Reviewer #4 (Public review):

Summary:

The manuscript by Graça et al. explores the role of MftG in the ethanol metabolism of mycobacteria. The authors hypothesise that MftG functions as a mycofactocin dehydrogenase, regenerating mycofactocin by shuttling electrons to the respiratory chain of mycobacteria. Although the study primarily uses M. smegmatis as a model microorganism, the findings have more general implications for understanding mycobacterial metabolism. Identifying the specific partner to which MftG transfers its electrons within the respiratory chain of mycobacteria would be an important next step, as pointed out by the authors.

Strengths:

The authors have used a wide range of tools to support their hypothesis, including co-occurrence analyses, gene knockout and complementation experiments, as well as biochemical assays and transcriptomics studies.<br /> An interesting observation that the mftG deletion mutant grown on ethanol as the sole carbon source exhibited a growth defect resembling a starvation phenotype.<br /> MftG was shown to catalyse the electron transfer from mycofactocinol to components of the respiratory chain, highlighting the flexibility and complexity of mycobacterial redox metabolism.

Weaknesses:

Could the authors elaborate more on the differences between the WT strains in Fig. 3C and 3E? in Fig. 3C, the ethanol concentration for the WT strain is similar to that of WT-mftG and ∆mftG-mftG, whereas the acetate concentration in thw WT strain differs significantly from the other two strains. How this observation relates to ethanol oxidation, as indicated on page 12.<br /> The authors conclude from their functional assays that MftG catalyses single-turnover reactions, likely using FAD present in the active site as an electron acceptor. While this is plausible, the current experimental set up doesn't fully support this conclusions, and the language around this claim should be softened.<br /> The authors suggest in the manuscript that the quinone pool (page 24) may act as the electron acceptor from mycofactocinol, but later in in the discussion section (page 30) they propose cytochromes as the potential recipients. If the authors consider both possibilities valid, I suggest discussing both options in the manuscript.

Reviewer #3 (Public review):

Here, Wang et al. aim to clarify the role of the centrosome and conserved polarity regulators in apical membrane formation during the polarization of MDCK cells cultured in 3D. Through well-presented and rigorous studies, the authors focused on the emergence of polarity as a single MDCK cell divided in 3D culture to form a two-cell cyst with a nascent lumen. Focusing on these very initial stages, rather than in later large cyst formation as in most studies, is a real strength of this study. The authors found that conserved polarity regulators Gp135/podocalyxin, Crb3, Cdc42, and the recycling endosome component Rab11a all localize to the centrosome before localizing to the apical membrane initiation site (AMIS) following cytokinesis. This protein relocalization was concomitant with a repositioning of centrosomes towards the AMIS. In contrast, Par3, aPKC, and the junctional components E-cadherin and ZO1 localize directly to the AMIS without first localizing to the centrosome. Based on the timing of the localization of these proteins, these observational studies suggested that Par3 is upstream of centrosome repositioning towards the AMIS and that the centrosome might be required for delivery of apical/luminal proteins to the AMIS.

To test this hypothesis, the authors generated numerous new cell lines and/or employed pharmacological inhibitors to determine the hierarchy of localization among these components. They found that removal of the centrosome via centrinone treatment severely delayed and weakened the delivery of Gp135 to the AMIS and single lumen formation, although normal lumenogenesis was apparently rescued with time. This effect was not due to the presence of CEP164, ODF2, CEP120, or Pericentrin. Par3 depletion perturbed the repositioning of the centrosome towards the AMIS and the relocalization of the Gp135 and Rab11 to the AMIS, causing these proteins to get stuck at the centrosome. Finally, the authors culture the MDCK cells in several ways (forced aggregation and ECM depleted) to try and further uncouple localization of the pertinent components, finding that Par3 can localize to the cell-cell interface in the absence of cell division. Par3 localized to the edge of the cell-cell contacts in the absence of ECM and this localization was not sufficient to orient the centrosomes to this site, indicating the importance of other factors in centrosome recruitment.

Together, these data suggest a model where Par3 positions the centrosome at the AMIS and is required for the efficient transfer of more downstream polarity determinants (Gp135 and Rab11) to the apical membrane from the centrosome. The authors present solid and compelling data and are well-positioned to directly test this model with their existing system and tools. In particular, one obvious mechanism here is that centrosome-based microtubules help to efficiently direct the transport of molecules required to reinforce polarity and/or promote lumenogenesis. This model is not really explored by the authors except by Pericentrin and subdistal appendage depletion and the authors do not test whether these perturbations affect centrosomal microtubules. Exploring the role of microtubules in this process could considerably add to the mechanisms presented here. In its current state, this paper is a careful observation of the events of MCDK polarization and will fill a knowledge gap in this field. However, the mechanism could be significantly bolstered with existing tools, thereby elevating our understanding of how polarity emerges in this system.

Reviewer #3 (Public review):

In the manuscript titled "Heat Shock Factor Regulation of Antimicrobial Peptides Expression Suggests a Conserved Defense Mechanism Induced by Febrile Temperature in Arthropods", the authors investigate the role of heat shock factor 1 (HSF1) in regulating antimicrobial peptides (AMPs) in response to viral infections, particularly focusing on febrile temperatures. Using shrimp (Litopenaeus vannamei) and Drosophila S2 cells as models, this study shows that HSF1 induces the expression of AMPs, which in turn inhibit viral replication, offering insights into how febrile temperatures enhance immune responses. The study demonstrates that HSF1 binds to heat shock elements (HSE) in AMPs, suggesting a conserved antiviral defense mechanism in arthropods. The findings are informative for understanding innate immunity against viral infections, particularly in aquaculture. However the logical flow of the paper can be improved.

Reviewer #3 (Public review):

This manuscript presents a number of interesting findings that have the potential to increase our understanding of the mechanism underlying homeostatic synaptic plasticity (HSP). The data broadly support that Rab3A plays a role in HSP, although the site and mechanism of action remain uncertain.

The authors clearly demonstrate the Rab3A plays a role in HSP at excitatory synapses, with substantially less plasticity occurring in the Rab3A KO neurons. There is also no apparent HSP in the Earlybird Rab3A mutation, although baseline synaptic strength seems already elevated. In this context, it is unclear if the plasticity is absent or just occluded by a ceiling effect due the synapses already being strengthened. Occlusion may also occur in the mixed cultures, with Rab3A missing from neurons but not astrocytes. The authors do appropriately discuss both options. There are also differences in genetic background between the Rab3A KO and Earlybird mutants that could also impact the results, which are also noted. The authors have solid data showing that Rab3A is unlikely to be active in astrocytes, Finally, they attempt to study the linkage between synaptic strength during HSP and AMPA receptor trafficking and conclude that trafficking may not be solely responsible for the changes in synaptic strength.

Strengths:

This work adds another player into the mechanisms underlying an important form of synaptic plasticity. The plasticity is likely only reduced, suggesting Rab3A is only partially required and perhaps multiple mechanisms contribute. The authors speculate about some possible novel mechanisms.

However, the conclusions on the partial dissociation of AMPAR trafficking and synaptic response are made from somewhat weaker data. On average, across 3 culture sets, they saw similar magnitude of change in mEPSC amplitude and GluA2 cluster area and integral, but the GluA2 data was not significant. This is likely due to the nature of the datasets. Their imaging method involves only assessing puncta pairs (GluA2/VGlut1) clearly associated with a MAP2 labeled dendrite. This is a small subset of synapses, with usually less than 20 synapses per neuron analyzed (as stated by the authors). The mEPSC recordings will be averaging across several hundred events, which likely represent a hundred or more synapses given reasonable expectations on release probability. It has been reported, in work from this lab as well as by direct monitoring of tagged AMPARs during HSP (Wang, et al., 2019), that individual synapses are quite variable in their response. So there will almost necessarily be higher variability in the imaging data due to the smaller number of synapses sampled. The overall trends, though, are in alignment with previous data implicating receptor trafficking as the mechanism for HSP. However, the authors go on to evaluate each of the individual cultures, where 2 show similar changes between the mEPSC data and GluA2 clusters, and 1 culture showing little/no change in GluA2 clusters. The n's are very low here, and none of the datasets are significant. They want to conclude for this culture, there was a change in mEPSC amplitude that was not accompanied by a change in GluA2 at synaptic sites. But these data are collected from different coverslips, and due to the low n's, the potential under-sampling of the GluA2 clusters, and neuron-to-neuron variability, it is very hard to distinguish if this apparent difference is a methodological issue rather than a biological one. Much stronger data would be necessary to conclude that additional factors beyond receptor trafficking are required for HSP.

Other questions arise from the NASPM experiments, used to justify looking at GluA2 (and not GluA1) in the immunostaining. First, there is a frequency effect that is unclear in origin. One would expect NASPM to merely block some fraction of the post-synaptic current, and not affect pre-synaptic release or block whole synapses. However the change in frequency seems to argue (as the authors do) that some synapses only have CP-AMPARs, while the rest of the synapses have few or none. Another possibility is that there are pre-synaptic NASPM-sensitive receptors that influence release probability. Further, the amplitude data show a strong trend towards smaller amplitude following NASPM treatment (Fig 3B). The p value for both control and TTX neurons was 0.08 - it is very difficult to argue that there is no effect. The decrease on average is larger in the TTX neurons, and some cells show a strong effect. It is possible there is some heterogeneity between neurons on whether GluA1/A2 heteromers or GluA1 homomers are added during HSP. This would impact the weakly supported conclusions about the GluA2 imaging vs mEPSC amplitude data.

Unaddressed issues that would greatly increase the impact of the paper:

(1) Is Rab3A acting pre-synaptically, post-synaptically or both? The authors provide good evidence that Rab3A is acting within neurons and not astrocytes. But where it is acting (pre or post) would aid substantially in understanding its role. They could use sparse knock-down of Rab3A, or simply mix cultures from KO and WT mice (with appropriate tags/labels). The general view in the field has been that HSP is regulated post-synaptically via regulation of AMPAR trafficking, and considerable evidence supports this view. The more support for their suggestion of a pre-synaptic site of control, the better.

(2) Rab3A is also found at inhibitory synapses. It would be very informative to know if HSP at inhibitory synapses is similarly affected. This is particularly relevant as at inhibitory synapses, one expects a removal of GABARs (ie the opposite of whatever is happening at excitatory synapses). If both processes are regulated by Rab3A, this might suggest a role for this protein more upstream in the signaling; an effect only at excitatory synapses would argue for a more specific role just at these synapses.

Reviewer #3 (Public review):

The authors apply multivoxel decoding analyses from fMRI during reward feedback about the cues previously chosen that led to that feedback. They compare two versions of the task - one in which the feedback is provided about the current trial, and one in which the feedback is provided about the previous trial. Reward probability changes slowly over time, so subjects need to identify which cues are leading to reward at a given time. They find that evidence for recall of the cue in the lateral orbitofrontal cortex (lOFC) and hippocampus (HC). They also find that in the second condition, where feedback is for the one-back trial, this representation is mediated by the lateral frontal pole (FPl).

Overall, the analyses are clean and elegant and seem to be complete. I have only a few comments.

(1) They do find (not surprisingly) that the one-back task is harder. It would be good to ensure that the reason that they had more trouble detecting direct HC & lOFC effects on the harder task was not because the task is harder and thus that there are more learning failures on the harder one-back task. (I suspect their explanation that it is mediated by FPl is likely to be correct. But it would be nice to do some subsampling of the zero-back task [matched to the success rate of the one-back task] to ensure that they still see the direct HC and lOFC there).

(2) The evidence that they present in the main text (Figure 3) that the HC and lOFC are mediated by FPl is a correlation. I found the evidence presented in Supplemental Figure 7 to be much more convincing. As I understand it, what they are showing in SF7 is that when FPl decodes the cue, then (and only then) HC and lOFC decode the cue. If my understanding is correct, then this is a much cleaner explanation for what is going on than the secondary correlation analysis. If my understanding here is incorrect, then they should provide a better explanation of what is going on so as to not confuse the reader.

(3) I like the idea of "credit spreading" across trials (Figure 1E). I think that credit spreading in each direction (into the past [lower left] and into the future [upper right]) is not equivalent. This can be seen in Figure 1D, where the two tasks show credit spreading differently. I think a lot more could be studied here. Does credit spreading in each of these directions decode in interesting ways in different places in the brain?

Reviewer #3 (Public review):

This study provides a useful insight into the proteomic analysis of several human induced pluripotent (hiPSC) and human embryonic stem cell (hESC) lines. Although the study is largely descriptive with limited validation of the differences found in the proteomic screen, the findings provide a solid platform for further mechanistic discovery.

Reviewer #3 (Public review):

Summary:

The manuscript by Witten et al., aims to investigate the link between acuity thresholds (and hyperacuity) and retinal sampling. Specifically, using in vivo foveal cone-resolved imaging and simultaneous microscopic photo stimulation, the researchers examined visual acuity thresholds in 16 volunteers and correlated them with each individual's retinal sampling capacity and the characteristics of ocular drift.

First, the authors found that although visual acuity was highly correlated with the individual spatial arrangement of cones, for all participants, visual resolution exceeded the Nyquist sampling.

Thus, the researchers hypothesized that this increase in acuity, which could not be explained in terms of spatial encoding mechanisms, might result from exploiting the spatiotemporal characteristics of the visual input associated with the dynamics of the fixational eye movements (and ocular drift in particular).

The authors reported a correlation between acuity threshold and drift amplitude, suggesting that the visual system benefits from transforming spatial input into a spatiotemporal flow. Finally, they showed that drift, contrary to the traditional view of it as random involuntary movement, appears to exhibit directionality: drift tends to move stimuli to higher cone density areas, therefore enhancing visual resolution.

I find the work of broad interest, its methods are clear, and the results solid.

Reviewer #3 (Public review):

Summary:

This paper examined the role of nucleus reuniens (RE) projections to dorsal CA1 neurons in context fear extinction learning. First, they show that RE neurons send excitatory projections to the stratum oriens (SO) and the stratum lacunosum moleculare (SLM), but not the stratum radiatum (SR). After context fear conditioning, the synaptic connections between RE and dCA1 neurons in the SLM (but not the SO) are weakened (reduced bouton and spine density) after mice undergo context fear conditioning. This weakening is reversed by extinction learning, which leads to enhanced synaptic connectivity between RE inputs and dendrites in the SLM. Control experiments demonstrate that the observed changes are due to extinction and not caused by simple exposure to the context. Extinction learning also induced increases in the size (volume and surface area) of the post-synaptic density (PSD) in SLM. To establish the functional role of RE inputs to dCA1, the researchers used an inhibitory DREADD to silence this pathway during extinction learning. They observe that extinction memory (measured 2-hours or 24-hours later) is impaired by this inhibition. Control experiments show that the extinction memory deficit is not simply due to increased freezing caused by inactivation of the pathway or injections of CNO. Inhibiting the RO projection during extinction learning also reduced the levels of PSD-95 protein levels in the spines of dCA1 neurons.

Strengths:

Based on their results, the authors conclude that, "the RE→SLM pathway participates in the updating of fearful context value by actively regulating CFE-induced molecular and structural synaptic plasticity in the SLM.". I believe the data are generally consistent with this hypothesis, although there is an important control condition missing from the behavioral experiments.

Weaknesses:

(1) A defining feature of extinction learning is that it is context specific (Bouton, 2004). It is expressed where it was learned, but not in other environments. Similarly, it has been shown that internal contexts (or states) also modulate the expression of extinction (Bouton, 1990). For example, if a drug is administered during extinction learning, it can induce a specific internal state. If this state is not present during subsequent testing, the expression of extinction is impaired just as it is when the physical context is altered (Bouton, 2004). It is possible that something similar is happening in Figure 6. In these experiments, CNO is administered to inactivate the RE-dCA1 projection during extinction learning. The authors observe that this manipulation impairs the expression of extinction the next day (or 2-hours later). However, the drug is not given again during the test. Therefore, it is possible that CNO (and/or inactivation of the RE-dCA1 pathway) induces a state change during extinction that is not present during subsequent testing. Based on the literature cited above, this would be expected to disrupt fear extinction as the authors observed. To determine if this alternative explanation is correct, the researchers need to add groups that receive CNO during extinction training and subsequent extinction testing. If the deficits in extinction expression reported in Figure 6 result from a state change, then these groups should not exhibit an impairment. In contrast, if the authors' account is correct, then the expression of extinction should still be disrupted in mice that receive CNO during training and testing.

(2) In their analysis of dCA1 synapses after contextual fear extinction (CFE) (Figure 4), the authors should have compared Ctx and Ctx-Ctx animals against naïve animals (as they did in Figure 3) when comparing 5US and Ext with naïve animals. Otherwise, the authors cannot make the following conclusion; "since changes of SLM synapses were not observed in the animals exposed to the familiar context that was not associated with the USs, our data support the role of the described structural plasticity at the RE→SLM synapses in CFE, rather than in processing contextual information in general.".

(3) In the materials and methods section, the description of cannula placements is confusing and needs to be rewritten.

Reviewer #3 (Public review):

Summary:

This manuscript by McDougal et al, demonstrates species-specific activities of diverse IFIT1 orthologs and seeks to utilize evolutionary analysis to identify key amino acids under positive selection that contribute to the antiviral activity of this host factor. While the authors identify amino acid residues as important for the antiviral activity of some orthologs and propose a possible mechanism by which these residues may function, the significance or applicability of these findings to other orthologs is unclear. However, the subject matter is of interest to the field, and these findings could be significantly strengthened with additional data.

Strengths:

Assessment of multiple IFIT1 orthologs shows the wide variety of antiviral activity of IFIT1, and identification of residues outside of the known RNA binding pocket in the protein suggests additional novel mechanisms that may regulate IFIT1 activity.

Weaknesses:

Consideration of alternative hypotheses that might explain the variable and seemingly inconsistent antiviral activity of IFIT1 orthologs was not really considered. For example, studies show that IFIT1 activity may be regulated by interaction with other IFIT proteins but was not assessed in this study.

Given that there appears to be very little overlap observed in orthologs that inhibited the viruses tested, it's possible that other amino acids may be key drivers of antiviral activity in these other orthologs. Thus, it's difficult to conclude whether the findings that residues 362/4/6 are important for IFIT1 activity can be broadly applied to other orthologs, or whether these are unique to human and chimpanzee IFIT1. Similarly, while the hypothesis that these residues impact IFIT1 activity in an allosteric manner is an attractive one, there is no data to support this.

DOI: 10.1038/s41467-024-52807-3

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

Reviewer #3 (Public review):

Summary:

In this manuscript, Yip and colleagues incorporated the pipette cleaning technique into their existing dual-patch robotic system, "the PatcherBot", to allow sequential patching of more cells for synaptic connection detection in living brain slices. During dual-patching, instead of retracting all two electrodes after each recording attempt, the system cleaned just one of the electrodes and reused it to obtain another recording while maintaining the other. With one new patch clamp recording attempt, new connections can be probed. By placing one pipette in front of the other in this way, one can "walk" across the tissue, termed "patch-walking." This application could allow for probing additional neurons to test the connectivity using the same pipette in the same preparation.

Strengths:

Compared to regular dual-patch recordings, this new approach could allow for probing more possible connections in brain slices with dual-patch recordings, thus having the potential to improve the efficiency of identifying synaptic connections

Weaknesses:

While this new approach offers the potential to increase efficiency, it has several limitations that could curtail its widespread use.

Loss of Morphological Information: Unlike traditional multi-patch recording, this approach likely loses all detailed morphology of each recorded neuron. This loss is significant because morphology can be crucial for cell type verification and understanding connectivity patterns by morphological cell type.

Spatial Restrictions: The robotic system appears primarily suited to probing connections between neurons with greater spatial separation (~100µm ISD). This means it may not reliably detect connections between neurons in close proximity, a potential drawback given that the connectivity is much higher between spatially close neurons. This limitation could help explain the low connectivity rate (5%) reported in the study.

Limited Applicability: While the approach might be valuable in specific research contexts, its overall applicability seems limited. It's important to consider scenarios where the trade-off between efficiency and specific questions that are asked.<br /> Scalability Challenges: Scaling this method beyond a two-pipette setup may be difficult. Additional pipettes would introduce significant technical and logistical complexities.

Reviewer #3 (Public review):

In this study, O'Brien et al. address the need for scalable and cost-effective approaches to finding lead compounds for the treatment of the growing number of Mendelian diseases. They used state-of-the-art phenotypic screening based on an established high-dimensional phenotypic analysis pipeline in the nematode C. elegans.

First, a panel of 25 C. elegans models was created by generating CRISPR/Cas9 knock-out lines for conserved human disease genes. These mutant strains underwent behavioral analysis using the group's published methodology. Clustering analysis revealed common features for genes likely operating in similar genetic pathways or biological functions. The study also presents results from a more focused examination of ciliopathy disease models.

Subsequently, the study focuses on the NALCN channel gene family, comparing the phenotypes of mutants of nca-1, unc-77, and unc-80. This initial characterization identifies three behavioral parameters that exhibit significant differences from the wild type and could serve as indicators for pharmacological modulation.

As a proof-of-concept, O'Brien et al. present a drug repurposing screen using an FDA-approved compound library, identifying two compounds capable of rescuing the behavioral phenotype in a model with UNC80 deficiency. The relatively short time and low cost associated with creating and phenotyping these strains suggest that high-throughput worm tracking could serve as a scalable approach for drug repurposing, addressing the multitude of Mendelian diseases. Interestingly, by measuring a wide range of behavioural parameters, this strategy also simultaneously reveals deleterious side effects of tested drugs that may confound the analysis.

Considering the wealth of data generated in this study regarding important human disease genes, it is regrettable that the data is not made accessible to researchers less versed in data analysis methods. This diminishes the study's utility. It would have a far greater impact if an accessible and user-friendly online interface were established to facilitate data querying and feature extraction for specific mutants. This would empower researchers to compare their findings with the extensive dataset created here.

Another technical limitation of the study is the use of single alleles. Large deletion alleles were generated by CRISPR/Cas9 gene editing. At first glance, this seems like a good idea because it limits the risk that background mutations, present in chemically-generated alleles, will affect behavioral parameters. However, these large deletions can also remove non-coding RNAs or other regulatory genetic elements, as found, for example, in introns. Therefore, it would be prudent to validate the behavioral effects by testing additional loss-of-function alleles produced through early stop codons or targeted deletion of key functional domains.

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 feature 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 epigentic 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 provide information in support of. Transcriptional condensates are an important "family" of condensates, regulating different types of genes and this work supports the hypothesis that they possess similar protein partner molecules as those thought to define such bodies.

Reviewer #3 (Public Review):

Summary:

(1) To further explore the genetic basis of asthenoteratozoospermia, the authors performed whole-exome sequencing analyses among infertile males affected by asthenoteratozoospermia. Four unrelated Han Chinese patients were found to carry biallelic variations of DNAH3, a gene encoding IDA-associated protein.<br /> (2) To verify the function of IDA associated protein DNAH3, the authors generated a Dnah3-KO mouse model and revealed that the loss of DNAH3 leads to severe male infertility as a result of the severe reduction in sperm movement with the abnormal IDA and mitochondrion structures.<br /> (3) Mechanically, they confirmed decreased expression of IDA-associated proteins (including DNAH1, DNAH6 and DNALI1) in the spermatozoa from patients with DNAH3 mutations and Dnah3-KO male mice.<br /> (4) Then, they also found that male infertility caused by DNAH3 deficiency could be rescued by intracytoplasmic sperm injection (ICSI) treatment in humans and mice.

Strengths:

(1) In addition to existing research, the authors provided novel variants of DNAH3 as important factors leading to asthenoteratozoospermia. This further expands the spectrum of pathogenic variants in asthenoteratozoospermia.<br /> (2) By mechanistic studies, they found that DNAH3 deficiency led to decreased expression of IDA-associated proteins, which may be used to explain the disruption of sperm motility and reduced fertility caused by DNAH3 deficiency.<br /> (3) Then, successful ICSI outcomes were observed in patients with DNAH3 mutations and Dnah3 KO mice, which will provide an important reference for genetic counselling and clinical treatment of male infertility.

Reviewer #3 (Public review):

Summary:

This manuscript presents a series of experiments aimed at investigating orientation to polarized lunar skylight in a nocturnal ant, the first report of its kind that I am aware of.

Strengths:

The study was conducted carefully and is clearly explained here.

Weaknesses:

The revised manuscript is much improved.

Reviewer #3 (Public review):

Summary:

The authors use cryo-electron tomography to thoroughly investigate the complexity of purified, excitatory synapses. They make several major interesting discoveries: polyhedral vesicles that have not been observed before in neurons; analysis of the intermembrane distance, and a link to potentiation, essentially updating distances reported from plastic-embedded specimen; and find that the postsynaptic density does not appear as a dense accumulation of proteins in all vitrified samples (less than half), a feature which served as a hallmark feature to identify excitatory plastic-embedded synapses.

Strengths:

(1) The presented work is thorough: the authors compare purified, endogenously labeled synapses to wild-type synapses to exclude artifacts that could arise through the homogenation step, and, in addition, analyse plastic embedded, stained synapses prepared using the same quick workflow, to ensure their findings have not been caused by way of purification of the synapses. Interestingly, the 'thick lines of PSD' are evident in most of their stained synapses.

(2) I commend the authors on the exceptional technical achievement of preparing frozen specimens from a mouse within two minutes.

(3) The approaches highlighted here can be used in other fields studying cell-cell junctions.

(4) The tomograms will be deposited upon publication which will enable neurobiologists and researchers from other fields to carry on data evaluation in their field of expertise since tomography is still a specialized skill and they collected and reconstructed over 100 excellent tomograms of synapses, which generates a wealth of information to be also used in future studies.

(5) The authors have identified ionotropic receptor positions and that they are linked to actin filaments, and appear to be associated with membrane and other cytosolic scaffolds, which is highly exciting.

(6) The authors achieved their aims to study neuronal excitatory synapses in great detail, were thorough in their experiments, and made multiple fascinating discoveries. They challenge dogmas that have been in place for decades and highlight the benefit of implementing and developing new methods to carefully understand the underlying molecular machines of synapses.

Weaknesses:

The authors show informative segmentations in their figures but none have been overlayed with any of the tomograms in the submitted videos. It would be helpful for data evaluation to a broad audience to be able to view these together as videos to study these tomograms and extract more information. Deposition of segmentations associated with the tomgrams would be tremendously helpful to Neurobiologists, cryo-ET method developers, and others to push the boundaries.

Impact on community:

The findings presented by Peukes et al. pertaining to synapse biology change dogmas about the fundamental understanding of synaptic ultrastructure. The work presented by the authors, particularly the associated change of intermembrane distance with potentiation and the distinct appearance of the PSD as an irregular amorphous 'cloud' will provide food for thought and an incentive for more analysis and additional studies, as will the discovery of large membranous and cytosolic protein complexes linked to ionotropic receptors within and outside of the synaptic cleft, which are ripe for investigation. The findings and tomograms available will carry far in the synapse fields and the approach and methods will move other fields outside of neurobiology forward. The method and impactful results of preparing cryogenic, unlabeled, unstained, near-native synapses may enable the study of how synapses function at high resolution in the future.

Reviewer #3 (Public review):

This paper provides an interesting description of the ventral parts of the Cambrian xandarellid Cindarella eucalla, derived from exceptionally preserved specimens of the Chengjiang Biota. These morphological data are useful for our broad understanding and future research on Xandarellida, and are generally well-represented in the description and accompanying figures. The strengths of this work rest in this morphological description of exceptional fossil material, and this is generally well supported. In addition, the authors put this description in the context of the morphology of other xandarellids and Cambrian arthropod groups, with most of these parallels being useful and reasonably supported, though in several places homology is assumed and this currently lacks evidence. The manuscript goes on to use these morphological data and comparisons to other groups (particularly trilobites) to make suggestions for the ecology of Cindarella eucalla and other xandarellids. The majority of my comments on this work relate to this latter aim - the ecological conclusions drawn are generally derived through morphological comparisons, where a specific morphology has been suggested as an adaption to a particular ecological function in another extinct arthropod group. However, the original suggestions for ecological function are untested, and so remain hypotheses. Despite this, they are frequently presented as truisms to enable ecological conclusions to be drawn for Cindarella eucalla. I have listed my comments and queries on the study below for the authors to address or respond to, and I hope they are useful to the authors.

Comments:

There are a number of ecological and functional morphology conclusions stated that seem put too strongly to be considered sufficiently supported by the evidence given. These relate to both the description of C. eucalla, and comparisons to other extinct arthropod taxa (notably trilobites). Many of these latter statements are assumptions of functional morphology, and should not be repeated as truisms, rather than they represent suggested functions and ecologies based on the known morphological descriptions. This aspect occurs throughout the article, and, for me, is the primary concern.

Reviewer #3 (Public review):

Summary:

The manuscript "Crispant analysis in zebrafish as a tool for rapid functional screening of disease-causing genes for bone fragility" describes the use of CRISPR gene editing coupled with phenotyping mosaic zebrafish larvae to characterize functions of genes implicated in heritable fragile bone disorders (FBDs). The authors targeted six high-confident candidate genes implicated in severe recessive forms of FBDs and four Osteoporosis GWAS-implicated genes and observed varied developmental phenotypes across all crispants, in addition to adult skeletal phenotypes.

A major strength of the paper is the streamlined method that produced significant phenotypes for all candidate genes tested.

A major weakness is a lack of new insights into underlying mechanisms that may contribute to disease phenotypes, nor any clear commonalities across gene sets. This was most evident in the qRT-PCR analysis of select skeletal developmental genes, which all showed varied changes in fold and direction, but with little insight into the implications of the results.

Ultimately, the authors were able to show their approach is capable of connecting candidate genes with perturbation of skeletal phenotypes. It was surprising that all four GWAS candidate genes (which presumably were lower confidence) also produced a result. These authors have previously demonstrated that crispants recapitulate skeletal phenotypes of stable mutant lines for a single gene, somewhat reducing the novelty of the study.

Reviewer #3 (Public review):

Summary:

In this study, Miyatake et al. present the interesting finding that ectopic expression of miR-195 in EBF1-deficient hematopoietic progenitor cells can partially rescue their developmental block and allow B cells to progress to a B220+ CD19+ cells stage. Notably, this is accompanied by an upregulation of B-cell-specific genes and, correspondingly, a downregulation of T, myeloid, and NK lineage-related genes, suggesting that miR-195 expression is at least in part equivalent to EBF1 activity in orchestrating the complex gene regulatory network underlying B cell development. Strengthening this point, ATAC sequencing of miR-195-expressing EBF1-deficient B220+CD19+ cells and a comparison of these data to public datasets of EBF1-deficient and -proficient cells suggest that miR-195 indirectly regulates gene expression and chromatin accessibility of some, but not all regions regulated by EBF1.

Mechanistically, the authors identify a subset of potential target genes of miR-195 involved in MAPK and PI3K signalling. Dampening of these pathways has previously been demonstrated to activate FOXO1, a key transcription factor for early B cells downstream of EBF1. Accordingly, the authors hypothesize that miR-195 exerts its function through FOXO1. Supporting this claim, also exogenous FOXO1 expression is able to promote the development of EBF1-deficient cells to the B220+CD19+ stage and thus recapitulates the miR-195 phenotype.

Strengths:

The strength of the presented study is the detailed assessment of the altered chromatin accessibility in response to ectopic miR-195 expression. This provides insight into how miR-195 impacts the gene regulatory network that governs B-cell development and allows the formation of mechanistic hypotheses.

Weaknesses:

The key weakness of this study is that its findings are based on the artificial and ectopic expression of a miRNA out of its normal context, which in my opinion strongly limits the biological relevance of the presented work.

While the authors performed qPCRs for miR-195 on different B cell populations and show that its relative expression peaks in early B cells, it remains unclear whether the absolute miR-195 expression is sufficiently high to have any meaningful biological activity. In fact, other miRNA expression data from immune cells (e.g. DOI 10.1182/blood-2010-10-316034 and DOI 10.1016/j.immuni.2010.05.009) suggest that miR-195 is only weakly, if at all, expressed in the hematopoietic system.

The authors support their finding by a CRISPR-derived miR-195 knockout mouse model which displays mild, but significant differences in the hematopoietic stem cell compartment and in B cell development. However, they fail to acknowledge and discuss a lymphocyte-specific miR-195 knockout mouse that does not show any B cell defects in the bone marrow or spleen and thus contradicts the authors' findings (DOI 10.1111/febs.15493). Of note, B-1 B cells in particular have been shown to be elevated upon loss of miR-15-16-1 and/or miR-15b-16-2, which contradicts the data presented here for loss of the family member miR-195.

A second weakness is that some claims by the authors appear overstated or at least not fully backed up by the presented data. In particular, the findings that miR-195-expressing cells can undergo VDJ recombination, express the pre-BCR/BCR and class switch needs to be strengthened. It would be beneficial to include additional controls to these experiments, e.g. a RAG-deficient mouse as a reference/negative control for the ddPCR and the surface IgM staining, and cells deficient in class switching for the IgG1 flow cytometric staining.

Moreover, the manuscript would be strengthened by a more thorough investigation of the hypothesis that miR-195 promotes the stabilization and activity of FOXO1, e.g. by comparing the authors' ATACseq data to the FOXO1 signature.

Reviewer #3 (Public review):

Summary:

Perlee et al. present a method for generating cell-type restricted knockouts in zebrafish, focusing on melanocytes. For this method, the authors knock-in a Cas9 encoding sequence into the mitfa locus. This mitfaCas9 line has restricted Cas9 expression, allowing the authors to generate melanocyte-specific knockouts rapidly by follow-up injection of sgRNA expressing transposon vectors.

The paper presents some interesting vignettes to illustrate the utility of their approach. These include 1) a derivation of albino mutant fish as a demonstration of the method's efficiency, 2) an interrogation and novel description of tuba1a as a potential non-autonomous contributor to melanocyte dispersion, and 3) the generation of sox10 deficient melanoma tumors that show "escape" of sox10 loss through upregulation of sox9. The latter two examples highlight the usefulness of cell-type targeted knockouts (Body-wide sox10 and tuba1a loss elicit developmental defects). Additionally, the tumor models involve highly multiplexed sgRNAs for tumor initiation which is nicely facilitated by the stable Cas9.

Strengths:

The approach is clever and could prove very useful for studying melanocytes and other cell types. As the authors hint at in their discussion, this approach would become even more powerful with the generation of other Cas9-restricted lineages so a single sgRNA construct can be screened across many lineages rapidly (or many sgRNA and fish lines screened combinatorially).

The biological findings used to demonstrate the power of the approach are interesting in their own right. If it proves true, tuba1a's non-autonomous effects on melanosome dispersion are striking, and this example demonstrates very nicely how one could use Perlee et al.'s approach to search for other non-autonomous mechanisms systematically. Similarly, the observation of the sox9 escape mechanism with sox10 loss is a beautiful demonstration of the relevance of SOX10/SOX9's reciprocal regulation in vivo. This system would be a very nice model for further interrogating mechanisms/interventions surrounding Sox10 in melanoma.

Finally, the figure presentation is very nice. This work involves complex genetic approaches including multiple fish generations and multiplexed construct injections. The vector diagrams and breeding schemes in the paper make everything very clear/"grok-able," and the paper was enjoyable to read.

Weaknesses:

The mitfa-driven GFP on their sgRNA-expressing cassette is elegant, but it makes one wonder why the endogenous knock-in is necessary. It would strengthen the motivation of the work if the authors could detail the potential advantages and disadvantages of their system compared to expressing Cas9 with a lineage-specific promoter from a transposon in their introduction or discussion.

Related to the above - is mitfa haplosufficient? If the mitfaCas9/+ fish have any notable phenotypes, it would be worth noting for others interested in using this approach to study melanoma and pigmentation.

A core weakness (and also potential strength) of the system is that introduced edits will always be non-clonal (Fig 2H/I). The activity of individual sgRNAs should always be validated in the absence of any noticeable phenotype to interpret a negative result. Additionally, caution should be taken when interpreting results from rare events involving positive outgrowth (like tumorogenesis) to account for the fact many cells in the population might not have biallelic null alleles (i.e., 100% of the gene product removed).

Along those lines: in my opinion, the tuba1a results are the most provocative finding in the paper, but they lack key validation. With respect to cutting activity, the Alt-R and transgenic sgRNA expression approaches are not directly comparable. Since there is no phenotype in the melanocyte specific tuba1a knockouts, the authors must confirm high knockout efficiency with this set of reagents before making the claim there is a non-autonomous phenotype. This can be achieved with GFP+ sorting and NGS like they performed with their albino melanocytes.

The whole-body tuba1a knockout phenotype is expected to be pleiotropic, and this expectation might mask off-target effects. Controls for knockout specificity should be included. For instance, confidence in the claims would greatly increase if the dispersed melanosome phenotype could be recovered with guide-resistant tuba1a re-expression and if melanocyte-restricted tuba1a re-expression failed to rescue. As a less definitive but adequate alternative, the authors could also test if another guide or a morpholino against tuba1a phenocopies the described Alt-R edited fish.

I have similar questions about the sox10 escapers, but these suggestions are less critical for supporting the authors claims (especially given the nice staining). Are the sox10 tumors relatively clonal with respect to sox10 mutations? And are the sox10 tumor mutations mostly biallelic frameshifts or potential missense mutations/single mutations that might not completely remove activity? I am particularly curious as SOX10 doesn't seem to be completely absent (and is still very high in some nuclei) in the immunohistochemistry.

Intermedia products don't show up in scope 3? That likely helps explain why there are so figures for making chips at all

Reviewer #3 (Public review):

In this study Barth et al. present results of detailed analyses of the relationships between menopausal hormone therapy (MHT), APOE ε4 genotype, and measures of anatomical brain age in women in the UK Biobank. While past studies have investigated the links between some of these variables (including works by the authors themselves), this new study adds more detailed MHT variables, surgical status, and additional brain aging measures. The UK biobank sample is large, but it is a population cohort and many of the MHT measures are self-reported (as the authors point out). However, the authors present a solid analysis of the available information which shows associations between MHT user status, length of MHT use, as well as surgical status with brain age. However, as the authors themselves state, the results do not unequivocally support the neuroprotective or adverse effect of MHT on the brain. I think this work strengthens the case for the need of better-designed longitudinal studies investigating the effect of MHT on the brain in the peri/post-menopausal stage.

Strengths:

The authors addressed the statistical analyses rigorously. For example, multiple testing corrections, outlier removal, and sensitivity analysis were performed carefully. Ample background information is provided in the introduction allowing even individuals not familiar with the field to understand the motivation behind the work. The discussion section also does a great job of addressing open questions and limitations. Very detailed results of all statistical tests are provided either in the main text or in the supplementary information.

Weaknesses:

For me, the biggest weakness was the presentation of the results. As many variables are involved and past studies have investigated several of these questions, it would have helped to better clarify the analysis and questions that are addressed by this study in particular and what sets this work apart from past studies. The information is present in the manuscript but better organization might have helped. For example, a figure depicting the key questions near the beginning of the manuscript would have been very helpful for me. The Tables also contain a lot of information but I wonder if there might be a way to capture the most relevant information more succinctly (either in Table format or in a figure) for the main text.<br /> Another concern I had was the linear models investigating the effects of these MHT variables on the brain age gap. The authors have included "age" as one of the parameters in this analysis. I wonder if adding a quadratic age factor age2 in the model might have improved the fit since many brain phenotypes tend to show quadratic brain age effects in the 40 to 80-year age range.

Reviewer #3 (Public review):

Summary:

This study examines the metabolic regulation of progenitor proliferation and differentiation in the developing retina. The authors observe dynamic changes in glycolytic gene expression in retinal progenitors and use various strategies to test the role of glycolysis. They find that elevated glycolysis in Pten-cKO retinas results in alteration of RPC fate, while inhibition of glycolysis has converse effects. They specifically test the role of elevated glycolysis using dominant active cytoPFKB3, which demonstrates the selective effects of elevated glycolysis on progenitor proliferation and rod differentiation. They then show that elevated glycolysis modulates both pHi and Wnt signaling, and provide evidence that these pathways impact proliferation and differentiation of progenitors, particularly affecting rod photoreceptor differentiation.

Strengths:

This is a compelling and rigorous study that provides an important advance in our understanding of metabolic regulation of retina development, addressing a major gap in knowledge. A key strength is that the study utilizes multiple genetic and pharmacological approaches to address how both increased or decreased glycolytic flux affect retinal progenitor proliferation and differentiation. They discover elevated Wnt signaling pathway genes in Pten cKO retina, revealing a potential link between glycolysis and Wnt pathway activation. Altogether the study is comprehensive and adds to the growing body of evidence that regulation of glycolysis plays a key role in tissue development.

Weaknesses:

(1) Following the expression of cytoPFKB3, which results in increased glycolytic flux, BrDU labeling was performed at e12.5 and increased labeled cells were detected in the outer nuclear layer. However whether these are cones or rods is not established. The rest of the analysis is focused on the precocious maturation of rhodopsin-labeled outer segments, and the major conclusions emphasize rod photoreceptor differentiation. Therefore it is unclear whether there is an effect on cone differentiation for either Pten cKO or cytoPFKB3 transgenic retina. It is also not established whether rods are born precociously. Presumably, this would be best detected by BrDU labeling at later embryonic stages.

(2) The authors find that there is upregulation of multiple Wnt pathway components in Pten cKO retina. They further show that inhibiting Wnt signaling phenocopies the effects of reducing glycolysis. However, they do not test whether pharmacological inhibition of Wnt signaling reverses the effects of high glycolytic activity in Pten cKO retinas. Thus the argument that Wnt is a key downstream effector pathway regulating rod photoreceptor differentiation is weak.

(3) The use of sodium acetate to force protein acetylation is quite non-specific and will have effects beyond beta-catenin acetylation (which the authors acknowledge). Thus it is a stretch to state that "forced activation of beta-catenin acetylation" mimics the impact of Pten loss/high glycolytic activity in RPCs since the effects could be due to acetylation of other proteins.

Reviewer #3 (Public review):

In this manuscript by Goldblatt et al. the authors study the development of a well-known sensorimotor system, the vestibulo-ocular reflex circuit, using Danio rerio as a model. The authors address whether motor neurons within this circuit are required to determine the identity, upstream connectivity and function of their presynaptic partners, central projection neurons. They approach this by generating a CRISPR-mediated knockout line for the transcription factor phox2a, which specifies the fate of extraocular muscle motor neurons. After showing that phox2a knockout ablates these motor neurons, the authors show that functionally, morphologically, and transcriptionally, projection neurons develop relatively normally.

Overall, the authors present a convincing argument for the dispensability of motor neurons in the wiring of this circuit, although their claims about the generalizability of their findings to other sensorimotor circuits should be tempered. The study is comprehensive and employs multiple methods to examine the function, connectivity and identity of projection neurons.

Comments on the revised version:

The authors have addressed all my previous concerns.

Reviewer #3 (Public review):

Summary:

The manuscript by Jaime Tobon and Moser uses patch-clamp electrophysiology in cochlear preparations to probe the pre- and post-synaptic specializations that give rise to diverse activity of spiral ganglion afferent neurons (SGN). The experiments are quite an achievement! They use paired recordings from pre-synaptic cochlear inner hair cells (IHC) that allow precise control of voltage and therefore calcium influx, with post-synaptic recordings from type I SGN boutons directly opposed to the IHC for both presynaptic control of membrane voltage and post-synaptic measurement of synaptic function with great temporal resolution.

Any of these techniques by themselves are challenging, but the authors do them in pairs, at physiological temperatures, and in hearing animals, all of which combined make these experiments a real tour de force. The data is carefully analyzed and presented, and the results are convincing. In particular, the authors demonstrate that post-synaptic features that contribute to the spontaneous rate (SR) of predominantly monophasic post-synaptic currents (PSCs), shorter EPSC latency, and higher PSC rates are directly paired with pre-synaptic features such as a lower IHC voltage activation and tighter calcium channel coupling for release to give a higher probability of release and subsequent increase in synaptic depression. Importantly, IHCs paired with Low and High SR afferent fibers had the same total calcium currents, indicating that the same IHC can connect to both low and high SR fibers. These fibers also followed expected organizational patterns, with high SR fibers primarily contacting the pillar IHC face and low SR fibers primarily contacting the modiolar face. The authors also use in vivo-like stimulation paradigms to show different RRP and release dynamics that are similar to results from SGN in vivo recordings. Overall, this work systematically examines many features giving rise to specializations and diversity of SGN neurons.

Reviewer #3 (Public review):

Summary:

This study used transcranial direct current stimulation administered using small 'high-definition' electrodes to modulate neural activity within the non-human primate prefrontal cortex during both wakefulness and anaesthesia. Functional magnetic resonance imaging (fMRI) was used to assess the neuromodulatory effects of stimulation. The authors report on the modification of brain dynamics during and following anodal and cathodal stimulation during wakefulness and following anodal stimulation at two intensities (1 mA, 2 mA) during anaesthesia. This study provides some possible support that prefrontal direct current stimulation can alter neural activity patterns across wakefulness and sedation in monkeys. However, the reported findings need to be considered carefully against several important methodological limitations.

Strengths:

A key strength of this work is the use of fMRI-based methods to track changes in brain activity with good spatial precision. Another strength is the exploration of stimulation effects across wakefulness and sedation, which has the potential to provide novel information on the impact of electrical stimulation across states of consciousness.

Weaknesses:

The lack of a sham stimulation condition is a significant limitation, for instance, how can the authors be sure that results were not affected by drowsiness or fatigue as a result of the experimental procedure?

In the anaesthesia condition, the authors investigated the effects of two intensities of stimulation (1 mA and 2 mA). However, a potential confound here relates to the possibility that the initial 1 mA stimulation block might have caused plasticity-related changes in neural activity that could have interfered with the following 2 mA block due to the lack of a sufficient wash-out period. Hence, I am not sure any findings from the 2 mA block can really be interpreted as completely separate from the initial 1 mA stimulation period, given that they were administered consecutively. Several previous studies have shown that same-day repeated tDCS stimulation blocks can influence the effects of neuromodulation (e.g., Bastani and Jaberzadeh, 2014, Clin Neurophysiol; Monte-Silva et al., J. Neurophysiology).

The different electrode placement for the two anaesthetised monkeys (i.e., Monkey R: F3/O2 montage, Monkey N: F4/O1 montage) is problematic, as it is likely to have resulted in stimulation over different brain regions. The authors state that "Because of the small size of the monkey's head, we expected that tDCS stimulation with these two symmetrical montages would result in nearly equivalent electric fields across the monkey's head and produce roughly similar effects on brain activity"; however, I am not totally convinced of this, and it really would need E-field models to confirm. It is also more likely that there would in fact be notable differences in the brain regions stimulated as the authors used HD-tDCS electrodes, which are generally more focal.

Given the very small sample size, I think it is also important to consider the possibility that some results might also be impacted by individual differences in response to stimulation. For instance, in the discussion (page 9, paragraph 2) the authors contrast findings observed in awake animals versus anaesthetised animals. However, different monkeys were examined for these two conditions, and there were only two monkeys in each group (monkeys J and Y for awake experiments [both male], and monkeys R and N [male and female] for the anaesthesia condition). From the human literature, it is well known that there is a considerable amount of inter-individual variability in response to stimulation (e.g., Lopez-Alonso et al., 2014, Brain Stimulation; Chew et al., 2015, Brain Stimulation), therefore I wonder if some of these differences could also possibly result from differences in responsiveness to stimulation between the different monkeys? At the end of the paragraph, the authors also state "Our findings also support the use of tDCS to promote rapid recovery from general anesthesia in humans...and suggest that a single anodal prefrontal stimulation at the end of the anesthesia protocol may be effective." However, I'm not sure if this statement is really backed-up by the results, which failed to report "any behavioural signs of awakening in the animals" (page 7)?

Reviewer #3 (Public review):

The authors make use of a large dataset of reaches from several studies run in their lab to try to identify the source of direction-dependent radial reaching errors. While this has been investigated by numerous labs in the past, this is the first study where the sample is large enough to reliably characterize isometries associated with these radial reaches to identify possible sources of errors.

The sample size is impressive, but the authors should include confidence intervals and ideally, the distribution of responses across individuals along with average performance across targets. It is unclear whether the observed "averaged function" is consistently found across individuals, or if it is mainly driven by a subset of participants exhibiting large deviations for diagonal movements. Providing individual-level data or response distributions would be valuable for assessing the ubiquity of the observed bias patterns and ruling out the possibility that different subgroups are driving the peaks and troughs. It is possible that the Transformation or some other model (see below) could explain the bias function for a substantial portion of participants, while other participants may have different patterns of biases that can be attributable to alternative sources of error.

The different datasets across different experimental settings/target sets consistently show that people show fewer deviations when making cardinal-directed movements compared to movements made along the diagonal when the start position is visible. This reminds me of a phenomenon referred to as the oblique effect: people show greater accuracy for vertical and horizontal stimuli compared to diagonal ones. While the oblique effect has been shown in visual and haptic perceptual tasks (both in the horizontal and vertical planes), there is some evidence that it applies to movement direction. These systematic reach deviations in the current study thus may reflect this epiphenomenon that applies across modalities. That is, estimating the direction of a visual target from a visual start position may be less accurate, and may be more biased toward the horizontal axis, than for targets that are strictly above, below, left, or right of the visual start position. Other movement biases may stem from poorer estimation of diagonal directions and thus reflect more of a perceptual error than a motor one. This would explain why the bias function appears in both the in-lab and on-line studies although the visual targets are very different locations (different planes, different distances) since the oblique effects arise independent of plane, distance, or size of the stimuli.

When the start position is not visible like in the Vindras study, it is possible that this oblique effect is less pronounced; masked by other sources of error that dominate when looking at 2D reach endpoint made from two separate start positions, rather than only directional errors from a single start position. Or perhaps the participants in the Vindras study are too variable and too few (only 10) to detect this rather small direction-dependent bias.

A bias in estimating visual direction or visual movement vector is a more realistic and relevant source of error than the proposed visual bias model. The Visual Bias model is based on data from a study by Huttenlocher et al where participants "point" to indicate the remembered location of a small target presented on a large circle. The resulting patterns of errors could therefore be due to localizing a remembered visual target, or due to relative or allocentric cues from the clear contour of the display within which the target was presented, or even movements used to indicate the target. This may explain the observed 4-peak bias function or zig-zag pattern of "averaged" errors, although this pattern may not even exist at the individual level, especially given the small sample size. The visual bias source argument does not seem well-supported, as the data used to derive this pattern likely reflects a combination of other sources of errors or factors that may not be applicable to the current study, where the target is continuously visible and relatively large. Also, any visual bias should be explained by a coordinates centre on the eye and should vary as a function of the location of visual targets relative to the eyes. Where the visual targets are located relative to the eyes (or at least the head) is not reported.

The Proprioceptive Bias Model is supposed to reflect errors in the perceived start position. However, in the current study, there is only a single, visible start position, which is not the best design for trying to study the contribution. In fact, my paradigms also use a single, visual start position to minimize the contribution of proprioceptive biases, or at least remove one source of systematic biases. The Vindras study aimed to quantify the effect of start position by using two sets of radial targets from two different, unseen start positions on either side of the body midline. When fitting the 2D reach errors at both the group and individual levels (which showed substantial variability across individuals), the start position predicted most of the 2D errors at the individual level - and substantially more than the target direction. While the authors re-plotted the data to only illustrate angular deviations, they only showed averaged data without confidence intervals across participants. Given the huge variability across their 10 individuals and between the two target sets, it would be more appropriate to plot the performance separately for two target sets and show confidential intervals (or individual data). Likewise, even the VT model predictions should differ across the two targets set since the visual-proprioceptive matching errors from the Wang et al study that the model is based on, are larger for targets on the left side of the body.

I am also having trouble fully understanding the V-T model and its associated equations, and whether visual-proprioception matching data is a suitable proxy for estimating the visuomotor transformation. I would be interested to first see the individual distributions of errors and a response to my concerns about the Proprioceptive Bias and Visual Bias models.

Reviewer #3 (Public review):

Summary:

This study reveals that sound exposure enhances drug delivery to the cochlea through the non-selective action of outer hair cells. The efficiency of sound-facilitated drug delivery is reduced when outer hair cell motility is inhibited. Additionally, low-frequency tones were found to be more effective than broadband noise for targeting substances to the cochlear apex. Computational model simulations support these findings.

Strengths:

The study provides compelling evidence that the broad action of outer hair cells is crucial for cochlear fluid circulation, offering a novel perspective on their function beyond frequency-selective amplification. Furthermore, these results could offer potential strategies for targeting and optimizing drug delivery throughout the cochlear spiral.

Weaknesses:

The primary weakness of this paper lies in the surgical procedure used for drug administration through the round window. Opening the cochlea can alter intracochlear pressure and disrupt the traveling wave from sound, a key factor influencing outer hair cell activity. However, the authors do not provide sufficient details on how they managed this issue during surgery. Additionally, the introduction section needs further development to better explain the background and emphasize the significance of the work.

Reviewer #3 (Public review):

Summary:

Authors try to challenge the mainstream scientific as well as popularly held view that Inattentional Blindness (IB) signifies subjects having no conscious awareness of what they report not seeing (after being exposed to unexpected stimuli). They show that even when subjects indicate NOT having seen the unexpected stimulus, they are at above chance level for reporting features such as location, color or movement of these stimuli. Also, they show that 'not seen' responses are in part due to a conservative bias of subjects, i.e. they tend to say no more than yes, regardless of actual visibility. Their conclusion is that IB may not (always) be blindness, but possibly amnesia, uncertainty etc.

Strengths:

A huge pool of (25.000) subjects is used. They perform several versions of the IB experiments, both with briefly presented stimuli (as the classic Mack and Rock paradigm), as well as with prolonged stimuli moving over the screen for 5 seconds (a bit like the famous gorilla version), and all these versions show similar results, pointing in the same direction: above chance detection of unseen features, as well as conservative bias towards saying not seen.

Weaknesses:

Results are all significant but effects are not very strong, typically a bit above chance. Also, it is unclear what to compare these effects to, as there are no control experiments showing what performance would have been in a dual task version where subjects have to also report features etc for stimuli that they know will appear in some trials

There are quite some studies showing that during IB, neural processing of visual stimuli continues up to high visual levels, for example, Vandenbroucke et al 2014 doi:10.1162/jocn_a_00530 showed preserved processing of perceptual inference (i.e. seeing a kanizsa illusion) during IB. Scholte et al 2006 doi: 10.1016/j.brainres.2005.10.051 showed preserved scene segmentation signals during IB. Compared to the strength of these neural signatures, the reported effects may be considered not all that surprising, or even weak.

Reviewer #3 (Public review):

Summary:

The authors first tested whether EAA supplementation increases olfactory preference for bacterial food for a variety of bacterial strains. Of the EAAs, they found only leucine supplementation increased olfactory preference (within a bacterial strain), and only for 3 of the bacterial strains tested. Leucine itself was not found to be intrinsically attractive.

They determined that leucine supplementation increases isoamyl alcohol (IAA) production in the 3 preferred bacterial strains. They identify the biochemical pathway that catabolizes leucine to IAA, showing that a required enzyme for this pathway is upregulated upon supplementation.

Consistent with earlier studies, they find that AWC olfactory neuron is primarily responsible for increased preference for IAA-producing bacteria.

Testing volatile compounds produced by bacteria and identified by GC/MS, and identified several as attractive, most of them require AWC for the full effect. Adaptation assays were used to show that odorant levels produced by bacterial lawns were sufficient to induce olfactory adaptation, and adaptation to IAA reduced chemotaxis to leucine-supplemented lawns. They then showed that IAA attractiveness is conserved across wild strains, while other compounds are more variable, suggesting IAA is a principal foraging cue.

Finally, using the CeNGEN database, they developed a list of candidate IAA receptors. Using behavioral tests, they show that mutation of srd-12 greatly impairs IAA chemotaxis without affecting locomotion or attraction to another AWC-sensed odor, PEA.

Comments

This study will be of great interest in the field of C. elegans behavior, chemical senses and chemical ecology, and understanding of the sensory biology of foraging.

Strengths:

The identification of a receptor for IAA is an excellent finding. The combination of microbial metabolic chemistry and the use of natural bacteria and nematode strains makes an extremely compelling case for the ecological and adaptive relevance of the findings.

Weaknesses:

AWC receives synaptic input from other chemosensory neurons, and thus could potentially mediate navigation behaviors to compounds detected in whole or in part by those neurons. Language concluding detection by AWC should be moderated (e.g. p9 "worms sense an extensive repertoire...predominantly using AWC") unless it has been demonstrated.

srd-12 is not exclusively expressed in AWC. Normally, cell-specific rescue or knockdown would be used to demonstrate function in a specific cell. The authors should provide such a demonstration or explain why they are confident srd-12 acts in AWC.

A comparison of AWC's physiological responses between WT and srd-12, preferably in an unc-13 background, would be nice. Even further, the expression of srd-12 in a different neuron type and showing that it confers responsiveness to IAA (in this case, inhibition) would be very convincing.

Reviewer #3 (Public review):

Summary:

In this work, Rossi et al. use a novel split-belt treadmill learning task to reveal distinct sub-components of gait adaptation. The task involved following a standard adaptation phase with a "ramp-down" phase that helped them dissociate implicit recalibration and more deliberate SR map learning. Combined with modeling and re-analysis of previous studies, the authors show multiple lines of evidence that both processes run simultaneously, with implicit learning saturating based on intrinsic learning constraints and SR learning showing sensitivity to a "perceptual" error. These results offer a parallel with work in reaching adaptation showing both explicit and implicit processes contributing to behavior; however, in the case of gait adaptation the deliberate learning component does not appear to be strategic but is instead a more implicit SR learning processes.

Strengths:

(1) The task design is very clever and the "ramp down" phase offers a novel way to attempt to dissociate competing models of multiple processes in gait adaptation.

(2) The analyses are thorough, as is the re-analysis of multiple previous data sets.

(3) The querying of perception of the different relative belt speeds is a very nice addition, allowing the authors to connect different learning components with error perception.

(4) The conceptual framework is compelling, highlighting parallels with work in reaching but also emphasizing differences, especially w/r/t SR learning versus strategic behaviors. Thus the discovery of an SR learning process in gait adaptation would be both novel and also help conjoin different siloed subfields of motor learning research.

Weaknesses:

(1) The behavior in the ramp-down phase does indeed appear to support multiple learning processes. However, I may have missed something, but I have a fundamental worry about the specific modeling and framing of the "SR" learning process. If I correctly understand, the SR process learns by adjusting to perceived L/R belt speed differences (Figure 7). What is bugging me is why that process would not cause the SR system to still learn something in the later parts of the ramp-down phase when the perceived speed differences flip (Figure 4). I do believe this "blunted learning" is what the SR component is actually modeled with, given this quote in the caption to Figure 7: "When the perturbation is perceived to be opposite than adaptation, even if it is not, mapping is zero and the Δ motor output is constant, reflecting recalibration adjustments only." It seems a priori odd and perhaps a little arbitrary to me that a SR learning system would just stop working (go to zero) just because the perception flipped sign. Or for that matter "generalize" to a ramp-up (i.e., just learn a new SR mapping just like the system did at the beginning of the first perturbation). What am I missing that justifies this key assumption? Or is the model doing something else? (if so that should be more clearly described).

(2) A more minor point, but given the sample size it is hard to be convinced about the individual difference analysis for structure learning (Figure 5). How clear is it that these two groups of subjects are fully separable and not on a continuum? The lack of clusters in another data set seems like a somewhat less than convincing control here.

Reviewer #3 (Public Review):

Hüttemeister et. al. describe a study where researchers utilized a genetic modification technique to knockin a red fluorescence protein variant mCherry into titin, a giant muscle protein, at the Z-disk in order to investigate skeletal muscle development and remodeling. The study revealed that titin's integration into the sarcomere is tightly regulated during muscle development, and its mobility allows for a homogeneous distribution of titin after cell fusion, which is crucial for syncytium formation and skeletal muscle maturation. Furthermore, in adult mice with mCherry-tagged titin, the researchers observed the process of muscle injury treatment by implanting myoblasts containing titin tagged with another fluorescent protein, eGFP. This experiment provided insights into how myocytes integrate, fuse, and contribute to the continuous myofilament system across cell boundaries during muscle regeneration. Interestingly, the behavior of titin proteins differed between immature primary cells and adult muscle tissue. The manuscripts point our interesting observation that develop treatment protocols that target the early postnatal patient or consider in utero cell therapy approaches based on controlling the ratio of therapeutic to diseased cells. though the approach is very interesting, the paper is very qualitative in its approaches. Community will benefit from better quantification of data as most of them are microscopic data that requires quantification.

Reviewer #3 (Public Review):

Fu et al. present a multi-model study using goose and mouse that investigates the protective effects of Lactobacillus plantarum against hyperuricaemia. They highlight this strain's significance and clarify its role in responding to intestinal nucleoside levels and affecting uric acid metabolism through modulation of host signaling pathways.

Strengths:<br /> (1) Fu et al. created two animal models for validation, yielding more reliable and extensive data. In addition, the in vitro tests were repeatedly tested by a multitude of methods, proving to be convincing.<br /> (2) This study integrates microbiomics, whole genomics, in vitro bacterial culture, and metabolomics, providing a wealth of data and valuable insights for future research.

Weakness:<br /> Fu et al. clearly described the role of Lactobacillus plantarum, but it is also important to explore its other mechanisms influencing uric acid metabolism in the host. While changes in hepatic and renal uric acid metabolism were confirmed, the gut's role in this process deserves investigation, particularly regarding whether Lactobacillus plantarum or its metabolites act within the gut. The authors have effectively conveyed the story outlined in the article's title, and the remainder can be explored later. In addition, further discussion is needed to highlight how this strain of Lactobacillus plantarum differs from other Lactobacillus strains or how it innovatively functions differ from some literature reported.

Reviewer #3 (Public review):

Summary:

In this manuscript, Devakinandan and colleagues have undertaken a thorough characterization of the cell types of the mouse vomeronasal organ, focusing on the vomeronasal sensory neurons (VSNs). VSNs are known to arise from a common pool of progenitors that differentiate into two distinct populations characterized by the expression of either the G protein subunit Gnao1 or Gnai2. Using single-cell RNA sequencing followed by unsupervised clustering of the transcriptome data, the authors identified three Gnai2+ VSN subtypes and a single Gnao1+ VSN type. To study VSN developmental trajectories, Devakinandan and colleagues took advantage of the constant renewal of the neuronal VSN pool, which allowed them to harvest all maturation states. All neurons were re-clustered and a pseudotime analysis was performed. The analysis revealed the emergence of two pools of Gap43+ clusters from a common lineage, which differentiate into many subclusters of mature Gnao1+ and Gnai2+ VSNs. By comparing the transcriptomes of these two pools of immature VSNs, the authors identified a number of differentially expressed transcription factors in addition to known markers. Next, by comparing the transcriptomes of mature Gnao1+ and Gnai2+ VSNs, the authors report an enrichment of ER-related genes in Gnao1+ VSNs. Using electron microscopy, they found that this enrichment was associated with specific ER morphology in Gnao1+ neurons. Finally, the authors characterized chemosensory receptor expression and co-expression (as well as H2-Mv proteins) in mature VSNs, which recapitulated known patterns.

Strengths:

The data presented here provide new and interesting perspectives on the distinguishing features between Gnao1+ and Gnai2+ VSNs. These features include newly identified markers, such as transcription factors, as well as an unsuspected ER-related peculiarity in Gnao1+ neurons, consisting in a hypertrophic ER and an enrichment in ER-related genes. In addition, the authors provide a comprehensive picture of specific co-expression patterns of V2R chemoreceptors and H2-Mv genes.

Importantly, the authors provide a browser (scVNOexplorer) for anyone to explore the data, including gene expression and co-expression, number and proportion of cells, with a variety of graphical tools (violin plots, feature plots, dot plots, ...).

Reviewer #3 (Public review):

Summary:

Understanding the mechanisms whereby animals restrict the timing of their reproduction according to day length is a critical challenge given that many of the most relevant species for agriculture are strongly photoperiodic. However, the principal animal models capable of detailed genetic analysis do not respond to photoperiod so this has inevitably limited progress in this field. The fish model medaka occupies a uniquely powerful position since its reproduction is strictly restricted to long days and it also offers a wide range of genetic tools for exploring, in depth, various molecular and cellular control mechanisms.

For these reasons, this manuscript by Tagui and colleagues is particularly valuable. It uses the medaka to explore links bridging photoperiod, feeding behaviour, and reproduction. The authors demonstrate that in female, but not male medaka, photoperiod-induced reproduction is associated with an increase in feeding, presumably explained by the high metabolic cost of producing eggs on a daily basis during the reproductive period. Using RNAseq analysis of the brain, they reveal that the expression of the neuropeptides agrp and npy that have been previously implicated in the regulation of feeding behaviour in mice are upregulated in the medaka brain during exposure to long photoperiod conditions. Unlike the situation in mice, these two neuropeptides are not co-expressed in medaka neurons, and food deprivation in medaka led to increases in agrp but also a decrease in npy expression. Furthermore, the situation in fish may be more complicated than in mice due to the presence of multiple gene paralogs for each neuropeptide. Exposure to long-day conditions increases agrp1 expression in medaka as the result of increases in the number of neurons expressing this neuropeptide, while the increase in npyb levels results from increased levels of expression in the same population of cells. Using ovariectomized medaka and in situ hybridization assays, the authors reveal that the regulation of agrp1 involves estrogen acting via the estrogen receptor esr2a. Finally, a loss of agrp1 function mutant is generated where the female mutants fail to show the characteristic increase in feeding associated with long-day enhanced reproduction as well as yielding reduced numbers of eggs during spawning.

Strengths:

This manuscript provides important foundational work for future investigations aiming to elucidate the coordination of photoperiod sensing, feeding activity, and reproduction function. The authors have used a combination of approaches with a genetic model that is particularly well suited to studying photoperiodic-dependent physiology and behaviour. The data are clear and the results are convincing and support the main conclusions drawn. The findings are relevant not only for understanding photopriodic responses but also provide more general insight into links between reproduction and feeding behaviour control.

Weaknesses:

Some experimental models used in this study, namely ovariectomized female fish and juvenile fish have not been analysed in terms of their feeding behaviour and so do not give a complete view of the position of this feeding regulatory mechanism in the context of reproduction status. Furthermore, the scope of the discussion section should be expanded to speculate on the functional significance of linking feeding behaviour control with reproductive function.

Reviewer #3 (Public review):

Summary:

In the manuscript entitled "Human Brain Barcodes", the author sought to use single-cell CpG methylation information to trace cell lineages in the human brain.

Strengths:

Tracing cell lineages in the human brain is important but technically challenging. Lineage tracing with single-cell CpG methylation would be interesting if convincing evidence exists.

Weaknesses:

As the author noted, "DNA methylation patterns are usually copied between cell division, but the replication errors are much higher compared to base replication". This unstable nature of CpG methylation would introduce significant problems in inferring the true cell lineage. The unreliable CpG methylation status also raises the question of what the "Barcodes" refer to in the title and across this study. Barcodes should be stable in principle and not dynamic across cell generations, as defined in Reference#1. It is not convincing that the "dynamic" CpG methylation fits the "barcodes" terminology. This problem is even more concerning in the last section of results, where CpG would fluctuate in post-mitotic cells.

Reviewer #3 (Public review):

Summary:

The goal of the paper is to examine the objective function of total reward rate in an environment to understand the behavior of humans and animals in two types of decision-making tasks: (1) stay/forgo decisions and (2) simultaneous choice decisions. The main aims are to reframe the equation of optimizing this normative objective into forms that are used by other models in the literature like subjective value and temporally discounted reward. One important contribution of the paper is the use of this theoretical analysis to explain apparent behavioral inconsistencies between forgo and choice decisions observed in the literature.

Strengths:

The paper provides a nice way to mathematically derive different theories of human and animal behavior from a normative objective of global reward rate optimization. As such, this work has value in trying to provide a unifying framework for seemingly contradictory empirical observations in literature, such as differentially optimal behaviors in stay-forgo v/s choice decision tasks. The section about temporal discounting is particularly well motivated as it serves as another plank in the bridge between ecological and economic theories of decision-making.

Weaknesses:

One broad issue with the paper is readability. Admittedly, this is a complicated analysis involving many equations that are important to grasp to follow the analyses that subsequently build on top of previous analyses.

But, what's missing is intuitive interpretations behind some of the terms introduced, especially the apportionment cost without referencing the equations in the definition so the reader gets a sense of how the decision-maker thinks of this time cost in contrast with the opportunity cost of time.

Re-analysis of some existing empirical data through the lens of their presented objective functions, especially later when they describe sources of error in behavior.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors used structural biology approaches to determine the molecular mechanism underlying the inactivation of the PIEZO1 ion channel. To this end, the authors presented structures of human PIEZO1 and its slow-inactivating mutants. The authors also determined the structures of these PIEZO1 constructs in complexes with the auxiliary subunit MDFIC, which substantially slows down PIEZO1 inactivation. From these structures, the authors suggested an anti-correlation between the inactivation kinetics and the resting curvature of PIEZO1 in detergent. The authors also observed a unique feature of human PIEZO1 in which the lipid molecules plugged the channel pore. The authors proposed that these lipid molecules could stabilize human PIEZO1 in a prolonged inactivated state.

Strengths:

Notedly, this manuscript reported the first structures of a human PIEZO1 channel, its channelopathy mutants, and their complexes with MDFIC. The evidence that lipid molecules could occupy the channel pore of human PIEZO1 is solid. The authors' proposals to correlate PIEZO1 resting curvature and pore-resident lipid molecules with the inactivation kinetics are novel and interesting.

Weaknesses:

However, in my opinion, additional evidence is needed to support the authors' proposals.

(1) The authors determined the apo structure of human PIEZO1, which showed a more flattened architecture than that of the mouse PIEZO1. Functionally, the inactivation kinetics of human PIEZO1 is faster than its mouse counterpart. From this observation (and some subsequent observations such as the complex with MDFIC), the authors proposed the anti-correlation between curvature and inactivation kinetics. However, the comparison between human and mouse PIEZO1 structure might not be justified. For example, the human and mouse structures were determined in different detergent environments, and the choice of detergent could influence the resting curvature of the PIEZO structures.

(2) Related to point 1), the 3.7 Å structure of the A1988V mutant presented by the authors showed a similar curvature as the WT but has a slower inactivating kinetics.

(3) Related to point 1), the authors stated that human PIEZO1 might not share the same mechanism as mouse PIEZO1 due to its unique properties. For example, MDFIC only modifies the curvature of human PIEZO1, and lipid molecules were only observed in the pore of the human PIEZO1. Therefore, it may not be justified to draw any conclusions by comparing the structures of PIEZO1 from humans and mice.

(4) Related to point 1), it is well established that PIEZO1 opening is associated with a flattened structure. If the authors' proposal were true, in which a more flattened structure led to faster inactivation, we would have the following prediction: more opening is associated with faster inactivation. In this case, we would expect a pressure-dependent increase in the inactivation kinetics. Could the authors provide such evidence, or provide other evidence along this direction?

(5) In Figure S2, the authors showed representative experiments of the inactivation kinetics of PIEZO1 using whole-cell poking. However, poking experiments have high cell-to-cell variability. The authors should also show statics of experiments obtained from multiple cells.

(6) In Figure 2 and Figure 5, when the authors show the pore diameter, it could be helpful to also show the side chain densities of the pore lining residues.

(7) The authors observed pore-plugging lipids in slow inactivating conditions such as channelopathy mutations or in complex with MDFIC. The authors propose that these lipid molecules stabilize a "deep resting state" of PIEZO1, making it harder to open and harder to inactivate once opened. This will lead to the prediction that the slow-inactivating conditions will lead to a higher activation threshold, such as the mid-point pressure in the activation curve. Is this true?

Reviewer #3 (Public review):

Summary:

In this work, the authors investigated the molecular and cellular basis of sour taste perception in Drosophila melanogaster, focusing on identifying receptors that mediate attractive responses to certain carboxylic acids. It builds on previous work from the same group that had identified the IR co-receptors IR25a and IR76b for this sensory process, screening a set of mutants in IRs to identify three, IR51b, IR94a, and IR94h, required for feeding preference responses to some or all of the tested acids.

Strengths:

The work is of interest because it assigns sensory roles to IRs of previously unknown function, in particular IR94a and IR94h, and points to pharyngeal neurons in which these receptors are expressed as the relevant sensory neurons (potentially with different roles for IR94a- and IR94h-expressing neurons). The work combines elegant genetics, simple but effective feeding and taste assays, chemo-/opto-genetic activation, and some calcium imaging. Overall the presented data look solid and well-controlled.

Weaknesses:

The in situ expression analysis relies entirely on transgenic driver lines for IR94a and IR94h (which had been previously described, though not fully cited in this work). Importantly, given that many of the behavioral experiments (genetic rescue, physiology, artificial activation) use the IR94a and IR94h GAL4 driver lines, it would be helpful to validate that these faithfully reflect IR94a and IR94h expression (as far as I can tell, such validation wasn't done in the original papers describing these lines as part of a large collection of IR drivers). For IR51b, pharyngeal expression is concluded indirectly from non-quantitative RT-PCR analysis (genetic reporters did not work). The lack of direct detection of gene/protein expression (for example, through RNA FISH, immunofluorescence, or protein tagging) would have made for a more complete characterization of these receptors (for example, there is no direct evidence that they also express IR25a and IR76b, as one might expect). Finally, the relationship of IR94a and IR94h neurons to other types of pharyngeal neurons remains unclear, as are their projection patterns in the SEZ.

Conceptually, the work is of interest mostly to those in the immediate field; there have been a very large number of studies in the past decade (several from this lab) characterizing the contributions of different IRs to various chemosensory processes. The current work doesn't lend much insight into the nature of the minimal functional unit of gustatory IRs (reconstitution of a functional IR in a heterologous neuron/cell has not been achieved here, but this is a limitation of many other previous studies), nor to how different pharyngeal sensory pathways might collaborate to control behavior. Nevertheless, the findings provide a useful contribution to the literature.

Reviewing Editor (Public Review):

Summary:

In this well-written paper, a pharmacological experiment is described in which a large group of volunteers is tested on a novel probabilistic reversal learning task with different levels of noise, once after intake of methamphetamine and once after intake of placebo. The design includes a separate baseline session, during which performance is measured. The key result is that drug effects on learning rate variability depend on performance in this separate baseline session.

The approach and research question are important, the results will have an impact, and the study is executed according to current standards in the field. Strengths include the interventional pharmacological design, the large sample size, the computational modeling, and the use of a reversal-learning task with different levels of noise.

(i) One novel and valuable feature of the task is the variation of noise (having 70-30 and 80-20 conditions). This nice feature is currently not fully exploited in the modeling of the task and the data. For example, recently reported new modeling approaches for disentangling two types of uncertainty (stochasticity vs volatility) could be usefully leveraged here (by Piray and Daw, 2021, Nat Comm). The current 'signal to noise ratio' analysis that is targeting this issue relies on separately assessing learning rates on true reversals and learning rates after misleading feedback, in a way that is experimenter-driven. As a result, this analysis cannot capture a latent characteristic of the subject's computational capacity.

(ii) An important caveat is that all the drug x baseline performance interactions, including for the key computational eta parameter did not reach the statistical threshold, and only tended towards significance.

(iii) Both the overlap and the differences between the current study and previous relevant work (that is, how this goes beyond prior studies in particular Rostami Kandroodi et al, which also assessed effects of catecholaminergic drug administration as a function of baseline task performance using a probabilistic reversal learning task) are not made explicit, particularly in the introduction.

(iv) In the discussion, it is stated that the existing literature has, to date, overlooked baseline performance effects, but this is not true in the general sense, given that an accumulating number of studies have shown that the effects of drugs like MA depend on baseline performance on working memory tasks, which often but certainly not always correlates positively with performance on the task under study.

Reviewer #3 (Public review):

Summary of the Study:

The authors investigate the organization of the human pulvinar by analyzing DWI, fMRI, and PET data. The authors explore the hypothesis of the "replication principle" in the pulvinar.

Strengths and Weaknesses of the Methods and Results:

The study effectively integrates diverse imaging modalities to provide a view of the pulvinar's organization. The use of analysis techniques, such as diffusion embedding-driven gradients combined with detailed interpretations of the pulvinar, is a strength.

Even though the study uses the best publicly available resolution possible with current MR-technology, the pulvinar is densely packed with many cell bodies, requiring even higher spatial resolution. In addition, the model order selection of gradients may vary with the acquired data quality. Therefore, the pulvinar's intricate organization needs further exploration with even higher spatial resolution to capture gradients closer to the biological organization of the pulvinar.

Appraisal of the Study's Aims and Conclusions:

The authors delineate the gradient organization of the pulvinar. The study provides a basis for understanding the pulvinar's role in mediating brain network communication.

Impact and Utility of the Work:

This work contributes to the field by offering insights into pulvinar organization.

DOI: 10.1038/s41598-018-20697-3

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

Reviewer #3 (Public review):

The current study examined 13 monosomic yeast strains that lost different individual chromosomes. By comparing the fitness of monosomic strains and several heterozygous deletion strains, the authors observed strong positive epistasis for fitness. The transcriptomes of monosomic strains indicated that general gene-dose compensation is not the reason for fitness gains. On the other hand, gene expression of ribosomal proteins was up-regulated and proteasome subunit expression was down-regulated in all tested monosomic strains. The authors speculated that overexpression in combination with decreased degradation of the insufficient proteins might explain the positive epistasis observed in monosomic strains. This study investigates an important biological question and has some interesting results. However, I have some reservations about the data interpretations listed below.

(1) In Figure 3b (and line 179), the authors stated that those haploinsufficient genes were not transcribed at elevated rates, but almost half of them are in reddish colors (indicating that the expression is higher than 1-fold). Obviously, many haploinsufficient genes are up-regulated in monosomic strains. What the data really show is that the level of overexpression is not correlated with the fitness effect of the deletion (since all the p values are not significant). The authors need to correct their conclusions.<br /> (2) Why are some monosomic strains removed from the transcriptomics analysis, especially when the chromosome IV and XV strains show very strong positive epistasis? The authors need to provide an explanation here.<br /> (3) The authors stated that diploidy observed in chromosome VII and XIII strains were due to endoreplication after losing the marked chromosomes (lines 97 and 117). Isn't chromosome missegregation an equally possible explanation? Since monosomic cells are generated by chromosome missegregation during mitosis, another chromosome missegregation event may occur to rescue the fitness (or viability) of monosomic cells in these strains.

Comments for the revised version:

The authors have addressed all my previous concerns and I have no further questions.

Reviewer #3 (Public review):

Summary:

Yang et al reported in this paper that TGF-beta induces SIRT4 activation, TGF-beta activated SIRT4 then modulates U2AF2 alternative splicing, U2AF2 in turn causes CCN2 for expression. The mechanism is described as this: mitochondrial SIRT4 transport into the cytoplasm in response to TGF-β stimulation, phosphorylated by ERK in the cytoplasm, and pathway and then undergo nuclear translocation by forming the complex with importin α1. In the nucleus, SIRT4 can then deacetylate U2AF2 at K413 to facilitate the splicing of CCN2 pre-mRNA to promote CCN2 protein expression. Moreover, they used exosomes to deliver Sirt4 antibodies to mitigate renal fibrosis in a mouse model. TGF-beta has been widely reported for its role in fibrosis induction.

Strengths:

TGF-beta induction of SIRT4 translocation from mitochondria to nuclei for epigenetics or gene regulation remains largely unknown. The findings presented here that SIRT4 is involved in U2AF2 deacetylation and CCN2 expression are interesting.

Comments on revised version:

I went through the revised manuscript and the letter from the authors. I have no further concerns.

Reviewer #3 (Public review):

Summary:

Regulated metabolism has only recently been recognized as a key component of cancer biology, and even more recently recognized as a significant modulator of the tumor microenvironment (TME). TAMs in the TME play a major role in supporting cancer cell survival and growth/spread, as well as generating an immunosuppressive ME to suppress anti-tumor immunity. Specific regulation of lipid metabolism in this context, in particular how lipids are stored and subsequently mobilized for metabolism, is largely unexplored - especially in the immunological components of the TME.

In this manuscript, the authors build on their previous observations that the fatty acid-binding protein FABP4 plays an important role in macrophage function and that FABP4 expression in tumor associated macrophages (TAM) promotes breast cancer progression. They demonstrate:

(1) Unlike saturated fatty acids (FA), unsaturated FA promotes lipid droplet (LD) accumulation in murine macrophages. LD is the primary intracellular storage depot for FA.

(2) Unsaturated FA activates the FABP4-C/EBPalpha axis to upregulate transcription of the enzymes involved in the synthesis of neutral triacylglycerol (TAG) is an essential step in the formation of the neutral lipid core of LD. It should be noted that the authors speculate that UFA-activated FABP4 translocates to the nucleus to activate PPARgamma, which is known to induce C/EBPalpha expression, but do not directly test the involvement of PPARgamma in this axis.

(3) FABP4 deficiency compromises unsaturated FA-mediated lipid accumulation and utilization in murine macrophages.

(4) FABP4-mediated lipid metabolism in macrophages (TAMS) contributes to breast cancer metastasis, in in-vitro of tumor migration induced by murine macrophages and in correlative studies from human patient breast cancer biopsies.

From these studies, the manuscript concludes that FABP4 plays a pivotal role in mediating lipid droplet formation and lipolysis in TAM, which provides lipids to breast cancer cells that contribute to their growth and metastasis.

These are significant findings, as they provide new insight into the mechanistic regulation of TAM biology via regulation of lipid metabolism, as well as define new biomarkers and potential novel therapeutic targets.

The findings are strong in the studies that mechanistically define the role of FAB4 in lipid accumulation and utilization in murine macrophages. However, evidence is less compelling regarding TAM biology and human breast cancer in 3 main areas:

First, while there is clear in vitro evidence that co-cultured murine macrophages genetically deficient in FABP4 (or their conditioned media) do not enhance breast cancer cell motility and invasion, these macrophages are not bonafide TAM - which may have different biology. The use of actual TAM in these experiments would be more compelling. Perhaps more importantly, there is no in vivo data in tumor-bearing mice that macrophage deficiency of FABP4 affects tumor growth or metastasis - which are doable experiments given the availability of the FABP4 KO mice.

Second, no data is presented that the mechanisms/biology that are elegantly demonstrated in the murine macrophages also occur in human macrophages - which would be foundational to translating these findings into human breast cancer. It seems like straightforward in vitro studies in human monocytes/macrophages could be done to recapitulate the main characteristics seen in the murine macrophages.

Third, while the data from the human breast cancer specimens is very intriguing, it is difficult to ascertain how accurate IHC is in determining that the CD163+ cells (TAM) are in fact the same cells expressing FABP4 - which is the central premise of these studies. Demonstrating that IHC has the resolution to do this would be important. Additionally, the in vitro characterization of FABP4 expression in human macrophages would also add strength to these findings.

In summary, the strengths of this manuscript are the significance of metabolic regulation of the immune tumor microenvironment (TME), and the careful mechanistic delineation of FABP4 involvement in mediating lipid droplet formation and lipolysis in murine macrophages. The weaknesses of the work are the lack of direct experimental evidence that human macrophages behave in the same way as murine macrophages, the incomplete characterization of the role of FABP4 expression in TAM in modulating tumor growth in vivo (in murine models), and whether it can be definitively determined that FABP4 is being primarily expressed in the CD163+ macrophages in human breast cancer samples.

Strengths:

(1) Regulated metabolism has only recently been recognized as a key component of cancer biology, and even more recently recognized as a significant modulator of the tumor microenvironment (TME). TAMs in the TME play a major role in supporting cancer cell survival and growth/spread, as well as generating an immunosuppressive ME to suppress anti-tumor immunity.

(2) Regulation of lipid metabolism in this context is largely unexplored, especially in the immunological components of the TME.

(3) The work builds on the authors' previous work on the role of FABP4 plays an important role in macrophage function including FABP4 expression in TAM promotes breast cancer progression (Hao et al, Cancer Res 2018). This paper identified FABP4-expressing macrophages as being pro-tumorigenic via upregulation of IL-6STAT3 signaling.

(4) The careful and thorough mechanistic delineation of FABP4 involvement in mediating lipid droplet formation and lipolysis in murine macrophages.

(5) The intriguing observations that FABP4-mediated lipid metabolism in macrophages contributes to breast cancer metastasis, in in vitro of tumor migration induced by murine macrophages and in correlative studies from human patient breast cancer biopsies that CD163+ cell numbers (putatively TAM) and FABP4 expression was associated with increased metastatic disease and poor overall survival.

(6) Identification of FABP4 both a prognostic biomarker and a potential therapeutic target to modulate the pro-tumor immune TME.

Weaknesses:

(1) While the authors speculate that UFA-activated FABP4 translocates to the nucleus to activate PPARgamma, which is known to induce C/EBPalpha expression, they do not directly test involvement of PPARgamma in this axis.

(2) While there is clear in vitro evidence that co-cultured murine macrophages genetically deficient in FABP4 (or their conditioned media) do not enhance breast cancer cell motility and invasion, these macrophages are not bonafide TAM - which may have different biology. Use of actual TAM in these experiments would be more compelling. Perhaps more importantly, there is no in vivo data in tumor bearing mice that macrophage-deficiency of FABP4 affects tumor growth or metastasis.

(3) Related to this, the authors find FABP4 in the media and propose that macrophage secreted FABP4 is mediating the tumor migration - but don't do antibody neutralizing experiments to directly demonstrate this.

(4) No data is presented that the mechanisms/biology that are elegantly demonstrated in the murine macrophages also occurs in human macrophages - which would be foundational to translating these findings into human breast cancer.

(5) While the data from the human breast cancer specimens is very intriguing, it is difficult to ascertain how accurate IHC is in determining that the CD163+ cells (TAM) are in fact the same cells expressing FABP4 - which is central premise of these studies. Demonstration that IHC has the resolution to do this would be important. Additionally, the in vitro characterization of FABP4 expression in human macrophages would also add strength to these findings.

Reviewer #3 (Public review):

Summary:

Landau et al. have submitted a manuscript describing for the first time that mammalian adenylyl cyclases can serve as membrane receptors. They have also identified the respective endogenouse ligands which act via AC membrane linkers to modify and control Gs-stimulated AC activity either towards enhancement or inhibition of ACs which is family and ligand-specific. Overall, they have used classical assays such as adenylyl cyclase and cAMP accumulation assays combined with molecular cloning and mutagenesis to provide exceptionally strong biochemical evidence for the mechanism of the involved pathway regulation.

Strengths:

The authors have gone the whole long classical way from having a hypothesis that ACs could be receptors to a series of MS studies aimed at ligand indentification, to functional studies of how these candidate substances affect the activity of various AC families in intact cells. They have used a large array of techniques with a paper having clear conceptual story and several strong lines of evidence.

Weaknesses:

(1) At the beginning of the results section, the authors say "We have expected lipids as ligands". It is not quite clear why these could not have been other substances. It is because they were expected to bind in the lipophilic membrane anchors? Various lipophilic and hydrophilic ligands are known for GPCR which also have transmembrane domains. Maybe 1-2 additional sentences could be helpful here.

(2) In stably transfected HEK cells expressing mAC3 or mAC5, they have used only one dose of isoproterenol (2.5 uM) for submaximal AC activation. The reference 28 provided here (PMID: 33208818) did not specifically look at Iso and endogenous beta2 adrenergic receptors expressed in HEK cells. As far as I remember from the old pharmacological literature, this concentration is indeed submaximal in receptor binding assays but regarding AC activity and cAMP generation (which happen after signal amplification with a so-called receptor reserve), lower Iso amounts would be submaximal. When we measure cAMP, these are rather 10 to 100 nM but no more than 1 uM at which concentration response dependencies usually saturate. Have the authors tried lower Iso concentrations to prestimulate intracellular cAMP formation? I am asking this because, with lower Iso prestimulation, the subsequent stimulatory effects of AC ligands could be even greater.

(3) The authors refer to HEK cell models as "in vivo". I agree that these are intact cells and an important model to start with. It would be very nice to see the effects of the new ligands in other physiologically relevant types of cells, and how they modulate cAMP production under even more physiological conditions. Probably, this is a topic for follow-up studies.

Appraisal of whether the authors achieved their aims, and whether the results support their conclusions:

The authors have achieved their aims to a very high degree, their results do nicely support their conclusions. There is only one point (various classical GPCR concentrations, please see above) that would be beneficial to address.

Without any doubt, this is a groundbreaking study that will have profound implications in the field for the next years/decades. Since it is now clear that mammalian adenylyl cyclases are receptors for aliphatic fatty acids and anandamide, this will change our view on the whole signaling pathway and initiate many new studies looking at the biological function and pathophysiological implications of this mechanism. The manuscript is outstanding.

Reviewer #3 (Public review):

Summary:

In this study the authors use the zebrafish model and in vitro co-cultures with human cell lines, to study how keratinocytes modulate the early stages of melanoma development/migration. The authors demonstrate that keratinocytes undergo an EMT-like transformation in the presence of melanoma cells which leads to a reduction in melanoma cell migration. This EMT transformation occurs via Twist; and resulted in an improvement in OS in zebrafish melanoma models. Authors suggest that the limitation of melanoma cell migration by Twist-overexpressing keratinocytes was through altered cell-cell interactions (Jam3b) that caused a physical blockage of melanoma cell migration.

Strengths:

The authors describe a new cross-talk between melanoma and its major initial microenvironment: the keratinocytes and how instructed by melanoma cells keratinocytes undergo an EMT transformation, which then controls melanoma migration.

Overall, the paper is very well written, and the results are clearly organized and presented.

Weaknesses:

(1) To really show their last point it would be important to CRISPR KO Jam3b in melanoma with twist OE keratinocytes, in vivo or in vitro.

(2) The use of patient biopsies from early-stage melanomas vs healthy tissue to assess if there is a similar alteration of morphology of adjacent keratinocytes and an increase in vimentin in human samples would strengthen the author's findings.

(3) The cell-cell junctions and borders between cells (melanoma/ keratinocytes) should be characterized better, with cellular and sub-cellular resolution. Since melanocytes can "touch" with their dendrites ~40 keratinocytes - can authors expand and explain better their model? Can this explain that in some images we cannot observe a direct interface between the cells?

Reviewer #3 (Public review):

In this study, the authors employed the protein complex structure prediction tool AlphaFold-Multimer to obtain a predicted structure of the protein complex composed of ULK1-ATG13-FIP200 and validated the structure using mutational analysis. This complex plays a central role in the initiation of autophagy in mammals. Previous attempts at resolving its structure have failed to obtain high-resolution structures that can reveal atomic details of the interactions within the complex. The results obtained in this study reveal extensive binary interactions between ULK1 and ATG13, between ULK1 and FIP200, and between ATG13 and FIP200, and pinpoint the critical residues at each interaction interface. Mutating these critical residues led to the loss of binary interactions. Interestingly, the authors showed that the ATG13-ULK1 interaction and the ATG13-FIP200 interaction are partially redundant for maintaining the complex.

The experimental data presented by the authors are of high quality and convincing. However, given the core importance of the AlphaFold-Multimer prediction for this study, I recommend the authors improve the presentation and documentation related to the prediction, including the following:

(1) I suggest the authors consider depositing the predicted structure to a database (e.g. ModelArchive) so that it can be accessed by the readers.

(2) I suggest the authors provide more details on the prediction, including explaining why they chose to use the 1:1:2 stoichiometry for ULK1-ATG13-FIP200 and whether they have tried other stoichiometries, and explaining why they chose to use the specific fragments of the three proteins and whether they have used other fragments.

(3) I suggest the authors present the PAE plot generated by AlphaFold-Multimer in Figure S1. The PAE plot provides valuable information on the prediction.

Reviewer #3 (Public review):

In this study, Bison et al. analyzed the role of the GATA6 transcription factor in patterning the early mesoderm and generating cardiomyocytes, using human embryonic stem cell differentiation assays and patient-derived hiPSCs with heart defects associated with mutations in the GATA6 gene. They identified a novel role for GATA6 in regulating genes involved in the WNT and BMP pathways -findings not previously noted in earlier analyses of GATA6 mutant hiPSCs during early cardiac mesoderm specification (Sharma et al., 2020). Modulation of the WNT and BMP pathways may partially rescue early cardiac mesoderm defects in GATA6 mutant hESCs. These results provide significant insights into how GATA6 loss-of-function and heterozygous mutations contribute to heart defects.

I have the following comments:

(1) Throughout the manuscript, Bison et al. alternate between different protocols to generate cardiomyocytes, which creates some confusion (e.g., Figure 1 vs. Supplemental Figure 2A). The authors should provide a clear justification for using alternative protocols.

(2) The authors should characterise the mesodermal identity and cardiomyocyte subtypes generated with the activin/BMP-induction protocol thoroughly and clarify whether defects in the expression of BMP and WNT-related gene affect the formation of specific cardiomyocyte subtypes in a chamber-specific manner. This analysis is important, as Sharma et al. suggested a role for GATA6 in orchestrating outflow tract formation, and Bison et al. similarly identified decreased expression of NRP1, a gene involved in outflow tract septation, in their GATA6 mutant cells.

(3) The authors developed an iPSC line derived from a congenital heart disease (CHD) patient with an atrial septal defect and observed that these cells generate cTnnT+ cells less efficiently. However, it remains unclear whether atrial cardiomyocytes (or those localised specifically at the septum) are being generated using the activin/BMP-induction protocol and the patient-derived iPSC line.

(4) The authors should also justify the necessity of using the patient-derived line to further analyse GATA6 function.

(5) Figure 3 suggests an enrichment of paraxial mesoderm genes in the context of GATA6 loss-of-function, which is intriguing given the well-established role of GATA6 in specifying cardiac versus pharyngeal mesoderm lineages in model organisms. Could the authors expand their analysis beyond GO term enrichment to explore which alternative fates GATA6 mutant cells may acquire? Additionally, how does the potential enrichment of paraxial mesoderm, rather than pharyngeal mesoderm, relate to the initial mesodermal induction from their differentiation protocol? Could the authors also rule out the possibility of increased neuronal cell fates?

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 toroidal gel within each well.

Addition upon revision:

Overall, the authors have adequately addressed most of the concerns raised. There are a few minor issues that require attention.

Minor comments:

Figure S10: There appears to be a discrepancy in the panel labeling. The current labels are E-H, but it is unclear whether panels A-D exist. Also, this reviewer thought that panels G and H would benefit from statistical testing to strengthen the conclusions. As a general rule for scientific graph presentation, the y-axis of all graphs should start at zero unless there is a compelling reason not to do so.

Reviewer #3 (Public Review):

Summary:

The authors set out to devise a system for the neural and behavioral study of socially cooperative behaviors in nonhuman primates (common marmosets). They describe instrumentation to allow for a "cooperative pulling" paradigm, the training process, and how both behavioral and neural data can be collected and analyzed. This is a valuable approach to an important topic, as the marmoset stands as a great platform to study primate social cognition. Given that the goals of such a methods paper are to (a) describe the approach and instrumentation, (b) show the feasibility of use, and (c) quantitatively compare to related approaches, the work is easily able to meet those criteria. My specific feedback on both strengths and weaknesses is therefore relatively limited in scope and depth.

Strengths:

The device is well-described, and the authors should be commended for their efforts in both designing this system but also in "writing it up" so that others can benefit from their R&D.

The device appears to generate more repetitions of key behavior than other approaches used in prior work (with other species).

The device allows for quantitative control and adjustment to control behaviour.

The approach also supports the integration of markerless behavioral analysis as well as neurophysiological data.

Reviewer #3 (Public Review):

Summary:

The work submitted by Dr. Jeong-Oh Shin and co-workers aims to investigate the therapeutic efficacy of rhPTH(1-34) and R25CPTH(1-34) on bone regeneration and osseointegration of titanium implants using a postmenopausal osteoporosis animal model.

In my opinion the findings presented are not strongly supported by the provided data since the methods utilized do not allow to significantly support the primary claims.

Strengths:

Strengths include certain good technologies utilized to perform histological sections (i.e. the EXAKT system).

Weaknesses:

Certain weaknesses continue to significantly lower the enthusiasm for this work. Most important: the limited number of samples/group. In fact, as presented, the work has an n=4 for each treatment group. This limited number of samples/group significantly impairs the statistical power of the study. In addition, the implants were surgically inserted following a "conventional implant surgery", implying that no precise/guided insertion was utilized. This weakness is, in my opinion, particularly significant since the amount of bone osteointegration may greatly depend on the bucco-lingual positioning of each implant at the time of the surgical insertion (which should, therefore, be precisely standardized across all animals and for all surgical procedures).

Reviewer #3 (Public review):

Summary:

Heterochromatin is characterized by low transcription activity and late replication timing, both dependent on the NAD-dependent protein deacetylase Sir2, the founding member of the sirtuins. This manuscript addresses the mechanism by which Sir2 delays replication timing at the rDNA in budding yeast. Previous work from the same laboratory (Foss et al. PLoS Genetics 15, e1008138) showed that Sir2 represses transcription-dependent displacement of the Mcm helicase in the rDNA. In this manuscript, the authors show convincingly that the repositioned Mcms fire earlier and that this early firing partly depends on the ATPase activity of the nucleosome remodeler Fun30. Using read-depth analysis of sorted G1/S cells, fun30 was the only chromatin remodeler mutant that somewhat delayed replication timing in sir2 mutants, while nhp10, chd1, isw1, htl1, swr1, isw2, and irc5 had no effect. The conclusion was corroborated with orthogonal assays including two-dimensional gel electrophoresis and analysis of EdU incorporation at early origins. Using an insightful analysis with an Mcm-MNase fusion (Mcm-ChEC), the authors show that the repositioned Mcms in sir2 mutants fire earlier than the Mcm at the normal position in wild type. This early firing at the repositioned Mcms is partially suppressed by Fun30. In addition, the authors show Fun30 affects nucleosome occupancy at the sites of the repositioned Mcm, providing a plausible mechanism for the effect of Fun30 on Mcm firing at that position. However, the results from the MNAse-seq and ChEC-seq assays are not fully congruent for the fun30 single mutant. Overall, the results support the conclusions providing a much better mechanistic understanding how Sir2 affects replication timing at rDNA,

Strengths

(1) The data clearly show that the repositioned Mcm helicase fires earlier than the Mcm in the wild type position.<br /> (2) The study identifies a specific role for Fun30 in replication timing and an effect on nucleosome occupancy around the newly positioned Mcm helicase in sir2 cells.

Weaknesses

(1) It is unclear which strains were used in each experiment.<br /> (2) The relevance of the fun30 phospho-site mutant (S20AS28A) is unclear.<br /> (3) For some experiments (Figs. 3, 4, 6) it is unclear whether the data are reproducible and the differences significant. Information about the number of independent experiments and quantitation is lacking. This affects the interpretation, as fun30 seems to affect the +3 nucleosome much more than let on in the description.

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.

Comment on revised version:

The authors have responded the majority of my criticism.

Reviewer #3 (Public review):

The manuscript "Regeneration following tissue necrosis is mediated by non-apoptotic caspase activity" by Klemm et al. is an exploration of what happens to a group of cells that experience caspase activation after necrosis occurs some distance away from the cells of interest. These experiments have been conducted in the Drosophila wing imaginal disc, which has been used extensively to study the response of a developing epithelium to damage and stress. The authors revise and refine their earlier discovery of apoptosis initiated by necrosis, here showing that many of those presumed apoptotic cells do not complete apoptosis. Thus, the most interesting aspect of the paper is the characterization of a group of cells that experience mild caspase activation in response to an unknown signal, followed by some effector caspase activation and DNA damage, but that then recover from the DNA damage, avoid apoptosis, and proliferate instead. Many questions remain unanswered, including the signal that stimulates the mild caspase activation, and the mechanism through which this activation stimulates enhanced proliferation.

The authors should consider answering additional questions, clarifying some points, and making some minor corrections:

Major concerns affecting the interpretation of experimental results:

Expression of STAT92E RNAi had no apparent effect on the ability of hinge cells to undergo NiA, leading the authors to conclude that other protective signals must exist. However, the authors have not shown that this STAT92E RNAi is capable of eliminating JAK/STAT signaling in the hinge under these experimental conditions. Using a reporter for JAK/STAT signaling, such as the STAT-GFP, as a readout would confirm the reduction or elimination of signaling. This confirmation would be necessary to support the negative result as presented.

Similarly, the authors should confirm that the Zfh2 RNAi is reducing or eliminating Zfh2 levels in the hinge under these experimental conditions, before concluding that Zfh2 does not play a role in stopping hinge cells from undergoing NiA.

EdU incorporation was quantified by measuring the fluorescence intensity of the pouch and normalizing it to the fluorescence intensity of the whole disc. However, the images show that EdU fluorescence intensity of other regions of the disc, especially the notum, varied substantially when comparing the different genetic backgrounds (for example, note the substantially reduced EdU in the notum of Figure 3 B' and B'). Indeed, it has been shown that tissue damage can lead to suppression of proliferation in the notum and elsewhere in the disc, unless the signaling that induces the suppression is altered. Therefore, the normalization may be skewing the results because the notum EdU is not consistent across samples, possibly because the damage-induced suppression of proliferation in the notum is different across the different genetic backgrounds.

The authors expressed p35 to attempt to generate "undead cells". They take an absence of mitogen secretion or increased proliferation as evidence that undead cells were not generated. However, there could be undead cells that do not stimulate proliferation non-autonomously, which could be detected by the persistence of caspase activity in cells that do not complete apoptosis. Indeed, expressing p35 and observing sustained effector caspase activation could help answer the later question of what percentage of this cell population would otherwise complete apoptosis (NiA, rescued by p35) vs reverse course and proliferate (NiCP, unaffected by p35).

It is unclear if the authors' model is that the NiCP cells lead to autonomous or non-autonomous cell proliferation, or both. Could the lineage-tracing experiments and/or the experiments marking mitosis relative to caspase activity answer this question?

Many of the conclusions rely on single images. Quantification of many samples should be included wherever possible.

Why does the reduction of Dronc appear to affect regenerative growth in females but not males?

Reviewer #3 (Public review):

The authors developed a useful methodology for generating all combinations of multiple reagents using standard lab equipment. This methodology has clear uses for studying microbial ecology as they demonstrated. The methodology will likely be useful for other types of experiments that require exhaustive testing of all possible combinations of a given set of reagents (e.g., drug-drug antagonism and synergy).

The authors provided a useful R script that generates a detailed experimental protocol for building the desired combination from any number of reagents. The produced document is useful and has clear instructions. The output of the computer script will be strengthened if graphical output is also provided (similar to the one provided in Figure 1C).

The authors show that the error rate of the method doesn't go up with the number of combinations using dyes (Figure 2).

The authors demonstrate the value of their methodology for studying interactions within microbial consortia by assembling all possible combinations of eight strains of Pseudomonas aeruginosa. The value of their methodology for this application is well-founded. However, it is also unclear why specific experimental choices were made for this application. It is unclear why authors continue to show the absorbance measurements of strain assemblies over the entire wavelength spectrum and not just for ABS 600 nm (Figures 3 and 4). It is also unclear why the authors provided information on the "sum of the three spectra" as this reference line is meaningless and not a reasonable null model for estimating how well specific strain combinations will grow together.

Figure 5 illustrates the various analysis types that can be performed on the data collected from growing combinations of eight Pseudomonas aeruginosa strains. It is a very informative figure since it provides a "roadmap" on the various ways in which the dataset produced can be explored. The information in Figures 5 and S6 will likely be very useful for a wide audience.

Reviewer #3 (Public review):

Summary:

Using flies, Kazama et al. combined behavioral analysis, electrophysiological recordings, and calcium imaging experiments to elucidate how odors activate gustatory receptor neurons (GRNs) and elicit a proboscis extension response, which is interpreted as a feeding response.

The authors used DeepLabCut v2.0 to estimate the extension of the proboscis, which represents an unbiased and more precise method for describing this behavior compared to manual scoring.

They demonstrated that the probability of eliciting a proboscis extension increases with higher odor concentrations. The most robust response occurs at a 0.5 v/v concentration, which, despite being diluted in the air stream, remains a relatively high concentration. Although the probability of response is not particularly high it is higher than control stimuli. Notably, flies respond with a proboscis extension to both odors that are considered positive and those regarded as negative.

The authors used various transgenic lines to show that the response is mediated by GRNs. Specifically, inhibiting Gr5a reduces the response, while inhibiting Gr66a increases it in fed flies. Additionally, they find that odors induce a strong positive response in both types of GRNs, which is abolished when the labella of the proboscis are covered. This response was also confirmed through electrophysiological tip recordings.

Finally, the authors demonstrated that the response increases when two stimuli of different modalities, such as sucrose and odors, are presented together, suggesting clear multimodal integration.

Strengths:

The integration of various techniques, that collectively support the robustness of the results.

The assessment of electrophysiological recordings in intact animals, preserving natural physiological conditions.

Weaknesses:

The behavioral response is observed in only a small proportion of animals.

Reviewer #3 (Public review):

Summary:

The study investigates reinforcement learning across the lifespan with a large sample of participants recruited for an online game. It finds that children gradually develop their abilities to learn reward probability, possibly hindered by their immature spatial processing and probabilistic reasoning abilities. Motor noise, reinforcement learning rate, and exploration after a failure all contribute to children's subpar performance.

Strengths:

(1) The paradigm is novel because it requires continuous movement to indicate people's choices, as opposed to discrete actions in previous studies.

(2) A large sample of participants were recruited.

(3) The model-based analysis provides further insights into the development of reinforcement learning ability.

Weaknesses:

(1) The adequacy of model-based analysis is questionable, given the current presentation and some inconsistency in the results.

(2) The task should not be labeled as reinforcement motor learning, as it is not about learning a motor skill or adapting to sensorimotor perturbations. It is a classical reinforcement learning paradigm.

Reviewer #3 (Public review):

Summary:

In this very thorough manuscript, the authors provide further evidence that the lectin-24A gene in Drosophila melanogaster is directly involved in the anti-parasitoid wasp humoral immune reaction.

Strengths:

In this study in particular they use a fluorescent reporter and promoter-bashing to determine how this gene is regulated. They find that JAK/STAT, Pannier, and NF-κB signaling are integral to the regulation of lectin-24A and to the humoral anti-parasitoid immune response. These claims are well supported by the experimental design, results, and analysis.

Weaknesses:

A bit of clarity is needed regarding Figure 4a as well as on the rationale for the lengths of the promoter intervals used.

DOI: 10.21203/rs.3.rs-4603170/v1

Resource: Addgene_135676

Curator: @olekpark

SciCrunch record: RRID:Addgene_135676

What is this?

DOI: 10.1038/s41467-024-51681-3

Resource: RRID:Addgene_47406

Curator: @olekpark

SciCrunch record: RRID:Addgene_47406

What is this?

DOI: 10.1186/s12967-024-05563-3

Resource: RRID:Addgene_138209

Curator: @olekpark

SciCrunch record: RRID:Addgene_138209

What is this?

DOI: 10.1038/s43018-024-00784-3

Resource: RRID:Addgene_92379

Curator: @olekpark

SciCrunch record: RRID:Addgene_92379

What is this?

DOI: 10.1038/s41467-024-51603-3

Resource: RRID:Addgene_109424

Curator: @olekpark

SciCrunch record: RRID:Addgene_109424

What is this?

In the article “These new tools let you see for yourself how biased AI image models are,” Melissa Heikkilä, argues that AI-generating image systems are applying harmful biases and stereotypes. Despite the company's attempts to fix these issues, Heikkila's research with Hugging Face and Leipzig University has created a tool to bring to light these biases. The tool highlights biases and stereotypical images based on gender and ethnicity. Heikkila blames these biases on the training data used which reflects off of American culture/values. Overall, the article clarifies these AI challenges and emphasizes making the system less biased.

Reviewer #3 (Public review):

Summary:<br /> The overarching goal of the authors was to understand whether emotional information conveyed through point-light biological motion can trigger automatic physiological responses, as reflected in pupil size.

Strengths:<br /> This manuscript has several noticeable strengths: it addresses an intriguing research question that fills that gap in existing literature, presents a clear and accurate presentation of the current literature, and conducts a series of experiments and control experiments with adequete sample size. Yet, it also entails several noticeable limitations - especially in the study design and statistical analyses.

Assessment of the revision:

The authors have done a thorough job revising the manuscript, effectively addressing all of my previous concerns.

Reviewer #3 (Public review):

Summary:

Das et al. discovered a maternal role for Caspar (Casp), the Drosophila orthologue of human Fas-associated factor-1 (FAF1), in embryonic development and germ cell formation. They find that Casp interacts with Transitional endoplasmic reticulum 94 (TER94). Loss of Casp or TER94 leads to partial embryonic lethality, correlated with aberrant centrosome behavior and cytoskeletal abnormalities. This suggests that Casp, along with TER94, promotes embryonic development through a still unidentified mechanism. They also find that Casp regulates germ cell number by controlling a key determinant of germ cell formation, Oskar, through its negative regulator, Smaug.

Strengths:

Overall, the experiments are well-conducted, and the conclusions of this paper are mostly well-supported by data.

Weaknesses:

Some additional controls could be included, and the language could be clarified for accuracy.

Reviewer #3 (Public review):

Summary:

Nguyen et al show data indicating that the vomeronasal organ (VNO) and ventromedial hypothalamus (VMH) are part of a circuit that elicits defensive responses induced by predator odors. They also suggest that using fresh or old predator saliva may be a method to change the perceived imminence of predation. The authors also identify a family of VNO receptors that are activated by cat saliva. Next, the authors show how different components of this defensive circuit are activated by saliva, as measured by fos expression. The work also shows that different VMH populations are activated by fresh and old saliva, demonstrating that these stimuli create qualitatively different neural activity profiles. However, the exact components that differ between fresh and old saliva remain unknown and may be identified in future studies.

Strengths:

(1) Predator saliva is a stimulus of high ethological relevance<br /> (2) The authors performed a careful quantification of fos induction across the anterior-posterior axis<br /> (3) Authors show that different VMH populations are activated by fresh and old saliva

Weaknesses:

(1) There is a lack of standard circuit dissection methods, such as characterizing the behavioral effects of increasing and decreasing neural activity of relevant cell bodies and axonal projections

(2) Some of the findings are disconnected from the story. For example, the authors show V2R-A4-expressing cells are activated by predator odors, but the causal role of these cells in generating defensive actions is not shown

DOI: 10.1038/s41598-017-18167-3

Resource: RRID:BDSC_37519

Curator: @maulamb

SciCrunch record: RRID:BDSC_37519

What is this?

DOI: 10.1038/s41598-018-19802-3

Resource: RRID:BDSC_28079

Curator: @maulamb

SciCrunch record: RRID:BDSC_28079

What is this?

Reviewer #3 (Public review):

Summary:

Using a mouse model of Staphylococcus aureus gut colonization, Lejeune et al. demonstrate that the microbiome, immune system, and sex are important contributing factors for whether this important human pathogen persists in the gut. The work begins by describing differential gut clearance of S. aureus in female B6 mice bred at NYU compared to those from Jackson Laboratories (JAX). NYU female mice cleared S. aureus from the gut but NYU male mice and mice of both sexes from JAX exhibited persistent gut colonization. Further experimentation demonstrated that differences between staphylococcal gut clearance in NYU and JAX female mice were attributed to the microbiome. However, NYU male and female mice harbor similar microbiomes, supporting the conclusion that the microbiome cannot account for the observed sex-dependent clearance of S. aureus gut colonization. To identify factors responsible for female clearance of S. aureus, the authors performed RNAseq on intestinal epithelial cells and cells enriched within the lamina propria. This analysis revealed sex-dependent transcriptional responses in both tissues. Genes associated with immune cell function and migration were distinctly expressed between the sexes. To determine which immune cell types contribute to S. aureus clearance Lejeune et al employed genetic and antibody-mediated immune cell depletion. This experiment demonstrated that CD4+ IL17+ cells and neutrophils promote the elimination of S. aureus from the gut. Subsequent experiments, including the use of the 'four core genotype model' were conducted to discern between the roles of sex chromosomes and sex hormones. This work demonstrated that sex-chromosome-linked genes are not responsible for clearance, increasing the likelihood that hormones play a dominant role in controlling S. aureus gut colonization.

Strengths:

A strength of the work is the rigorous experimental design. Appropriate controls were executed and, in most cases, multiple approaches were conducted to strengthen the authors' conclusions. The conclusions are supported by the data.

The following suggestions are offered to improve an already strong piece of scholarship.

Weaknesses:

The correlation between female sex hormones and the elimination of S. aureus from the gut could be further validated by quantifying sex hormones produced in the four core genotype mice in response to colonization. Additionally, and this may not be feasible, but according to the proposed model administering female sex hormones to male mice should decrease colonization. Finally, knowing whether the quantity of IL-17a CD4+ cells change in the OVX mice has the potential to discern whether abundance/migration of the cells or their activation is promoted by female sex hormones.

In the Discussion, the authors highlight previous work establishing a link between immune cells and sex hormone receptors, but whether the estrogen (and progesterone) receptor is differentially expressed in response to S. aureus colonization could be assessed in the RNAseq dataset. Differential expression of known X and Y chromosome-linked genes were discussed but specific sex hormones or sex hormone receptors, like the estrogen receptor, were not. This potential result could be highlighted.

Reviewer #3 (Public review):

Summary:

Avila and colleagues investigate the role of glutamate signaling in the dorsomedial striatum in a treadmill-based task where rats learn to turn or stop their walking based on learning cue-associations that allow them to acquire rewards. Phenotypic variation in Pavlovian conditioned sign and goal-tracking behavior was examined, where behavioral differences in stopping and turning were observed. Glutamate signals in the DMS were recorded during the treadmill task and were related to features of cue-controlled movement, with a stronger relationship seen for goal trackers. Finally, chemogenic inhibition of prelimbic neurons projecting to the DMS (the predicted source of those glutamate signals), preferentially affected cued movement in goal trackers. The authors couch these experiments in the context of cognitive control-attentional mechanisms, movement disorders, and individual differences in cue reactivity.

Strengths:

Overall these studies are interesting and are of general relevance to a number of research questions in neurology and psychiatry. The assessment of the intersection of individual differences in cue-related learning strategies with movement-related questions - in this case, cued turning behavior - is an interesting and understudied question. The link between this work and growing notions of corticostriatal control of action selection makes it timely.

Weaknesses:

The clarity of the manuscript could be improved in several places, including in the graphical visualization of data. It is sometimes difficult to interpret the glutamate results, as presented, in the context of specific behavior, for example.

Reviewer #3 (Public review):

Summary:

Loss of cell attachment to extracellular matrix (ECM) triggers aniokis (a type of programmed cell death), and resistance to aniokis plays a role in cancer development. However, mechanisms underlying anoikis resistance, and the precise role of F-actin, are not fully known.

Here authors describe the formation of a new organelle, giant unilocular vacuole (GUVac), in cells whose F-actin is disrupted during loss of matrix attachment. GUVac formation (diameter >500 nm) resulted from a previously unrecognised macropinocytosis-like process, characterized by inwardly curved micron-sized plasma membrane invaginations, dependent on F-actin depolymerization, septin recruitment and PI(3)P. Finally, the authors show GUVac formation after loss of matrix attachment promotes resistance to anoikis.

From these results, authors conclude that GUVac formation promotes cell survival in environments where F-actin is disrupted and conditions of cell stress.

Strengths:

The manuscript is clear and well-written, figures are all presented at a very high level.

A variety of cutting edge cell biology techniques (eg time-lapse imaging, EM, super-resolution microscopy) are used to study the role of cytoskeleton in GUVac formation, discovering (i) a macropinocytosis-like process dependent on F-actin depolymerisation, SEPT6 recruitment and PI(3)P contributes to GUVac formation, and (ii) GUVac formation is associated with resistance to cell death.

Experimental work was advanced in response to reviewers' comments, improving the manuscript message and mechanistic advance.

Weaknesses:

The manuscript is highly reliant on the use of drugs, or combinations of drugs, for long periods of time (6hr, 18hr). However, in the revised manuscript, authors test conclusions drawn from experiments involving drugs using other canonical cell biology approaches.

The molecular characterisation of GUVacs has been advanced, although not fully resolved.

The authors show (mostly using pharmacological inhibition) that F-actin is key for GUVac formation. The precise role of F-actin / GUVac formation in anoikis resistance will be the focus of future work.

Reviewer #3 (Public review):

Abidi et al. investigated the role of Notch signalling for sebaceous gland differentiation and sebocyte progenitor proliferation in adult mouse skin. By injecting antagonising antibodies against different Notch receptors and ligands into mice, the authors identified that the Notch1 receptor and, to a lesser extent, Notch2 receptor, as well as the Notch ligand Jagged2, contribute to the regulation of sebaceous gland differentiation. In situ hybridisation confirmed that treatment with anti-Jagged2 dramatically reduced the number of basal sebocytes staining for the transcriptionally active intracellular domain of Notch1. Loss of Notch activity in sebocyte progenitors robustly inhibited sebaceous gland differentiation. Under these conditions, the number of sebocyte progenitors marked by Lrig1 was not affected, while the number of proliferating basal sebocytes was increased. Upon recovery of Notch activity, sebaceous gland differentiation could likewise be recovered. By suggesting that Notch activity in sebocyte progenitors is required to balance proliferation and differentiation, these data bring valuable new and relevant findings for the skin field on the sebaceous gland homeostasis.

Reviewer #3 (Public review):

Summary:

The authors investigate how polar flagellation is achieved in gamma-proteobacteria. By probing for proteins that interact with the known flagellar placement factor FlhF, they uncover a new regulator (FipA) for flagellar assembly and polar positioning in three flagellated gamma-proteobacteria. They convincingly demonstrate that FipA interacts genetically and biochemically with previously known spatial regulators HubP and FlhF. FipA is a membrane protein with a cytoplasmic DUF2802 and it co-localizes to the flagellated pole with HubP and FlhF. The DUF2802 mediates the interaction between FipA and FlhF and this interaction is required for FipA function. FipA localization depends on HubP and FlhF.

Strengths:

The work is throughly executed, relying on bacterial genetics, cell biology and protein interaction studies. The analysis is deep, beginning with the discovery af a new and conserved factor, to the molecular dissection of the protein and probing localisation and interaction determinants. Finally, they show that these determinants are important for function and they perform these studies in parallel in three model systems.

Weaknesses:

Because some of the phenotypes and localisation dependencies differ somewhat between model systems, the comparison is challenging to the reader because it is sometimes not obvious what these differences mean and why they arise.

Reviewer #3 (Public Review):

Hu et al in their manuscript attempt to interrogate the interplay between glycolysis, TCA activity, and OXPHOS using LDHA/B knockouts as well as LDH-specific inhibitors. Before I discuss the specifics, I have a few issues with the overall manuscript. First of all, based on numerous previous studies it is well established that glycolysis inhibition or forcing pyruvate into the TCA cycle (studies with PDKs inhibitors) leads to upregulation of TCA cycle activity, and OXPHOS, activation of glutaminolysis, etc (in this work authors claim that lowered glycolysis leads to lower levels of TCA activity/OXPHOS). The authors in the current work completely ignore recent studies that suggest that lactate itself is an important signaling metabolite that can modulate metabolism (actual mechanistic insights were recently presented by at least two groups (Thompson, Chouchani labs). In addition, extensive effort was dedicated to understanding the crosstalk between glycolysis/TCA cycle/OXPHOS using metabolic models (Titov, Rabinowitz labs). I have several comments on how experiments were performed. In the Methods section, it is stated that both HeLa and 4T1 cells were grown in RPMI-1640 medium with regular serum - but under these conditions, pyruvate is certainly present in the medium - this can easily complicate/invalidate some findings presented in this manuscript. In LDH enzymatic assays as described with cell homogenates controls were not explained or presented (a lot of enzymes in the homogenate can react with NADH!). One of the major issues I have is that glycolytic intermediates were measured in multiple enzyme-coupled assays. Although one might think it is a good approach to have quantitative numbers for each metabolite, the way it was done is that cell homogenates (potentially with still traces of activity of multiple glycolytic enzymes) were incubated with various combinations of the SAME enzymes and substrates they were supposed to measure as a part of the enzyme-based cycling reaction. I would prefer to see a comparison between numbers obtained in enzyme-based assays with GC-MS/LC-MS experiments (using calibration curves for respective metabolites, of course). Correct measurements of these metabolites are crucial especially when thermodynamic parameters for respective reactions are calculated. Concentrations of multiple graphs (Figure 1g etc.) are in "mM", I do not think that this is correct.

Reviewer #3 (Public review):

This manuscript reports the temporal history dependence of central complex TL/ring neuron spiking activity to polarized light patterns. Using sharp recording in tethered bumblebees with synthetic and natural visual stimulation, the authors nicely measured activities to rotating polarized UV light, and made the interesting finding that spiking activity depends on not just current stimulus but also recent activity.

(1) History dependence has been reported before in ring neurons in Drosophila (Sun et al., Nature Neuroscience, 2017; Shiozaki et al., Nature Neuroscience, 2017). While there are differences in the nature of the visual stimulation used, the basic phenomenology of temporal history dependence bears some resemblance. Where are the differences in the physiological properties of ring/TL neurons between different insect species in relevance to history dependence? What are the structural similarities and differences in the circuits that may help to explain history dependence? Just to name a few. To gain further insight into this question, the manuscript may benefit from putting the findings here into context.

(2) Figure 3b serves as a critical evidence for history-dependence. However, it is unclear from this data if this is history dependence, or other physiological processes such as OFF response to sensory stimulation, or sensory adaptation. One way to test this is to examine whether such an effect can be detected after a delay period. For example, history dependence in fly ring neurons is mediated by delay period activity present for several seconds. This can be easily tested here as well.

(3) The properties of the history dependence can be better characterized to help understand its nature. What are the statistical characteristics of post-stimulus inhibition to preferred AoP and post-stimulus excitation to anti-preferred AoP? What are the temporal dynamics of such an effect, e.g., how long does it take to return to baseline? Are the differences in these properties recorded across the TL neuron population? Is it possible to categorize these TL neurons based on these properties and morphology? These properties are important to under the physiological basis of such effect. The authors only presented two traces in Figure 3b, beautiful example traces, but without any further population data and statistical analysis.

(4) A major point of the manuscript is energy efficiency via reduction of firing rate. However, the only evidence comes from simulation, and it seems to be a weak effect of 0.5 APs/s.

(5) Another major point of the manuscript is "increases sensitivity for course deviations during straight flight". However, this again is supported by simulation only. To validate these claims, empirical support of behavioral experiments is highly desired. Otherwise, it is recommended to minimize emphasizing such behavioral predictions.

(6) A substantial portion of the text emphasizes the importance of natural stimulation. While natural stimulation is indeed a desirable experimental approach, it is unclear if natural stimulation is exploited to its full in this manuscript. History dependence can be explored with synthetic stimulation.

(7) A phenomenological model was used to account for the history effect, by assuming a linear integration process and a linear history effect. However, such an assumption is not adequately backed up by rigorous statistical analysis of experiment data or at least proper conceptual discussion.

(8) Population responses, as in Figure 4, are based on strong assumptions of neuronal properties without clear experimental support, thus seeming to be quite a stretch.

(9) There are interesting observations in simulation results from Figure 5; it would be nice to experimentally test at least some of these ideas.

(10) "anticipate future head directions" seems to be quite a stretch to me without mechanistic explanations.

(11) The visual stimulation design used can be improved and expanded. The synthetic stimulation used in Figure 1c follows a stereotyped order, according to angular velocities. As the focus of the manuscript is to probe the history effect and to test again the findings made with this stimulation, randomized stimulation should ideally be examined.

(12) State dependence was observed in ring neurons in Drosophila (Sun et al., Nature Neuroscience, 2017) which might be related to ongoing neural activity and history dependence. While I realize that the animal is tethered, I was wondering if there was any signature of neural activity state dependence observed in this study.

Kalluri reveals that AI-generated images are often generated with biased and stereotypical images due to how they were trained. Efforts are made to reduce these biases with new data training and development to improve their algorithms. Kalluri addresses these biases since she believes AI-generated images must become widely accepted in various parts.

Reviewer #3 (Public review):

Summary:

The authors present new observations related to the gliding motility of the multicellular filamentous cyanobacteria Fluctiforma draycotensis. The bacteria move forward by rotating their about their long axis, which causes points on the cell surface to move along helical paths. As filaments glide forward they form visible tracks. Filaments preferentially move within the tracks. The authors devise a simple model in which each cell in a filament exerts a force that either pushes forward or backwards. Mechanical interactions between cells cause neighboring cells to align the forces they exert. The model qualitatively reproduces the tendency of filaments to move in a concerted direction and reverse at the end of tracks.

Strengths:

The observations of the helical motion of the filament are compelling.

The biophysical model used to describe cell-cell coordination of locomotion is clear and reasonable. The qualitative consistency between theory and observation suggests that this model captures some essential qualities of the true system.

The authors suggest that molecular studies should be directly coupled to the analysis and modeling of motion. I agree.

Weaknesses:

There is very little quantitative comparison between theory and experiment. It seems plausible that mechanisms other than mechano-sensing could lead to equations similar to those in the proposed model. As there is no comparison of model parameters to measurements or similar experiments, it is not certain that the mechanisms proposed here are an accurate description of reality. Rather the model appears to be a promising hypothesis.

Reviewer #3 (Public review):

Summary:

This paper presents a systematic analylsis of the role of the hyperpolarization-activated inward current (the h current) in the response of the pyloric rhythm of the stomatogastric ganglion (STG) of the crab. In a detailed set of experiments, they analyze the effect of blocking h current with bath infusion of the h current blocker cesium (perfused as CsCl). They show interesting and reproducible effects that blockade of h current results in a period of frequency decrease after an upward step in temperature, followed by a slow increase in frequency. This contrasts with the normal temperature response that shows an increase in frequency with an increase in temperature without a downward "jag" in the frequency response. This is an important paper for showing the role of h current in stabilizing network dynamics in response to perturbations such as a temperature change.

Strengths of the paper:

The major effects are shown very clearly and convincingly in a range of experiments with combined intracellular recording from neurons during changes in temperature.

Weaknesses

The Marder lab has detailed models of the pyloric rhythm. These temperature effects have not yet been modeled and could be the focus of future modeling studies.

Reviewer #3 (Public review):

Summary:

The authors examine how distinct cellular environments differentially control Mtb following BCG vaccination. The key findings are that IL17-producing PMNs harbor a significant Mtb load in both wild-type and IFNg-/- mice. Targeting IL17 and Cox2 improved disease and enhanced BCG efficacy over 12 weeks and neutrophils/IL17 are associated with treatment failure in humans. The authors suggest that targeting these pathways, especially in MSMD patients may improve disease outcomes.

Strengths:

The experimental approach is generally sound and consists of low-dose aerosol infections with distinct readouts including cell sorting followed by CFU, histopathology, and RNA sequencing analysis. By combining genetic approaches and chemical/antibody treatments, the authors can probe these pathways effectively.

Understanding how distinct inflammatory pathways contribute to control or worsen Mtb disease is important and thus, the results will be of great interest to the Mtb field.

Weaknesses:

A major limitation of the current study is overlooking the role of non-hematopoietic cells in the IFNg/IL17/neutrophil response. Chimera studies from Ernst and colleagues (PMCID: PMC2807991) previously described this IDO-dependent pathway following the loss of IFNg through an increased IL17 response. This study is not cited nor discussed even though it may alter the interpretation of several experiments.

Several of the key findings in mice have previously been shown (albeit with less sophisticated experimentation) and human disease and neutrophils are well described - thus the real new finding is how intracellular Mtb in neutrophils are more refractory to BCG-mediated control. However, given there are already high levels of Mtb in PMNs compared to other cell types, and there is a decrease in intracellular Mtb in PMNs following BCG immunization the strength of this finding is a bit limited.

Reviewer #3 (Public review):

Summary:

This study presents a valuable finding on the mechanism used by WTAP to modulate the IFN-β stimulation. It describes the phase transition of WTAP driven by IFN-β-induced dephosphorylation. The evidence supporting the claims of the authors is solid, although major analysis and controls would strengthen the impact of the findings. Additionally, more attention to the figure design and to the text would help the reader to understand the major findings.

Strength:

The key finding is the revelation that WTAP undergoes phase separation during virus infection or IFN-β treatment. The authors conducted a series of precise experiments to uncover the mechanism behind WTAP phase separation and identified the regulatory role of 5 phosphorylation sites. They also succeeded in pinpointing the phosphatase involved.

Weaknesses:

However, as the authors acknowledge, it is already widely known in the field that IFN and viral infection regulate m6A mRNAs and ISGs. Therefore, a more detailed discussion could help the reader interpret the obtained findings in light of previous research.

It is well-known that protein concentration drives phase separation events. Similarly, previous studies and some of the figures presented by the authors show an increase in WTAP expression upon IFN treatment. The authors do not discuss the contribution of WTAP expression levels to the phase separation event observed upon IFN treatment. Similarly, METTL3 and METTL14, as well as other proteins of the MTC are upregulated upon IFN treatment. How does the MTC protein concentration contribute to the observed phase separation event?

How is PP4 related to the IFN signaling cascade?

In general, it is very confusing to talk about WTAP KO as WTAPgRNA.

Reviewer #3 (Public review):

Summary:

In this study, Piersma et al. successfully generated a mouse model with all Ly49 genes knocked out, resulting in the complete absence of Ly49 receptor expression on the cell surface. The absence of Ly49 expression led to the loss of NK cell education/licensing and consequently, a failure in responsiveness against missing-self target cells. The experimental work and findings are partially overlapping with the previous work by Zhang et al. (2019), who also performed knockout of the entire Ly49 locus in mice and demonstrated that loss of NK responsiveness was due to the removal of inhibitory, and not activating Ly49 genes. The authors demonstrate the restoration of NK cell licensing by knocking in a single Ly49 gene, Ly49A, in a mouse expressing the H-2Dd ligand for this receptor, which is a novel and important finding.

Strengths:

The authors established a novel mouse model enabling them to have a clean and thorough study on the function of Ly49 on NK cell licensing. Also, by knocking in a single Ly49, they were able to investigate the function of a given Ly49 receptor excluding the "contamination" of co-expression of any other Ly49 genes. Their idea and method were novel though the mouse model was somehow genetically similar to a previous study. The experiment design and data interpretation were logically clear and the evidence was solid.

Weaknesses:

The paper is very poorly written and confusing. The authors should be more accurate in the usage of terminology, provide more details on experimental procedures, and revise much of the text to improve clarity and coherence. A thorough revision aiming to clarify the paper would be helpful.

Reviewer #3 (Public review):

Summary:

Targeted covalent inhibition of therapeutically relevant proteins is an attractive approach in drug development. This manuscript now reports a series of covalent inhibitors for human carbonic anhydrase (CA) isozymes (CAI, CAII, and CAIX, CAXIII) for irreversible binding to a critical histidine amino acid in the active site pocket. To support their findings, they included co-crystal structures of CAI, CAII, and CAIX in the presence of three such inhibitors. Mass spectrometry and enzymatic recovery assays validate these findings, and the results and cellular activity data are convincing.

Strengths:

The authors designed a series of covalent inhibitors and carefully selected non-covalent counterparts to make their findings about the selectivity of covalent inhibitors for CA isozymes quite convincing. The supportive X-ray crystallography and MS data are significant strengths. Their approach of targeted binding of the covalent inhibitors to histidine in CA isozyme may have broad utility for developing covalent inhibitors.

Weaknesses:

This reviewer did not find any significant weaknesses. However, I suggest several points in the recommendation for the authors' section for authors to consider.

Reviewer #3 (Public review):

Summary:

The current study on the mutant zebrafish for IBD modeling is worth trying. The author provided lots of evidence, including histopathological observation, gut microflora, as well as intestinal tissue or mucosa cells' transcriptomic data. The multi-omic study has demonstrated the enteritis pathology at multi levels in zebrafish model. However, poor writing of methods and insufficient discussion of current findings were the main defects.

Strengths:

The important immune checkpoint of Treg cells was knocked out in zebrafish, and the enteritis was found then. It could be a substitution of the mouse knockout model to investigate the molecular mechanism of gut disease.

Weaknesses:

(1) The use of the English language requires further editing.

(2) The background of this study has not been introduced sufficiently.

(3) The medical concepts were overstated for immune cell populations.

(4) A lot of methods were not provided.

(5) The age of fish varied a lot in this study.

(6) The pathological index can't reflect the detailed changes in intestinal mucosa.

(7) A lot of findings reflected by the current were not discussed.

(8) The structuring of the text is poor and lacks good logic.

Reviewer #3 (Public review):

Sun et al. present a comprehensive study using a novel photoacoustic microscopy setup and mitochondrial analysis to investigate the impact of hypoxia-ischemia (HI) on brain metabolism and the protective role of therapeutic hypothermia. The authors elegantly demonstrate three connected findings: (1) HI initially suppresses brain metabolism, (2) subsequently triggers a metabolic surge linked to oxidative phosphorylation uncoupling and brain damage, and (3) therapeutic hypothermia mitigates HI-induced damage by blocking this surge and reducing mitochondrial stress.

The study's design and execution are great, with a clear presentation of results and methods. Data is nicely presented, and methodological details are thorough.

However, a minor concern is the extensive use of abbreviations, which can hinder readability. As all the abbreviations are introduced in the text, their overuse may render the text hard to read to non-specialist audiences. Additionally, sharing the custom Matlab and other software scripts online, particularly those used for blood vessel segmentation, would be a valuable resource for the scientific community. In addition, while the study focuses on the short-term effects of HI, exploring the long-term consequences and definitively elucidating HI's impact on mitochondria would further strengthen the manuscript's impact.

Despite these minor points, this manuscript is very interesting.

Reviewer #3 (Public review):

The aim of the study was to map, a) whether different tissues exhibit different metabolic profiles (this is known already), what differences are found between female and male mice and how the profiles changes with age. In particular, the study recorded the activity of respirasomes, i.e. the concerted activity of mitochondrial respiratory complex chains consisting of CI+CIII2+CIV, CII+CIII2+CIV or CIV alone.

The strength is certainly the atlas of oxidative metabolism in the whole mouse body, the inclusion of the two different sexes and the comparison between young and old mice. The measurement was performed on frozen tissue, which is possible as already shown (Acin-Perez et al, EMBO J, 2020).

Weakness:

The assay reveals the maximum capacity of enzyme activity, which is an artificial situation and may differ from in vivo respiration, as the authors themselves discuss. The material used was a very crude preparation of cells containing mitochondria and other cytosolic compounds and organelles. Thus, the conditions are not well defined and the respiratory chain activity was certainly uncoupled from ATP synthesis. Preparation of more pure mitochondria and testing for coupling would allow evaluation of additional parameters: P/O ratios, feedback mechanism, basal respiration, and ATP-coupled respiration, which reflect in vivo conditions much better. The discussion is rather descriptive and cautious and could lead to some speculations about what could cause the differences in respiration and also what consequences these could have, or what certain changes imply.<br /> Nevertheless, this study is an important step towards this kind of analysis.

Reviewer #3 (Public Review):

Summary:

In this study Bomba-Warczak et al focused on the reproductive aging, and they presented a map for long-lived proteins which were stable during the reproductive lifespan. The authors used MIMS to examine and show distinct molecules in different cell types in the ovary and tissue regions in 6 months mice, and they also used proteomic analysis to present different LLPs in ovaries between these two timepoints in 6 months and 10 months mice; besides, the authors also examined the LLPs in oocytes in 6 months mice and indicated that these were nuclear, cytoskeleton and mitochondria proteins.

Strengths:

Overall, this study provided important information about the pattern of long-lived proteins during aging, which will contribute to the understanding of the defects caused by reproductive aging.

Weaknesses:

12 months mice were not examined as the typical aged model.

Comments on revised version:

The authors responded to my comments and suggestions. Due to the limitation of the manuscript type, most suggestions of my comments in first round could be considered for future studies by the authors.

Reviewer #3 (Public review):

Summary:

The paper offers a systematic and rigorous description of the layer-and sublayer specific outputs of the somatosensory cortex using a modern toolbox for the analysis of brain connectivity which combines: 1) Layer-specific genetic drivers for conditional viral tracing; 2) whole brain analyses of axon tracts using tissue clearing and imaging; 3) Segmentation and quantification of axons with normalization to the number of transduced neurons; 4) registration of connectivity to a widely used anatomical reference atlas; 5) functional validation of the connectivity using optogenetic approaches in vivo.

Strengths:

Although the connectivity of the somatosensory cortex is already known, precise data are dispersed in different accounts (papers, online resources, ) using different methods. So the present account has the merit of condensing this information in one very precisely documented report. It also brings new insights on the connectivity, such as the precise comparison of layer specific outputs, and of the primary and secondary somatosensory areas. It also shows a topographic organization of the circuits linking the somatosensory and motor cortices. The paper also offers a clear description of the methodology and of a rigorous approach to quantitative anatomy.

Weaknesses:

The weakness relates to the intrinsic limitations of the in toto approaches, that currently lack the precision and resolution allowing to identify single axons, axon branching or synaptic connectivity. These limitations are identified and discussed by the authors.

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. 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 use of genome-edited cells (for addition of the tag on one of the G proteins) is a great choice to prevent effects of overexpression. Moreover, use of bystander BRET allowed authors to probe 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. Moreover, authors also looked at the dynamics of G protein trafficking by tracking them over multiple time points in different compartments.

Weaknesses:

While 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 include more quantitative details considering G-protein distribution in different compartments as well as more detailed dynamic data on G protein internalization as well as intracellular trafficking kinetics.

Reviewer #3 (Public review):

The manuscript by Fargeot and colleagues assesses the relative effects of species and genetic diversity on ecosystem functioning. This study is very well written and examines the interesting question of whether within-species or among-species diversity correlates with ecosystem functioning, and whether these effects are consistent across trophic levels. The main findings are that genetic diversity appears to have a stronger positive effect on function than species diversity (which appears negative). These results are interesting and have value.

However, I do have some concerns that could influence the interpretation.

(1) Scale: the different measures of diversity and function for the different trophic levels are measured over very different spatial scales, for example, trees along 200 m transects and 15 cm traps. It is not clear whether trees 200 m away are having an effect on small-scale function.

(2) Size of diversity gradients: More information is needed on the actual diversity gradients. One of the issues with surveys of natural systems is that they are of species that have already gone through selection filters from a regional pool, and theoretically, if the environments are similar, you should get similar sets of species, without monocultures. So, if the species diversity gradients range from say, 6 to 8 species, but genetic diversity gradients span an order of magnitude more, you can explain much more variance with genetic diversity. Related to this, species diversity effects on function are often asymptotic at high diversity and so if you are only sampling at the high diversity range, we should expect a strong effect.

(3) Ecosystem functions: The functions are largely biomass estimates (expect decomposition), and I fail to see how the biomass of a single species can be construed as an ecosystem function. Aren't you just estimating a selection effect in this case?

Note that the article claims to be one of the only studies to look at function across trophic levels, but there are several others out there, for example:

Li, F., Altermatt, F., Yang, J., An, S., Li, A., & Zhang, X. (2020). Human activities' fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China. Global change biology, 26(12), 6867-6879.

Luo, Y. H., Cadotte, M. W., Liu, J., Burgess, K. S., Tan, S. L., Ye, L. J., ... & Gao, L. M. (2022). Multitrophic diversity and biotic associations influence subalpine forest ecosystem multifunctionality. Ecology, 103(9), e3745.

Moi, D. A., Romero, G. Q., Antiqueira, P. A., Mormul, R. P., Teixeira de Mello, F., & Bonecker, C. C. (2021). Multitrophic richness enhances ecosystem multifunctionality of tropical shallow lakes. Functional Ecology, 35(4), 942-954.

Wan, B., Liu, T., Gong, X., Zhang, Y., Li, C., Chen, X., ... & Liu, M. (2022). Energy flux across multitrophic levels drives ecosystem multifunctionality: Evidence from nematode food webs. Soil Biology and Biochemistry, 169, 108656.

And the case was made strongly by:

Seibold, S., Cadotte, M. W., MacIvor, J. S., Thorn, S., & Müller, J. (2018). The necessity of multitrophic approaches in community ecology. Trends in ecology & evolution, 33(10), 754-764.

Reviewer #3 (Public Review):

Summary:

This paper by Martin et al. describes the contribution of a Kv channel subunit (Kv1.8, KCNA10) to voltage-dependent K+ conductances and membrane properties of type I and type II hair cells of the mouse utricle. Previous work has documented striking differences in K+ conductances between vestibular hair cell types. In particular amniote type I hair cells are known to express a non-typical low-voltage-activated K+ conductance (GK,L) whose molecular identity has been elusive. K+ conductances in hair cells from 3 different mouse genotypes (wildtype, Kv1.8 homozygous knockouts and heterozygotes) are examined here and whole cell patch-clamp recordings indicate a prominent role for Kv1.8 subunits in generating GK,L. Results also interestingly support a role for Kv1.8 subunits in type II hair cell K+ conductances; inactivating conductances in null mice are reduced in type II hair cells from striola and extrastriola regions of the utricle. Kv1.8 is therefore proposed to contribute as a pore-forming subunit for 3 different K+ conductances in vestibular hair cells. The impact of these conductances on membrane responses to current steps is studied in current clamp. Pharmacological experiments use XE991 to block some residual Kv7-mediated current in both hair cell types, but no other pharmacological blockers are used. In addition immunostaining data are presented and raise some questions about Kv7 and Kv1.8 channel localization. Overall, the data present compelling evidence that removal of Kv1.8 produces profound changes in hair cell membrane conductances and sensory capabilities. These changes at hair cell level suggest vestibular function would be compromised and further assessment in terms of balance behavior in the different mice would be interesting.

Strengths:

This study provides strong evidence that Kv1.8 subunits are major contributors to the unusual K+ conductance in type I hair cells of the utricle. It also indicates that Kv1.8 subunits are important for type II hair cell K+ conductances because Kv1.8-/- mice lacked an inactivating A conductance and had reduced delayed rectifier conductance compared to controls. A comprehensive and careful analysis of biophysical profiles is presented of expressed K+ conductances in 3 different mouse genotypes. Voltage-dependent K+ currents are rigorously characterized at a range of different ages and their impact on membrane voltage responses to current input is studied. Some pharmacological experiments are performed in addition to immunostaining to bolster the conclusions from the biophysical studies. The paper has a significant impact in showing the role of Kv1.8 in determining utricular hair cell electrophysiological phenotypes.

Weaknesses:

(1) From previous work it is known that GK,L in type I hair cells has unusual ion permeation and pharmacological properties that differ greatly from type II hair cell conductances. Notably GK,L is highly permeable to Cs+ as well as K+ ions and is slightly permeable to Na+. It is blocked by 4-aminopyridine and divalent cations (Ba2+, Ca2+, Ni2+), enhanced by external K+ and modulated by cyclic GMP. The question arises-if Kv1.8 is a major player and pore-forming subunit in type I and type II cells (and cochlear inner hair cells as shown by Dierich et al. 2020) how are subunits modified to produce channels with very different properties? A role for Kv1.4 channels (gA) is proposed in type II hair cells based on previous findings in bird hair cells. However, hair cell specific partner interactions with Kv1.8 that result in GK, L in type I hair cells and Cs+ impermeable, inactivating currents in type II hair cells remain for the most part unexplored.

(2) Data from patch-clamp and immunocytochemistry experiments are not in close alignment. XE991 (Kv7 channel blocker) decreases remaining K+ conductance in type I and type II hair cells from null mice supporting the presence of Kv7 channels in hair cells (Fig. 7). Also, Holt et al. (2007) previously showed inhibition of GK,L in type I hair cells (but not delayed rectifier conductance in type II hair cells) using a dominant negative construct of Kv7.4 channels. However, immunolabelling indicates Kv7.4 channels on the inner face of calyx terminals adjacent to hair cells (Fig. 5). Some reconciliation of these findings is needed.

(3) A previous paper reported that a vestibular evoked potential was abnormal in Kv1.8-/- mice (Lee et al. 2013) as briefly mentioned (lines 94-95). It would be really interesting to know if any vestibular-associated behaviors and/or hearing loss were observed in the mice populations. If responses are compromised at the sensory hair cell level across different zones, degradation of balance function would be anticipated and should be elucidated.

Reviewer #3 (Public review):

Summary:

The systematic way in which path selection is parametrically investigated is the main contribution.

Strengths:

The authors have developed an impressive workflow to study gait and gaze in natural terrain. They are able to determine footholds and gaze points in the 3D world, and explore different path selections in the terrain.

Weaknesses:

The finding that walkers prefer less tortuous, demanding paths is hardly surprising, and from the data it is still not clear what actual visual features are used to choose among alternative routes or what the nature of the decision process is. The authors discuss energetic cost and other "factors" that might influence path selection, but as yet there is no way to express these ideas rigorously in such complex natural settings.

Reviewer #3 (Public review):

This paper analyses self-citation rates in the field of Neuroscience, comprising in this case, Neurology, Neuroscience and Psychiatry. Based on data from Scopus, the authors identify self-citations, that is, whether references from a paper by some authors cite work that is written by one of the same authors. They separately analyse this in terms of first-author self-citations and last-author self-citations. The analysis is well-executed and the analysis and results are written down clearly. The interpretation of some of the results might prove more challenging. That is, it is not always clear what is being estimated.

This issue of interpretability was already raised in my review of the previous revision, where I argued that the authors should take a more explicit causal framework. The authors have now revised some of the language in this revision, in order to downplay causal language. Although this is perfectly fine, this misses the broader point, namely that it is not clear what is being estimated. Perhaps it is best to refer to Lundberg et al. (2021) and ask the authors to clarify "What is your Estimand?" In my view, the theoretical estimands the authors are interested in are causal in nature. Perhaps the authors would argue that their estimands are descriptive. In either case, it would be good if the authors could clarify that theoretical estimand.

Finally, in my previous review, I raised the issue of when self-citations become "problematic". The authors have addressed this issue satisfactorily, I believe, and now formulate their conclusions more carefully.

Lundberg, I., Johnson, R., & Stewart, B. M. (2021). What Is Your Estimand? Defining the Target Quantity Connects Statistical Evidence to Theory. American Sociological Review, 86(3), 532-565. https://doi.org/10.1177/00031224211004187

Reviewer #3 (Public Review):

In this manuscript by Berrocal and coworkers, the authors do a deep dive into the transcriptional regulation of the eve gene in both an endogenous and ectopic background. The idea is that by looking at eve expression under non-native conditions, one might infer how enhancers control transcriptional bursting. The main conclusion is that eve enhancers have not evolved to have specific behaviors in the eve stripes, but rather the same rates in the telegraph model are utilized as control rates even under ectopic or 'de novo' conditions. For example, they achieve ectopic expression (outside of the canonical eve stripes) through a BAC construct where the binding sites for the TF Giant are disrupted along with one of the eve enhancers. Perhaps the most general conclusion is that burst duration is largely constant throughout at ~ 1 - 2 min. This conclusion is consistent with work in human cell lines that enhancers mostly control frequency and that burst duration is largely conserved across genes, pointing to an underlying mechanistic basis that has yet to be determined.

Reviewer #3 (Public review):

Summary:

Mitochondrial injury activates eiF2α kinases - PERK, GCN2, HRI, and PKR - which collectively regulate the Integrated Stress Response (ISR) to preserve mitochondrial function and integrity. Previous work has demonstrated that stress-induced and pharmacologic stress-independent ISR activation promotes adaptive mitochondrial elongation via the PERK and GCN2 kinases, respectively. Here, the authors demonstrate that pharmacologic ISR inducers of HRI and GCN2 enhance mitochondrial elongation and suppress mitochondrial fragmentation in two disease models, illustrating the therapeutic potential of pharmacologic ISR activators. Specifically, the authors first used an innovative ISR translational reporter to screen for nucleoside mimetic compounds that induce ISR signaling and identified two compounds, 0357 and 3610, that preferentially activate HRI. Using a mitochondrial-targeted GFP MEF cell line, the authors next determined that these compounds (as well as the GCN2 activator, halofuginone) enhance mitochondrial elongation in an ISR-dependent manner. Moreover, pretreatment of MEFs with these ISR kinase activators suppressed pathological mitochondrial fragmentation caused by a calcium ionophore. Finally, pharmacologic HRI and GCN2 activation were found to preserve mitochondrial morphology in human fibroblasts expressing a pathologic variant in MFN2, a defect that leads to mitochondrial fragmentation and is a cause of Charcot Marie Tooth Type 2A disease.

Strengths:

This well-written manuscript has several notable strengths, including the demonstration of the potential therapeutic benefit of ISR modulation. New chemical entities with which to further interrogate this stress response pathway are also reported. In addition, the authors used an elegant screen to isolate compounds that selectively activate the ISR and identify which of the four kinases was responsible for activation. Special attention was also paid to a thorough evaluation of the effect of their compounds on other stress response pathways (i.e. the UPR, and heat and oxidative stress responses), thereby minimizing the potential for off-target effects. The implementation of automated image analysis rather than manual scoring to quantify mitochondrial elongation is not only practical but also adds to the scientific rigor, as does the complementary use of both the calcium ionophore and MFN2 models to enhance confidence and the broad therapeutic potential for pharmacology ISR manipulation.

Weaknesses:

The only minor concerns are with regard to effects on cell health and the timing of pharmacological administration.

Reviewer #3 (Public review):

Summary:

Dong et al tackle the mechanism leading to polarized migration of tracheal progenitors during Drosophila metamorphosis. This work fits in the stem cell research field and its crucial role in growth and regeneration. While it has been previously reported by others that tracheal progenitors migrate in response to FGF and Insulin signals emanating from the fat body in order to regenerate tracheal branches, the authors identified an additional mechanism involved in the communication of the fat body and tracheal progenitors.

Strengths:

The data presented were obtained using a wide range of complementary techniques combining genetics, molecular biology, quantitative, and live imaging techniques. The authors provide convincing evidence that the fat body, found in close proximity to the trachea, secrete vesicles containing the Upd2 cytokine that reach tracheal progenitors leading to JAK-STAT pathway activation, which is required for their polarized migration. In addition, the authors show that genes regulating planar cell polarity are also involved in this inter-organ communication.

Weaknesses:

(1) Affecting this inter-organ communication leads to a quite discrete phenotype where polarized migration of tracheal progenitors is partially compromised. The study lacks data showing the consequences of this phenotype on the final trachea morphology, function, and/or regeneration capacities at later pupal and adult stages. This could potentially increase the significance of the findings.

(2) The conclusions of this paper are mostly well supported by data, but some aspects of data acquisition and analysis need to be clarified and corrected, such as recurrent errors in plotting of tracheal progenitor migration distance that mislead the reader regarding the severity of the phenotype.

(3) The number of tracheal progenitors should be assessed since they seem to be found in excess in some genetic conditions that affect their behavior. A change in progenitor number could lead to crowding, thus affecting their localization rather than migration capacities, thereby changing the proposed interpretation. In addition, the authors show data suggesting a reduced progenitor migration speed when the fat body is affected, which would also be consistent with a crowding of progenitors.

(4) The authors claim that tracheal progenitors display a polarized distribution of PCP proteins that is controlled by JAK-STAT signaling. However, this conclusion is made from a single experiment that is not quantified and for which there is no explanation of how the plot profile measurements were performed. It also seems that this experiment was done only once. Altogether, this is insufficient to support the claim. Finally, a quantification of the number of posterior edges presenting filopodia rather than the number of filopodia at the anterior and posterior leading edges would be more appropriate.

(5) The authors demonstrate that Upd2 is transported through vesicles from the fat body to the tracheal progenitors where they propose they are internalized. Since the Upd2 receptor Dome ligand binding sites are exposed to the extracellular environment, it is difficult to envision in the proposed model how Upd2 would be released from vesicles to bind Dome extracellularly and activate the JAK-STAT pathway. Moreover, data regarding the mechanism of the vesicular transport of Upd2 are not fully convincing since the PLA experiments between Upd2 and Rab5, Rab7, and Lbm are not supported by proper positive and negative controls and co-immunoprecipitation data in the main figure do not always correlate to the raw data.

Reviewer #3 (Public review):

Summary:

In this study, Sanchez-Leon et al. combined extracellular recordings of Purkinje cell activity in awake and anesthetized mice with juxtacellular recordings and Purkinje cell staining to link Purkinje cell orientation to their stimulation response. The authors find a relationship between neuron orientation and firing rate, dependent on stimulation type (anodal/cathodal). They also show the effects of stimulation intensity and rebound effects.

Strengths:

Overall, the work is methodologically sound and the manuscript is well written. The authors have taken great care to explain their rationale and methodological choices.

Weaknesses:

My only reservation is the lack of reporting of the precise test statistics, p-values, and multiple comparison corrections. The work would benefit from adding this and other information.

Major Comments:

(1) The authors should report the exact test statistics. These are missing for all comparisons and hinder the reader from understanding what exactly was tested for each of the experiments. For example, having the exact test statistics would help better understand the non-significant differences in Figure 1h where there is at least a numeric difference in CS firing rate during tDCS.

(2) Did the authors apply any corrections for multiple comparisons? Generally, it would be helpful if they could clarify the statistical analysis (which values were subjected to the tests, how many tests were performed for each question, etc.).

(3) The relationship shown in Figure 2g seems to be influenced by the two outliers. Have the authors confirmed the results using a robust linear regression method?

(4) The authors conclude that tDCS modulates vermal PCs more than Crus I/II PCs - but they don't seem to test this statistically. It would be helpful to submit the firing rate change values to an actual statistical test to conclude this directly from the data

Reviewer #3 (Public review):

Experimentally, this study provides sufficient data to support the authors' conclusion that MinD dimerization but not ATPase activity is both necessary and sufficient for concentrating it and its binding partner, the division inhibitor MinC, at cell poles. Biochemical data appears to be rigorously acquired and includes proper controls. Although cytological data are consistent with the authors' model, quantitative information on MinD localization in a statistically relevant set of cells is missing (e.g. Figure 2B). 

The study's other major conclusion, as outlined in their discussion, that a reaction-diffusion model explains MinD localization in wild-type cells, is unsubstantiated. If they would like to make this a major conclusion of the final manuscript, they will need to include modeling that takes into account biochemical and cytological data. 

From a presentation perspective, the manuscript is challenging to read and will require substantial rewriting and revision prior to publication.

Reviewer #3 (Public review):

The manuscript reports data collected in awake toddlers recording BOLD while watching videos. The authors analyse the BOLD time series using two different statistical approaches, both very complex but that do not require any a priori determination of the movies features or contents to be associated with regressors. The two main messages are that 1) toddlers have occipital visual areas very similar to adults, given that a SRM model derive from adults BOLD is consistent with the infant brains as well; 2) the retinotopic organization and the spatial frequency selectivity of the occipital maps derived by applying correlation analysis are consistent with the maps obtained by standard and conventional mapping.

Comments on revised version:

The authors did a thorough revision of the manuscript which now is very clear. All the missing information has been added and the technical issue clarified. I think that it is a very good and important paper.

Reviewer #3 (Public review):

Summary:

In the current manuscript, Piccin et al. identify a role for CRF type 1 receptors in morphine-induced social deficits using a 3-chamber social interaction task in mice. They demonstrate that pre-treatment with a CRFR1 antagonist blocks morphine-induced social deficits in male, but not female, mice, and this is associated with the CRF R1 antagonist blocking morphine-induced increases in PVN neuronal excitability in male but not female mice. They followed up by using a transgenic mouse CRFR1 knockout mouse line. CRFR1 genetic deletion also blocked morphine-induced social deficits, similar to the pharmacological approach, in male mice. This was also associated with morphine-induced increases in PVN neuronal excitability being blocked in CRFR1 knockout mice. Interestingly they found that the pharmacological antagonism of the CRFR1 specifically blocked morphine-induced increases in oxytocin/AVP neurons in the PVN in male mice.

Strengths:

The authors used both male and female mice where possible and the studies were fairly well controlled. The authors provided sufficient methodological detail and detailed statistical information. They also examined measures of locomotion in all of the behavioral tasks to separate changes in sociability from overall changes in locomotion. The experiments were well thought out and well controlled. The use of both the pharmacological and genetic approaches provides converging lines of evidence for the role of CRFR1 in morphine-induced social deficits. Additionally, they have identified the PVN as a potential site of action for these CRFR1 effects.

Weaknesses:

While the authors included both sexes they analyzed them independently. This was done for simplicity's sake as they have multiple measures but there are several measures where the number of factors is reduced and the inclusion of sex as a factor would be possible. Additionally, single doses of both the CRFR1 antagonist and morphine are used within an experiment without justification for the doses. In fact, a lower dose of morphine was needed for the genetic CRFR1 mouse line. This would suggest that the dose of morphine being used is likely causing some aversion that may be more present in the females, as they have lower overall time in the ROI areas of both the object and the mouse following morphine exposure. As for the discussion, the authors do not sufficiently address why CRFR1 has an effect in males but not females and what might be driving that difference, or why male and female mice have different distribution of PVN cell types during the recordings. Additionally, the authors attribute their effect to CRF and CRFR1 within the PVN but do not consider the role of extrahypothalamic CRF and CRFR1. While the PVN does contain the largest density of CRF neurons there are other CRF neurons, notably in the central amygdala and BNST, that have been shown to play important roles in the impact of stress on drug-related behavior. This also holds true for the expression of CRFR1 in other regions of the brain, including the VTA, which is important for drug-related behavior and social behavior. The treatments used in the current manuscript were systemic or brain-wide deletion of CRFR1. Therefore, the authors should consider that the effects could be outside the PVN.

Reviewer #3 (Public Review):

Summary:

Kearns et al. explored a computational approach DASAr to identify stable peptide epitopes on SARS-CoV-2 proteins. They find that the computational approach has a high success rate at identifying stable and soluble peptides that may reserve the native conformation. The approach identified multiple peptides in Spike, Nucleoprotein, Membrane, and Envelope proteins of SARS-CoV-2. Most surprisingly, a high prevalence of IgM response is to recognize a newly exposed Membrane epitope, M1. Anti-M1 IgM titer is associated with a protective anti-Spike titer, severe disease and long COVID. The data also indicate that anti-M1 IgM may arise from T cell-independent B cell activation.

Strengths:

The computational approach can be widely applied to study antibody epitopes in many pathogens. The observations from this study provide clues to further understanding the role of anti-M1 response and the mechanisms of anti-M1 IgM response to SARS-CoV-2 associated diseases.

Weaknesses:

A subset of the conclusions of this paper are well supported by data, but some statements and analyses need to be clarified, revised, and extended.

Reviewer #3 (Public Review):

Vazquez-Fernandez et al. present a comprehensive and detailed analysis of the S. cerevisiae APC/C complex, providing new insights into its structure and function. The authors determined the medium-resolution structures of three recombinant S. cerevisiae APC/C complexes, including unphosphorylated apo-APC/C (4.9 Å), the ternary APC/CCDH1-substrate complex (APC/CCDH1:Hsl1 , 4.0 Å), and phosphorylated apo-APC/C (4.4 Å). Prior structures of human, E. cuniculi, S. cerevisiae, and S. pombe APC/C subunits, as well as AlphaFold2 predictions were used to guide model building. Although the determined structures are not sufficient to fully explain the molecular mechanism of APC/C activation and regulation in S. cerevisiae, they provide valuable insights into the similarities and differences with the human complex, shedding light on the conserved and divergent features of APC/C function.

The manuscript synthesizes the structural analysis of the APC/C complex in S. cerevisiae, with literature into a cohesive and clear picture of the complex's structure and function. It is well-written and clear, making the complex biology of the APC/C complex accessible to a wide range of readers. The complex forms a triangular shape, with a central cavity surrounded by two modules: the TPR lobe and the platform module. The TPR lobe consists of three TPR proteins (APC3, APC6, and APC8), which stack on top of each other to form a quasi-symmetric structure. The platform module is composed of the large APC1 subunit, together with APC4 and APC5. The authors also analyzed the structure of several smaller subunits that are involved in regulating the activity of the APC/C complex and showed their structural similarities to and discrepancies from their human counterparts. These subunits, including CDC26/APC12, SWM1/APC13, APC9, and MND2/APC15, form extended, irregular structures that simultaneously contact multiple large globular APC/C subunits.

While the authors report the similarity between the overall structure of S. cerevisiae and human APC/C complexes, they also found two unexpected differences. First, in the S. cerevisiae apo-complex, the E2 binding site on APC11RING is accessible, whereas, in humans, it requires CDH1 binding. Second, a structural element similar to the human APC1 auto-inhibitory segment is missing in S. cerevisiae. In humans, the phosphorylation-dependent displacement of this segment allows CDC20 binding to APC/C. In S. cerevisiae, the binding requires phosphorylation however the structures reported here are suggestive that this could involve a different (presently unknown) mechanism. These structural insights highlight the importance of understanding the species-specific features of APC/C function.

Strengths:

The manuscript does a great job of revealing new structures.

Opportunity for increasing impact: It would have been nice if some functional differences were demonstrated, for example regarding the mechanism of CDC20 binding, and the comparison between apo-APC/C and ternary APC/CCDH1:Hsl1 does not explain the molecular activation mechanism of S. cerevisiae APC/C. Nonetheless, the authors nicely integrate their data with well-established literature on the similarities and differences between yeast and human systems.

Reviewer #3 (Public review):

Summary:

Lin et al., performed a scRNA-seq-based study of tea roots, as an example, to elucidate the biosynthesis and regulatory processes for theanine, a root-specific secondary metabolite, and established the first map of tea roots comprised of 8 cell clusters. Their findings contribute to deepening our understanding of the regulation of the synthesis of important flavor substances in tea plant roots. They have presented some innovative ideas.

Comment on revised version:

The reviewer has addressed all my concerns and I have no further comments.

Reviewer #3 (Public review):

Summary:

This paper identifies GTSE1 as a potential substrate of cyclin D1-CDK4/6 and shows that GTSE1 correlates with cancer prognosis, probably through an effect on cell proliferation. The main problem is that the phosphorylation analysis relies on the over-expression of cyclin D1. It is unclear if the endogenous cyclin D1 is responsible for any phosphorylation of GTSE1 in vivo, and what, if anything, this moderate amount of GTSE1 phosphorylation does to drive proliferation.

Strengths:

There are few bonafide cyclin D1-Cdk4/6 substrates identified to be important in vivo so GTSE1 represents a potentially important finding for the field. Currently, the only cyclin D1 substrates involved in proliferation are the Rb family proteins.

Weaknesses:

The main weakness is that it is unclear if the endogenous cyclin D1 is responsible for phosphorylating GTSE1 in the G1 phase. For example, in Figure 2G there doesn't seem to be a higher band in the phos-tag gel in the early time points for the parental cells. This experiment could be redone with the addition of palbociclib to the parental to see if there is a reduction in GTSE1 phosphorylation and an increase in the amount in the G1 phase as predicted by the authors' model.

The experiments involving palbociclib do not disentangle cell cycle effects. Adding Cdk4 inhibitors will progressively arrest more and more cells in the G1 phase and so there will be a reduction not just in Cdk4 activity but also in Cdk2 and Cdk1 activity. More experiments, like the serum starvation/release in Figure 2G, with synchronized populations of cells would be needed to disentangle the cell cycle effects of palbociclib treatment.

It is unclear if GTSE1 drives the G1/S transition. Presumably, this is part of the authors' model and should be tested.

The proliferation assays need to be more quantitative. Figure 4B should be plotted on a log scale so that the slope can be used to infer the proliferation rate of an exponentially increasing population of cells. Figure 4c should be done with more replicates and error analysis since the effects shown in the lower right-hand panel are modest.

Reviewer #3 (Public review):

Summary:

In this study, the authors aim to uncover how 3D tongue direction is represented in the Motor (M1o) and Somatosensory (S1o) cortex. In non-human primates implanted with chronic electrode arrays, they use X-ray-based imaging to track the kinematics of the tongue and jaw as the animal is either chewing food or licking from a spout. They then correlate the tongue kinematics with the recorded neural activity. Using linear regressions, they characterize the tuning properties and distributions of the recorded population during feeding and licking. Then, they recharacterize the tuning properties after bilateral lidocaine injections in the two sensory branches of the trigeminal nerve. They report that their nerve block causes a reorganization of the tuning properties. Overall, this paper concludes that M1o and S1o both contain representations of the tongue direction, but their numbers, their tuning properties, and susceptibility to perturbed sensory input are different.

Strengths:

The major strengths of this paper are in the state-of-the-art experimental methods employed to collect the electrophysiological and kinematic data.

Weaknesses:

However, this paper has a number of weaknesses in the analysis of this data.

It is unclear how reliable the neural responses are to the stimuli. The trial-by-trial variability of the neural firing rates is not reported. Thus, it is unclear if the methods used for establishing that a neuron is modulated and tuned to a direction are susceptible to spurious correlations. The authors do not use shuffling or bootstrapping tests to determine the robustness of their fits or determining the 'preferred direction' of the neurons. This weakness colors the rest of the paper.

The authors compare the tuning properties during feeding to those during licking but only focus on the tongue-tip. However, the two behaviors are different also in their engagement of the jaw muscles. Thus many of the differences observed between the two 'tasks' might have very little to do with an alternation in the properties of the neural code - and more to do with the differences in the movements involved. Many of the neurons are likely correlated with both Jaw movements and tongue movements - this complicates the interpretations and raises the possibility that the differences in tuning properties across tasks are trivial.

The population analyses for decoding are rudimentary and provide very coarse estimates (left, center, or right), it is also unclear what the major takeaways from the population decoding analyses are. The reduced classification accuracy could very well be a consequence of linear models being unable to account for the complexity of feeding movements, while the licking movements are 'simpler' and thus are better accounted for.

The nature of the nerve block and what sensory pathways are being affected is unclear - the trigeminal nerve contains many different sensory afferents - is there a characterization of how effectively the nerve impulses are being blocked? Have the authors confirmed or characterized the strength of their inactivation or block, I was unable to find any electrophysiological evidence characterizing the perturbation.

Overall, while this paper provides a descriptive account of the observed neural correlations and their alteration by perturbation, a synthesis of the observed changes and some insight into neural processing of tongue kinematics would strengthen this paper.

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