electrophysiological and morphological characteristics of serotonergic and dopaminergic neurons in the DRN and examined the alterations of these neurons in the 6-OHDA-induced mouse PD model. Using whole-cell patch clamp recording, they found that 5-HT and dopamine (DA) neurons in the DRN are electrophysiologically distinct from each other. Additionally, they characterized distinct morphological features of 5-HT and DA neurons in the DRN. Notably, these specific features of 5-HT and DA neurons in the DRN exhibited different changes in the 6-OHDA-induced PD model. Then the authors utilized desipramine (DMI) to separate the effects of nigrostriatal DA depletion and noradrenaline (NA) depletion induced by 6-OHDA. Interestingly, protection from NA depletion by DMI pretreatment reversed the changes in 5-HT neurons, while having a minor impact on the changes in DA neurons in the DRN. These data indicate that the role of NA lesion in the altered properties of DRN 5-HT neurons by 6-OHDA is more critical than that of DA lesions.

Overall, this study provides foundational data on the 5-HT and DA neurons in the DRN and their potential involvement in PD symptoms. Given the deficits of the DRN in PD, this paper may offer insights into the cellular mechanisms underlying non-motor symptoms associated with PD.

Reviewer #2 (Public Review):

Summary:

Tian et al. aimed to assess differences in biological motion (BM) perception between children with and without ADHD, as well as relationships to indices of social functioning and possible predictors of BM perception (including demographics, reasoning ability and inattention). In their study, children with ADHD showed poorer performance relative to typically developing children in three tasks measuring local, global, and general BM perception. The authors further observed that across the whole sample, performance in all three BM tasks was negatively correlated with scores on the social responsiveness scale (SRS), whereas within groups a significant relationship to SRS scores was only observed in the ADHD group and for the local BM task. Local and global BM perception showed a dissociation in that global BM processing was predicted by age, while local BM perception was not. Finally, general (local & global combined) BM processing was predicted by age and global BM processing, while reasoning ability mediated the effect of inattention on BM processing.

Strengths:

Overall, the manuscript is presented in a clear fashion and methods and materials are presented with sufficient detail so the study could be reproduced by independent researchers. The study uses an innovative, albeit not novel, paradigm to investigate two independent processes underlying BM perception. The results are novel and have the potential to have wide-reaching impact on multiple fields.

Weaknesses:

The manuscript has improved in clarity and conceptual and methodological considerations in response to the last review. However, the reported results still provide incomplete support for the claims the authors make in the paper.

In relation to other reviewers' earlier comments, the model notation used is still not consistent and model results are reported incompletely, which make it difficult to gain a full picture of the data and how they support the authors' secondary claims. For instance, across the models in the supplementary materials, ß coefficients are only reported selectively which makes it difficult to assess the model as a whole. Furthermore, different terms (task 1, task 2 vs. BM-Local, BM-global) are used to refer to the same levels of a variable, and it is unclear which levels of a dummy variable correspond to which task, making it overall very difficult to comprehend the modelling procedure.

Reviewer #3 (Public Review):

The authors presented point light displays of human walkers to children (mean = 9 years) with and without ADHD to compare their biological motion perception abilities, and relate them to IQ, social responsiveness scale (SRS) scores and age. They report that children with ADHD were worse at all three biological motion tasks, but that those loading more heavily on local processing related to social interaction skills and global processing to age. The valuable and solid findings are informative for understanding this complex condition, as well as biological motion processing mechanisms in general. However, the correlations present a pattern that needs further examination in future studies because many of the differences between correlations are not significant.

Strengths:

The authors present differences between ADHD and TD children in biological motion processing, and this question has not received as much attention as equivalent processing capabilities in autism. They use a task that appears well controlled. They raise some interesting mechanistic possibilities for differences in local and global motion processing, which are distinctions worth exploring. The group differences will therefore be of interest to those studying ADHD, as well as other developmental conditions, and those examining biological motion processing mechanisms in general.

Weaknesses:

The data are not strong enough to support claims about differences between global and lobal processing wrt social communication skills and age. The mechanistic possibilities for why these abilities may dissociate in such a way are interesting, but the crucial tests of differences between correlations do not present a clear picture. Further empirical work would be needed to test this further. Specifics:

The authors state frequently that it was the local BM task that related to social communication skills (SRS) and not the global tasks. However, the results section shows a correlation between SRS and all three tasks. The only difference is that when looking specifically within the ADHD group, the correlation is only significant for the local task. The supplementary materials demonstrate that tests of differences between correlations present an incomplete picture. Currently they have small samples for correlations, so this is unsurprising.

Theoretical assumptions. The authors make some statements about local vs global biological motion processing that may have been made in previous studies, but would appear controversial and not definitive. E.g., that local BM processing does not improve with age and is uninfluenced by attention.

Reviewer #3 (Public Review):

In this work, Jarc et al. describe a method to decouple the mechanisms supporting progenitor self-renewal and expansion from feed-forward mechanisms promoting their differentiation.

The authors aimed at expanding pancreatic progenitor (PP) cells, strictly characterized as PDX1+/SOX9+/NKX6.1+ cells, for several rounds. This required finding the best cell culture conditions that allow sustaining PP cell proliferation along cell passages while avoiding their further differentiation. They achieve this by comparing the transcriptome of PP cells that can be expanded for several passages against the transcriptome of unexpanded (just differentiated) PP cells.

The optimized culture conditions enabled the selection of PDX1+/SOX9+/NKX6.1+ PP cells and their consistent, 2000-fold, expansion over ten passages and 40-45 days. Transcriptome analyses confirmed the stabilization of PP identity and the effective suppression of differentiation. These optimized culture conditions consisted in substituting the Vitamin A containing B27 supplement with a B27 formulation devoid of vitamin A (to avoid retinoic acid (RA) signaling from an autocrine feed-forward loop), substituting A38-01 with the ALK5 II inhibitor (ALK5i II) that targets primarily ALK5, supplementation of medium with FGF18 (in addition to FGF2) and the canonical Wnt inhibitor IWR-1, and cell culture on vitronectin-N (VTN-N) as a substrate instead of Matrigel.

The strength of this work relies on a clever approach to identify cell culture modifications that allow expansion of PP cells (once differentiated) while maintaining, if not reinforcing, PP cell identity. Along the work, it is emphasized that PP cell identity is associated to the co-expression of PDX1, SOX9 and NKX6.1. The optimized protocol is unique (among the other datasets used in the comparison shown here) at inducing a strong upregulation of GP2, a unique marker of human fetal pancreas progenitors. Importantly GP2+ enriched hPS cell-derived PP cells are more efficiently differentiating into pancreatic endocrine cells (Aghazadeh et al., 2022; Ameri et al., 2017).

The unlimited expansion of PP cells reported here would allow scaling-up the generation of beta cells, for the cell therapy of diabetes, by eliminating a source of variability derived from the number of differentiation procedures to be carried out when starting at the hPS cell stage each time. The approach presented here would allow selection of the most optimally differentiated PP cell population for subsequent expansion and storage. Among other conditions optimized, the authors report a role for Vitamin A in activating retinoic acid signaling in an autocrine feed-forward loop, and the supplementation with FGF18 to reinforce FGF2 signaling.

This is a relevant topic in the field of research, and some of the cell culture conditions reported here for PP expansion might have important implications in cell therapy approaches. Thus, the approach and results presented in this study could be of interest for researchers working in the field of in vitro pancreatic beta cell differentiation from hPSCs. Table S1 and Table S4 are clearly detailed and extremely instrumental to this aim.

Reviewer #2 (Public Review):

The paper presents a novel approach to expand iPSC-derived pdx1+/nkx6.1+ pancreas progenitors, making them potentially suitable for GMP-compatible protocols. This advancement represents a significant breakthrough for diabetes cell replacement therapies, as one of the current bottlenecks is the inability of expanding PP without compromising their differentiation potential. The study employs a robust dataset and state-of-the-art methodology, unveiling crucial signaling pathways (eg TGF, Notch...) responsible for sustaining pancreas progenitors while preserving their differentiation potential in vitro.

The current version of the paper has improved, increasing the clarity and providing clear explanations to the comments raised regarding quantifications, functionality of the cells in vivo etc...

The discussion on challenges adds depth to the study and encourages future research to build upon these important findings

Reviewer #1 (Public Review):

Summary:

The authors use innovative CRISPRi method to uncover regulators of cell density and volume in neutrophils. The results show that cells require NHE activity during chemoattractant-driven cell migration. Before migration occurs, cells also undergo a rapid cell volume increase. These results indicate that water flux, driven by ion channels, appears to play a central role in neutrophil migration. The paper is very well written and clear. The revised version has addressed all of my questions.

Reviewer #2 (Public Review):

Nagy et al investigated the role of volume increase and swelling in neutrophils in response to the chemoattractant. Authors show that following chemoattractant response cells lose their volume slightly owing to the cell spreading phase and then have a relatively rapid increase in the cell volume that is concomitant with cell migration. Authors performed an impressive genome-wide CRISPR screen and buoyant density assay to identify the regulators of neutrophil swelling. This assay showed that stimulating cells with chemoattractant fMLP lead to an increase in the cell volume that was abrogated with the FPR1 receptor knockout. The screen revealed a cascade that could potentially be involved cell swelling including NHE1 (sodium-proton antiporter) and PI3K. NHE1 and PI3K is required for chemoattractant-induced swelling in human primary neutrophils. Authors also suggest slightly different functions of NHE1 and PI3K activity where PI3K is also required for maintain chemoattractant-induced cell shape changes. Authors convincingly show that chemoattractant induced cell swelling is linked to cell migration and NHE1 is required for swelling at the later stages of swelling since the cells at the early point work on low-volume and low-velocity regime. Interesting authors also show that lack of swelling in NHE1 inhibited cells could be rescued by mild hypo-osmotic swelling strengthening the argument that water influx followed chemoattractant stimulation is important for potentiation for migration.

The conclusions of this paper are mostly well supported by data and is pretty convincing

Reviewer #1 (Public Review):

This study presents a novel application of the inverted encoding (i.e., decoding) approach to detect the correlates of crossmodal integration in the human EEG (electrophysiological) signal. The method is successfully applied to data from a group of 41 participants, performing a spatial localization task on auditory, visual, and audio-visual events. The analyses clearly show a behavioural superiority for audio-visual localization. Like previous studies, the results when using traditional univariate ERP analyses were inconclusive, showing once more the need for alternative, more sophisticated approaches. Instead, the principal approach of this study, harnessing the multivariate nature of the signal, captured clear signs of super-additive responses, considered by many as the hallmark of multisensory integration. Unfortunately, the manuscript lacks many important details in the descriptions of the methodology and analytical pipeline. Although some of these details can eventually be retrieved from the scripts that accompany this paper, the main text should be self-contained and sufficient to gain a clear understanding of what was done. (A list of some of these is included in the comments to the authors). Nevertheless, I believe the main weakness of this work is that the positive results obtained and reported in the results section are conditioned upon eye movements. When artifacts due to eye movements are removed, then the outcomes are no longer significant.

Therefore, whether the authors finally achieved the aims and showed that this method of analysis is truly a reliable way to assess crossmodal integration, does not stand on firm ground. The worst-case scenario is that the results are entirely accounted for by patterns of eye movements in the different conditions. In the best-case scenario, the method might truly work, but further experiments (and/or analyses) would be required to confirm the claims in a conclusive fashion.

If finally successful, this approach could bring important advances in the many fields where multisensory integration has been shown to play a role, by providing a way to bring much-needed coherence across levels of analysis, from behaviour to single-cell electrophysiology. To achieve this, one would have to make sure that the pattern of super-additive effects, the standard self-imposed by the authors as a proxy for multisensory integration, shows up reliably regardless of eye movement or artifact corrections. One first step toward this goal would be, perhaps, to facilitate the understanding of results in context by reporting both the uncorrected and corrected analyses in the main results section. Second, one could try to support the argument given in the discussion, pointing out the origin of the super-additive effects in posterior electrode sites, by also modelling frontal electrode clusters and showing they aren't informative as to the effect of interest.

Reviewer #2 (Public Review):

Summary:

This manuscript seeks to reconcile observations in multisensory perception - from behavior and neural responses. It is intuitively obvious that perceiving a stimulus via two senses results in better performance than one alone. In fact, it is not uncommon to observe that for a perceptual task, the percentage of correct responses seen with two senses is higher than the sum of the percentage correct obtained with each modality individually. i.e. the gains are "superadditive". The gains of adding a second sense are typically larger when the performance with the first sense is relatively poor - this effect is often called the principle of inverse effectiveness. More generally, what this tells us is that performance in a multisensory perceptual task is a non-linear sum of performance for each sensory modality alone.

Despite this abundant evidence of behavioral non-linearity in multisensory integration, evoked responses (EEG) to such sensory stimuli often show little evidence of it - and this is the problem this manuscript tackles. The key assertion made is that univariate analysis of the EEG signal is likely to average out the non-linear effects of integration. This is a reasonable assertion, and their analysis does indeed provide evidence that a multivariate approach can reveal non-linear interactions in the evoked responses.

Strengths:

It is of great value to understand how the process of multisensory integration occurs, and despite a wealth of observations of the benefits of perceiving the world with multiple senses, we still lack a reasonable understanding of how the brain integrates information. For example - what underlies the large individual differences in the benefits of two senses over one? One way to tackle this is via brain imaging, but this is problematic if important features of the processing - such as non-linear interactions are obscured by the lack of specificity of the measurements. The approach they take to the analysis of the EEG data allows the authors to look in more detail at the variation in activity across EEG electrodes, which averaging across electrodes cannot.

This version of the manuscript is well-written and for the most part clear. It shows a good understanding of the non-linear effects described above (where many studies show a poor understanding of "superadditivity" of perceptual performance) and the report of non-linear summation of neural responses is convincing.

A particular strength of the paper is their use of a statistical model of multisensory integration as their "null" model of neural responses, and the "inverted-encoder" which infers an internal representation of the stimulus which can explain the EEG responses. This encoder generates a prediction of decoding performance, which can be used to generate predictions of multisensory decoding from unisensory decoding, or from a sum of the unisensory internal representations.

In behavioural performance, it is frequently observed that the performance increase from two senses is close to what is expected from the optimal integration of information across the senses, in a statistical sense. It can be plausibly explained by assuming that people are able to weigh sensory inputs according to their reliability - and somewhat optimally. Critically the apparent "superadditive" effect on performance described above does not require any non-linearity in the sum of information across the senses but can arise from correctly weighting the information according to reliability.

The authors apply a similar model to predict the neural responses expected to audiovisual stimuli from the neural responses to audio and visual stimuli alone, assuming optimal statistical integration of information. The neural responses to audiovisual stimuli exceed the predictions of this model and this is the main evidence supporting their conclusion, and it is convincing.

Weaknesses:

The main weakness of the manuscript is that their behavioural data show no evidence of performance that exceeds the predictions of these statistical models. In fact, the models predict multisensory performance from unisensory performance pretty well. So this manuscript presents the opposite problem to that which motivated the study - neural interactions across the senses which appear to be more non-linear than perception. This makes it hard to interpret their results, as surely if these nonlinear neural interactions underlie the behaviour, then we should be able to see evidence of it in the behaviour? I cannot offer an easy explanation for this.

Overall, therefore, I applaud the motivation and the sophistication of the analysis method and think it shows great promise for tackling these problems, but the manuscript unfortunately brushes over an important problem specific to the results. It appeals to the higher-level reasoning - that non-linearity is a behavioural hallmark of integration and therefore we should see it in neural responses. Yet it ignores the fact that the behaviour observed here does not exceed the predictions of the "null" model applied to the neural response.

Part of the problem, I think, is that the authors never explain the difference between superadditivity of perceptual performance (proportion correct) and superadditivity of the underlying processing, which is implied by the EEG results but not their behavior. This is of course a difficult matter to describe succinctly or clearly (I somehow doubt I have). It is however worth addressing. The literature is full of confusing claims of superadditivity. I believe these authors understand this distinction and have an opportunity to represent it clearly for the benefit of all.

Joint Public Review:

Mahapatra and Takahashi report on the physiological consequences of pharmacologically blocking either clathrin and dynamin function during compensatory endocytosis or of the cortical actin scaffold both in the calyx of Held synapse and hippocampal boutons in acute slice preparations.

Although many aspects of these pharmacological interventions have been studied in detail during the past decades, this is a comprehensive and comparative study, which reveals some interesting differences between a fast synapse (Calyx of Held) tuned to reliably transmit at several 100 Hz and a more slow hippocampal CA1 synapse. In particular the authors find that acute disturbance of the synaptic actin network leads to a marked frequency-dependent enhancement of synaptic depression in the Calyx, but not in the hippocampal synapse. This striking difference between both preparations is the most interesting finding.

Comments on latest version:

The authors have done a great job revising the paper and only minor revisions are suggested to the Discussion of the paper.

Two quite relevant and recent papers should be cited and briefly discussed because they relate directly to Pitstop2 effects and actin-myosin-scaffold proteins in the calyx of Held synapse.

One is: Paksoy A et al, (2022) "Effects of the clathrin inhibitor Pitstop-2 on synaptic vesicle recycling at a central synapse in vivo." Front. Synaptic Neurosci. 14:1056308. doi: 10.3389/fnsyn.2022.1056308. This paper shows with EM that changes caused by PitStop2 perturbation of "clathrin function suggest that clathrin plays a role in SV recycling from both, the plasma membrane and large endosomes, under physiological activity patterns, in vivo."

Second: A role for actin-myosin and MLCK in short-term plasticity has been shown by Srinivasan G., et al. (2008) "The Pool of Fast Releasing Vesicles Is Augmented by Myosin Light Chain Kinase Inhibition at the Calyx of Held Synapse." J Neurophysiol 99: 1810-1824, 2008. The data here suggests that MLCK plays a crucial role in determining the size of the pool of synaptic vesicles that undergo fast release but not the Pr of the synapse. In other words, MLCK inhibition augments super-priming of vesicles at the calyx of Held synapse.

Reviewer #1 (Public Review):

Summary:

The authors aim to test the sensory recruitment theory of visual memory, which assumes that visual sensory areas are recruited for working memory and that these sensory areas represent visual memories in a similar fashion to how perceptual inputs are represented. To test the overlap between working memory (WM) and perception, the authors use coarse stimulus (aperture) biases that are known to account for (some) orientation decoding in visual cortex (i.e., stimulus energy is higher for parts of an image where a grating orientation is perpendicular to an aperture edge, and stimulus energy drives decoding). Specifically, the authors show gratings (with a given "carrier" orientation) behind two different apertures: One is a radial modulator (with maximal energy aligned with the carrier orientation) and the other an angular modulator (with maximal energy orthogonal to the carrier orientation). When subject detect contrast changes in these stimuli (the perceptual task), orientation decoding only works when training and testing within each modulator, but not across modulators, showing the impact of stimulus energy on decoding performance. Instead, when subjects remember the orientation over a 12s delay, orientation decoding works irrespective of the modulator used. The authors conclude that representations during WM are therefore not "sensory-like", given that they are immune to aperture biases. This invalidates the sensory recruitment hypothesis, or at least the part assuming that when sensory areas that are recruited during WM, they are recruited in a manner that resembles how these areas are used during perception.

Strengths:

Duan and Curtis very convincingly show that aperture effects that are present during perception, do not appear to be present during the working memory delay. Especially when the debate about "why can we decode orientations from human visual cortex" was in full swing, many may have quietly assumed this to be true (e.g., "the memory delay has no stimuli, and ergo no stimulus aperture effects"), but it is definitely not self-evident and nobody ever thought to test it directly until now. In addition to the clear absence of aperture effects during the delay, Duan and Curtis also show that when stimulus energy aligns with the carrier orientation, cross-generalization between perception and memory does work (which could explain why perception-to-memory cross decoding also works). All in all, this is a clever manipulation, and I'm glad someone did it, and did it well.

Weaknesses:

There seems to be a major possible confound that prohibits strong conclusions about "abstractions" into "line-like" representation, which is spatial attention. What if subjects simply attend the end points of the carrier grating, or attend to the edge of the screen where the carrier orientation "intersects" in order to do the task? This may also result in reconstructions that have higher bold at areas close to the stimulus/screen edges along the carrier orientation. The question then would be if this is truly an "abstracted representation", or if subjects are merely using spatial attention to do the task.

Alternatively (and this reaches back to the "fine vs coarse" debate), another argument could be that during memory, what we are decoding is indeed fine-scale inhomogenous sampling of orientation preferences across many voxels. This is clearly not the most convincing argument, as the spatial reconstructions (e.g., Figure 3A and C) show higher BOLD for voxels with receptive fields that are aligned to the remembered orientation (which is in itself a form of coarse scale bias), but could still play a role.

To conclude that the spatial reconstruction from the data indeed comes from a line-like representation, you'd need to generate modeled reconstructions of all possible stimuli and representations. Yes, Figure 4 shows that a line results in a modeled spatial map that resembles the WM data, but many other stimuli might too, and some may better match the data. For example, the alternative hypothesis (attention to grating endpoints) may very well lead to a very comparable model output to the one from a line. But testing this would not suffice, as there may be an inherent inverse problem (with multiple stimuli that can lead to the same visual field model).

The main conclusion, and title of the paper, that visual working memories are abstractions of percepts, is therefore not supported. Subjects could be using spatial attention, for example. Furthermore, even if it is true that gratings are abstracted into lines, this form of abstraction would not generalize to any non-spatial feature (e.g., color cannot become a line, contrast cannot become a line, etc.), which means it has limited explanatory power.

Additional context:

The working memory and perception tasks are rather different. In this case, the perception task does not require the subject to process the carrier orientation (which is largely occluded, and possibly not that obvious without paying attention to it), but attention is paid to contrast. In this scenario, stimulus energy may dominate the signal. In the WM task, subjects have to work out what orientation is shown to do the task. Given that the sensory stimulus in both tasks is brief (1.5s during memory encoding, and 2.5s total in the perceptual task), it would be interesting to look at decoding (and reconstructions) for the WM stimulus epoch. If abstraction (into a line) happens in working memory, then this perceptual part of the task should still be susceptible to aperture biases. It allows the authors to show that it is indeed during memory (and not merely the task or attentional state of the subject) that abstraction occurs.

What's also interesting is what happens in the passive perceptual condition, and the fact that spatial reconstructions for areas beyond V1 and V2 (i.e., V3, V3AB, and IPS0-1) align with (implied) grating endpoints, even when an angular modulator is used (Figure 3C). Are these areas also "abstracting" the stimulus (in a line-like format)?

Review after revision:

(1) It's nice of the authors to simulate how a dot stimulus affects the image computable model, but this does not entirely address my concern about attention to endpoints. The assumption that attention can be used in the same manner as a physical stimulus to calculate stimulus energy is questionable. (also, why would a dot at 15º lead to high stimulus energy tangential to that orientation?). This simulation also does not at all address my concern about model mimicry (many possible inputs can lead to a line-like output).

(2) It's also nice that the authors agree that much more work needs to be done, and these results may not generalize to all forms of memory. Given this agreement, and until that "more work" is done, I strongly believe we should refrain from making hyperbolic claims that might preemptively imply all visual working memories are abstractions of percepts. Time (and much more work) will likely show things to be much more subtle and complex.

The work presented in this paper is cool, but it uses a specific case: spatial stimuli (gratings) with the task to remember orientation. This limits possible conclusions for several reasons (1) These results are specific to EVC, as visual maps are a prerequisite meaning that these results will not hold up in other, non-retinotopic areas. (2) The fact that subjects are "focusing" along the main stimulus axis (attention or not) can simply be a strategy employed by the majority of (but not all) subjects - a strategy that may not be necessary to do the task, and therefore not a canonical method of Abstraction. It may be a "shared preferred strategy" or something. (3) If subjects had to (for example) remember contrast, and not orientation, results may have been entirely different (I would hypothesize there is no line-like abstraction in this case). Vice versa, if the perceptual task would have been on orientation (instead of contrast), the authors admit that "participants would reformat the grating into a line-like representation to make the judgments" (quote from author's response under "Additional context"). Thus, the results may be entirely about the task/ cognitive state, and not about how perceptual information is abstracted into memory.

Instead of unveiling *the* working memory Abstraction, this work (very nicely) shows a specific instance of possible abstraction. A more correct (but admittedly, less "sexy") conclusion may be "Visual working memories of orientation can be abstracted into a line in early visual cortex". As it stands, the authors still do not acknowledge any of the alternatives that myself (see above) and the other reviewers have put forth, nor do they acknowledge recent work by Chunharas et al. (2023, BioRxiv), that directly applies principles of efficient coding to address the exact same question of working memory abstraction. The link between a "line-like" representation and efficient coding implied by the authors (in their response) is merely tentative to me, but it would be great if the authors could explain this further.

These were, and remain, the major weaknesses in the original submission, that in my view have not been adequately addressed by the authors, as many overly broad conclusions about abstractions are currently still present in the manuscript (in for example the title).

Reviewer #2 (Public Review):

Summary:

In this work, Duan and Curtis addressed an important issue related to the nature of working memory representations. This work is motivated by findings illustrating that orientation decoding performance for perceptual representations can be biased by the stimulus aperture (modulator). Here, the authors examined whether the decoding performance for working memory representations is similarly influenced by these aperture biases. The results provide convincing evidence that working memory representations have a different representational structure, as the decoding performance was not influenced by the type of stimulus aperture.

Strengths:

The strength of this work lies in the direct comparison of decoding performance for perceptual representations with working memory representations. The authors take well-motivated approach and illustrate that perceptual and working memory representations do not share a similar representational structure. The authors test a clear question, with a rigorous approach and provide compelling evidence. First, the presented oriented stimuli are carefully manipulated to create orthogonal biases introduced by the stimulus aperture (radial or angular modulator), regardless of the stimulus carrier orientation. Second, the authors implement advanced methods to decode the orientation information, in visual and parietal cortical regions, when directly perceiving or holding an oriented stimulus in memory. The data illustrates that working memory decoding is not influenced by the type of aperture, while this is the case in perception. In sum, the main claims are important and shed light on the nature of working memory representations.

Weaknesses:

After the authors revised the original manuscript, a few of my initial concerns remain.

(1) Theoretical framing in the introduction. The introduction proposes that decoding of orientation information during perception does not reflect orientation selectivity, and it is instead driven by coarse scale biases. This is an overstatement. Recent work shows that orientation decoding is indeed influenced by coarse biases, but also reflects orientation selectivity (Roth, Kay & Merriam, 2022).

(2) The description of the image computable V1 model remains incomplete. The steerable pyramid is a model that simulates the responses of V1 neurons. To do so, it incorporates a set of linear receptive fields with varying orientation and spatial frequency tuning. However, the information that is lacking in the Methods is whether the implemented pyramid also included two quadrature phase pairs (odd and even phase Gabor filters making the output phase invariant). The sum of the squares of the responses to these offset phase filters computes the stimulus energy within each orientation and spatial frequency channel. Without this description, it is unclear what the model output represents.

Reviewer #1 (Public Review):

In this study, Gonzalez Alam et al. report a series of functional MRI results about the neural processing from the visual cortex to high-order regions in the default-mode network (DMN), compiling evidence from task-based functional MRI, resting-state connectivity, and diffusion-weighted imaging. Their participants were first trained to learn the association between objects and rooms/buildings in a virtual reality experiment; after the training was completed, in the task-based MRI experiment, participants viewed the objects from the earlier training session and judged if the objects were in the semantic category (semantic task) or if they were previously shown in the same spatial context (spatial context task). Based on the task data, the authors utilised resting-state data from their previous studies, visual localiser data also from previous studies, as well as structural connectivity data from the Human Connectome Project, to perform various seed-based connectivity analysis. They found that the semantic task causes more activation of various regions involved in object perception while the spatial context task causes more activation in various regions for place perception, respectively. They further showed that those object perception regions are more connected with the frontotemporal subnetwork of the DMN while those place perception regions are more connected with the medial-temporal subnetwork of the DMN. Based on these results, the authors argue that there are two main pathways connecting the visual system to high-level regions in the DMN, one linking object perception regions (e.g., LOC) leading to semantic regions (e.g., IFG, pMTG), the other linking place perception regions (e.g., parahippocampal gyri) to the entorhinal cortex and hippocampus.

Below I provide my takes on (1) the significance of the findings and the strength of evidence, (2) my guidance for readers regarding how to interpret the data, as well as several caveats that apply to their results, and finally (3) my suggestions for the authors.

(1) Significance of the results and strength of the evidence

I would like to praise the authors for, first of all, trying to associate visual processing with high-order regions in the DMN. While many vision scientists focus specifically on the macroscale organisation of the visual cortex, relatively few efforts are made to unravel how neural processing in the visual system goes on to engage representations in regions higher up in the hierarchy (a nice precedent study that looks at this issue is by Konkle and Caramazza, 2017). We all know that visual processing goes beyond the visual cortex, potentially further into the DMN, but there's no direct evidence. So, in this regard, the authors made a nice try to look at this issue.

Having said this, the authors' characterisation of the organisation of the visual cortex (object perception/semantics vs. place perception/spatial contexts) does not go beyond what has been known for many decades by vision neuroscience. Specifically, over the past two decades, numerous proposals have been put forward to explain the macroscale organisation of the visual system, particularly the ventrolateral occipitotemporal cortex. A lateral-medial division has been reliably found in numerous studies. For example, some researchers found that the visual cortex is organised along the separation of foveal vision (lateral) vs. peripheral vision (medial), while others found that it is structured according to faces (lateral) vs. places (medial). Such a bipartite division is also found in animate (lateral) vs. inanimate (medial), small objects (lateral) vs. big objects (medial), as well as various cytoarchitectonic and connectomic differences between the medial side and the lateral side of the visual cortex. Some more recent studies even demonstrate a tripartite division (small objects, animals, big objects; see Konkle and Caramazza, 2013). So, in terms of their characterisation of the visual cortex, I think Gonzalez Alam et al. do not add any novel evidence to what the community of neuroscience has already known.

However, the authors' effort to link visual processing with various regions of the DMN is certainly novel, and their attempt to gather converging evidence with different methodologies is commendable. The authors are able to show that, in an independent sample of resting-state data, object-related regions are more connected with semantic regions in the DMN while place-related regions are more connected with navigation-related regions in the DMN, respectively. Such patterns reveal a consistent spatial overlap with their Kanwisher-type face/house localiser data and also concur with the HCP white-matter tractography data. Overall, I think the two pathways explanation that the authors seek to argue is backed by converging evidence. The lack of travelling wave type of analysis to show the spatiotemporal dynamics across the cortex from the visual cortex to high-level regions is disappointing though because I was expecting this type of analysis would provide the most convincing evidence of a 'pathway' going from one point to another. Dynamic caudal modelling or Granger causality may also buttress the authors' claim of pathway because many readers, like me, would feel that there is not enough evidence to convincingly prove the existence of a 'pathway'.

(2) Guidance to the readers about interpretation of the data

The organisation of the visual cortex and the organisation of the DMN historically have been studied in parallel with little crosstalk between different communities of researchers. Thus, the work by Gonzalez Alam et al. has made a nice attempt to look at how visual processing goes beyond the realm of the visual cortex and continues into different subregions of the DMN.

While the authors of this study have utilised multiple methods to obtain converging evidence, there are several important caveats in the interpretation of their results:

(1) While the authors choose to use the term 'pathway' to call the inter-dependence between a set of visual regions and default-mode regions, their results have not convincingly demonstrated a definitive route of neural processing or travelling. Instead, the findings reveal a set of DMN regions are functionally more connected with object-related regions compared to place-related regions. The results are very much dependent on masking and thresholding, and the patterns can change drastically if different masks or thresholds are used.

(2) Ideally, if the authors could demonstrate the dynamics between the visual cortex and DMN in the primary task data, it would be very convincing evidence for characterising the journey from the visual cortex to DMN. Instead, the current connectivity results are derived from a separate set of resting state data. While the advantage of the authors' approach is that they are able to verify certain visual regions are more connected with certain DMN regions even under a task-free situation, it falls short of explaining how these regions dynamically interact to convert vision into semantic/spatial decision.

(3) There are several results that are difficult to interpret, such as their psychophysiological interactions (PPI), representational similarity analysis, and gradient analysis. For example, typically for PPI analysis, researchers interrogate the whole brain to look for PPI connectivity. Their use of targeted ROI is unusual, and their use of spatially extensive clusters that encompass fairly large cortical zones in both occipital and temporal lobes as the PPI seeds is also an unusual approach. As for the gradient analysis, the argument that the semantic task is higher on Gradient 1 than the spatial task based on the statistics of p-value = 0.027 is not a very convincing claim (unhelpfully, the figure on the top just shows quite a few blue 'spatial dots' on the hetero-modal end which can make readers wonder if the spatial context task is really closer to the unimodal end or it is simply the authors' statistical luck that they get a p-value under 0.05). While it is statistically significant, it is weak evidence (and it is not pertinent to the main points the authors try to make).

(3) My suggestion for the authors

There are several conceptual-level suggestions that I would like to offer to the authors:

(1) If the pathway explanation is the key argument that you wish to convey to the readers, an effective connectivity type of analysis, such as Granger causality or dynamic caudal modelling, would be helpful in revealing there is a starting point and end point in the pathway as well as revealing the directionality of neural processing. While both of these methods have their issues (e.g., Granger causality is not suitable for haemodynamic data, DCM's selection of seeds is susceptible to bias, etc), they can help you get started to test if the path during task performance does exist. Alternatively, travelling wave type of analysis (such as the results by Raut et al. 2021 published in Science Advances) can also be useful to support your claims of the pathway.

(2) I think the thresholding for resting state data needs to be explained - by the look of Figure 2E and 3E, it looks like whole-brain un-thresholded results, and then you went on to compute the conjunction between these un-thresholded maps with network templates of the visual system and DMN. This does not seem statistically acceptable, and I wonder if the conjunction that you found would disappear and reappear if you used different thresholds. Thus, for example, if the left IFG cluster (which you have shown to be connected with the visual object regions) would disappear when you apply a conventional threshold, this means that you need to seriously consider the robustness of the pathway that you seek to claim... it may be just a wild goose that you are chasing.

(3) There are several analyses that are hard to interpret and you can consider only reporting them in the supplementary materials, such as the PPI results and representational similarity analysis, as none of these are convincing. These analyses do not seem to add much value to make your argument more convincing and may elicit more methodological critiques, such as statistical issues, the set-up of your representational theory matrix, and so on.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Alam et al. sought to understand how memory interacts with incoming visual information to effectively guide human behavior by using a task that combines spatial contexts (houses) with objects of one or multiple semantic categories. Three additional datasets (all from separate participants) were also employed: one that functionally localized regions of interest (ROIs) based on subtractions of different visually presented category types (in this case, scenes, objects, and scrambled objects); another consisting of resting-state functional connectivity scans, and a section of the Human Connectome Project that employed DTI data for structural connectivity analysis. Across multiple analyses, the authors identify dissociations between regions preferentially activated during scene or object judgments, between the functional connectivity of regions demonstrating such preferences, and in the anatomical connectivity of these same regions. The authors conclude that the processing streams that take in visual information and support semantic or spatial processing are largely parallel and distinct.

Strengths:

(1) Recent work has reconceptualized the classic default mode network as two parallel and interdigitated systems (e.g., Braga & Buckner, 2017; DiNicola et al., 2021). The current manuscript is timely in that it attempts to describe how information is differentially processed by two streams that appear to begin in visual cortex and connect to different default subnetworks. Even at a group level where neuroanatomy is necessarily blurred across individuals, these results provide clear evidence of stimulus-based dissociation.

(2) The manuscript contains a large number of analyses across multiple independent datasets. It is therefore unlikely that a single experimenter choice in any given analysis would spuriously produce the overall pattern of results reported in this work.

Weaknesses:

(1) Throughout the manuscript, a strong distinction is drawn between semantic and spatial processing. However, given that only objects and spatial contexts were employed in the primary experiment, it is not clear that a broader conceptual distinction is warranted between "semantic" and "spatial" cognition. There are multiple grounds for concern regarding this basic premise of the manuscript.<br /> a. One can have conceptual knowledge of different types of scenes or spatial contexts. A city street will consistently differ from a beach in predictable ways, and a kitchen context provides different expectations than a living room. Such distinctions reflect semantic knowledge of scene-related concepts, but in the present work spatial and "all other" semantic information are considered and discussed as distinct and separate.<br /> b. As a related question, are scenes uniquely different from all other types of semantic/category information? If faces were used instead of scenes, could one expect to see different regions of the visual cortex coupling with task-defined face > object ROIs? The current data do not speak to this possibility, but as written the manuscript suggests that all (non-spatial) semantic knowledge should be processed by the FT-DMN.<br /> c. Recent precision fMRI studies characterizing networks corresponding to the FT-DMN and MTL-DMN have associated the former with social cognition and the latter with scene construction/spatial processing (DiNicola et al., 2020; 2021; 2023). This is only briefly mentioned by the authors in the current manuscript (p. 28), and when discussed, the authors draw a distinction between semantic and social or emotional "codes" when noting that future work is necessary to support the generality of the current claims. However, if generality is a concern, then emphasizing the distinction between object-centric and spatial cognition, rather than semantic and spatial cognition, would represent a more conservative and better-supported theoretical point in the current manuscript.

(2) Both the retrosplenial/parieto-occipital sulcus and parahippocampal regions are adjacent to the visual network as defined using the Yeo et al. atlas, and spatial smoothness of the data could be impacting connectivity metrics here in a way that qualitatively differs from the (non-adjacent) FT-DMN ROIs. Although this proximity is a basic property of network locations on the cortical surface, the authors have several tools at their disposal that could be employed to help rule out this possibility. They might, for instance, reduce the smoothing in their multi-echo data, as the current 5 mm kernel is larger than the kernel used in Experiment 2's single-echo resting-state data. Spatial smoothing is less necessary in multi-echo data, as thermal noise can be attenuated by averaging over time (echoes) instead of space (see Gonzalez-Castillo et al., 2016 for discussion). Some multi-echo users have eschewed explicit spatial smoothing entirely (e.g., Ramot et al., 2021), just as the authors of the current paper did for their RSA analysis. Less smoothing of E1 data, combined with a local erosion of either the MTL-DMN and VIS masks (or both) near their points of overlap in the RSFC data, would improve confidence that the current results are not driven, at least in part, by spatial mixing of otherwise distinct network signals.

(3) The authors identify a region of the right angular gyrus as demonstrating a "potential role in integrating the visual-to-DMN pathways." This would seem to imply that lesion damage to right AG should produce difficulties in integrating "semantic" and "spatial" knowledge. Are the authors aware of such a literature? If so, this would be an important point to make in the manuscript as it would tie in yet another independent source of information relevant to the framework being presented. The closest of which I am aware involves deficits in cued recall performance when associates consisted of auditory-visual pairings (Ben-Zvi et al., 2015), but that form of multi-modal pairing is distinct from the "spatial-semantic" integration forwarded in the current manuscript.

Reviewer #1 (Public Review):

The study by Chikermane and colleagues investigates the functional, structural, and dopaminergic network substrates of cortical beta oscillations (13-30 Hz). The major strength of the work lies in the methodology taken by the authors, namely a multimodal lesion network mapping. First, using invasive electrophysiological recordings from healthy cortical territories of epileptic patients they identify regions with the highest beta power. Next, they leverage open-access MRI data and PET atlases and use the identified high-beta regions as seeds to find (1) the whole-brain functional and structural maps of regions that form the putative underlying network of high-beta regions and (2) the spatial distribution of dopaminergic receptors that show correlation with nodal connectivity of the identified networks. These steps are achieved by generating aggregate functional, structural, and dopaminergic network maps using lead-DBS toolbox, and by contrasting the results with those obtained from high-alpha regions.

The main findings are:<br /> (1) Beta power is strongest across frontal, cingulate, and insular regions in invasive electrophysiological data, and these regions map onto a shared functional and structural network.<br /> (2) The shared functional and structural networks show significant positive correlations with dopamine receptors across the cortex and basal ganglia (which is not the case for alpha, where correlations are found with GABA).

Nevertheless, a few clarifications regarding the choice of high-power electrodes and distributions of functional connectivity maps (i.e., strength and sign across cortex and sub-cortex) can help with understanding the results.

Reviewer #2 (Public Review):

Summary:

This is a very interesting paper that leveraged several publicly available datasets: invasive cortical recording in epilepsy patients, functional and structural connectomic data, and PET data related to dopaminergic and gaba-ergic synapses. These were combined to create a unified hypothesis of beta band oscillatory activity in the human brain. They show that beta frequency activity is ubiquitous, not just in sensorimotor areas, and cortical regions where beta predominated had high connectivity to regions high in dopamine re-update.

Strengths:

The authors leverage and integrate three publicly available human brain datasets in a creative way. While these public datasets are powerful tools for human neuroscience, it is innovative to combine these three types of data into a common brain space to generate novel findings and hypotheses. Findings are nicely controlled by separately examining cortical regions where alpha predominates (which have a different connectivity pattern). GABA uptake from PET studies is used as a control for the specificity of the relationship between beta activity and dopamine uptake. There is much interest in synchronized oscillatory activity as a mechanism of brain function and dysfunction, but the field is short on unifying hypotheses of why particular rhythms predominate in particular regions. This paper contributes nicely to that gap. It is ambitious in generating hypotheses, particularly that modulation of beta activity may be used as a "proxy" for modulating phasic dopamine release.

Weaknesses:

As the authors point out, the use of normative data is excellent for exploring hypotheses but does not address or explore individual variations which could lead to other insights. It is also biased to resting state activity; maps of task-related activity (if they were available) might show different findings.

The figures, results, introduction, and methods are admirably clear and succinct but the discussion could be both shorter and more convincing.

Reviewer #3 (Public Review):

Summary:

In this paper, Chikermane et al. leverages a large open dataset of intracranial recordings (sEEG or ECoG) to analyze resting state (eyes closed) oscillatory activity from a variety of human brain areas. The authors identify a dominant proportion of channels in which beta band activity (12-30Hz) is most prominent and subsequently seek to relate this to anatomical connectivity data by using the sEEG/ECoG electrodes as seeds in a large set of MRI data from the human connectome project. This reveals separate regions and white matter tracts for alpha (primarily occipital) and beta (prefrontal cortex and basal ganglia) oscillations. Finally, using a third available dataset of PET imaging, the authors relate the parcellated signals to dopamine signaling as estimated by spatial uptake patterns of dopamine, and reveal a significant correlation between the functional connectivity maps and the dopamine reuptake maps, suggesting a functional relationship between the two.

Strengths:

Overall, I found the paper well justified, focused on an important topic, and interesting. The authors' use of 3 different open datasets was creative and informative, and it significantly adds to our understanding of different oscillatory networks in the human brain, and their more elusive relation with neuromodulator signaling networks by adding to our knowledge of the association between beta oscillations and dopamine signaling. Even my main comments about the lack of a theta network analysis and discussion points are relatively minor, and I believe this paper is valuable and informative.

Weaknesses:

The analyses were adequate, and the authors cleverly leveraged these different datasets to build an interesting story. The main aspect I found missing (in addition to some discussion items, see below) was an examination of the theta network. Theta oscillations have been involved in a number of cognitive processes including spatial navigation and memory, and have been proposed to have different potential originating brain regions, and it would be informative to see how their anatomical networks (e.g. as in Figure 2) look like under the author's analyses.

The authors devote a significant portion of the discussion to relating their findings to a popular hypothesis for the function of beta oscillations, the maintenance of the "status quo", mostly in the context of motor control. As the authors acknowledge, given the static nature of the data and lack of behavior, this interpretation remains largely speculative and I found it a bit too far-reaching given the data shown in the paper. In contrast, I missed a more detailed discussion on the growing literature indicating a role for beta in mood (e.g. in Kirkby et al. 2018), especially given the apparent lack of hippocampal and amygdala involvement in the paper, which was surprising.

Major comment:

• Although the proportion of electrodes with theta-dominant oscillations was lower (~15%) than alpha (~22%) or beta (~57%), it would be very valuable to also see the same analyses the authors carried out in these frequency bands extended to theta oscillations.