Reviewer #3 (Public Review):

Summary:

Prior research on SCC3, a cohesin subunit protein, in yeast and Arabidopsis has underscored its vital role in cell division. This study investigated into the specific functions of SCC3 in rice mitosis and meiosis. In a weakened SCC3 mutant, sister chromatids separating was observed in anaphase I, resulting in 24 univalents and subsequent sterility. The authors meticulously documented SCC3's loading and degradation dynamics on chromosomes, noting its impact on DNA replication. Despite the loss of homologous chromosome pairing and synapsis in the mutant, chromosomes retained double-strand breaks without fragmenting. Consequently, the authors inferred that in the scc3 mutant, DNA repair more frequently relies on sister chromatids as templates compared to the wild type.

Strengths:

The study presents exceptionally well-executed research in the field of rice cytogenetics.

Weaknesses:

While the paper's conclusions are generally well-supported, further substantiation is needed for the claim that SCC3 inhibits template choice for sister chromatids. To bolster this conclusion, I recommend that the authors perform whole-genome sequencing on parental and F1 individuals from two rice variants, subsequently calculating the allele frequencies at heterozygous sites in the F1 individuals. If SCC3 indeed inhibits inter-sister chromatid repair in the wild type, we would anticipate a higher frequency of inter-homologous chromosome repair (i.e., gene conversion). This should be manifested as a bias away from the Mendelian inheritance ratio (50:50) in the offspring of the wild type compared to the offspring of the scc3+/- mutant.

Reviewer #3 (Public Review):

Summary:

In this report, Ravala et al demonstrate that IP4, the soluble head-group of phosphatiylinositol 3,4,5 - trisphosphate (PIP3), is an inhibitor of pREX-1, a guanine nucleotide exchange factor (GEF) for Rac1 and related small G proteins that regulate cell cell migration. This finding is perhaps unexpected since pREX-1 activity is PIP3-dependent. By way of Cryo-EM (revealing the structure of the p-REX-1/IP4 complex at 4.2Å resolution), hydrogen-deuterium mass spectrometry and small angle X-ray scattering, they deduce a mechanism for IP4 activation, and conduct mutagenic and cell-based signaling assays that support it. The major finding is that IP4 stabilizes two interdomain interfaces that block access of the DH domain, which conveys GEF activity towards small G protein substrates. One of these is the interface between the PH domain that binds to IP4 and a 4-helix bundle extension of the IP4 Phosphatase domain and the DEP1 domain. The two interfaces are connected by a long helix that extends from PH to DEP1. Although the structure of fully activated pREX-1 has not been determined, the authors propose a "jackknife" mechanism, similar to that described earlier by Chang et al (2022) (referenced in the author's manuscript) in which binding of IP3 relieves a kink in a helix that links the PH/DH modules and allows the DH-PH-DEP triad to assume an extended conformation in which the DH domain is accessible. While the structure of the activated pREX-1 has not been determined, cysteine mutagenesis that enforces the proposed kink is consistent with this hypothesis. SAXS and HDX-MS experiments suggest that IP4 acts by stiffening the inhibitory interfaces, rather than by reorganizing them. Indeed, the cryo-EM structure of ligand-free pREX-1 shows that interdomain contacts are largely retained in the absence of IP4.

Strengths:

The manuscript thus describes a novel regulatory role for IP4 and is thus of considerable significance to our understanding of regulatory mechanisms that control cell migration, particularly in immune cell populations. Specifically, they show how the inositol polyphosphate IP4 controls the activity of pREX-1, a guanine nucleotide exchange factor that controls the activity of small G proteins Rac and CDC42. In their clearly-written discussion, the authors explain how PIP3, the cell membrane and the Gbeta-gamma subunits of heterotrimeric membranes together localize pREX-1 at the membrane and induce activation. The quality of experimental data is high and both in vitro and cell-based assays of site-directed mutants designed to test the author's hypotheses are confirmatory. The results strongly support the conclusions. The combination of cryo-EM data, that describe the static (if heterogeneous) structures with experiments (small angle x-ray scattering and hydrogen-deuterium exchange-mass spectrometry) that report on dynamics are well employed by the authors

Manuscript revision:

The reviewers noted a number of weaknesses, including error analysis of the HDX data, interpretation of the mutagenesis data, the small fraction of the total number of particles used to generate the EM reconstruction, the novelty of the findings in light of the previous report by Cheng et al, 2022, various details regarding presentation of structural results and questions regarding the interpretation of the inhibition data (Figure 1D). The authors have responded adequately to these critiques. It appears that pREX-1 is a highly dynamic molecule, and considerable heterogeneity among particles might be expected.

While, indeed, the conformation of pREX presented in this report is not novel, the finding that this inactive conformational state is stabilized by IP4 is significant and important. The evidence for this is both structural and biochemical, as indicated by micromolar competition of IP4 with PI3-enriched vesicles resulting in the inhibition of pREX-1 GEF activity.

Reviewer #3 (Public Review):

Summary:

This study aims to demonstrate that cortical feedback is not necessary to signal behavioral outcome to shell neurons of the inferior colliculus during a sound detection task. The demonstration is achieved in a very clear manner by the observation of the activity of cortico-recepient neurons in animals which have received lesions of the auditory cortex. The experiment shows that neither behavior performance nor neuronal responses are significantly impacted by cortical lesions except for the case of partial lesions which seem to have a disruptive effect on behavioral outcome signaling.

Strengths:

The demonstration of the main conclusions is based on state-of-the-art, carefully controlled methods and is highly convincing. There is an in depth discussion of the different effects of auditory cortical lesions on sound detection behavior.

Weaknesses:

The description of feedback signals could be more detailed although it is difficult to achieve good temporal resolution with the calcium imaging technique necessary for targeting cortico-recipient neurons.

Reviewer #3 (Public Review):

Summary:

Leveraging zebra fish as a research model, Wang et al identified "cytoneme-like structures" as a mechanism for mediating cell-cell communications among skin epidermal cells. The authors further demonstrated that the "cytoneme-like structures" can mediate Notch signaling, and the "cytoneme-like structures" are influenced by IL17 signaling.

Strengths:

Elegant zebrafish genetics, reporters, and live imaging.

Weaknesses: (minor)<br /> This paper focused on characterizing the "cytoneme-like structures" between different layers and the NOTCH signaling. However, these "cytoneme-like structures" observed in undifferentiated KC (Figure 2B), although at a slightly lower frequency, were not interpreted. In addition, it is unclear if these "cytoneme-like structures" can mediate other signaling pathways than NOTCH.

Overall, this is a solid paper with convincing data reporting the "cytoneme-like structures" in vivo, and with compelling data demonstrating the roles in NOTCH signaling and the regulation by IL17.

These findings provide a foundation for future work exploring the "cytoneme-like structures" in the mammalian system and other epithelial tissue types. This paper also suggests a potential connection between the "cytoneme-like structures" and psoriasis, which needs to be further explored in clinical samples.

Reviewer #3 (Public Review):

Summary:

In this study, Li et al. identified CAD96CA and FGF1 among 20 receptor tyrosine kinase receptors as mediators of JH signaling. By performing a screen in HaEpi cells with overactivated JH signaling, the authors pinpointed two main RTKs that contribute to the transduction of JH. Using the CRISPR/Cas9 system to generate mutants, the authors confirmed that these RTKs are required for normal JH activation, as precocious pupariation was observed in their absence. Additionally, the authors demonstrated that both CAD96CA and FGF1 exhibit a high affinity for JH, and their activation is necessary for the proper phosphorylation of Tai and Met, transcription factors that promote the transcriptional response. Finally, the authors provided evidence suggesting that the function of CAD96CA and FGF1 as JH receptors is conserved across insects.

Strengths:

The data provided by the authors are convincing and support the main conclusions of the study, providing ample evidence to demonstrate that phosphorylation of the transducers Met and Tai mainly depends on the activity of two RTKs. Additionally, the binding assays conducted by the authors support the function of CAD96CA and FGF1 as membrane receptors of JH. The study's results validate, at least in H. amigera, the predicted existence of membrane receptors for JH.

Weaknesses:

The study has several weaknesses that need to be addressed. Firstly, it is not clear what criteria were used by the authors to discard several other RTKs that were identified as repressors of JH signaling. For example, while NRK and Wsck may not fulfill all the requirements to become JH receptors, other evidence, such as depletion analysis and target gene expression, suggests they are involved in proper JH signaling activation.

Secondly, the expression of the six RTKs, which, when knocked down, were able to revert JH signaling activation, was mainly detected in the last larval stage of H. amigera. However, since JH signaling is active throughout larval development, it is unclear whether these RTKs are completely required for pathway activation or only needed for high activation levels at the last larval stage.<br /> Additionally, the mechanism by which different RTKs exert their functions in a specific manner is not clear. According to the expression profile of the different RTKs, one might expect some redundant role of those receptors. In fact the no reversion of phosphorilation of tai and met upon depletion of Wsck in cells with overactivated JH signalling seems to support this idea.

Nevertheless, and despite the overlapping expression of the different receptors, all RTKs seem to be required for proper pathway activation, even in the case of FGF1 which seems to be only expressed in the midgut. This is an intriguing point unresolved in the study.

Finally, the study does not explain how RTKs with known ligands could also bind JH and contribute to JH signaling activation. in Drosophila, FGF1 is activated by pyramus and thisbe for mesoderm development, while CAD96CA is activated by collagen during wound healing. Now the authors claim that in addition to these ligands, the receptors also bind to JH. However, it is unclear whether these RTKs are activated by JH independently of their known ligands, suggesting a specific binding site for JH, or if they are only induced by JH activation when those ligands are present in a synergistic manner. Alternatively, another explanation could be that the RTK pathways by their known ligands activation may induce certain levels of JH transducer phosphorylation, which, in the presence of JH, contributes to the full pathway activation without JH-RTK binding being necessary.

DOI: 10.21203/rs.3.rs-3592641/v1

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

DOI: 10.21203/rs.3.rs-3592641/v1

Resource: (BDSC Cat# 8121,RRID:BDSC_8121)

Curator: @maulamb

SciCrunch record: RRID:BDSC_8121

What is this?

DOI: 10.21203/rs.3.rs-3592641/v1

Resource: (BDSC Cat# 458,RRID:BDSC_458)

Curator: @maulamb

SciCrunch record: RRID:BDSC_458

What is this?

Reviewer #3 (Public Review):

Summary:

The work by Kalita et al. reports regulation of RecB expression by Hfq protein in E.coli cell. RecBCD is an essential complex for DNA repair and chromosome maintenance. The expression level needs to be regulated at low level under regular growth conditions but upregulated upon DNA damage. Through quantitative imaging, the authors demonstrate that recB mRNAs and proteins are expressed at low level under regular conditions. While the mRNA copy number demonstrates high noise level due to stochastic gene expression, the protein level is maintained at a lower noise level compared to expected value. Upon DNA damage, the authors claim that the recB mRNA concentration is decreased, however RecB protein level is compensated by higher translation efficiency. Through analyzing CLASH data on Hfq, they identified two Hfq binding sites on RecB polycistronic mRNA, one of which is localized at the ribosome binding site (RBS). Through measuring RecB mRNA and protein level in the ∆hfq cell, the authors conclude that binding of Hfq to the RBS region of recB mRNA suppresses translation of recB mRNA. This conclusion is further supported by the same measurement in the presence of Hfq sequestrator, the sRNA ChiX, and the deletion of the Hfq binding region on the mRNA.

Strengths:

(1) The manuscript is well-written and easy to understand.<br /> (2) While there are reported cases of Hfq regulating translation of bound mRNAs, its effect on reducing translation noise is relatively new.<br /> (3) The imaging and analysis are carefully performed with necessary controls.

Weaknesses:

The major weaknesses include a lack of mechanistic depth, and part of the conclusions are not fully supported by the data.

(1) Mechanistically, it is still unclear why upon DNA damage, translation level of recB mRNA increases, which makes the story less complete. The authors mention in the Discussion that a moderate (30%) decrease in Hfq protein was observed in previous study, which may explain the loss of translation repression on recB. However, given that this mRNA exists in very low copy number (a few per cell) and that Hfq copy number is on the order of a few hundred to a few thousand, it's unclear how 30% decrease in the protein level should resides a significant change in its regulation of recB mRNA.<br /> (2) Based on the experiment and the model, Hfq regulates translation of recB gene through binding to the RBS of the upstream ptrA gene through translation coupling. In this case, one would expect that the behavior of ptrA gene expression and its response to Hfq regulation would be quite similar to recB. Performing the same measurement on ptrA gene expression in the presence and absence of Hfq would strengthen the conclusion and model.<br /> (3) The authors agree that they cannot exclude the possibility of sRNA being involved in the translation regulation. However, this can be tested by performing the imaging experiments in the presence of Hfq proximal face mutations, which largely disrupt binding of sRNAs.<br /> (4) The data on construct with a long region of Hfq binding site on recB mRNA deleted is less convincing. There is no control to show that removing this sequence region itself has no effect on translation, and the effect is solely due to the lack of Hfq binding. A better experiment would be using a Hfq distal face mutant that is deficient in binding to the ARN motifs.<br /> (5) Ln 249-251: The authors claim that the stability of recB mRNA is not changed in ∆hfq simply based on the steady-state mRNA level. To claim so, the lifetime needs to be measured in the absence of Hfq.<br /> (6) What's the labeling efficiency of Halo-tag? If not 100% labeled, is it considered in the protein number quantification? Is the protein copy number quantification through imaging calibrated by an independent method? Does Halo tag affect the protein translation or degradation?<br /> (7) Upper panel of Fig S8a is redundant as in Fig 5B. Seems that Fig S8d is not described in the text.

Reviewer #3 (Public Review):

Strength:

The development of an automated Barnes maze allows for more naturalistic and uninterrupted behavior, facilitating the study of spatial learning and memory, as well as the analysis of the brain's neural networks during behavior when combined with neurophysiological techniques. The system's design has been thoughtfully considered, encompassing numerous intricate details. These details include the incorporation of flexible options for selecting start, goal, and proximal landmark positions, the inclusion of a rotating platform to prevent the accumulation of olfactory cues, and careful attention given to atomization, taking into account specific considerations such as the rotation of the maze without causing wire shortage or breakage. When combined with neurophysiological manipulations or recordings, the system provides a powerful tool for studying spatial navigation system.<br /> The behavioral experiment protocols, along with the analysis of animal behavior, are conducted with care, and the development of behavioral modeling to capture the animal's search strategy is thoughtfully executed. It is intriguing to observe how the integration of these innovative stochastic models can elucidate the evolution of mice's search strategy within a variant of the Barnes maze.

Comments on revised version:

The authors have addressed all the points I outlined in the previous round of review, resulting in significant improvements to the manuscript. However, I have one remaining comment. Given the updated inter-animal analysis (Supplementary Figure 8), it appears that male and female mice develop strategies differently across days. Male mice seem to progressively increase their employment of spatial strategy across days, at the expense of the random strategy. Conversely, female mice exhibit both spatial and serial strategies at their highest levels on day 2, with minimal changes observed on the subsequent days.<br /> These findings could alter the interpretation of Figure 5 and the corresponding text in the section "Evolution of search strategy across days".<br /> For instance, this statement on page 6 doesn't hold for female mice: "The spatial strategy was increased across days, ... largely at the expense of the random strategy."

Reviewer #3 (Public Review):

Summary:

The authors investigate the hypothesis that neurexins serve a crucial role as regulators of the synaptic strength and timing at the glycinergic synapse between neurons of the medial nucleus of the trapezoid body (MNTB) and the lateral superior olivary complex (LSO). It is worth mentioning that LSO neurons are an integration station of the auditory brainstem circuit displaying high reliability and temporal precision. These features are necessary for computing interaural cues to derive sound source location from comparing the intensities of sounds arriving at the two ears. In this context, the authors' findings build up according to the hypothesis first by displaying that neurexins were expressed in the MNTB at varying levels. They followed this up with deletion of all neurexins in the MNTB through the employment of a triple knock-out (TKO). Using electrophysiological recordings in acute brainstem slices of these TKO mice, they gathered solid evidence for the role of neurexins in synaptic transmission at this glycinergic synapse primarily by ensuring tight coupling of Ca2+ channels and vesicular release sites. Additionally, the authors uncovered a connection between the deletion of neurexins and a higher number of glycinergic synapses of TKO mice, for which they provided evidence in the form of immunostainings and related it to electrophysiological data on spontaneous release. Consequently, this investigation expands our knowledge on the molecular regulation of synaptic transmission at glycinergic synapses, as well as on the auditory processing at the level of the brainstem.

Strengths:

The authors demonstrate substantial results in support of the hypothesis of a critical role of neurexins for regulating glycinergic transmission in the LSO using various techniques. They provide evidence for the expression of neurexins in the MNTB and consecutively successfully generate and characterize the neurexin TKO. For their study on LSO IPSCs the authors transduced MNTB neurons by co-injection of virus carrying Cre and ChR2 and subsequently optogenetically evoke release of glycine. As a result, they observed a significant reduction in amplitude and significantly slower rise and decay times of the IPSCs of the TKO in comparison with control mice in which MNTB neurons were only transduced with ChR2. Furthermore, they observed an increased paired pulse ratio (PPR) of LSO IPSCs in the TKO mice, indicating lower release probability. Elaborating on the hypothesis that neurexins are essential for the coupling of synaptic vesicles to Ca2+ channels, the authors show lowered Ca2+ sensitivity in the TKO mice. Additionally, they reveal convincing evidence for the connection between the increased frequency of spontaneous IPSC and the higher number of glycinergic synapses of the LSO in the TKO mice, revealed by immunolabeling against the glycinergic presynaptic markers GlyT2 or VGAT.

Weaknesses:

A concern is on novelty as this work on the effects of pan-neurexin deletion in a glycinergic synapse is quite consistent with the authors prior work on glutamatergic synapses (Luo et al., 2020).

Reviewer #3 (Public Review):

Summary

In this manuscript, Weng et al. identify the neuron specific transcriptome that impacts age dependent cognitive decline. The authors design a pipeline to profile neurons from wild type and long-lived insulin receptor/IGF-1 mutants using timepoints when memory functions are declining. They discover signatures unique to neurons which validates their approach. The authors identify that genes related to neuronal identity are lost with age in wild type worms. For example, old neurons reduce the expression of genes linked to synaptic function and neuropeptide signaling and increase the expression of chromatin regulators, insulin peptides and glycoproteins. Depletion of selected genes which are upregulated in old neurons (utx-1, ins-19 and nmgp-1) leads to improved short memory function. This indicates that some genes that increase with age have detrimental effects on learning and memory. The pipeline is then used to test neuronal profiles of long-lived insulin/IGF-1 daf-2 mutants. Genes related to stress response pathways are upregulated in long lived daf-2 mutants (e.g. dod-24, F08H9.4) and those genes are required for improved neuron function.

Strengths

The manuscript is well written, and the experiments are well described. The authors take great care to explain their reasoning for performing experiments in a specific way and guide the reader through the interpretation of the results, which makes this manuscript an enjoyable and interesting read. The authors discover novel regulators of learning and memory using neuron-specific transcriptomic analysis in aged animals, which underlines the importance of cell specific deep sequencing. The timepoints of the transcriptomic profiling are elegantly chosen, as they coincide with the loss of memory and can be used to specifically reveal gene expression profiles related to neuron function. The authors discuss on the dod-24 example how powerful this approach is. In daf-2 mutants whole-body dod-24 expression differs from neuron specific profiles, which underlines the importance of precise cell specific approaches. This dataset will provide a very useful resource for the C. elegans and aging community as it complements existing datasets with additional time points and neuron specific deep profiling.

Weakness

This study nicely describes the neuron specific profiles of aged long-lived daf-2 mutants. Selected neuronal genes that were upregulated in daf-2 mutants (e.g. F08H9.4, mtl-1, dod-24, alh-2, C44B7.5) decreased learning/memory when knocked down. However, the knock down of these genes was not specific to neurons. The authors use a neuron-sensitive RNAi strain to address this concern and acknowledge this caveat in the text. While it is likely that selected candidates act only in neurons it is possible that other tissues participate as well.

Reviewer #3 (Public Review):

Summary:

The authors address a very important issue of going beyond a single-copy model obtained by the two principal experimental methods of structural biology, macromolecular crystallography and cryo electron microscopy (cryo-EM). Such multiconformer model is based on the fact that experimental data from both these methods represent a space- and time-average of a huge number of the molecules in a sample, or even in several samples, and that the respective distributions can be multimodal. Differently from structure prediction methods, this approach is strongly based on accurate high-resolution experimental information and requires validated single-copy high-quality models as input. In overall, the results support the authors' conclusions.

In fact, the method addresses two problems which could be considered separately:

- an automation of construction of multiple conformations when they can be identified visually;<br /> - a determination of multiple conformations when their visual identification is difficult or impossible.

The former is a known problem, when missing alternative conformations may cost a few percent in R-factors. While these conformations are relatively easy to detect and build manually, the current procedure may save significant time being quite efficient, as the test results show. It is an indisputably useful tool for such a goal. The second problem is important from the physical point of view and has been considered first thirty years ago by Burling & Brünger. The manuscript does not specify clearly how much the current tool addresses the second case. To model such maps, the authors introduced errors in structure factors, however, being independent, as in this work, such errors, even quite high, may leave the maps reasonably well interpretable. Obviously, it is impossible to model all kinds of errors and this modeling of noise is appreciated but it would helpful for understanding if the manuscript shows, for example, the worst map when the procedure was successful.

The new procedure deals with a second-order variation in the R-factors, of about 1% or less, like placing riding hydrogen atoms, modeling density deformation or variation of the bulk solvent. In such situations, it is hard to justify model improvement. Keeping Rfree values or their marginal decreasing can be considered as a sign that the model does not overfit data but hardly as a strong argument in favor of the model.

In general, global targets are less appropriate for this kind of problems and local characteristics may be better indicators. Improvement of the model geometry is a good choice. Indeed, yet Cruickshank (1956) showed that averaged density images may lead to a shortening of covalent bonds when interpreting such maps by a single model. However, a total absence of geometric outliers is not necessarily required for the structures solved at a high resolution where diffraction data should have a more freedom to place the atoms where the experiments "see" them.

The key local characteristic for multicomformer models is a closeness of the model map to the experimental one. Actually, the procedure uses a kind of such measure, the Bayesian information criteria (BIC). Unfortunately, the manuscript does not describe how sharply it identifies the best model and how much it changes between the initial and final models; in general, there is no feeling about its values. The Q-score (page 17) can be an appropriate tool for the first problem where the multiple conformations and individual atomic images are clearly separated and not for the second problem where the contributions from neighboring conformations and atoms are merged. In addition to BIC or to even more conventional global target functions such as LS or map correlation, the extreme values of the local difference maps may help to validate, or not, the model.

This described method with the results presented is a strong argument for a need in experimental data and information they contain, differently from a pure structure prediction. This tool is important to produce user-unbiased multiconformer models rapidly and automatically. At the same time, absence of strong density-based validation components may limit its impact.

Strengths:<br /> Addressing an important problem and automatisation of model construction for alternative conformations using high-resolution experimental data.

Weaknesses:<br /> An insufficient validation of the models when no discrete alternative conformations visible and insufficiency of local real-space validation indicators.

Reviewer #3 (Public Review):

Summary:

This is a well prepared manuscript which presented interesting research result.

Strengths:

The omics method produced unbiased results.

Weaknesses:

LPS neutralization is not new method for treating leptospiral infection.

Reviewer #4 (Public Review):

Summary:

In the present study, Spikol et al. explore the projection patterns and functional characteristics of two distinct and genetically defined populations in the larval zebrafish Nucleus Incertus (NI), expressing the transcription factor gsc2 or the neuropeptide rln3a. To label in vivo these neurons two transgenic lines were generated by CRISPR/Cas9 mediated Knock-in. These genetic tools allowed the analysis of the projection patterns of these neuronal populations showing that the NI neurons expressing gsc2 and rln3a exhibit markedly different projection patterns, targeting separate subregions within the midbrain interpeduncular nucleus (IPN).<br /> Functional imaging and behavioral analysis revealed that while gsc2 neurons respond to electric shock stimuli, rln3a neurons show high spontaneous activity and play a role in regulating locomotor activity.

Strengths:

The paper relies on a series of rigorous experimental approaches including molecular genetic, neuroanatomical, functional and behavioral analysis. The resources generated including the two knock-in transgenic reporter lines will be of great value for the zebrafish neurobiology community as well as inspire further studies of the NI in other model systems.

Weaknesses:

Technical weaknesses present in the first version of the manuscript have largely been addressed in the present revision.

Reviewer #3 (Public Review):

Summary:

This manuscript describes RNAi depletion of isp-1 or spg-7 in the GABAergic neurons of C. elegans leads to: lifespan extension; increased resistance to paraquat oxidative stress and heat stress; decreased brood size and mitotic germ cell numbers in the gonad and increased DNA aggregates in the oocytes; increased mitochondrial membrane potential, ATP levels, mitochondrial mass, mitochondrial DNA copies, mitochondrial DNA polymerase gamma polg-1 levels, and decreased ROS levels. The authors further show that daf-16 is necessary for GABAergic depletion of isp-1 mediated lifespan extension, stress resistance, increased mitochondrial membrane potential, mitochondrial mass and DNA copies, and decreased brood size. Unc-25 for GABA synthesis, unc-31 for neuropeptide secretion, and flp-13 neuropeptide are all in the same pathway of isp-1 RNAi in GABAergic neurons for lifespan extension and stress resistance.

Strengths:

The topic is interesting and relatively novel in terms of GABAergic mitochondrial dysfunction. The data provided support the conclusions well.

Weaknesses:

The mechanistic evidence needs to be improved substantially.

Reviewer #3 (Public Review):

Summary:

Mou and Ji investigated neuro-computational mechanisms behind observational spatial learning in rats and reported several signs of functional coupling between the ACC and CA1 at the single neuron level. Using multi-site tetrode recording, they found that ACC cells encoding a path on a maze were activated while a rat observed another rat took that path. This activation was also correlated with the activation of CA1 cells encoding the same path and facilitated their replay during sharp-wave ripples (SWRs) before the recording rat ran on the maze by itself. These activity patterns were associated with correct path choice during self-running and were absent in control conditions where the recording rat did not learn the correct choice through observations. Based on these findings, the authors argue that ACC cells capture the critical information during observation to organize hippocampal cell activity for subsequent spatial decisions.

Strengths:

The authors used multiple outcome measures to build a strong case for path-specific spike coordination between ACC and CA1 cells. The analyses were conducted carefully, and proper control measures were used to establish the statistical significance of the detected effects. The authors also demonstrated tight correlations between the spike coordination patterns and the successful use of observed information for future decisions.

Weaknesses:

(1) As evidence for the activation of path information in the ACC during observation, the authors showed positive correlations between firing rates during observation and those during self-running. This argument will be solidified if the authors use a decoding approach to demonstrate the activation of path-selective ACC ensemble activity patterns during observation. This approach will also open the door to uncovering how the activation of ACC path representation is related to the moment-to-moment position of the demonstrator rat and whether it is coupled with the timing of SWRs.

(2) The authors argued that the ACC biases the content of awake replay in CA1 during SWRs in the observation period. The reviewer wonders if a similar bias also occurs during SWRs in the self-run period (i.e., water consumption after the correct choice). This analysis will be helpful in testing if the biased replay occurs due to the need to convert observed information into future choices.

(3) Although the authors demonstrated the necessity of the ACC for the task, it still remains to be determined firing coordination between the ACC and CA1 during observation is necessary for the correct path choice during self-runs. Some discussion on this point, along with future direction, would be beneficial for readers.

Reviewer #3 (Public Review):

Summary:

In the present work, Deganutti et al. report a structural study on GPCR functional dynamics using a computational approach called supervised molecular dynamics.

Strengths:

The study has the potential to provide novel insight into GPCR functionality. An example is the interaction between loops of GPCR and G proteins, which are not resolved experimentally, or the interaction between D344 and R385 identified during the Gs coupling by GLP-1R. However, validation of the findings, even computationally through for instance in silico mutagenesis study, is advisable.

Weaknesses:

In its current form, the manuscript seems immature and in particular, the described results grasp only the surface of the complex molecular mechanisms underlying GPCR activation. No significant advance of the existing structural data on GPCR and GPCR/G protein coupling is provided. Most of the results are a reproduction of the previously reported structures.

Reviewer #3 (Public Review):

Summary:

The study presented by Leitao et al., represents an important advancement in comprehending the social learning processes of sperm whales across various communicative and socio-cultural contexts. The authors introduce the concept of "vocal style" as an addition to the previously established notion of "vocal repertoire," thereby enhancing our understanding of sperm whale vocal identity.

Strengths:

A key finding of this research is the correlation between the similarity of clan vocal styles for non-ID codas and spatial overlap (while no change occurs for ID codas), suggesting that social learning plays a crucial role in shaping symbolic cultural boundaries among sperm whale populations. This work holds great appeal for researchers interested in animal cultures and communication. It is poised to attract a broad audience, including scholars studying animal communication and social learning processes across diverse species, particularly cetaceans.

Weaknesses:

In terms of terminology, while the authors use the term "saying" to describe whale vocalizations, it may be more conservative to employ terms like "vocalize" or "whale speech" throughout the manuscript. This approach aligns with the distinction between human speech and other forms of animal communication, as outlined in prior research (Hockett, 1960; Cheney & Seyfarth, 1998; Hauser et al., 2002; Pinker & Jackendoff, 2005; Tomasello, 2010).

Reviewer #3 (Public Review):

Summary:

This paper describes a new mechanism of clearance of protein aggregates occurring during mitosis.

The authors have observed that animal cells can clear misfolded aggregated proteins at the end of mitosis. The images and data gathered are solid, convincing, and statistically significant. However, there is a lack of insight into the underlying mechanism. They show the involvement of the ER, ATPase-dependent, BiP chaperone, and the requirement of Cdk1 inactivation (a hallmark of mitotic exit) in the process. They also show that the mechanism seems to be independent of the APC/C complex (anaphase-promoting complex). Several points need to be clarified regarding the mechanism that clears the aggregates during mitosis:

• What happens in the cell substructure during mitosis to explain the recruitment of BiP towards the aggregates, which seem to be relocated to the cytoplasm surrounded by the ER membrane.

• How the changes in the cell substructure during mitosis explain the relocation of protein aggregates during mitosis.

• Why BiP seems to be the main player of this mechanism and not the cyto Hsp70 first described to be involved in protein disaggregation.

Strengths:

Experimental data showing clearance of protein aggregates during mitosis is solid, statistically significant, and very interesting.

Weaknesses:

Weak mechanistic insight to explain the process of protein disaggregation, particularly the interconnection between what happens in the cell substructure during mitosis to trigger and drive clearance of protein aggregates.

Reviewer #3 (Public Review):

Summary:

In this manuscript, Boudjerna and Balagé et al. aim to elucidate the spatial origin of centriole amplification and the mechanisms behind the formation of an apical-basal body patch in multiciliated cells (MCCs). To this end, they focused on the role of microtubules and developed new tools for spatiotemporal and high-resolution analysis of different stages of centriole amplification, including the centrosome stages, A-stage, G-stage, and MCC-stage. Among these tools, the MEF-MCC cells grown on micropatterns stands out for its versatility as it is not tissue-specific and does not require epithelial cell-to-cell contact for differentiation. Additionally, the Cen2-GFP; mRuby-Deup1 knock-in mouse model was used to study different stages of centriole amplification in physiological brain MCCs. This model offers an advantage over the previously described Cen2-GFP model by enabling the resolution of early events in centriole amplification through the visualization of Deup1-positive structures and their dynamics. Finally, the authors leveraged powerful imaging techniques, including super-resolution microscopy, the U-ExM, and high-resolution live cell imaging in order to detect and track centriole amplification, elongation, disengagement, and migration.

By combining the MEF-MCC and knock-in mouse model with spatiotemporal imaging in control and nocodazole-treated cells(treated acutely or chronically), the authors define the sequence of events during centriole amplification, revealing the critical roles of microtubules for the first time. Initially, the centrosome-mediated microtubule network forms, organizing a pericentrosomal nest from which procentrioles and deuterosomes emerge. Their findings indicate the importance of microtubules in recruiting and maintaining pericentriolar material clouds that contain DEUP1, PCNT, SAS6, PLK1, PLK4, and tubulins. Following the amplification stage, the procentrioles mature, leading to cells displaying numerous MTOCs, as demonstrated by regrowth experiments. Mature centrioles then disengage from deuterosomes, attach to the nuclear envelope, and migrate to the apical surface facilitated by microtubules.

Strengths:

The manuscript provides new insights into the regulatory function of microtubules in centriole amplification. Addressing the role of microtubules during different stages of centriole amplification required the development of new tools to study brain MCCs, which will be useful in future studies of MCCs. A notable strength of this manuscript is the authors' thorough and quantitative analysis of highly dynamic processes in MCCs. The precision and detail in describing these dynamic events are impressive. This comprehensive analysis advances our understanding of MCC biology.

Weaknesses:

The role of microtubules and other molecular players during different stages of centriole amplification in brain MCCs can be further studied and strengthened using the tools developed in the manuscript. A more quantitative description of some of the analysis performed in the manuscript is required to strengthen the conclusions.

Reviewer #3 (Public Review):

Summary:

The authors want to prove that there is a redox potential between germline stem cells (GSCs) and somatic cyst stem cells (CySCs) in the Drosophila testis, with ROS being higher in the former compared to the latter. They also want to prove that ROS travels from CySCs to GSCs. Finally, they begin to characterize the phenotypes caused by loss of SOD (which normally lowers ROS levels) in the tj- lineage and how this impacts the germline.

Strengths:

The role of SOD in somatic support cells is an under-explored area.

Weaknesses:

The authors fall short of accomplishing their goals. There are issues with the concept of the paper (ROS gradient between cells that causes a transfer of ROS across membranes for homeostasis), the data, the figures, and the scholarship of the testis. I have discussed each of the points in detail below. These weaknesses negatively impact the conclusions put forward by the authors. In short, their data is not compelling: there is no evidence provided by the authors that ROS diffuses from CySCs to GSCs as most of the claims about stem cells are founded on data about differentiating germ and somatic cells. The somatic SOD depletion phenotype is incompletely characterized and several pathways appear to change in these cells, including reduced Egfr signaling, increased Tor signaling, and increased Hh signaling. None of these results are sufficiently followed up on. And none of them are considered relative to their known roles in the testis. For example, high Hh signaling in CySCs increases their competitiveness with GSCs. Increased Tor signaling in all CySCs does not affect the CySC lineage. Reduced Egfr signaling in CySCs reduces the number of CySCs and reduces/inhibits abscission between GSCs-gonialblasts.

Major issues:

(1) Data<br /> a. Problems proving which mitochondria are associated with which lineage.<br /> b. There is no evidence that ROS diffuses from CySCs into GSCs.<br /> c. The changes in gst-GFP (redox readout) are possibly seen in differentiating germ cells (i.e., spermatogonia) but not in GSCs. This weakens their model that ROS in CySC is transferred to GSCs.<br /> d. Most of the paper examines the effect of SOD depletion (which should increase ROS) on the CySC lineage and GSC lineage. One big caveat is that tj-Gal4 is expressed in hub cells (Fairchild, 2016) so the loss of SOD from hub cells may also contribute to the phenotype. In fact, the niche in Figure 2D looks larger than the niche in the control in Figure 2C, arguing that the expression of Tj in niche cells may be contributing to the phenotype. The authors need to better characterize the niche in tj>SOD-RNAi testes.<br /> e. The tj>SOD-RNAi phenotype is an expansion of the Zfh1+ CySC pool, expansion of the Tj+ Zfh1- cyst cells (both due to increased somatic proliferation) and a non-autonomous disruption of the germline.<br /> f. I am not convinced that MAPK signaling is decreased in tj>SOD-i testes. Not only is this antibody finicky, but the authors don't have any follow-up experiments to see if they can restore SOD-depleted CySCs by expressing an Egfr gain of function. Additionally, reduced Egfr activity causes fewer somatic cells (not more) (Amoyel, 2016) and also inhibits abscission between GSCs and gonialblasts (Lenhart 2015), which causes interconnected cysts of 8- to 16 germ cells with one GSC emanating from the hub.<br /> g. The increase in Hh signaling in SOD-depleted CySCs would increase their competitiveness against GSCs and GSCs would be lost (Amoyel 2014). The authors need to validate that Hh protein expression is indeed increased in SOD-depleted CySCs/cyst cells and which cells are producing this Hh. Normally, only hub cells produce Hh (Michel, 2012; Amoyel 2013) to promote self-renewal in CySCs.<br /> h. The increase in p4E-BP is an indication that Tor signaling is increased, but an increase in Tor in the CySC lineage does not significantly affect the number of CySCs or cyst cells (Chen, 2021). So again I am not sure how increased Tor factors into their phenotype.<br /> i. The over-expression of SOD in CySCs part is incomplete. The authors would need to monitor ROS in these testes. They would also need to examine with tj>SOD affects the size of the hub.

(2) Concept<br /> Why would it be important to have a redox gradient across adjacent cells? The authors mention that ROS can be passed between cells, but it would be helpful for them to provide more details about where this has been documented to occur and what biological functions ROS transfer regulates.

(3) Issues with scholarship of the testis<br /> a. Line 82 - There is no mention of BMPs, which are the only GSC-self-renewal signal. Upd/Jak/STAT is required for adhesion of GSCs to the niche but not self-renewal (Leatherman and Dinardo, 2008, 2010). The author should read a review about the testis. I suggest Greenspan et al 2015. The scholarship of the testis should be improved.<br /> b. Line 82-84 - BMPs are produced by both hub cells and CySCs. BMP signaling in GSCs represses bam. So it is not technically correct to say the CySCs repress bam expression in GSCs.<br /> c. Throughout the figures the authors score Vasa+ cells for GSCs. This is technically not correct. What they are counting is single, Vasa+ cells in contact with the niche. All graphs should be updated with the label "GSCs" on the Y-axis.

(4) Issues with the text<br /> a. Line 1: multi-lineage is not correct. Multi-lineage refers to stem cells that produce multiple types of daughter cells. GSCs produce only one type of offspring and CySCs produce only one type of offspring. So both are uni-lineage. Please change accordingly.<br /> b. Lines 62-75 - Intestinal stem cells have constitutively high ROS (Jaspar lab paper) so low ROS in stem cell cells is not an absolute.<br /> c. Line 79: The term cystic is not used in the Drosophila testis. There are cyst stem cells (CySCs) that produce cyst cells. Please revise.<br /> d. Line 90 - perfectly balanced is an overstatement and should be toned down.<br /> e. Line 98 - division of labour is not supported by the data and should be rephrased.<br /> f. Line 200 - the authors provide no data on BMPs - the GSC self-renewal cue - so they should avoid discussing an absence of self-renewal cues.

(5) Issues with the figures<br /> a. The images are too small to appreciate the location of mitochrondria in GSCs and CySCs.<br /> b. Figure 1<br /> i. cell membranes are not marked, reducing the precision of assigning mitochondria to GSC or CySCs. It would be very helpful if the authors depleted ATP5A from GSCs and showed that the puncta are reduced in these cells and did a similar set of experiments for the tj-Gal4 lineage. It would also be very helpful if the authors expressed membrane markers (like myr-GFP) in the GSC and then in the CySC lineage and then stained with ATP5A. This would pinpoint in which cells ATP5A immunoreactivity is occurring.<br /> ii. The presumed changes in gst-GFP (redox readout) are possibly seen in differentiating germ cells (i.e., spermatogonia) but not in GSC.<br /> iii. Panels F, Q, and S are not explained and currently are irrelevant.<br /> c. Figure 3K - The evidence to support less Ecad in GSCs in tj>SOD-i testes is not compelling as the figure is too small and the insets show changes in Ecad in somatic cells, not GSC.<br /> d. Figure 4:<br /> i. Panel A, B The apparent decline (not quantified) may not contribute to the phenotype.<br /> ii. dpERK is a finicky antibody and the authors are showing a single example of each genotype. This is an important experiment because the authors are going to use it to conclude that MAPK is decreased in the tj>SOD-i samples. However, the authors don't have any positive (dominant-active Egfr) or negative (tj>mapk-i). As is standing the data are not compelling. The graph in F does not convey any useful information.<br /> e. Figure S1D - cannot discern green on black. It is critical for the authors to show monochromes (gray scale) for the readouts that they want to emphasize. I cannot see the green on black in Figure S1D.<br /> f. Figure S4 - there is no quantification of the number of Tj cells in K-N.

(6) Issues with Methods<br /> a. Materials and Methods are not described in sufficient depth - please revise.<br /> b. Note that tj-Gal4 has real-time expression in hub cells and this is not considered by the authors. The ideal genotype for targeting CySCs is tjGal4, Gal80TS, hh-Gal80. Additionally, the authors do not mention whether they are depleting throughout development into adulthood or only in adults. If the latter, then they must have used a temperature shift like growing the flies at 18C and then upshifting to 25C or 29C during adult stages.<br /> c. The authors need to show data points in all of the graphs. Some graphs do this but others do not.<br /> d. The authors state that all data points are from three biological replicates. This is not sufficient for GSC and CySC counts. Most labs count GSCs and CySCs from at least 10 testes of the correct genotype.

Reviewer #3 (Public Review):

The authors tested a dietary intervention focused on improving meal regularity in this interesting paper. The study, a two-group, single-center, randomized, controlled, single-blind trial, utilized a smartphone application to track participants' meal frequencies and instructed the experimental group to confine their eating to these times for six weeks. The authors concluded that improving meal regularity reduced excess body weight despite food intake not being altered and contributed to overall improvements in well-being.

The concept is interesting, but the need for more rigor is of concern.

A notable limitation is the reliance on self-reported food intake, with the primary outcome being self-reported body weight/BMI, indicating an average weight loss of 2.62 kg. Despite no observed change in caloric intake, the authors assert weight loss among participants.

The trial's reliance on self-reported caloric intake is problematic, as participants tend to underreport intake; for example, in the NEJM paper (DOI: 10.1056/NEJM199212313272701), some participants underreported caloric intake by approximately 50%, rendering such data unreliable and hence misleading. More rigorous methods for assessing food intake are available and should have been utilized. Merely acknowledging the unreliability of self-reported caloric intake is insufficient as it would still leave the reader with the impression that there is no change in food intake when we actually have no idea if food intake was altered. A more robust approach to assessing food intake is imperative. Even if a decrease in caloric intake is observed through rigorous measurement, as I am convinced a more rigorous study would unveil testing this paradigm, this intervention may merely represent another short-term diet among countless others that show that one may lose weight by going on a diet, principally due to heightened dietary awareness.

Furthermore, the assessment of circadian rhythm using the MCTQ, a self-reported measure of chronotype, may not be as reliable as more objective methods like actigraphy.

Given the potential limitations associated with self-reported data in both dietary intake and circadian rhythm assessment, the overall impact of this manuscript is low. Increasing rigor by incorporating more objective and reliable measurement techniques in future studies could strengthen the validity and impact of the findings.

Reviewer #3 (Public Review):

Summary:

In this study, the authors have started off using an immortalized human cell line and then gene-edited it to decrease the levels of VEGF1 (in order to influence vascularization), and the levels of Runx2 (to decrease chondro/osteogenesis). They first transplanted these cells with a collagen scaffold. The modified cells showed a decrease in vascularization when VEGF1 was decreased, and suggested an increase in cartilage formation.

In another study, the matrix generated by these cells was subsequently remodeled into a bone marrow organ. When RUNX2 was decreased, the cells did not mineralize in vitro, and their matrices expressed types I and II collagen but not type X collagen in vitro, in comparison with unedited cells. In vivo, the author claims that remodeling of the matrices into bone was somewhat inhibited. Lastly, they utilized matrices generated by RUNX2 edited cells to regenerate chondro-osteal defects. They suggest that the edited cells regenerated cartilage in comparison with unedited cells.

Strengths:

-The notion that inducing changes in the ECM by genetically editing the cells is a novel one, as it has long been thought that ECM composition influences cell activity.

-If successful, it may be possible to make off-the-shelf ECMS to carry out different types of tissue repair.

Weaknesses:

-The authors have not generated histologically identifiable cartilage or bone in their transplants of the cells with a type I scaffold.

-In many cases, they did not generate histologically identifiable cartilage with their cell-free-edited scaffold. They did generate small amounts of bone but this is most likely due to BMPs that were synthesized by the cells and trapped in the matrix.

-There is a great deal of missing detail in the manuscript.

-The in vivo study is underpowered, the results are not well documented pictorially, and are not convincing.

-Given the fact that they have genetically modified cells, they could have done analyses of ECM components to determine what was different between the lines, both at the transcriptome and the protein level. Consequently, the study is purely descriptive and does not provide any mechanistic understanding of what mixture of matrix components and growth factors works best for cartilage or bone. But this presupposes that they actually induced the formation of bona fide cartilage, at least.

DOI: 10.21203/rs.3.rs-4166090/v1

Resource: Fiji (RRID:SCR_002285)

Curator: @evieth

SciCrunch record: RRID:SCR_002285

What is this?

DOI: 10.21203/rs.3.rs-4166090/v1

Resource: ImageJ (RRID:SCR_003070)

Curator: @evieth

SciCrunch record: RRID:SCR_003070

What is this?

Reviewer #3 (Public Review):

Summary:

This manuscript describes some biochemical experiments on the crucial virulence factor EsxA (ESAT-6) of Mycobacterium tuberculosis. EsxA is secreted via the ESX-1 secretion system. Although this system is recognized to be crucial for virulence the actual mechanisms employed by the ESX-1 substrates are still mostly unknown. The EsxA substrate is attracting most attention as the central player in virulence, especially phagosomal membrane disruption. EsxA is secreted as a dimer together with EsxB. The authors show that EsxA is also able to form homodimers and even tetramers, albeit at very low pH (below 5). Furthermore addition of a nanobody that specifically binds EsxA is blocking intracellular survival, also if the nanobody is produced in the cytosol of the infected macrophages.

Strengths:

Decent biochemical characterization of EsxA and identification of a new and interesting tool to study the function of EsxA (nanobody). Well written.

Weaknesses:

The findings are not critically evaluated using extra experiments or controls.<br /> For instance, tetrameric EsxA in itself is interesting and could reveal how EsxA works. But one would say that this is a starting point to make small point mutations that specifically affect tetramer formation and then evaluate what the effect is on phagosomal membrane lysis. Also one would like to see experiments to indicate whether these structures can be produced under in vitro conditions, especially because it seems that this mainly happens when the pH is lower than 5, which is not normally happening in phagosomes that are loaded with M. tuberculosis.<br /> Also the fact that the addition of the nanobody, either directly to the bacteria or produced in the cytosol of macrophages is interesting, but again the starting point for further experimentation. As a control one would like to se the effect on an Esx-1 secretion mutant. Furthermore, does cytososlic production or direct addition of the nanobody affect phagosomal escape? What happens if an EsxA mutant is produced that does not bind the nanobody?<br /> Finally, it is a bit strange that the authors use a non-native version of esxA that has not only an additional His-tag but also an additional 12 amino acids, which makes the protein in total almost 20% bigger. Of course these additions do not have to alter the characteristics, but they might. On the other hand they easily discard the natural acetylation of EsxA by mycobacteria itself (proven for M. marinum) as not relevant for the function because it might not happen in (the close homologue) M. tuberculosis.

Reviewer #3 (Public Review):

Summary:

Mäkelä et al. here investigate genome concentration as a limiting factor on growth. Previous work has identified key roles for transcription (RNA polymerase) and translation (ribosomes) as limiting factors on growth, which enable an exponential increase in cell mass. While a potential limiting role of genome concentration under certain conditions has been explored theoretically, Mäkelä et al. here present direct evidence that when replication is inhibited, genome concentration emerges as a limiting factor.

Strengths:

A major strength of this paper is the diligent and compelling combination of experiment and modeling used to address this core question. The use of origin- and ftsZ-targeted CRISPRi is a very nice approach that enables dissection of the specific effects of limiting genome dosage in the context of a growing cytoplasm. While it might be expected that genome concentration eventually becomes a limiting factor, what is surprising and novel here is that this happens very rapidly, with growth transitioning even for cells within the normal length distribution for E. coli. Fundamentally, it demonstrates the fine balance of bacterial physiology, where the concentration of the genome itself (at least under rapid growth conditions) is no higher than it needs to be.

Weaknesses:

One limitation of the study is that genome concentration is largely treated as a single commodity. While this facilitates their modeling approach, one would expect that the growth phenotypes observed arise due to copy number limitation in a relatively small number of rate-limiting genes. The authors do report shifts in the composition of both the proteome and the transcriptome in response to replication inhibition, but while they report a positional effect of distance from the replication origin (reflecting loss of high-copy, origin-proximal genes), other factors shaping compositional shifts and their functional effects on growth are not extensively explored. This is particularly true for ribosomal RNA itself, which the authors assume to grow proportionately with protein. More generally, understanding which genes exert the greatest copy number-dependent influence on growth may aid both efforts to enhance (biotechnology) and inhibit (infection) bacterial growth.

Overall, this study provides a fundamental contribution to bacterial physiology by illuminating the relationship between DNA, mRNA, and protein in determining growth rate. While coarse-grained, the work invites exciting questions about how the composition of major cellular components is fine-tuned to a cell's needs and which specific gene products mediate this connection. This work has implications not only for biotechnology, as the authors discuss, but potentially also for our understanding of how DNA-targeted antibiotics limit bacterial growth.

Reviewer #3 (Public Review):

Summary:

Kundu et al. investigated the effects of pre-exposure to a non-pathogenic Leptospira strain in the prevention of severe disease following subsequent infection by a pathogenic strain. They utilized a single or double exposure method to the non-pathogen prior to challenge with a pathogenic strain. They found that prior exposure to a non-pathogen prevented many of the disease manifestations of the pathogen. Bacteria, however, were able to disseminate, colonize the kidneys, and be shed in the urine. This is an important foundational work to describe a novel method of vaccination against leptospirosis. Numerous studies have attempted to use recombinant proteins to vaccinate against leptospirosis, with limited success. The authors provide a new approach that takes advantage of the homology between a non-pathogen and a pathogen to provide heterologous protection. This will provide a new direction in which we can approach creating vaccines against this re-emerging disease.

Strengths:

The major strength of this paper is that it is one of the first studies utilizing a live non-pathogenic strain of Leptospira to immunize against severe disease associated with leptospirosis. They utilize two independent experiments (a single and double vaccination) to define this strategy. This represents a very interesting and novel approach to vaccine development. This is of clear importance to the field.

The authors use a variety of experiments to show the protection imparted by pre-exposure to the non-pathogen. They look at disease manifestations such as death and weight loss. They define the ability of Leptospira to disseminate and colonize the kidney. They show the effects infection has on kidney architecture and a marker of fibrosis. They also begin to define the immune response in both of these exposure methods. This provides evidence of the numerous advantages this vaccination strategy may have. Thus, this study provides an important foundation for future studies utilizing this method to protect against leptospirosis.

Weaknesses:

Although they provide some evidence of the utility of pretreatment with a non-pathogen, there are some areas in which the paper needs to be clarified and expanded.

The authors draw their conclusions based on the data presented. However, they state the graphs only represent one of two independent experiments. Each experiment utilized 3-4 mice per group. In order to be confident in the conclusions, a power analysis needs to be done to show that there is sufficient power with 3-4 mice per group. In addition, it would be important to show both experiments in one graph which would inherently increase the power by doubling the group size, while also providing evidence that this is a reproducible phenotype between experiments. Overall, this weakens the strength of the conclusions drawn and would require additional statistical analysis or additional replicates to provide confidence in these conclusions.

A direct comparison between single and double exposure to the non-pathogen is not able to be determined. The ages of mice infected were different between the single (8 weeks) and double (10 weeks) exposure methods, thus the phenotypes associated with LIC infection are different at these two ages. The authors state that this is expected, but do not provide a reasoning for this drastic difference in phenotypes. It is therefore difficult to compare the two exposure methods, and thus determine if one approach provides advantages over the other. An experiment directly comparing the two exposure methods while infecting mice at the same age would be of great relevance to and strengthen this work.

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

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

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

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

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

Weaknesses:

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

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

Reviewer #3 (Public Review):

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

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

Weaknesses:

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #4 (Public Review):

Summary:

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

Strengths:

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

Other considerations :

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

Reviewer #3 (Public Review):

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

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

Reviewer #3 (Public Review):

Summary:

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

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

The analyses are clearly presented, applied, and visualized.

The supplemental data provides important transparency.

Weaknesses:

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

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #4 (Public Review):

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

Strengths:

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

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

The shown interaction of TDR1 with DNA.

Weaknesses:

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

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

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

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

Weaknesses:

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

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

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

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

Impact:

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

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

Reviewer #3 (Public Review):

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

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

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

General comments:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Comments:

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

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

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

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Critique:

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

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

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

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

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

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

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

Recommendation:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

(2) Some control data needs to be included.

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

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

Reviewer #3 (Public Review):

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

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

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

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

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

Strengths:

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

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

Weaknesses:

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

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

Reviewer #3 (Public Review):

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

I have run across Jeff Shelton's Analog system (originally via Kickstarter) before. Thanks for the reminder.

There's also a slew of others, especially for folks looking at commercially preprinted cards (though I tend to think they're overpriced compared to blank cards): - The Hipster PDA (Parietal Disgorgement Aid) https://web.archive.org/web/20040906150523/https://merlin.blogs.com/43folders/2004/09/introducing_the.html - Pile of Index Cards (PoIC) https://www.flickr.com/photos/hawkexpress/albums/72157594200490122/ - Levenger https://www.levenger.com/products/triple-decker-pocket-planner?variant=42485422424213 (among others they carry including pocket briefcases) - Notsu https://notsubrand.com/ - Baronfig / Strategist: https://baronfig.com/products/strategist?variant=39787199529043 - Jeff Shelton's Analog system https://ugmonk.com/ - 3x5 Life https://www.3x5life.com/ - Foglietto https://www.nerosnotes.co.uk/collections/foglietto - Jot & Mark https://amzn.to/3Qs26Je

Am I missing any significant or influential examples, particularly branded ones?

Hubnote for 3 x 5" index cards for productivity

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

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

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

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

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #3 (Public Review):

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

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

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

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

Reviewer #3 (Public Review):

Summary:

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

Strengths:

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

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

Weaknesses:

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

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

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

Reviewer #3 (Public Review):

This study begins with a chemogenetic screen to discover previously unrecognized regulators of the cell cycle. Using a CRISPR-Cas9 library in HAP1 cells and an assay that scores cell fitness, the authors identify genes that sensitize or desensitize cells to the presence of palbociclib, colchicine, and camptothecin. These three drugs inhibit proliferation through different mechanisms, and with each treatment, expected and unexpected pathways were found to affect drug sensitivity. The authors focus the rest of the experiments and analysis on the polycomb complex PRC2, as the deletion of several of its subunits in the screen conferred palbociclib resistance. The authors find that PRC2, specifically a complex dependent on the MTF2 subunit, methylates histone 3 lysine 27 (H3K27) in promoters of genes associated with various processes including cell-cycle control. Further experiments demonstrate that Cyclin D expression increases upon loss of PRC2 subunits, providing a potential mechanism for palbociclib resistance.

The strengths of the paper are the design and execution of the chemogenetic screen, which provides a wealth of potentially useful information. The data convincingly demonstrate in the HAP1 cell line that the MTF2-PRC2 complex sustains the effects of palbociclib (Figure 4), methylates H3K27 in CpG-rich promoters (Figure 5), and represses Cyclin D expression (Figure 6). These results could be of great interest to those studying cell-cycle control, resistance mechanisms to therapeutic cell-cycle inhibitors, and chromatin regulation and gene expression.

There are several weaknesses that limit the overall quality and potential impact of the study. First, none of the results from the colchicine and camptothecin screens (Figures 1 and 2) are experimentally validated, which lessens the rigor of those data and conclusions. Second, all experiments validating and further exploring results from the palbociclib screen are restricted to the Hap1 cell line, so the reproducibility and generality of the results are not established. While it is reasonable to perform the initial screen to generate hypotheses in the Hap1 line, other cancer and non-transformed lines should be used to test further the validity of conclusions from data in Figures 4-6. Third, conclusions drawn from data in Figures 3D and 4D are not fully supported by the experimental design or results. Finally, there have been other similar chemogenetic screens performed with palbociclib, most notably the study described by Chaikovsky et al. (PMID: 33854239). Results here should be compared and contrasted to other similar studies.

Reviewer #3 (Public Review):

Summary:

The manuscript introduces PAClight1P78A, a novel genetically encoded sensor designed to facilitate the study of class-B1 G protein-coupled receptors (GPCRs), focusing on the human PAC1 receptor. Addressing the significant challenge of investigating these clinically relevant drug targets, the sensor demonstrates a high dynamic range, excellent ligand selectivity, and rapid activation kinetics. It is validated across a variety of experimental contexts including in vitro, ex vivo, and in vivo models in mice and zebrafish, showcasing its utility for high-throughput screening, basic research, and drug development efforts related to GPCR dynamics and pharmacology.

Strengths:

The innovative design of PAClight1P78A successfully bridges a crucial gap in GPCR research by enabling real-time monitoring of receptor activation with high specificity and sensitivity. The extensive validation across multiple models emphasizes the sensor's reliability and versatility, promising significant contributions to both the scientific understanding of GPCR mechanisms and the development of novel therapeutics. Furthermore, by providing the research community with detailed methodologies and access to the necessary viral vectors and plasmids, the authors ensure the sensor's broad applicability and ease of adoption for a wide range of studies focused on GPCR biology and drug targeting.

Weaknesses<br /> To further strengthen the manuscript and validate the efficacy of PAClight1P78A as a selective PACAP sensor, it is crucial to demonstrate the sensor's ability to detect endogenous PACAP release in vivo under physiological conditions. While the current data from artificial PACAP application in mouse brain slices and microinfusion in behaving mice provide foundational insights into the sensor's functionality, these approaches predominantly simulate conditions with potentially higher concentrations of PACAP than naturally occurring levels.

Although the sensor's specificity for the PAC1 receptor and its primary ligand is a pivotal achievement, exploring its potential application to other GPCRs within the class-B1 family or broader categories could enhance the manuscript's impact, suggesting ways to adapt this technology for a wider array of receptor studies. Additionally, while the sensor's performance is convincingly demonstrated in short-term experiments, insights into its long-term stability and reusability in more prolonged or repeated measures scenarios would be valuable for researchers interested in chronic studies or longitudinal behavioral analyses. Addressing these aspects could broaden the understanding of the sensor's practical utility over extended research timelines.

Furthermore, the current in vivo experiments involving microinfusion of PACAP near sensor-expressing areas in behaving mice are based on a relatively small sample size (n=2), which might limit the generalizability of the findings. Increasing the number of subjects in these experimental groups would enhance the statistical power of the results and provide a more robust assessment of the sensor's in vivo functionality. Expanding the sample size will not only validate the findings but also address potential variability within the population, thereby reinforcing the conclusions drawn from these crucial experiments.

Reviewer #3 (Public Review):

Summary:

In this study, the authors probe the connections between clustering of the Met4/32 transcription factors (TFs), clustering of their regulatory targets, and transcriptional regulation. While there is an increasing number of studies on TF clustering in vitro and in vivo, there is an important need to probe whether clustering plays a functional role in gene expression. Another important question is whether TF clustering leads to the clustering of relevant gene targets in vivo. Here the authors provide several lines of evidence to make a compelling case that Met4/32 and their target genes cluster and that this leads to an increase in transcription of these genes in the induced state. First, they found that, in the induced state, Met4/32 forms co-localized puncta in vivo. This is supported by in vitro studies showing that these TFs can form condensates in vitro with Med32 being the driver of these condensates. They found that two target genes, MET6 and MET13 have a higher probability of being co-localized with Met4 puncta compared with non-target loci. Using a targeted DNA methylation assay, they found that MET13 and MET6 show Met4-dependent long-range interactions with other Met4-regulated loci, consistent with the clustering of at least some target genes under induced conditions. Finally, by inserting a Met4-regulated reporter gene at variable distances from MET6, they provide evidence that insertion near this gene is a modest hotspot for activity.

Weaknesses:

(1) Please provide more information on the assay for puncta formation (Figure 1). It's unclear to me from the description provided how this assay was able to quantitate the number of puncta in cells.

2) How does the number of puncta in cells correspond with the number of Met-regulated genes? What are the implications of this calculation?

3) A control for chromosomal insertion of the Met-regulated reporter was a GAL4 promoter derivative reporter. However, this control promoter seems 5-10 fold more active than the Met-regulated promoter (Figure 6). It's possible that the high activity from the control promoter overcomes some other limiting step such that chromosomal location isn't important. It would be ideal if the authors used a promoter with comparable activity to the Met-reporter as a control.

(4) It seems like transcription from a very large number of genes is altered in the Met4 IDR mutant (Figure 7F). Why is this and could this variability affect the conclusions from this experiment?

Reviewer #3 (Public Review):

The manuscript by Ruan et al. addresses an important issue in Panx1 research, i.e. the activation of the channel formed by Panx1 via protein phosphorylation. If the authors' conclusions are correct, the previous claims for Panx1 phosphorylation on the basis of the commercial anti-phospho-Panx1 antibodies would be in question.

This is a very detailed and comprehensive analysis making use of state-of-the-art techniques, including mass spectrometry and phos-tag gel electrophoresis.

In general, the study is well-controlled as relating to negative controls.

The value of this manuscript is, that it could spawn new, more function-oriented studies on the activation of Panx1 channels.

The weaknesses identified previously are reproduced below:

Weaknesses:

Although the manuscript addresses an important issue, the activation of the ATP-release channel Panx1 by protein phosphorylation, the data provided do not support the firm conclusion that such activation does not exist. The failure to reproduce published data obtained with commercial anti-phospho Panx1 antibodies can only be of limited interest for a subfield.

(1) The title claiming that "Panx1 is NOT phosphorylated..." is not justified by the failure to reproduce previously published data obtained with these antibodies. If, as claimed, the antibodies do not recognize Panx1, their failure cannot be used to exclude tyrosine phosphorylation of the Panx1 protein. There is no positive control for the antibodies.

(2) The authors claim that exogenous SRC expression does not phosphorylate Y198. DeLalio et al. 2019 show that Panx1 is constitutively phosphorylated at Y198, so an effect of exogenous SRC expression is not necessarily expected.

(3) The authors argue that the GFP tag of Panx1at the COOH terminus does not interfere with folding since the COOH modified (thrombin cleavage site) Panx1 folds properly, forming an amorphous glob in the cryo-EM structure. However, they do not show that the COOH-modified Panx1 folds properly. It may not, because functional data strongly suggest that the terminal cysteine dives deep into the pore. For example, the terminal cysteine, C426, can form a disulfide bond with an engineered cysteine at position F54 (Sandilos et al. 2012).

(4) The authors dismiss the additional arguments for tyrosine phosphorylation of Panx1 given by the various previous studies on Panx1 phosphorylation. These studies did not, as implied, solely rely on the commercial anti-phospho-Panx1 antibodies, but also presented a wealth of independent supporting data. Contrary to the authors' assertion, in the previous papers the pY198 and pY308 antibodies recognized two protein bands in the size range of glycosylated and partial glycosylated Panx1.

(5) A phosphorylation step triggering channel activity of Panx1 would be expected to occur exclusively on proteins embedded in the plasma membrane. The membrane-bound fraction is small in relation to the total protein, which is particularly true for exogenously expressed proteins. Thus, any phosphorylated protein may escape detection when total protein is analyzed. Furthermore, to be of functional consequence, only a small fraction of the channels present in the plasma membrane need to be in the open state. Consequently, only a fraction of the Panx1 protein in the plasma membrane may need to be phosphorylated. Even the high resolution of mass spectroscopy may not be sufficient to detect phosphorylated Panx1 in the absence of enrichment processes.

(6) In the electrophysiology experiments described in Figure 7, there is no evidence that the GFP-tagged Panx1 is in the plasma membrane. Instead, the image in Figure 7a shows prominent fluorescence in the cytoplasm. In addition, there is no evidence that the CBX-sensitive currents in 7b are mediated by Panx1-GFP and are not endogenous Panx1. Previous literature suggests that the hPanx1 protein needs to be cleaved (Chiu et al. 2014) or mutated at the amino terminus (Michalski et al 2018) to see voltage-activated currents, so it is not clear that the currents represent hPANX1 voltage-activated currents.

Note from the editors: The authors provided a rebuttal to the latest review, but no additional data, so we encourage readers to read the concerns and the author responses.

Reviewer #3 (Public Review):

Summary and Strengths:

The manuscript by Lewis et al, investigates whether myosin ATP activity may differ between states of hibernation and activity in both large and small mammals. The study interrogates (primarily) permeabilized muscle strips or myofibrils using several state-of-the-art assays, including the mant-ATP assay to investigate ATP utilization of myosin, X-ray diffraction of muscles, proteomics studies, metabolic tests, and computational simulations. The overall data suggests that ATP utilization of myosin during hibernation is different than in active conditions.

A clear strength of this study is the use of multiple animals that utilize two different states of hibernation or torpor. Two large animal hibernators (Eurasian Brown Bear, American Black Bear) represent large animal hibernators that typically undergo a prolonged hibernation. Two small animal hibernators (Garden Dormouse, 13 Lined Ground Squirrel) undergo torpor with more substantial reductions in heart rate and body temperature, but whose torpor bouts are interrupted by short arousals that bring the animals back to near-summer like metabolic conditions.

Especially interesting, the investigators analyze the impact that body temperature may have on myosin ATP utilization by performing assays at two different temperatures (8 and 20 degrees C, in 13 Lined Ground Squirrels).

The multiple assays utilized provide a more comprehensive set of methods with which to test their hypothesis that muscle myosins change their metabolic efficiency during hibernation.

Suggestions and potential Weaknesses:

The following highlight comments from the first Public Review that this reviewer acknowledges authors may not be able to address in the current study but may merit carrying to the revised article of record.

(1) Statistical Analysis<br /> The revised manuscript addresses the substantial issues. The two remaining questions may be noted for future experimental design(s): 1.c. That myosin isoforms may be considered a main effect and 1.e. The importance of biological vs statistical significance, especially for the mant-ATP chase data from the American Black Bear, where there appear to be shifts between the summer and winter data.

(2). Consistency of DRX/SRX data.<br /> The responses to the first Public Review on the prior version of this manuscript highlight that a potential disconnect between the mant-ATP-predicted SRX:DRX proportions and x-ray diffraction studies measuring the position of the myosin heads (Mohran et al PMID 38103642) may be outside of the scope of the current manuscript. The reviewer accepts that a substantial discussion is outside of this article, but considers a brief mention possible differences between ATP kinetics and structural movements of value.

Overall, the manuscript represents a valuable data set comparing myosin properties of skeletal muscles multiple species exhibiting different forms of hibernation/torpor.

Reviewer #3 (Public Review):

This is interesting biology. Vitamin B6 deficiency has been linked to cognitive impairment. It is not clear whether supplements are effective in restoring functional B6 levels. Vitamin B6 is composed of pyridoxal compounds and their phosphorylated forms, with pyridoxal 5-phosphate (PLP) being of particular importance. The levels of PLP are determined by the balance between pyridoxal kinase and phosphatase activities. The authors are testing the hypothesis that inhibition of pyridoxal phosphatase (PDXP) would arrest the age-dependent decline in PLP, offering an alternative therapeutic strategy to supplements. Published data illustrating that ablation of the Pdxp gene in mice led to increases in PLP levels and improvement in learning and memory trials are consistent with this hypothesis.

In this report, the authors conduct a screen of a library of ~40k small molecules and identify 7,8-dihydroxyflavone (DHF) as a candidate PDXP inhibitor. They present an initial characterization of this micromolar inhibitor, including a co-crystal structure of PDXP and 7,8-DHF. In addition, they demonstrate that treatment of cells with 7,8 DHP increases PLP levels. Overall, this study provides further validation of PDXP as a therapeutic target for the treatment of disorders associated with vitamin B6 deficiency and provides proof-of-concept for inhibition of the target with small-molecule drug candidates.

Strengths include the biological context, the focus on an interesting and under-studied class of protein phosphatases that includes several potential therapeutic targets, and the identification of a small molecule inhibitor that provides proof-of-concept for a new therapeutic strategy. Overall, the study has the potential to be an important development for the phosphatase field in general.

Weaknesses include the fact that the compound is very much an early-stage screening hit. It is an inhibitor with micromolar potency for which mechanisms of action other than inhibition of PDXP have been reported. Extensive further development will be required to demonstrate convincingly the extent to which its effects in cells are due to on-target inhibition of PDXP.

Reviewer #3 (Public Review):

Summary:

The manuscript by Yeo et al. investigates the intracellular trafficking of Botulinum neurotoxin A (BoNT/A), a potent toxin used in clinical and cosmetic applications. Contrary to the prevailing understanding of BoNT/A translocation into the cytosol, the study suggests a retrograde migration from the synapse to the soma-localized Golgi in neurons. Using a genome-wide siRNA screen in genetically engineered neurons, the researchers identify over three hundred genes involved in this process. The study employs organelle-specific split-mNG complementation, revealing that BoNT/A traffics through the Golgi in a retromer-dependent manner before moving to the endoplasmic reticulum (ER). The Sec61 complex is implicated in the retro-translocation of BoNT/A from the ER to the cytosol. Overall, the research challenges the conventional model of BoNT/A translocation, uncovering a complex route from synapse to cytosol for efficient intoxication. The findings are based on a comprehensive approach, including the introduction of a fluorescent reporter for BoNT/A catalytic activity and genetic manipulations in neuronal cell lines. The conclusions highlight the importance of retrograde trafficking and the involvement of specific genes and cellular processes in BoNT/A intoxication.

Strengths:

The major part of the experiments are convincing. They are well-controlled and the interpretation of their results is balanced and sensitive.

Weaknesses:

To my opinion, the main weakness of the paper is that all experiments are performed using a single cellular system (RenVM neurons), as stated in the title. It is therefore unclear at the moment to what extent the findings in this paper can be generalized to other neuronal cell models / in vivo situation.

Reviewer #3 (Public Review):

Summary:

This paper presents novel and innovative force measurements of the biophysics of gliding cyanobacteria filaments. These measurements allow for estimates of the resistive force between the cell and substrate and provide potential insight into the motility mechanism of these cells, which remains unknown.

Strengths:

The authors used well-designed microfabricated devices to measure the bending modulus of these cells and to determine the critical length at which the cells buckle. I especially appreciated the way the authors constructed an array of pillars and used it to do 3-point bending measurements and the arrangement the authors used to direct cells into a V-shaped corner in order to examine at what length the cells buckled at. By examining the gliding speed of the cells before buckling events, the authors were able to determine how strongly the buckling length depends on the gliding speed, which could be an indicator of how the force exerted by the cells depends on cell length; however, the authors did not comment on this directly.

Weaknesses:

There are no major weaknesses in the paper.

Reviewer #3 (Public Review):

In this study, the authors utilized mass spectrometry-based quantification of polar metabolites and lipids in normal and cancerous tissue interstitial fluid and plasma. This showed that nutrient availability in tumor interstitial fluid was similar to that of interstitial fluid in adjacent normal kidney tissue, but that nutrients found in both interstitial fluid compartments were different from those found in plasma. This suggests that the nutrients in kidney tissue differ from those found in blood and that nutrients found in kidney tumors are largely dictated by factors shared with normal kidney tissue. Those data could be useful as a resource to support further study and modeling of the local environment of RCC and normal kidney physiology.

Reviewer #3 (Public Review):

Summary:

Secondary metabolites are produced by numerous microorganisms and have important ecological functions. A major problem is that neither the function of a secondary metabolite enzyme nor the resulting metabolite can be precisely predicted from gene sequence data.

In the current paper, the authors addressed this highly relevant question.

The authors developed a bioinformatic pipeline to reconstruct the complete secondary metabolism pathway of pyoverdines, a class of iron-scavenging siderophores produced by Pseudomonas spp. These secondary metabolites are biosynthesized by a series of non-ribosomal peptide synthetases and require a specific receptor (FpvA) for uptake. The authors combined knowledge-guided learning with phylogeny-based methods to predict with high accuracy encoding NRPSs, substrate specificity of A domains, pyoverdine derivatives, and receptors. After validation, the authors tested their pipeline with sequence data from 1664 phylogenetically distinct Pseudomonas strains and were able to determine 18,292 enzymatic A domains involved in pyoverdine synthesis, reliably predicted 97.8% of their substrates, identified 188 different pyoverdine molecule structures and 4547 FpvA receptor variants belonging to 94 distinct groups. All the results and predictions were clearly superior to predictions that are based on antiSMASH. Novel pyoverdine structures were elucidated experimentally by UHPLC-HR-MS/MS.

To assess the extendibility of the pipeline, the authors chose Burkholderiales as a test case which led to the results that the pipeline consistently maintains high prediction accuracy within Burkholderiales of 83% which was higher than for antiSMASH (67%).

Together, the authors concluded that supervised learning based on a few known compounds produced by species from the same genus probably outperforms generalized prediction algorithms trained on many products from a diverse set of microbes for NRPS substrate predictions. As a result, they also show that both pyoverdine and receptor diversity have been vastly underestimated.

Strengths:

The authors developed a very useful bioinformatic pipeline with high accuracy for secondary metabolites, at least for pyoverdines. The pipelines have several advantages compared to existing pipelines like the extensively used antiSMASH program, e.g. it can be applied to draft genomes, shows reduced erroneous gene predictions, etc. The accuracy was impressively demonstrated by the discovery of novel pyoverdines whose structures were experimentally substantiated by UHPLC-HR-MS/MS.

The manuscript is very well written, and the data and the description of the generation of pipelines are easy to follow.

Weaknesses:

The only major comment I have is the uncertainty of whether the pipeline can be applied to more complex non-ribosomal peptides. In the current study, the authors only applied their pipeline to a very narrow field, i.e., pyoverdines of Pseudomonas and Burkholderia strains.

Reviewer #3 (Public Review):

The study presents strong evidence for allosteric activation of plant receptor kinases, which enhances our understanding of the non-catalytic mechanisms employed by this large family of receptors.

Plant receptor kinases (RKs) play a critical role in transducing extracellular signals. The activation of RKs involves homo- or heterodimerization of the RKs, and it is believed that mutual phosphorylation of their intracellular kinase domains initiates downstream signaling. However, this model faces a challenge in cases where the kinase domain exhibits pseudokinase characteristics. In their recent study, Mühlenbeck et al. reveal the non-catalytic activation mechanisms of the EFR-BAK1 complex in plant receptor kinase signaling. Specifically, they aimed to determine that the EFR kinase domain activates BAK1 not through its kinase activity, but rather by utilizing a "conformational toggle" mechanism to enter an active-like state, enabling allosteric trans-activation of BAK1. The study sought to elucidate the structural elements and mutations of EFR that affect this conformational switch, as well as explore the implications for immune signaling in plants. To investigate the activation mechanisms of the EFR-BAK1 complex, the research team employed a combination of mutational analysis, structural studies, and hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis. For instance, through HDX-MS analysis, Mühlenbeck et al. discovered that the EFR (Y836F) mutation impairs the accessibility of the active-like conformation. On the other hand, they identified the EFR (F761H) mutation as a potent intragenic suppressor capable of stabilizing the active-like conformation, highlighting the pivotal role of allosteric regulation in BAK1 kinase activation. The data obtained from this methodology strengthens their major conclusion. Moreover, the researchers propose that the allosteric activation mechanism may extend beyond the EFR-BAK1 complex, as it may also be partially conserved in the Arabidopsis LRR-RK XIIa kinases. This suggests a broader role for non-catalytic mechanisms in plant RK signaling.

The allosteric activation mechanism was demonstrated for receptor tyrosine kinases (RTKs) many years ago. A similar mechanism has been suggested for the activation of plant RKs, but experimental evidence for this conclusion is lacking. Data in this study represent a significant advancement in our understanding of non-catalytic mechanisms in plant RK signaling. By shedding light on the allosteric regulation of BAK1, the study provides a new paradigm for future research in this area.

Reviewer #3 (Public Review):

This paper compares the synaptic and membrane properties of two main subtypes of interneurons (PV+, SST+) in the auditory cortex of control mice vs mutants with Syngap1 haploinsufficiency. The authors find differences at both levels, although predominantly in PV+ cells. These results suggest that altered PV-interneuron functions in the auditory cortex may contribute to the network dysfunction observed in Syngap1 haploinsufficiency-related intellectual disability. The subject of the work is interesting, and most of the approach is direct and quantitative, which are major strengths. There are also some weaknesses that reduce its impact for a broader field.

(1) The choice of mice with conditional (rather than global) haploinsufficiency makes the link between the findings and Syngap1 relatively easy to interpret, which is a strength. However, it also remains unclear whether an entire network with the same mutation at a global level (affecting also excitatory neurons) would react similarly.

(2) There are some (apparent?) inconsistencies between the text and the figures. Although the authors appear to have used a sophisticated statistical analysis, some datasets in the illustrations do not seem to match the statistical results. For example, neither Fig 1g nor Fig 3f (eNMDA) reach significance despite large differences. Also, the legend to Fig 9 indicates the presence of "a significant decrease in AP half-width from cHet in absence or presence of a-DTX", but the bar graph does not seem to show that.

(3) The authors mention that the lack of differences in synaptic current kinetics is evidence against a change in subunit composition. However, in some Figures, for example, 3a, the kinetics of the recorded currents appear dramatically different. It would be important to know and compare the values of the series resistance between control and mutant animals.

(4) A significant unexplained variability is present in several datasets. For example, the AP threshold for PV+ includes points between -50-40 mV, but also values at around -20/-15 mV, which seems too depolarized to generate healthy APs (Fig 5c, Fig7c).

(5) I am unclear as to how the authors quantified colocalization between VGluts and PSD95 at the low magnification shown in Supplementary Figure 2.

(6) The authors claim that "cHet SST+ cells showed no significant changes in active and passive membrane properties", but this claim would seem to be directly refused by the data of Fig 8f. In the absence of changes in either active or passive membrane properties shouldn't the current/#AP plot remain unchanged?

(7) The plots used for the determination of AP threshold (Figs 5c, 7c, and 7h) suggest that the frequency of acquisition of current-clamp signals may not have been sufficient, this value is not included in the Methods section.

Reviewer #3 (Public Review):

Building on their previous work that defined four major subgroups, or clades, of V1 interneurons largely by their transcriptional signatures, they do meticulous yet comprehensive analysis of the birth timing of V1 interneurons by clade, and even intra-clade, subtypes. This analysis establishes new relationships between the molecular identity, settling position, and birth time with extraordinary precision.

These relationships are then explored from the lens of synaptic connectivity. Focusing on the FoxP2 clade, they show tight spatial correspondence between V1 and motor neuron position, and through detailed synaptic analysis, find the FoxP2 V1 clade, as compared to Renshaw cells and other V1s, are the major contributors to V1-to-limb motor neuron connectivity. Finally, by analyzing sensory-to-V1 connectivity too, they show that the FoxP2 clade exhibits Ia-reciprocal interneuron-like convergence of proprioceptive and Renshaw cell synapses.

Taking the development and connectivity analysis together, their work substantially advances our understanding of spinal interneurons and yields fundamental basic information about how cell type heterogeneity corresponds across developmental, molecular and anatomical features.

An additional strength of this study is that they generate new genetic tools for labeling interneuron subpopulations, and provide insider knowledge into antibody, genetic and viral labeling that often get tucked under the rug, providing a very useful resource for further studies.

My only criticism is that some of the main messages of the paper are buried in technical details. Better separation of the main conclusions of the paper, which should be kept in the main figures and text, and technical details/experimental nuances, which are essential but should be moved to the supplement, is critical. This will also correct the other issue with the text at present, which is that it is too long.

Reviewer #3 (Public Review):

Summary:

This study explored how the motor system adapts to new environments by modifying redundant body movements. Using a novel bimanual stick manipulation task, participants manipulated a virtual stick to reach targets, focusing on how tip-movement direction perturbations affected both tip movement and stick-tilt adaptation. The findings indicated a consistent strategy among participants who flexibly adjusted the tilt angle of the stick in response to errors. The adaptation patterns are influenced by physical space relationships, guiding the motor system's choice of movement patterns. Overall, this study highlights the adaptability of the motor system through changes in redundant body movement patterns.

Strengths:

This paper introduces a novel bimanual stick manipulation task to investigate how the motor system adapts to novel environments by altering the movement patterns of our redundant body.

Weaknesses:

The generalizability of the findings is quite limited. It would have been interesting to see if the same relationships were held for different stick lengths (i.e., the hands positioned at different start locations along the virtual stick) or when reaching targets to the left and right of a start position, not just at varying angles along one side. Alternatively, this study would have benefited from a more thorough investigation of the existing literature on redundant systems instead of primarily focusing on the lack of redundancy in endpoint-reaching tasks. Although the novel task expands the use of endpoint robots in motor control studies, the utility of this task for exploring motor control and learning may be limited.

Reviewer #3 (Public Review):

Summary:

Bennion et al. investigate how semantic relatedness proactively benefits the learning of new word pairs. The authors draw predictions from Osgood (1949), which posits that the degree of proactive interference (PI) and proactive facilitation (PF) of previously learned items on to-be-learned items depends on the semantic relationships between the old and new information. In the current study, participants learn a set of word pairs ("supplemental pairs"), followed by a second set of pairs ("base pairs"), in which the cue, target, or both words are changed, or the pair is identical. Pairs were drawn from either a narrower or wider stimulus set and were tested after either a 5-minute or 48-hour delay. The results show that semantic relatedness overwhelmingly produces PF and greater memory interdependence between base and supplemental pairs, except in the case of unrelated pairs in a wider stimulus set after a short delay, which produced PI. In their final analyses, the authors compare their current results to previous work from their group studying the analogous retroactive effects of semantic relatedness on memory. These comparisons show generally similar, if slightly weaker, patterns of results. The authors interpret their results in the framework of recursive reminders (Hintzman, 2011), which posits that the semantic relationships between new and old word pairs promote reminders of the old information during the learning of the new to-be-learned information. These reminders help to integrate the old and new information and result in additional retrieval practice opportunities that in turn improve later recall.

Strengths:

Overall, I thought that the analyses were thorough and well-thought-out and the results were incredibly well-situated in the literature. In particular, I found that the large sample size, inclusion of a wide range of semantic relatedness across the two stimulus sets, variable delays, and the ability to directly compare the current results to their prior results on the retroactive effects of semantic relatedness were particular strengths of the authors' approach and make this an impressive contribution to the existing literature. I thought that their interpretations and conclusions were mostly reasonable and included appropriate caveats (where applicable).

Weaknesses:

Although I found that the paper was very strong overall, I have three main questions and concerns about the analyses.

My first concern lies in the use of the narrow versus wider stimulus sets. I understand why the initial narrow stimulus set was defined using associative similarity (especially in the context of their previous paper on the retroactive effects of semantic similarity), and I also understand their rationale for including an additional wider stimulus set. What I am less clear on, however, is the theoretical justification for separating the datasets. The authors include a section combining them and show in a control analysis that there were no directional effects in the narrow stimulus set. The authors seem to imply in the Discussion that they believe there are global effects of the lower average relatedness on differing patterns of PI vs PF across stimulus sets (lines 549-553), but I wonder if an alternative explanation for some of their conflicting results could be that PI only occurs with pairs of low semantic relatedness between the supplemental and base pair and that because the narrower stimulus set does not include the truly semantically unrelated pairs, there was no evidence of PI.

My next concern comes from the additive change in both measures (change in Cue + change in Target). This measure is simply a measure of overall change, in which a pair where the cue changes a great deal but the target doesn't change is treated equivalently to a pair where the target changes a lot, but the cue does not change at all, which in turn are treated equivalently to a pair where the cue and target both change moderate amounts. Given that the authors speculate that there are different processes occurring with the changes in cue and target and the lack of relationship between cue+target relatedness and memorability, it might be important to tease apart the relative impact of the changes to the different aspects of the pair.

Finally, it is unclear to me whether there was any online spell-checking that occurred during the free recall in the learning phase. If there wasn't, I could imagine a case where words might have accidentally received additional retrieval opportunities during learning - take for example, a case where a participant misspelled "razor" as "razer." In this example, they likely still successfully learned the word pair but if there was no spell-checking that occurred during the learning phase, this would not be considered correct, and the participant would have had an additional learning opportunity for that pair.

Reviewer #3 (Public Review):

Summary:

This work investigates the role of cellular senescence in the progression of Periodontitis using a combination of in vivo and in vitro mouse modelling experiments, human periodontitis samples, and transcriptomic analyses.

The authors propose that gum fibroblasts from either patient periodontitis samples or a mouse model of periodontitis can enter a state of cellular senescence (Figure 1). Treatment of their periodontitis mouse model with the compound Metformin attenuated this senescent phenotype and mildly reduced symptom severity. Therefore providing a potential mechanistic link between the senescent state and disease progression (Figure 2).

Leveraging analysis of published single-cell RNA-sequencing datasets of human healthy and periodontitis gum samples, the authors identify CD81+ gum fibroblasts as the cell type with the greatest enrichment of senescence-associated gene expression (Figures 3 and 4) as well as possessing metabolic alterations (Figure 5). Finally, the authors propose that these senescent gum fibroblasts are able to recruit neutrophils through C3 signalling, generating a sustained inflammatory environment that promotes disease progression (Figure 6).

The conclusions of this research are mostly well supported by that data. However, the characterisation of the senescent state and its causal involvement in disease progression could be further improved.

Strengths:

(1) The authors' use of both human and mouse samples provides important translational relevance to their research by finding analogous populations of putatively senescent fibroblasts in both systems.

(2) The use of single-cell RNA-sequencing datasets derived from patient control and periodontitis samples provides a powerful system for interrogating specific cell types. Such an analysis allowed for the characterisation of fibroblast heterogeneity revealing the unique CD81-expressing subset as having the greatest senescent characteristics. Importantly, this result was validated by immunofluorescence in both mouse and human periodontitis systems.

Weaknesses:

(1) The assessment of cellular senescence induction during periodontitis is rather superficial, relying on p16 and p21 Immunohistochemical staining and geneset enrichment analysis (Figure 1). This could be bolstered by their in vitro human fibroblast culture system utilising LPS stimulation. Specifically, their assessment could be more robust by including further markers of senescence such as (i) expression of DNA-damage markers, (ii) evidence of proliferative arrest, and (iii) assessment of an induced secretory phenotype. While a SASP signature was defined in Figure 5A, this was derived from a published single-cell RNA-sequencing dataset. Finding an analogous SASP signature in their human fibroblast cultures/bulk RNA-sequencing comparison of mouse normal-versus-periodontitis tissue would provide more compelling evidence for senescence induction.

(2) While Metformin treatment has an existing basis in the literature as a therapeutic strategy for treating periodontitis, the authors of the current study provide novelty by proposing that Metformin acts by reducing the senescent cell burden during periodontitis. While Metformin treatment is able to significantly reduce the severity of bone damage in ligation-induced periodontitis, the effect is quite mild and the evidence presented does not compellingly show an effect on the putatively senescent p16+ and p21+ cell populations in the gum (Figures 2E and F). Moreover, while the authors show that Metformin treatment is able to attenuate senescence by reducing the expression of senescence-associated Beta-galactosidase (Supplementary Figure 2E), this raises several questions. Namely, (i) Does Metformin prevent the acquisition of a senescent state or (ii) is it acting as a senolytic by actively killing the senescent fibroblasts? It would be important to address these questions to better assess whether Metformin treatment is efficacious only prophylactically, or whether it can have an effect during disease progression. Furthermore, experimental testing if other, widely utilised, senolytics strategies (i.e Navitoclax, Dasatinib+Quercetin, Fisetin etc...) or testing if a p16-/- genetic background is able to attenuate senescence and produce similar protective response would provide more compelling evidence to support their conclusion that cellular senescence is having a causal role in disease progression.

(3) The authors' metabolic profiling of their senescent gum fibroblasts, through interrogation of the transcriptomic datasets, reveals an upregulated synthesis of arachidonic acid. Through this they propose that it can be converted into prostaglandins and leukotrienes, by COXs expressed by the fibroblasts, fuelling tissue inflammation. However, this mechanism promoting inflammation is speculative and lacks experimental demonstration. To support this mechanism it would be important to show (i) increased prostaglandin/leukotrienes expression in periodontitis (relative to healthy control) and (ii) the ability to reduce this by attenuating the senescent phenotype (either by Metformin or other senolytics strategies).

for - sleep hygiene - 3 - temperature

advice - sleep hygiene - 3 - temperature - sleep cool - 18.5 Deg C is ideal

Reviewer #3 (Public Review):

Summary:

This paper assesses the size and clearance kinetics of proviral HIV DNA (intact and total) in women in South Africa with clade C virus. who started ART at different time points of infection (very early vs late).

Strengths:

The cohort is excellent. The paper is easy to read. The methodology is appropriate. Some conclusions, particularly the differing kinetics of total HIV DNA despite a similar amount of virus in early vs late treated women are novel and thought-provoking. I really enjoyed reading this paper!

Weaknesses:

There are several areas in the paper that could be explicated a bit more accurately with more detailed references to past work.

(1) The word reservoir should not be used to describe proviral DNA soon after ART initiation. It is generally agreed upon that there is still HIV DNA from actively infected cells (phase 1 & 2 decay of RNA) during the first 6-12 months of ART. Only after a full year of uninterrupted ART is it really safe to label intact proviral HIV DNA as an approximation of the reservoir. This should be amended throughout.

(2) All raw, individualized data should be made available for modelers and statisticians. It would be very nice to see the RNA and DNA data presented in a supplementary figure by an individual to get a better grasp of intra-host kinetics.

(3) The legend of Supplementary Figure 2 should list when samples were taken.

Reviewer #3 (Public Review):

Summary:

The paper by Gao et al. describes that capsaicin (CAP) might act as a novel NRF2 agonist capable of suppressing ethanol (EtOH)-induced oxidative damage in the gastric mucosa by disrupting the KEAP1-NRF2 interaction. Initially, the authors established and validated a cell model for EtOH-induced oxidative stress which they used to experiment with different CAP concentrations and to determine changes in a variety of parameters such as cell morphology, ROS production, status of redox balance to mitochondrial function, amongst others.

The proposed mechanism by which CAP activates NRF2 and mitigates oxidative stress is thought to be via non-covalent binding to the Kelch domain of KEAP1. A variety of assays such as BLI, CETSA, Pull-down, Co-IP, and HDX-MS were employed to investigate the KEAP1 binding behavior of CAP both in vitro and in GES1 cells. Consequently, the authors developed in vivo nanoparticles harboring CAP and tested those in a rat model. They found that pretreatment with the CAP-nanoparticles led to significant upregulation of NRF2 and subsequent effects on pro- (suppression of IL-1β, TNF-α, IL-6, and CXCL1) and anti-inflammatory (activation of IL-10) cytokines pointing to a resolved state of inflammation and oxidative stress.

Strengths:

The work comprises a comprehensive approach with a variety of in vitro assays as well as cell culture experiments to investigate CAP binding behaviour to KEAP1. In addition, the authors employ in vivo validation by establishing an ethanol-induced acute gastric mucosal damage rat model and providing evidence of the potential therapeutic effect of CAP.

The study further provides novel insights into the mode of CAP action by elucidating the mechanism by which CAP promotes NRF2 expression and downstream antioxidant target gene activation.

The design of IR-Dye800 modified albumin-coated CAP nanoparticles for enhanced drug solubility and delivery efficiency demonstrates a valuable practical application of the research findings.

In summary, the study's findings suggest that CAP could be a safe and novel NRF2 agonist with implications for the development of lead drugs for oxidative stress-related diseases. Collectively, the data support the significance and potential impact of CAP as a therapeutic agent for oxidative stress-related conditions.

Weaknesses:

While the study provides valuable insights into the molecular mechanisms and in vivo effects of CAP, further clinical studies are needed to validate its efficacy and safety in human subjects. The study primarily focuses on the acute effects of CAP on ethanol-induced gastric mucosa damage. Long-term studies are necessary to assess the sustained therapeutic effects and potential side effects of CAP treatment.

Furthermore, the study primarily focuses on the interaction between CAP and the KEAP1-NRF2 axis in the context of ethanol-induced gastric mucosa damage. It may be beneficial to explore the broader effects of CAP on other pathways or conditions related to oxidative stress. CAP has been known for its interaction with the Transient Receptor Potential Vanilloid type 1 (TRPV1) channel and subsequent NRF2 signaling pathway activation. Those receptors are also expressed within the gastric mucosa and could potentially cross-react with CAP leading to the observed outcome. Including experiments to investigate this route of activation could strengthen the present study.

While the design of CAP nanoparticles is innovative, further research is needed to optimize the nanoparticle formulation for enhanced efficacy and targeted delivery to specific tissues.

Addressing these weaknesses through additional research and clinical trials can strengthen the validity and applicability of CAP as a therapeutic agent for oxidative stress-related conditions.

Reviewer #3 (Public Review):

Summary:

The authors. sought to quantify the influence of the gut microbiome on metabolite cycling in a Drosophila model with extensive metabolomic profiling over a 24-hour period. The major strength of the work is the production of a large dataset of metabolites that can be the basis for hypothesis generation for more specific experiments. There are several weaknesses that make the conclusions difficult to evaluate. Additional experiments to quantify food intake over time will be required to determine the direct role of the microbiome in metabolite cycling.

Strengths:

An extensive metabolomic dataset was collected with treatments designed to determine the influence of the gut microbiome on metabolite circadian cycling.

Weaknesses:

(1) The major strength of this study is the extensive metabolomic data, but as far as I can tell, the raw data is not made publicly available to the community. The presentation of highly processed data in the figures further underscores the need to provide the raw data (see comment 3).

(2) Feeding times heavily influence the metabolome. The authors use timed feeding to constrain when flies can eat, but there is no measurement of how much they ate and when. That needs to be addressed.

Since food is the major source of metabolites, the timing of feeding needs to be measured for each of the treatment groups. In the previous paper (Zhang et al 2023 PNAS), the feeding activity of groups of 4 male flies was measured for the wildtype flies. That is not sufficient to determine to what extent feeding controls the metabolic profile of the flies. Additionally, timed feeding opportunities do not equate to the precise time of feeding. They may also result in dietary restriction, leading to the loss of stress resistance in the TF flies. The authors need to measure food consumption over time in the exact conditions under which transcriptomic and metabolomic cycling are measured. I suggest using the EX-Q assay as it is much less effort than the CAFE assay and can be more easily adapted to the rearing conditions of the experiments.

(3) The data on the cycling of metabolites is presented in a heavily analyzed form, making it difficult to evaluate the validity of the findings, particularly when a lack of cycling is detected. The normalization to calculate the change in cycling due to particular treatments is particularly unclear and makes me question whether it is affecting the conclusions. More presentation of the raw data to show when cycling is occurring versus not would help address this concern, as would a more thorough explanation of how the normalization is calculated - the brief description in the methods is not sufficient.

For instance, the authors state that "timed feeding had less effect on flies containing a microbiome relative to sterile flies." One alternative interpretation of that result is that both treatments are cycling but that the normalization of one treatment to the other removes the apparent effect. This concern should be straightforward to address by showing the raw data for individual metabolites rather than the group.

Reviewer #3 (Public Review):

This study was focused on the conserved mechanisms across the Transmembrane Channel/Scramblase superfamily, which includes members of the TMEM16, TMEM63/OSCA, and TMC families. The authors show that the introduction of lysine residues at the TM4-TM6 interface can disrupt gating and confer scramblase activity to non-scramblase proteins. Specifically, they show this to be true for conserved TM4 residues across TMEM16F, TMEM16A, OSCA1.2, and TMEM63A proteins. This breadth of data is a major strength of the paper and provides strong evidence for an underlying linked mechanism for ion conduction and phospholipid transport. Overall, the confocal imaging experiments, patch clamping experiments, and data analysis are performed well.

However, there are several concerns regarding the scope of experiments supporting some claims in the paper. Although the authors propose that the TM4/TM6 interface is critical to ion conduction and phospholipid scramblase activity, in each case, there is very narrow evidence of support consisting of 1-3 lysine substitutions at specific residues on TM4. Given that the authors postulate that the introduction of a positive charge via the lysine side chain is essential to the constitutive activity of these proteins, additional mutation controls for side chain size (e.g. glutamine/methionine) or negative charge (e.g. glutamic acid), or a different positive charge (i.e. arginine) would have strengthened their argument. To more comprehensively understand the TM4/TM6 interface, mutations at locations one turn above and one turn below could be studied until there is no phenotype. In addition, the equivalent mutations on the TM6 side should be explored to rule out the effects of conformational changes that arise from mutating TM4 and to increase the strength of evidence for the importance of side-chain interactions at the TM6 interface. The experiments for OSCA1.2 osmolarity effects on gating and scramblase in Figure 4 could be improved by adding different levels of osmolarity in addition to time in the hypotonic solution.

Reviewer #3 (Public Review):

Summary:

The manuscript by Wang and colleagues describes single molecule localization microscopy to quantify the distribution and organization of Nipah virus F expressed on cells and on virus-like particles. Notably the crystal structure of F indicated hexameric assemblies of F trimers. The authors propose that F clustering favors membrane fusion.

Strengths:

The manuscript provides solid data on imaging of F clustering with the main findings of:<br /> - F clusters are independent of expression levels<br /> - Proteolytic cleavage does not affect F clustering<br /> - Mutations that have been reported to affect the hexamer interface reduce clustering on cells and its distribution on VLPs<br /> - - F nanoclusters are stabilized by AP

Weaknesses:

The relationship between F clustering and fusion is per se interesting, but looking at F clusters on the plasma membrane does not exclude that F clustering occurs for budding. Many viral glycoproteins cluster at the plasma membrane to generate micro domains for budding. This does not exclude that these clusters include hexamer assemblies or clustering requires hexamer assemblies.<br /> Assuming that the clusters are important for entry, hexameric clusters are not unique to Nipah virus F. Similar hexameric clusters have been described for the HEF on influenza virus C particles (Halldorsson et al 2021) and env organization on Foamy virus particles (Effantin et al 2016), both with specific interactions between trimers. What is the organization of F on Nipah virus particles? If F requires to be hexameric for entry, this should be easily imaged by EM on infectious or inactivated virus particles.<br /> AP stabilization of the F clusters is curious if the clusters are solely required for entry? Virus entry does not recruit the clathrin machinery. Is it possible that F clusters are endocytosed in the absence of budding?

Other points:<br /> Fig. 3: Some of the V108D and L53D clusters look similar in size than wt clusters. It seems that the interaction is important but not absolutely essential? Would a double mutant abrogate clustering completely?<br /> Fig. 4: The distribution of F on VLPs should be confirmed by cryoEM analyses. This would also confirm the symmetry of the clusters.

The manuscript by Chernomordik et al. JBC 2004 showed that influenza HA outside the direct contact zone affects fusion, which could be further elaborated in the context of F clusters and the fusion mechanism.

Reviewer #3 (Public Review):

Summary:

In this work, Link and colleagues have investigated the localization and function of the actomyosin system in the parasite Trypanosoma brucei, which represents a highly divergent and streamlined version of this important cytoskeletal pathway. Using a variety of cutting-edge methods, the authors have shown that the T. brucei Myo1 homolog is a dynamic motor that can translocate actin, suggesting that it may not function as a more passive crosslinker. Using expansion microscopy, iEM, and CLEM, the authors show that MyoI localizes to the endosomal pathway, specifically the portion tasked with internalizing and targeting cargo for degradation, not the recycling endosomes. The glycosomes also appear to be associated with MyoI, which was previously not known. An actin chromobody was employed to determine the localization of filamentous actin in cells, which was correlated with the localization of Myo1. Interestingly, the pool of actomyosin was not always closely associated with the flagellar pocket region, suggesting that portions of the endolysomal system may remain at a distance from the sole site of parasite endocytosis. Lastly, the authors used actin-perturbing drugs to show that disrupting actin causes a collapse of the endosomal system in T. brucei, which they have shown recently does not comprise distinct compartments but instead a single continuous membrane system with subdomains containing distinct Rab markers.

Strengths:

Overall, the quality of the work is extremely high. It contains a wide variety of methods, including biochemistry, biophysics, and advanced microscopy that are all well-deployed to answer the central question. The data is also well-quantitated to provide additional rigor to the results. The main premise, that actomyosin is essential for the overall structure of the T. brucei endocytic system, is well supported and is of general interest, considering how uniquely configured this pathway is in this divergent eukaryote and how important it is to the elevated rates of endocytosis that are necessary for this parasite to inhabit its host.

Weaknesses:

(1) Did the authors observe any negative effects on parasite growth or phenotypes like BigEye upon expression of the actin chromobody?

(2) The Garcia-Salcedo EMBO paper cited included the production of anti-actin polyclonal antibodies that appeared to work quite well. The localization pattern produced by the anti-actin polyclonals looks similar to the chromobody, with perhaps a slightly larger labeling profile that could be due to differences in imaging conditions. I feel that the anti-actin antibody labeling should be expressly mentioned in this manuscript, and perhaps could reflect differences in the F-actin vs total actin pool within cells.

(3) The authors showed that disruption of F-actin with LatA leads to disruption of the endomembrane system, which suggests that the unique configuration of this compartment in T. brucei relies on actin dynamics. What happens under conditions where endocytosis and endocyctic traffic is blocked, such as 4 C? Are there changes to the localization of the actomyosin components?

(4) Along these lines, the authors suggest that their LatA treatments were able to disrupt the endosomal pathway without disrupting clathrin-mediated endocytosis at the flagellar pocket. Do they believe that actin is dispensable in this process? That seems like an important point that should be stated clearly or put in greater context.

Reviewer #3 (Public Review):

Summary:

This paper used RNAseq, ATACseq, and Hi-C to assess gene expression, chromatin accessibility, and chromatin physical associations for native CD4+ T cells as they respond to stimulation through TCR and CD28. With these data in hand, the author identified 423 GWAS signals to their respective target genes, where most of these were not in the proximal promoter, but rather distal enhancers. The IL-2 gene was used as an example to identify new distal cis-regulatory regions required for optimal IL-2 gene transcription. These distal elements interact with the proximal IL2 promoter region. When the distal enhancer contained an autoimmune SNP, it affected IL-2 gene transcription. The authors also identified genetic risk variants that were associated with genes upon activation. Some of these regulate proliferation and cytokine production, but others are novel.

Strengths:

This paper provides a wealth of data related to gene expression after CD4 T cells are activated through the TCR and CD28. An important strength of this paper is that these data were intensively analyzed to uncover autoimmune disease SNPs in cis-acting regions. Many of these could be assigned to likely target genes even though they often are in distal enhancers. These findings help to provide a better understanding concerning the mechanism by which GWAS risk elements impact gene expression.

Another strength of this study was the proof-of-principle studies examining the IL-2 gene. Not only were new cis-acting enhancers discovered, but they were functionally shown to be important in regulating IL-2 expression, including susceptibility to colitis. Their importance was also established with respect to such distal enhancers harboring disease-relevant SNPs, which were shown to affect IL-2 transcription.

The data from this study were also mined against past CRISPR screens that identified genes that control aspects of CD4 T cell activation. From these comparisons, novel genes were identified that function during T cell activation.

Weaknesses:

A weakness of this study is that few individuals were analyzed, i.e., RNAseq and ATACseq (n=3) and HiC (n=2). Thus, the authors may have underestimated potentially relevant risk associations by their chromatin capture-based methodology. This might account for the low overlap of their data with the eQTL-based approach or the HIEI truth set.

Impact:

This study indicates that defining distal chromatin interacting regions helps to identify distal genetic elements, including relevant variants, that contribute to gene activation.

Reviewer #3 (Public Review):

Summary:

In their manuscript "Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans", Lenka et al present data that could suggest an "in trans" model of Parkin ubiquitination activity. Parkin is an intensely studied E3 ligase implicated in mitophagy, whereby missense mutations to the PARK2 gene are known to cause autosomal recessive juvenile parkinsonism. From a mechanistic point of view, Parkin is extremely complex. Its activity is tightly controlled by several modes of auto-inhibition that must be released by queues of mitochondrial damage. While the general overview of Parkin activation has been mapped out in recent years, several details have remained murky. In particular, whether Parkin dimerizes as part of its feed-forward signaling mechanism, and whether said dimerization can facilitate ligase activation, has remained unclear. Here, Lenka et al. use various truncation mutants of Parkin in an attempt to understand the likelihood of dimerization (in support of an "in trans" model for catalysis).

Strengths:

The results are bolstered by several distinct approaches including analytical SEC with cleavable Parkin constructs, ITC interaction studies, ubiquitination assays, protein crystallography, and cellular localization studies.

Weaknesses:

As presented, however, the storyline is very confusing to follow and several lines of experimentation felt like distractions from the primary message. Furthermore, many experiments could only indirectly support the author's conclusions, and therefore the final picture of what new features can be firmly added to the model of Parkin activation and function is unclear.

Major concerns:

(1) This manuscript solves numerous crystal structures of various Parkin components to help support their idea of in trans transfer. The way these structures are presented more resemble models and it is unclear from the figures that these are new complexes solved in this work, and what new insights can be gleaned from them.

(2) There are no experiments that definitively show the in trans activation of Parkin. The binding experiments and size exclusion chromatography are a good start, but the way these experiments are performed, they'd be better suited as support for a stronger experiment showing Parkin dimerization. In addition, the rationale for an in trans activation model is not convincingly explained until the concept of Parkin isoforms is introduced in the Discussion. The authors should consider expanding this concept into other parts of the manuscript.

2a. For the in trans activation experiment using wt Parkin and pParkin (T270R/C431A) (Figure 3D), there needs to be a large excess of pParkin to stimulate the catalytic activity of wt Parkin. This experiment has low cellular relevance as these point mutations are unlikely to occur together to create this nonfunctional pParkin protein. In the case of pParkin activating wt Parkin (regardless of artificial point mutations inserted to study specifically the in trans activation), if there needs to be much more pParkin around to fully activate wt Parkin, isn't it just more likely that the pParkin would activate in cis?

2ai. Another underlying issue with this experiment is that the authors do not consider the possibility that the increased activity observed is a result of increased "substrate" for auto-ubiquitination, as opposed to any role in catalytic activation. Have the authors considered looking at Miro as a substrate in order to control for this?

2b. The authors mention a "higher net concentration" of the "fused domains" with RING0, and use this to justify artificially cleaving the Ubl or RING2 domains from the Parkin core. This fact should be moot. In cells, it is expected there will only be a 1:1 ratio of the Parkin core with the Ubl or RING2 domains. To date, there is no evidence suggesting multiple pUbls or multiple RING2s can bind the RING0 binding site. In fact, the authors here even show that either the RING2 or pUbl needs to be displaced to permit the binding of the other domain. That being said, there would be no "higher net concentration" because there would always be the same molar equivalents of Ubl, RING2, and the Parkin core.

2c. A larger issue remaining in terms of Parkin activation is the lack of clarity surrounding the role of the linker (77-140); particularly whether its primary role is to tether the Ubl to the cis Parkin molecule versus a role in permitting distal interactions to a trans molecule. The way the authors have conducted the experiments presented in Figure 2 limits the possible interactions that the activated pUbl could have by (a) ablating the binding site in the cis molecule with the K211N mutation; (b) further blocking the binding site in the cis molecule by keeping the RING2 domain intact. These restrictions to the cis parkin molecule effectively force the pUbl to bind in trans. A competition experiment to demonstrate the likelihood of cis or trans activation in direct comparison with each other would provide stronger evidence for trans activation.

(3) A major limitation of this study is that the authors interpret structural flexibility from experiments that do not report directly on flexibility. The analytical SEC experiments report on binding affinity and more specifically off-rates. By removing the interdomain linkages, the accompanying on-rate would be drastically impacted, and thus the observations are disconnected from a native scenario. Likewise, observations from protein crystallography can be consistent with flexibility, but certainly should not be directly interpreted in this manner. Rigorous determination of linker and/or domain flexibility would require alternative methods that measure this directly.

(4) The analysis of the ACT element comes across as incomplete. The authors make a point of a competing interaction with Lys48 of the Ubl domain, but the significance of this is unclear. It is possible that this observation could be an overinterpretation of the crystal structures. Additionally, the rationale for why the ACT element should or shouldn't contribute to in trans activation of different Parkin constructs is not clear. Lastly, the conclusion that this work explains the evolutionary nature of this element in chordates is highly overstated.

(5) The analysis of the REP linker element also seems incomplete. The authors identify contacts to a neighboring pUb molecule in their crystal structure, but the connection between this interface (which could be a crystallization artifact) and their biochemical activity data is not straightforward. The analysis of flexibility within this region using crystallographic and AlphaFold modeling observations is very indirect. The authors also draw parallels with linker regions in other RBR ligases that are involved in recognizing the E2-loaded Ub. Firstly, it is not clear from the text or figures whether the "conserved" hydrophobic within the linker region is involved in these alternative Ub interfaces. And secondly, the authors appear to jump to the conclusion that the Parkin linker region also binds an E2-loaded Ub, even though their original observation from the crystal structure seems inconsistent with this. The entire analysis feels very preliminary and also comes across as tangential to the primary storyline of in trans Parkin activation.

Reviewer #3 (Public Review):

Summary:

The authors combine classical theories of phase separation and self-assembly to establish a framework for explaining the coupling between the two phenomena in the context of protein assemblies and condensates. By starting from a mean-field free energy for monomers and assemblies immersed in solvent and imposing conditions of equilibrium, the authors derive phase diagrams indicating how assemblies partition into different condensed phases as temperature and the total volume fraction of proteins are varied. They find that phase separation can promote assembly within the protein-rich phase, providing a potential mechanism for spatial control of assembly. They extend their theory to account for the possibility of gelation. They also create a theory for the kinetics of self-assembly within phase separated systems, predicting how assembly size distributions change with time within the different phases as well as how the volumes of the different phases change with time.

Strengths:

The theoretical framework that the authors present is an interesting marriage of classic theories of phase separation and self-assembly. Its simplicity should make it a powerful general tool for understanding the thermodynamics of assembly coupled to phase separation, and it should provide a useful framework for analyzing experiments on assembly within biomolecular condensates.

The key advance over previous work is that the authors now account for how self-assembly can change the boundaries of the phase diagram.

A second interesting point is the explicit theoretical consideration for the possibility that gelation (i.e. self-assembly into a macroscopic aggregate) could account for widely observed solidification of condensates. While this concept has been broadly discussed, to date I have yet to see a rigorous theoretical analysis of the possibility.

The kinetic theory in sections 5 and 6 is also interesting as it extends on previous work by considering the kinetics of phase separation as well as those of self-assembly.

Weaknesses:

A key point the authors make about their theory is that it allows, as opposed to previous research, to study non-dilute limits. It is true that they consider gelation when the 3D assemblies become macroscopic. However, dilute solution theory assumptions seem to be embedded in many aspects of their theory, and it is not always clear where else the non-dilute limits are considered. Is it in the inter-species interaction \chi_{ij}? Why then do they never explore cases for which \chi_{ij} is nonzero in their analysis?

The connection between this theory and biological systems is described in the introduction but lost along the main text. It would be very helpful to point out, for instance, that the presence of phase separation might induce aggregation of proteins. This point is described formally at the end of Section 3, but a more qualitative connection to biological systems would be very useful here.

Building on the previous point, it would be helpful to give an intuitive sense of where the equations derived in the Appendices and presented in the main text come from and to spell out clear physical interpretations of the results. For example, it would be helpful to point out that Eq. 4 is a form of the law of mass action, familiar from introductory chemistry.

It would be useful to better explain how the current work extends on existing previous work from these authors as well as others. Along these lines, closely related work by W. Jacobs and B. Rogers [O. Hedge et al. 2023, https://arxiv.org/abs/2301.06134; T. Li et al. 2023, https://arxiv.org/abs/2306.13198] should be cited in the introduction.

The results discussed in the first paragraph of Section 3 on assembly size distributions in a homogeneous system are well-known from classic theories of self-assembly. This should be acknowledged and appropriate references should be added; see for instance Rev. Mod. Phys. 93, 025008 and Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes by Sam Safran.

Equation 14 for the kinetic of volume fractions is given with a reference to Bauermann et al 2022, but it should be accompanied by a better intuitive interpretation of its terms in the main text. In particular, how should one understand the third term in this equation? Why does the change in volume impact the change of volume fraction in this way?

The discussion in the last paragraph of Section 6 should be clarified. How can the total amount of protein in both phases decrease? This would necessarily violate either mass or volume conservation. Also, the discussion of why the volume is non-monotonic in time is not clear.

Reviewer #3 (Public Review):

In this manuscript, the authors detail improvements in the core CTFFIND (CTFFIND5 as implemented in cisTEM) algorithm that better estimates CTF parameters from titled micrographs and those that exhibit signal attenuation due to ice thickness. These improvements typically yield more accurate CTF values that better represent the data. Although some of the improvements result in slower calculations per micrograph, these can be easily overcome through parallelization.

There are some concerns outlined below that would benefit from further evaluation by the authors.

For the examples shown in Figure 3b, given the small differences in estimated defocus1 and 2, what type of improvements would be expected in the reconstructed tomograms? Do such improvements in estimates manifest in better tilt-series reconstruction?

Similarly, the data shown in Figure 3C shows minimal improvements in the CTF resolution estimate (e.g., 4.3 versus 4.2 Å), but exhibited several hundred Å difference in defocus values. How do such differences impact downstream processing? Is such a difference overcame by per-particle (local) CTF refinements (like the authors mention in the discussion, see below)?

At which point does the thickness of the specimen preclude the ice thickness modulation to be included for "accurate" estimate? 500Å? 1000Å? 2000Å? Based on the data shown in Figure 3B, as high as 969 Å thick specimens benefit moderately (4.6 versus 3.4 Å fit estimate), but perhaps not significantly, from the ice thickness estimation. Considering the increased computational time for ice thickness estimation, such an estimate of when to incorporate for single-particle workflows would be beneficial.

It would seem that this statement could be evaluated herein: "the analysis of images of purified samples recorded at lower acceleration voltages, e.g., 100 keV (McMullan et al., 2023), may also benefit since thickness-dependent CTF modulations will appear at lower resolution with longer electron wavelengths". There are numerous examples of 300kV, 200kV, and 100kV EMPIAR datasets to be compared and recommendations would be welcomed.

Although logical, this statement is not supported by the data presented in this manuscript: "The improvements of CTFFIND5 will provide better starting values for this refinement, yielding better overall CTF estimation and recovery of high-resolution information during 3D reconstruction."

Moreso, the lack of single-particle data evaluation does present a concern. Naively, these improvements would benefit all cryoEM data, regardless of modality.

Reviewer #3 (Public Review):

Summary:

The authors conducted a time-resolved EEG decoding study where they presented sequences of dot locations (4 locations onscreen) or single elements of those sequences, presented at the correct temporal epoch for if they had been presented in the full sequence. They were interested in examining whether presenting single items would activate representations of the anticipated following events that were never presented. Stimuli were presented for 100 ms and separated by 200 ms ISIs. They also had pattern estimation blocks with 600 ms ISIs. They found indeed, that anticipated events could be decoded at their correct moment in time, although future anticipated elements could not.

The decoding of presented dots was fairly confined to the diagonal of the decoding matrix (training time x testing time), suggesting little temporal generalisation. This was in contrast with successor representations which were temporally more diffuse. The subsequent successor could be decoded but not future successors.

Strengths:

I liked this paper. The design was simple and clean and the implications of the findings are clear. The authors achieved their aims with this design, with the results supporting the conclusions. The findings will be of interest to a range of researchers studying learning and perception mechanisms, as well as the more generic role of prediction in the brain.

Weaknesses:

The sample size is fairly low for an EEG study. The authors justify it according to a previous Hogendoorn study, but not according to effect sizes in that study and particular power values.

For understandable reasons, the long ISI blocks were presented before the main test blocks (I would have made the same decision) but there is the risk that participants then come to expect stimuli at larger temporal separations in the main blocks. I do wonder whether this is part of the reason for the greater temporal generalisation for anticipated event representations.

Additional context:

My memory of Ekman et al. 2017 is that single events (presented at position 1) elicited predictive activation of anticipated future events, but that there was a temporal compression. The present study appears to show no temporal compression but that the representations are activated at the correct moment in time. This seems like a potentially interesting difference and one with mechanistic implications for the field.

Reviewer #3 (Public Review):

Summary:

Huang et al. investigated the phenotype of Bend2 mutant mice which expressed a truncated isoform. This mutant male showed increasing apoptosis due to unrepaired double-strand breaks. However, this mutant male has fertility, and this enabled them to analyze Bend2 function in females. They revealed that Bend2 mutation in females showed decreasing follicle numbers which leads to loss of ovarian reserve.

Strengths:

Since their Bend2 mutant males were fertile, they were able to analyze the function of Bend2 in females and they revealed that loss of Bend2 causes less follicle formation.

Weaknesses:

Why the phenotype of their mutant male is different from previous work (Ma et al.) is not clear enough although they discuss it.

Reviewer #3 (Public Review):

Summary:

In this work, MacFarland et.al. show that difference in the time of contact between axons of LC4 and LPLC2 visual projection neurons (VPNs) in the optic glomeruli and dendrites of large descending neuron, the giant fiber (GF) shapes the differential connectivity between these neurons.

Strengths:

The authors analyzed the development of a well-known circuit between GF dendrites and LC4 andLPLC2 axons using different approaches. Additionally, they developed an ex-vivo patch clamping technique to show, together with correlative RNA-sequencing data, that contact site restriction is not dependent on neuronal activity. Based on this study, the connectivity pattern between GF and the adjacent different sets of VPNs now provides a very interesting model to investigate developmental programs that lead to synaptic specificity.

Weaknesses:

Following are the concerns that significantly impact the veracity of conclusions drawn based on the data provided.

(1) All the data related to the activity of VPNs and GF and how this activity is related to the connectivity and/or maintaining and stabilizing this connectivity is correlative. The expression profiles of synaptic molecules (only at RNA level) over time or the appearance of pre and post synaptic proteins or the spontaneous spike patterns in GF do not show the role of activity in synapse specificity program. Synaptic molecules have been previously shown to be present at presynaptic sites without being involved in activity (Chen et al., 2014, Jin et al., 2018). To show whether activity is indeed not required for connectivity for either of the cell types (LC4 and LPLC2), they should silence each and also both cell types as early as possible (with the LC4 driver that does not ablate them) and then quantify the contacts with GF. In the same vein, the authors should knock down components of the synaptic machinery as early as possible to show directly the effect on 1) contact formation and 2) contact stabilization. For example, authors state in the lines 267-269 "VPN cholinergic machinery arrives too late to contribute to the initial targeting and localization of VPN axons on GF dendrites. Cholinergic activity instead is likely to participate in VPN and GF synapse refinement and stabilization." This statement would only be valid if the authors knock down the cholinergic machinery and find the contact numbers unchanged in the early stages but significantly different in later stages in comparison to the controls. Furthermore, authors only show increase in the VAChT and ChAT in the presynaptic cells but do not show if the cholinergic receptor AChRs are even expressed in GF cells or at what point they are expressed. Without these receptor expression, cholinergic system might not even be involved in the process. Also, there might be other neurotransmitter systems involved. Authors should at least check if other neurotransmitter systems are expressed in these cells, both pre-and post-synaptic.<br /> Line 371-374: "In the later stages of development, the frequency of synaptic events increase as gap junction proteins are downregulated and cholinergic presynaptic machinery is upregulated to enhance and stabilize synapses with intended synaptic partners while refining unintended contacts". The authors did not show the activity they observed in GF is due to the contacts they make with LC4s and LPLC2s. The functionality of these contacts can be shown by silencing the LC4s and LPLC2s and then doing the patch clamping in GF to see a decrease in the activity. Further, the authors did not show that the reduction in contacts are only by refining "unintended" contacts. There is no evidence that can support this statement.

(2) In the LC4 ablation experiments, authors claim that LC4_4 split Gal4 line is expressed around 18APF, prior to GF LC4 initial contact (Line 387). However, authors do not show the time point of first contact between GF dendrites and LC4 cells. In Fig. 2 the first time point shown is at P36, where there is already significant overlap between GF dendrites and LC4 axons. Authors should show the very first time point where they see any, even if minimal, overlap and/or contact between GFs and LC4s. Once the LC4s are ablated, is the increase in the colocalization between GF and LPLC2 due to LPLC2s increasing their contact numbers or due to them not decreasing the maximum contact numbers that the authors observed at P72 (Fig 2G)? In other words, once the LC4s are ablated, what would the new graph for temporal contact numbers for LPLC2 look like and how it would compare to Fig2G?

(3) If the developmental stages for different lines match, that would be more helpful for comparison. Also, as the authors analyzed expression every 12 hours from 0APF, the panel should also contain earlier time points (e.g. P0, P12) for all lines. This is critical to understand at what point the axons of LC4, LPLC2 and LPLC1 reach their position. From the scale bar in Supp Fig.4, it seems LC4 axons have already reached final position at P24 and there is no extension between P24 and P60. Do the authors know at what point LC4 axons start extending and reach the final position? If the LC4 and LPLC2 arbors are already separated medio-laterally even before GF dendrites extend towards them, it would explain why GF dendrites extending from medial region of the brain would encounter LC4 axons first and LPLC2 axons later, just based on their localization in space.<br /> Further to this point, the authors show in the section two of the paper that it is the GF dendrites that extend, elaborate and refine during the phase the authors analyzed and the authors do not show any morphological change in the axons of the VPNs. Therefore, the title of the paper is 'axon arrival times and physical occupancy establish visual projection neuron integration on developing dendrites in the Drosophila optic glomeruli' is slightly misguided.

(4) In the absence of LC4s, does the LPLC1 and GF colocalization increase or do they still stay disconnected?

(5) Does the absence of LC4s have any effect on GF arbor complexity? Does the graph in Fig 2B and C change? Can the increase in colocalization between LPLC2 and GF be at least partially due to the expansion of GF dendritic volume?

(6) Why is there a segregation in the medial-lateral axis but not in the dorso-ventral axis? Wouldn't the same segregation mechanism be in play in both axes? Also, the authors should clarify if this reduction in dorsal-ventral distribution is because dorso-ventral expansion of GF dendrites beyond the LC4 and LPLC2 axons? Theoretically that would seem to make the LC4s move more ventrally and LPLC2 move more dorsally in comparison to the total arbor.

(7) Why the LPLC2 medial connections are regarded as "mistargeting" in the heading of Supplemental Figure 1? Both in EM data and in some of the confocal datasets, these connections are observed. What is the criteria to label a connection "mistargeting" if it is observed, albeit occasionally, both in EM and confocal datasets?

(8) In Line 126-127, authors state that "we sought to determine how the precise VPN localization along GF dendrites arises across development". However, based in EM and microscopic data, there is considerable variability in the contact numbers and distribution. With such variability present, how can the localization be termed "precise"? Authors should clarify.

Reviewer #3 (Public Review):

Summary:

In the present manuscript, the authors use a few minutes of voltage imaging of CA1 pyramidal cells in head-fixed mice running on a track while local field potentials (LFPs) are recorded. The authors suggest that synchronous ensembles of neurons are differentially associated with different types of LFP patterns, theta and ripples. The experiments are flawed in that the LFP is not "local" but rather collected in the other side of the brain, and the investigation is flawed due to multiple problems with the point process analyses. The synchrony terminology refers to dozens of milliseconds as opposed to the millisecond timescale referred to in prior work, and the interpretations do not take into account theta phase locking as a simple alternative explanation.

Weaknesses:

The two main messages of the manuscript indicated in the title are not supported by the data. The title gives two messages that relate to CA1 pyramidal neurons in behaving head-fixed mice: (1) synchronous ensembles are associated with theta (2) synchronous ensembles are not associated with ripples.

There are two main methodological problems with the work: (1) experimentally, the theta and ripple signals were recorded using electrophysiology from the opposite hemisphere to the one in which the spiking was monitored. However, both signals exhibit profound differences as a function of location: theta phase changes with the precise location along the proximo-distal and dorso-ventral axes, and importantly, even reverses with depth. And ripples are often a local phenomenon - independent ripples occur within a fraction of a millimeter within the same hemisphere, let alone different hemispheres. Ripples are very sensitive to the precise depth - 100 micrometers up or down, and only a positive deflection/sharp wave is evident. (2) The analysis of the point process data (spike trains) is entirely flawed. There are many technical issues: complex spikes ("bursts") are not accounted for; differences in spike counts between the various conditions ("locomotion" and "immobility") are not accounted for; the pooling of multiple CCGs assumes independence, whereas even conditional independence cannot be assumed; etc.

Beyond those methodological issues, there are two main interpretational problems: (1) the "synchronous ensembles" may be completely consistent with phase locking to the intracellular theta (as even shown by the authors themselves in some of the supplementary figures). (2) The definition of "synchrony" in the present work is very loose and refers to timescales of 20-30 ms. In previous literature that relates to synchrony of point processes, the timescales discussed are 1-2 ms, and longer timescales are referred to as the "baseline" which is actually removed (using smoothing, jittering, etc.).

Reviewer #3 (Public Review):

Summary:

In the present manuscript, the authors propose that soluble Uric acid (sUA) is an enzymatic inhibitor of the NADase CD38 and that it controls levels of NAD modulating inflammatory response. Although interesting the studies are at this stage preliminary and validation is needed.

Strengths:

The study characterizes the potential relevance of sUA in NAD metabolism.

Weaknesses:

(1) A full characterization of the effect of sUA in other NAD-consuming and synthesizing enzymes is needed to validate the statement that the mechanism of regulation of NAD by sUA is mediated by CD38, The CD38 KO may not serve as the ideal control since it may saturate NAD levels already. Analysis of multiple tissues is needed.

(2) The physiological role of sUA as an endogenous inhibitor of CD38 needs stronger validation (sUA deficient model?).

(3) Flux studies would also be necessary to make the conclusion stronger.

Reviewer #3 (Public Review):

Summary:

Suzuki-Okutani and collogues reported a new live-attenuated SARS-CoV-2 vaccine (BK2102) containing multiple deletion/substitution mutations. They show that the vaccine candidate is highly attenuated and demonstrates a great safety profile in multiple animal models (hamsters and Tg-Mice). Importantly, their data show that single intranasal immunization with BK2102 leads to strong protection of hamsters against D614G and BA.5 challenge in both lungs and URT (nasal wash). Both humoral and cellular responses were induced, and neutralization activity remained for >360 after a single inoculation.

Strengths:

The manuscript describes a comprehensive study that evaluates the safety, immunogenicity, and efficacy of a new live-attenuated vaccine. Strengths of the study include (1) strong protection against immune evasive variant BA.5 in both lungs and NW; (2) durability of immunity for >360 days; (3) confirmation of URT protection through a transmission experiment.

While first-generation COVID-19 vaccines have achieved much success, new vaccines that provide mucosal and durable protection remain needed. Thus, the study is significant.

Weaknesses:

Lack of a more detailed discussion of this new vaccine approach in the context of reported live-attenuated SARS-CoV-2 vaccines in terms of its advantages and/or weaknesses.

Antibody endpoint titers could be presented.

Lack of elaboration on immune mechanisms of protection at the upper respiratory tract (URT) against an immune evasive variant in the absence of detectable neutralizing antibodies.

Reviewer #3 (Public Review):

Summary:

Day et al. introduced high-throughput expansion microscopy (HiExM), a method facilitating the simultaneous adaptation of expansion microscopy for cells cultured in a 96-well plate format. The distinctive features of this method include 1) the use of a specialized device for delivering a minimal amount (~230 nL) of gel solution to each well of a conventional 96-well plate, and 2) the application of the photochemical initiator, Irgacure 2959, to successfully form and expand the toroidal gel within each well.

Strengths:

This configuration eliminates the need for transferring gels to other dishes or wells, thereby enhancing the throughput and reproducibility of parallel expansion microscopy. This methodological uniqueness indicates the applicability of HiExM in detecting subtle cellular changes on a large scale.

Weaknesses:

To demonstrate the potential utility of HiExM in cell phenotyping, drug studies, and toxicology investigations, the authors treated hiPS-derived cardiomyocytes with a low dose of doxycycline (dox) and quantitatively assessed changes in nuclear morphology. However, this reviewer is not fully convinced of the validity of this specific application. Furthermore, some data about the effect of expansion require reconsideration.

Reviewer #3 (Public Review):

Summary:

infectious bursal disease virus (IBDV) is a birnavirus and an important avian pathogen. Interestingly, IBDV appears to be a unique dsRNA virus that uses early endosomes for RNA replication that is more common for +ssRNA viruses such as for example SARS-CoV-2.

This work builds on previous studies showing that IBDV VP3 interacts with PIP3 during virus replication. The authors provide further biophysical evidence for the interaction and map the interacting domain on VP3.

Strengths:

Detailed characterization of the interaction between VP3 and PIP3 identified R200D mutation as critical for the interaction. Cryo-EM data show that VP3 leads to membrane deformation.

Weaknesses:

The work does not directly show that the identified R200 residues are directly involved in VP3-early endosome recruitment during infection. The majority of work is done with transfected VP3 protein (or in vitro) and not in virus-infected cells.

Additional controls such as the use of PIP3 antagonizing drugs in infected cells together with a colocalization study of VP3 with early endosomes would strengthen the study.

In addition, it would be advisable to include a control for cryo-EM using liposomes that do not contain PIP3 but are incubated with HIS-VP3-FL. This would allow ruling out any unspecific binding that might not be detected on WB.

The authors also do not propose how their findings could be translated into drug development that could be applied to protect poultry during an outbreak. The title of the manuscript is broad and would improve with rewording so that it captures what the authors achieved.

Reviewer #3 (Public Review):

In this study, Zhang and colleagues proposed an ELMo-based embedding model (catELMo) for TCRβ CDR3 amino acid sequences. They showed the effectiveness of catELMo in both supervised TCR binding prediction and unsupervised clustering, surpassing existing methods in accuracy and reducing annotation costs. The study provides insights on the effect of model architectures to TCR specificity prediction and clustering tasks.

The authors have addressed our prior critiques of the manuscript.

Reviewer #3 (Public Review):

This paper studies chromatic coding in mouse primary visual cortex. Calcium responses of a large collection of cells are measured in response to a simple spot stimulus. These responses are used to estimate chromatic tuning properties - specifically sensitivity to UV and green stimuli presented in a large central spot or a larger still surrounding region. Cells are divided based on their responses to these stimuli into luminance or chromatic sensitive groups. The results are interesting and many aspects of the experiments and conclusions are well done; several technical concerns, however, limit the support for several main conclusions,

Limitations of stimulus choice<br /> The paper relies on responses to a large (37.5 degree diameter) modulated spot and surround region. This spot is considerably larger than the receptive fields of both V1 cells and retinal ganglion cells (it is twice the area of the average V1 receptive field). As a result, the spot itself is very likely to strongly activate both center and surround mechanisms, and responses of cells are likely to depend on where the receptive fields are located within the spot (and, e.g., how much of the true neural surround samples the center spot vs the surround region). Most importantly, the surrounds of most of the recorded cells will be strongly activated by the central spot. This brings into question statements in the paper about selective activation of center and surround (e.g. page 2, right column). This in turn raises questions about several subsequent analyses that rely on selective center and surround activation.

Comparison with retina<br /> A key conclusion of the paper is that the chromatic tuning in V1 is not inherited from retinal ganglion cells. This conclusion comes from comparing chromatic tuning in a previously-collected data set from retina with the present results. But the retina recordings were made using a considerably smaller spot, and hence it is not clear that the comparison made in the paper is accurate. For example, the stimulus used for the V1 experiments almost certainly strongly stimulates both center and surround of retinal ganglion cells. The text focuses on color opponency in the receptive field centers of retinal ganglion cells, but center-surround opponency seems at least as relevant for such large spots. This issue needs to be described more clearly and earlier in the paper.

Limitations associated with ETA analysis<br /> One of the reviewers in the previous round of reviews raised the concern that the ETA analysis may not accurately capture responses of cells with nonlinear receptive field properties such as On/Off cells. This possibility and whether it is a concern should be discussed.

Discrimination performance poor<br /> Discriminability of color or luminance is used as a measure of population coding. The discrimination performance appears to be quite poor - with 500-1000 neurons needed to reliably distinguish light from dark or green from UV. Intuitively I would expect that a single cell would provide such discrimination. Is this intuition wrong? If not, how do we interpret the discrimination analyses?

Reviewer #3 (Public Review):

Summary:

The authors conducted a human fMRI study investigating the omission of expected electrical shocks with varying probabilities. Participants were informed of the probability of shock and shock intensity trial-by-trial. The time point corresponding to the absence of the expected shock (with varying probability) was framed as a prediction error producing the cognitive state of relief/pleasure for the participant. fMRI activity in the VTA/SN and ventral putamen corresponded to the surprising omission of a high probability shock. Participants' subjective relief at having not been shocked correlated with activity in brain regions typically associated with reward-prediction errors. The overall conclusion of the manuscript was that the absence of an expected aversive outcome in human fMRI looks like a reward-prediction error seen in other studies that use positive outcomes.

Strengths:

Overall, I found this to be a well-written human neuroimaging study investigating an often overlooked question on the role of aversive prediction errors, and how they may differ from reward-related prediction errors. The paper is well-written and the fMRI methods seem mostly rigorous and solid.

Comments on revised version:

The authors were extremely responsive to the comments and provided a comprehensive rebuttal letter with a lot of detail to address the comments. The authors clarified their methodology, and rationale for their task design, which required some more explanation (at least for me) to understand. Some of the design elements were not clear to me in the original paper.

The initial framing for their study is still in the domain of learning. The paper starts off with a description of extinction as the prime example of when threat is omitted. This could lead a reader to think the paper would speak to the role of prediction errors in extinction learning processes. But this is not their goal, as they emphasize repeatedly in their rebuttal letter. The revision also now details how using a conditioning/extinction framework doesn't suit their experimental needs.

It is reasonable to develop a new task to answer their experimental questions. By no means is there a requirement to use a conditioning/extinction paradigm to address their questions. As they say, "it is not necessary to adopt a learning paradigm to study omission responses", which I agree with.

But the authors seem to want to have it both ways: they frame their paper around how important prediction errors are to extinction processes, but then go out of their way to say how they can't test their hypotheses with a learning paradigm.

Part of their argument that they needed to develop their own task "outside of a learning context" goes as follows:<br /> (1) "...conditioning paradigms generally only include one level of aversive outcome: the electrical stimulation is either delivered or omitted. As a result, the magnitude-related axiom cannot be tested."<br /> (2) "....in conditioning tasks people generally learn fast, rendering relatively few trials on which the prediction is violated. As a result, there is generally little intra-individual variability in the PE responses"<br /> (3) "...because of the relatively low signal to noise ratio in fMRI measures, fear extinction studies often pool across trials to compare omission-related activity between early and late extinction, which further reduces the necessary variability to properly evaluate the probability axiom"

These points seem to hinge on how tasks are "generally" constructed. However, there are many adaptations to learning tasks:<br /> (1) There is no rule that conditioning can't include different levels of aversive outcomes following different cues. In fact, their own design uses multiple cues that signal different intensities and probabilities. Saying that conditioning "generally only include one level of aversive outcome" is not an explanation for why "these paradigms are not tailored" for their research purposes. There are also several conditioning studies that have used different cues to signal different outcome probabilities. This is not uncommon, and in fact is what they use in their study, only with an instruction rather than through learning through experience, per se.<br /> (2) Conditioning/extinction doesn't have to occur fast. Just because people "generally learn fast" doesn't mean this has to be the case. Experiments can be designed to make learning more challenging or take longer (e.g., partial reinforcement). And there can be intra-individual differences in conditioning and extinction, especially if some cues have a lower probability of predicting the US than others. Again, because most conditioning tasks are usually constructed in a fairly simplistic manner doesn't negate the utility of learning paradigms to address PE-axioms.<br /> (3) Many studies have tracked trial-by-trial BOLD signal in learning studies (e.g., using parametric modulation). Again, just because other studies "often pool across trials" is not an explanation for these paradigms being ill-suited to study prediction errors. Indeed, most computational models used in fMRI are predicated on analyzing data at the trial level.

Again, the authors are free to develop their own task design that they think is best suited to address their experimental questions. For instance, if they truly believe that omission-related responses should be studied independent of updating. The question I'm still left puzzling is why the paper is so strongly framed around extinction (the word appears several times in the main body of the paper), which is a learning process, and yet the authors go out of their way to say that they can only test their hypotheses outside of a learning paradigm.

The authors did address other areas of concern, to varying extents. Some of these issues were somewhat glossed over in the rebuttal letter by noting them as limitations. For example, the issue with comparing 100% stimulation to 0% stimulation, when the shock contaminates the fMRI signal. This was noted as a limitation that should be addressed in future studies, bypassing the critical point.

Reviewer #3 (Public Review):

Kang, Huang, and colleagues have provided new data to address concerns regarding confirmation of LRRK1 and LRRK2 deletion in their mouse model and the functional impact of the modest loss of TH+ neurons observed in the substantia nigra of their double KO mice. In the revised manuscript, the new data around the characterization of the germline-deleted LRRK1 and LRRK2 mice add confidence that LRRK1 and LRRK2 can be deleted using the genetic approach. They have also added new text to the discussion to try and address some of the comments and questions raised regarding how LRRK1/2 loss may impact cell survival and the implications of this work for PD-linked variants in LRRK2 and therapeutic approaches targeting LRRK2. The new data provides additional support for the author's claims.

Reviewer #3 (Public Review):

Summary:

Unlike most eukaryotes Blastocystis has a branched glycolysis pathway, which is split between the cytoplasm and the mitochondrial matrix. An outstanding question was how the glycolytic intermediates generated in the 'preparatory' phase' are transported into the mitochondrial matrix for the 'pay off' phase. Here, the authors use bioinformatic analysis to identify two candidate solute carrier genes, bGIC-1 and bGIC-2, and use biochemical and biophysical methods to characterise their substrate specificity and transport properties. The authors demonstrate that bGIC-2 can transport dihydroxyacetone phosphate, glyceraldehyde-3-phosphate, 3-phosphoglycerate and phosphoenolpyruvate, establishing this protein as the 'missing link' connecting the two split branches of glycolysis in this branch of single celled eukaryotes. The authors also present their data on bGIC-1, which suggests a role in anion transport and bOGC, which is a close functional homologue of the human oxoglutarate carrier (hOGC, SLC25A11) and human dicarboxylate carrier (hDIC, SLC25A10).

Strengths:

The results are presented in a clear and logical arrangement, which nicely leads the reader through the process of gene identification and subsequent ligand screening and functional reconstitution. The results are compelling and well supported - the thermal stabilisation data is supported by the exchange studies. Caveats, where apparent, are discussed and rational explanations given.

Weaknesses:

The study does not contain any significant weaknesses in my view. I would like to see the authors include the initial rate plots used in the main figures (possibly as insets), so we can observe the data points used for these calculations. It would also have been interesting to include the AlphaFold models for bGIC-1 and bGIC-2 and a discussion/rationalisation for the substrate specificity discussed in the study.

Reviewer #3 (Public Review):

Summary:

This is an elegant study investigating possible mechanisms underlying the hysteresis effect in the perception of perceptually ambiguous Shepard tones. The authors make a fairly convincing case that the adaptation of pitch direction sensitive cells in auditory cortex is likely responsible for this phenomenon.

Strengths:

The manuscript is overall well written. My only slight criticism is that, in places, particularly for non-expert readers, it might be helpful to work a little bit more methods detail into the results section, so readers don't have to work quite so hard jumping from results to methods and back.

The methods seem sound and the conclusions warranted and carefully stated. Overall I would rate the quality of this study as very high, and I do not have any major issues to raise.

Weaknesses:

I think this study is about as good as it can be with the current state of the art. Generally speaking, one has to bear in mind that this is an observational, rather than an interventional study, and therefore only able to identify plausible candidate mechanisms rather than making definitive identifications. However, the study nevertheless represents a significant advance over the current state of knowledge, and about as good as it can be with the techniques that are currently widely available.

Reviewer #3 (Public Review):

Summary:

How short-term isolation acts on the brain to promote social behavior remains incompletely understood. The authors found that social interactions after a period of acute isolation increased investigation promoted mounting, and increased the production of ultrasonic vocalizations (USVs). This was true for females during same-sex interactions as well as for males interacting with females. Concomitant with these increased behavioral readouts, cFos expression in the preoptic area of the hypothalamus (POA) was found to increase selectively in single-housed females. Chemogenetic silencing of these POA neurons attenuated all three behavioral measures in socially isolated females. Surprisingly, ablation of the same POA neurons decreased mounting duration without impacting social investigation or USV production. While optogenetic activation was sufficient to evoke USV production, it did not affect either mounting or social investigation. In males, chemogenetic silencing of POA neurons decreased mounting but not other behaviors. Together, these data point towards a role of POA neurons in mediating social behaviors after acute isolation but the exact nature of that control appears to depend on the choice of perturbation method, sex, and social context in complex ways that are hard to parse. This study is an essential first step; additional experiments will be needed to explain the apparent discrepancy between the various circuit perturbation results and to gain a more comprehensive understanding of the role of POA in social isolation.

Strengths:

The goal of understanding the neural circuit mechanisms underlying acute social isolation is clearly important and topical. Using a state-of-the-art technique to tag specific neurons that were active during certain behavioral epochs, the authors managed to identify the POA as a critical circuit locus for the effects of social isolation. The experimental design is perfectly reasonable and the quality of the data is good. The control experiments (Figures 2B-D) showing that chemogenetic inactivation of other hypothalamic regions (AH and VMH) do not affect social behavior is indeed quite satisfying and points towards a specific role of POA within the hypothalamus. Using a combination of behavioral assays, activity-dependent neural tagging, and circuit manipulation techniques, the authors present convincing evidence for the role of the preoptic area of the hypothalamus in mediating certain behaviors following social isolation. These data are likely to be a valuable resource for understanding how hypothalamic circuits adjust to the challenges of social isolation.

Weaknesses:

While the authors should be commended for performing and reporting multiple circuit perturbation experiments (e.g., chemogenetics, ablation), the conflicting effects on behavior are hard to interpret without additional experiments. For example, chemogenetic silencing of the POA neurons (using DREADDs) attenuated all three behavioral measures but the ablation of the same POA neurons (using CASPACE) decreased mounting duration without impacting social investigation or USV production. Similarly, optogenetic activation of POA neurons was sufficient to generate USV production as reported in earlier studies but mounting or social investigation remained unaffected. Do these discrepancies arise due to the efficiency differences between DREADD-mediated silencing vs. Casp3 ablation? Or does the chemogenetic result reflect off-manifold effects on downstream circuitry whereas a more permanent ablation strategy allows other brain regions to compensate due to redundancy? It is important to resolve whether these arise due to technical reasons or whether these reflect the underlying (perhaps messy) logic of neural circuitry. Therefore, while it is clear that POA neurons likely contribute to multiple behavioral readouts of social isolation, understanding their exact roles in any greater detail will require further experiments.

Reviewer #3 (Public Review):

Summary:

This study focuses on changes in brain organization associated with congenital deafness. The authors investigate differences in functional connectivity (FC) and differences in the variability of FC. By comparing congenitally deaf individuals to individuals with normal hearing, and by further separating congenitally deaf individuals into groups of early and late signers, the authors can distinguish between changes in FC due to auditory deprivation and changes in FC due to late language acquisition. They find larger FC variability in deaf than normal-hearing individuals in temporal, frontal, parietal, and midline brain structures, and that FC variability is largely driven by auditory deprivation. They suggest that the regions that show a greater FC difference between groups also show greater FC variability.

Strengths:

- The manuscript is well written.

- The methods are clearly described and appropriate.

- Including the three different groups enables the critical contrasts distinguishing between different causes of FC variability changes.

- The results are interesting and novel.

Weaknesses:

- Analyses were conducted for task-based data rather than resting-state data. It was unclear whether groups differed in task performance. If congenitally deaf individuals found the task more difficult this could lead to changes in FC.

- No differences in overall activation between groups were reported. Activation differences between groups could lead to differences in FC. For example, lower activation may be associated with more noise in the data, which could translate to reduced FC.

- Figure 2B shows higher FC for congenitally deaf individuals than normal-hearing individuals in the insula, supplementary motor area, and cingulate. These regions are all associated with task effort. If congenitally deaf individuals found the task harder (lower performance), then activation in these regions could be higher, in turn, leading to FC. A study using resting-state data could possibly have provided a clearer picture.

- The correlation between the FC map and the FC variability map is 0.3. While significant using permutation testing, the correlation is low, and it is not clear how great the overlap is.

Reviewer #3 (Public Review):

Summary:

This manuscript by Peng et al. presents intriguing data indicating that high-frequency terahertz stimulation (HFTS) of the anterior cingulate cortex (ACC) can alleviate neuropathic pain behaviors in mice. Specifically, the investigators report that terahertz (THz) frequency stimulation widens the selectivity filter of potassium channels thereby increasing potassium conductance and leading to a reduction in the excitability of cortical neurons. In voltage clamp recordings from layer 5 ACC pyramidal neurons in acute brain slice, Peng et al. show that HFTS enhances K current while showing minimal effects on Na current. Current clamp recording analyses show that the spared nerve injury model of neuropathic pain decreases the current threshold for action potential (AP) generation and increases evoked AP frequency in layer 5 ACC pyramidal neurons, which is consistent with previous studies. Data are presented showing that ex-vivo treatment with HFTS in slice reduces these SNI-induced changes to excitability in layer 5 ACC pyramidal neurons. The authors also confirm that HFTS reduces the excitability of layer 5 ACC pyramidal neurons via in vivo multi-channel recordings from SNI mice. Lastly, the authors show that HFTS is effective at reducing mechanical allodynia in SNI using both the von Frey and Catwalk analyses. Overall, there is considerable enthusiasm for the findings presented in this manuscript given the need for non-pharmacological treatments for pain in the clinical setting.

Strengths:

The authors use a multifaceted approach that includes modeling, ex-vivo and in-vivo electrophysiological recordings, and behavioral analyses. Interpretation of the findings is consistent with the data presented. This preclinical work in mice provides new insight into the potential use of directed high-frequency stimulation to the cortex as a primary or adjunctive treatment for chronic pain.

Weaknesses:

There are a few concerns noted that if addressed, would significantly increase enthusiasm for the study.

(1) The left Na current trace for SNI + HFTS in Figure 2B looks to have a significant series resistance error. Time constants (tau) for the rate of activation and inactivation for Na currents would be informative.

(2) It is unclear why an unpaired t-test was performed for paired data in Figure 2. Also, statistical methods and values for non-significant data should be presented.

(3) It would seem logical to perform HFTS on ACC-Pyr neurons in acute slices from sham mice (i.e. Figure 3 scenario). These experiments would be informative given the data presented in Figure 4.

(4) As the data are presented in Figure 4g, it does not seem as if SNI significantly increased the mean firing rate for ACC-Pyr neurons, which is observed in the slice. The data were analyzed using a paired t-test within each group (sham and SNI), but there is no indication that statistical comparisons across groups were performed. If the argument is that HFTS can restore normal activity of ACC-Pyr neurons following SNI, this is a bit concerning if no significant increase in ACC-Pyr activity is observed in in-vivo recordings from SNI mice.

(5) The authors indicate that the effects of HFTS are due to changes in Kv1.2. However, they do not directly test this. A blocking peptide or dendrotoxin could be used in voltage clamp recordings to eliminate Kv1.2 current and then test if this eliminates the effects of HFTS. If K current is completely blocked in VC recordings then the authors can claim that currents they are recording are Kv1.1 or 1.2.

(6) The ACC is implicated in modulating the aversive aspect of pain. It would be interesting to know whether HFTS could induce conditioned place preference in SNI mice via negative reinforcement (i.e. alleviation of spontaneous pain due to the injury). This would strengthen the clinical relevance of using HFTS in treating pain.

Reviewer #3 (Public Review):

This paper builds on the authors' original development of a near infrared (NIR) FRET sensor by reporting in vivo real-time measurements for gamma-secretase activity in the mouse cortex. The in vivo application of the sensor using state of the art techniques is supported by a clear description and straightforward data, and the project represents significant progress because so few biosensors work in vivo. Notably, the NIR biosensor is detectable to ~ 100 µm depth in the cortex. A minor limitation is that this sensor has a relatively modest ΔF as reported in Houser et al, which is an additional challenge for its use in vivo. Thus, the data is fully dependent on post-capture processing and computational analyses. This can unintentionally introduce biases but is not an insurmountable issue with the proper controls that the authors have performed here.

The observation of gamma-secretase signaling that spreads across cells is potentially quite interesting, but it can be better supported. An alternative interpretation is that there exist pre-formed and clustered hubs of high gamma-secretase activity, and that DAPT has stochastic or differential accessibility to cells within the cluster. This could be resolved by an experiment of induction, for example, if gamma-secretase activity is induced or activated at a specific locale and there was observed coordinated spreading to neighboring neurons with their sensor.

Furthermore, to rule out the possibility that uneven viral transduction was not simply responsible for the observed clustering, it would be helpful to see an analysis of 670nm fluorescence alone.

Reviewer #3 (Public Review):

Summary:

The authors use in vitro grown cells and mouse xenografts to show that a combination of drugs, Sulfopin and Vorinostat, can impact the growth of cells derived from Diffuse midline gliomas, in particular the ones carrying the H3 K27M-mutations (clinically classified as DMG, H3 K27M-mutant). The authors use gene expression studies, and chromatin profiling to attempt to better understand how these drugs exert an effect on genome regulation. Their main findings are that the drugs reduce cell growth in vitro and in mouse xenografts of patient tumours, that DMG, H3 K27M-mutant tumours are particularly sensitive, identify potential markers of gene expression underlying this sensitivity, and broadly characterize the correlations between chromatin modification changes and gene expression upon treatment, identifying putative pathways that may be affected and underlie the sensitive (and thus how the drugs may affect the tumour cell biology).

Strengths:

It is a neat, mostly to-the-point work without exploring too many options and possibilities. The authors do a good job not overinterpreting data and speculating too much about the mechanisms, which is a very good thing since the causes and consequences of perturbing such broad epigenetic landscapes of chromatin may be very hard to disentangle. Instead, the authors go straight after testing the performance of the drugs, identifying potential markers and characterizing consequences.

Weaknesses:

If anything, the experiments done on Figure 3 could benefit from an additional replicate.

Reviewer #3 (Public Review):

Summary:

Gularte-Mérida and colleagues took advantage of the existence of so-called consomic strains in the mouse, which result from the substitution of one of their chromosomes by that of another strain, to ask through appropriate crosses whether information carried by this substitution chromosome impacts progeny that do not inherit it. With one exception, the authors did not detect any significant effect for any of the four non-transmitted chromosomes tested. Given these results, the authors conclude that such effects, if they exist, must be extremely rare in the mouse.

Strengths:

This is a very convincing and impressive study, with effects assessed in almost 2500 mice. The negative results obtained should put to rest once and for all the notion that intergenerational, let alone transgenerational, non-DNA sequence-based inheritance via the male germline could be substantial in the mouse.

Weaknesses:

The terminology used (epigenetics, nurture-independent TGE, etc. ) is somewhat confusing and unnecessary.

Reviewer #3 (Public Review):

In this important work, the authors show compelling evidence that the Rapid Alkalinisation Factor1 (RALF1) peptide acts as an interlink between pectin methyl esterification status and FERONIA receptor-like kinase in mediating extracellular sensing. Moreover, the RALF1-mediated pectin perception is surprisingly independent of LRX-mediated extracellular sensing in roots. The authors also show that the peptide directly binds demethylated pectin and the positively charged amino acids are required for pectin binding as well as for its physiological activity.

Some present findings are surprising; previously, the FERONIA extracellular domain was shown to bind pectin directly, and the mode of operation in the pollen tube involves the LRX8-RALF4 complex, which seems not the case for RALF1 in the present study. Although some aspects remain controversial, this work is a very valuable addition to the ongoing debate about this elusive complex regulation and signaling.

The authors drafted the manuscript well, so I do not have a lot of criticism or suggestions. The experiments are well-designed, executed, and presented, and they solidly support the authors' claims.

Reviewer #3 (Public Review):

Summary and Strengths:

In this interesting manuscript, the authors identify a large number of alternative transcription start sites (TSS) and focus their functional analysis on an alternative TSS that is expected to produce a micro-protein (miP) encoding the C-terminus of ATHB2 (ATHB2miP). ATHB2miP is expected to comprise the leucine zipper part of ATHB2 and hence interact with the full-length protein through this dimerization motif. Such interactions are shown using yeast two-hybrid and FRET-FLIM assays. ATHB2 is a well-known shade-induced gene that has been implicated in shade-regulated growth responses. The authors then test the potential role for ATHB2miP genetically by comparing several athb2 loss-of-function (LOF) alleles: one does not express either full-length ATHB2 or the short ATHB2miP (t-ATHB2), two CRISPR alleles give rise to frameshift mutations in the full-length transcript but still express a potentially functional short ATHB2miP (athb2deltaLZ and athb2delta). The authors also use plants that over and ectopically express ATHB2miP (35S:miP). Overall, the results are consistent with the hypothesis that ATHB2miP inhibits the function of ATHB2, which constitutes a novel negative feedback loop. Potentially ATHB2miP may also inhibit the activity of other related HD ZIP proteins (based on 35S:miP). The effects of these genetic alterations on shade-regulated hypocotyl growth are relatively modest. Effects on root growth are also investigated and in one intriguing case, the negative feedback model does not appear to explain the data (Figure 4D, effect on lateral roots, because for this phenotype 35S:miP is very different from the lof alleles). The authors also identify a potentially interesting link between shade-regulated hypocotyl growth and iron uptake. A number of text changes and corrections to the figures would be important for clarity. They primarily concern three issues: names of the alleles, names of the studied shade conditions, and statements about significant differences between genotypes. Also, it would be interesting to know whether the effects of ATHB2 on iron uptake are due to local effects of ATHB2. Is ATHB2 expressed in roots?

Weaknesses: