Reviewer #1 (Public Review):

The Calcium Homeostasis Modulators (CALHM) are a family of large pore channels, of which the physiological role of CALHM1 and 3 is well understood, in particular their key role in taste sensation via the release of the neurotransmitter ATP. The activation mechanism of CALHM1 involves membrane depolarization and a decrease in extracellular Ca concentration, allowing the passage of large cellular metabolites. However, the activation mechanism and physiological roles of other family members are much less well understood. Many structures of homomeric CALHM proteins have been determined, revealing distinct oligomeric assemblies despite a common transmembrane domain topology. CALHM1 and 3 have been shown functionally to form heteromeric assemblies with properties distinct from those of homomeric CALHM1. However, the structural basis of heteromeric CALHM1 and 3 remains unexplored.

In this paper, Drozdzyk et al. present an important study on the structures of heteromeric channels composed of CALHM2 and CALHM4, extending the structural understanding of the CALHM family beyond homomeric channels. The study relies primarily on cryo-EM. Despite the inherent challenges of structural determination due to the similar structural features of CALHM2 and CALHM4, the authors innovatively use synthetic nanobodies to distinguish between the subunits. Their results show a broad distribution of different heteromeric assemblies, with CALHM4 conformation similar to its homomeric form and CALHM2 conformation influenced by its proximity to CALHM4, and provide detailed insights into the interaction between CALHM2 and CALHM4.

The manuscript is well-structured and presents clear results that support the conclusions drawn. The discovery of heteromeric CALHM channels, although currently limited to an overexpressed system, represents a significant advance in the field of large-pore channels and will certainly encourage further investigation into the physiological relevance and roles of heteromeric CALHM channels. The manuscript would benefit from further insight into the functional properties of these heteromeric channels. However, this is not a weakness as the identification of precise activation stimuli for CALHM2 and 4 is beyond the scope of this work.

A challenge noted is the wide distribution of heteromeric assemblies in the 3D classification, resulting in insufficient particles for high-resolution structure determination of each assembly. The authors choose to combine particles from assemblies with 2-4 copies of CALHM4, which reveals the interface between CALHM2 and 4 but may compromise the quality of structural details. I recommend an alternative data processing strategy. First, refine particles with 2-4 CALHM4 subunits with symmetry imposed. This is followed by symmetry expansion, signal subtraction of two adjacent subunits, and subsequent classification and refinement of the subtracted particles. This approach, while not guaranteed, can potentially provide a clearer definition of CALHM2 and CALHM4 interfaces and show whether CALHM2 subunits adopt different conformations based on their proximity to CALHM4 subunits.

Reviewer #1 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #1 (Public Review):

Summary:

This paper provides a straightforward mechanism of how mycobacterial cAMP level is increased under stressful conditions and shows that the increase is important for the survival of the bacterium in animal hosts. The cAMP level is increased by decreasing the expression of an enzyme that degrades cAMP.

Strengths:

The paper shows that under different stresses the response regulator PhoP represses a phosphodiesterase (PDE) that degrades cAMP specifically. Identification of<br /> PhoP as a regulator of cAMP is significant progress in understanding Mtb pathogenesis, as increase in cAMP apparently increases bacterial survival upon infection. On the practical side, reduction of cAMP by increasing PDE can be a means to attenuate the growth of the bacilli. The results have wider implications since PhoP is implicated in controlling diverse mycobacterial stress responses and many bacterial pathogens modulate host cell cAMP level. The results here are straightforward, internally consistent, and of both theoretical and applied interests. The results also open considerable future work, especially how increases in cAMP level help to increase survival of the pathogen.

Weaknesses:

It is not clear whether PhoP-PDE Rv0805 is the only pathway to regulate cAMP level under stress.

Reviewer #1 (Public Review):

Summary:

This work describes the mechanism of protein disaggregation by the ClpL AAA+ protein of Listeria monocytogenes. Using several model subtrate proteins the authors first show that ClpL possesses a robust disaggregase activity that does not further require the endogenous DnaK chaperone in vitro. In addition, they found that ClpL is more thermostable than the endogenous L. monocytogenes DnaK and has the capacity to unfold tightly folded protein domains. The mechanistic basis for the robust disaggregase activity of ClpL was also dissected in vitro and in some cases, supported by in vivo data performed in chaperone-deficient E. coli strains. The data presented show that the two AAA domains, the pore-2 site and the N-terminal domain (NTD) of ClpL are critical for its disaggregase activity. Remarkably, grafting the NTD of ClpL to ClpB converted ClpB into an autonomous disaggregase, highlighting the importance of such a domain in the DnaK-independent disaggregation of proteins. The role of the ClpL NTD domain was further dissected, identifying key residues and positions necessary for aggregates recognition and disaggregation. Finally, using sets of SEC and negative staining EM experiments combined with conditional covalent linkages and disaggregation assays the authors found that ClpL shows significant structural plasticity, forming dynamic hexameric and heptameric active single rings that can further form higher assembly states via their middle domains.

Strengths:

The manuscript is well written and the experimental work well executed. It contains a robust and complete set of in vitro data that push further our knowledge of such important disaggregases. It shows the importance of the atypical ClpL N-terminal domain in the disaggregation process as well as the structural malleability of such AAA+ proteins. More generally, this work expands our knowledge of heat resistance in bacterial pathogens.

Weaknesses:

There is no specific weakness in this work, although it would have helped to have a drawing model showing how ClpL performs protein disaggregation based on their new findings. The function of the higher assembly states of ClpL remains unresolved and will need further extensive research. Similarly, it will be interesting in the future to see whether the sole function of the plasmid encoded ClpL is to cope with general protein aggregates under heat stress.

Joint Public Review:

Summary:

Previously, this group showed that Tgfbr1 regulates the reorganization of the epiblast and primitive streak into the chordo-neural hinge and tailbud during the trunk-to-tail transition. Gdf11 signaling plays a crucial role in orchestrating the transition from trunk to tail tissues in vertebrate embryos, including the reallocation of axial progenitors into the tailbud and Tgfbr1 plays a key role in mediating its signaling activity. Progenitors that contribute to the extension of the neural tube and paraxial mesoderm into the tail are located in this region. In this work, the authors show that Tgfbr1 also regulates the reorganization of the posterior primitive streak/base of allantois and the endoderm as well.

By analyzing the morphological phenotypes and marker gene expression in Tgfbr1 mutant mouse embryos, they show that it regulates the merger of somatic and splanchnic layers of the lateral plate mesoderm, the posterior streak derivative. They also present evidence suggesting that Tgfbr1 acts upstream of Isl1 (key effector of Gdf11 signaling for controlling differentiation of lateral mesoderm progenitors) and regulates the remodelling of the major blood vessels, the lateral plate mesoderm and endoderm associated with the trunk-to-tail transition. Through a detailed phenotypic analysis, the authors observed that, similarly to Isl1 mutants, the lack of Tgfbr1 in mouse embryos hinders the activation of hindlimb and external genitalia maker genes and results in a failure of lateral plate mesoderm layers to converge during tail development. As a result, they interpret that ventral lateral mesoderm, which generates the peri cloacal mesenchyme and genital tuberculum, fails to specify.

They also show defects in the morphogenesis of the dorsal aorta at the trunk/tail juncture, resulting in an aberrant embryonic/extraembryonic vascular connection. Endoderm reorganization defects following abnormal morphogenesis of the gut tube in the Tgfbr1 mutants cause failure of tailgut formation and cloacal enlargement. Thus, Tgfbr1 activity regulates the morphogenesis of the trunk/tail junction and the morphogenetic switch in all germ layers required for continuing post-anal tail development. Taken together with the previous studies, this work places Gdf11/8 - Tgfbr1 signaling at the pivot of trunk-to-tail transition and the authors speculate that critical signaling through Tgfbr1 occurs in the posterior-most part of the caudal epiblast, close to the allantois.

Strengths:

The data shown is solid with excellent embryology/developmental biology. This work demonstrates meticulous execution and is presented in a comprehensive and coherent manner. Although not completely novel, the results/conclusions add to the known function of Gdf11 signaling during the trunk-to-tail transition.

Weaknesses:

The authors rely on the expression of a small number of key regulatory genes to interpret the developmental defects. The alternative possibilities remain to be ruled out thoroughly. The manuscript is also quite descriptive and would benefit from more focused highlighting of the novelty regarding the absence of Tgfbr1 in the mouse embryo. They should also strengthen some of their conclusions with more details in the results.

Reviewer #1 (Public Review):

Summary:<br /> In the present study, Rincon-Torroella et al. developed ME3BP-7, a microencapsulated formulation of 3BP, as an agent to target MCT1 overexpressing PDACs. They provided evidence showing the specific killing of PDAC cells with MCT1 overexpressing in vitro, along with demonstrating the safety and anti-tumor efficacy of ME3BP-7 in PDAC orthotopic mouse models.

Strengths:<br /> * Developed a novel agent.<br /> * Well-designed experiments and an organized presentation of data that support the conclusions drawn.

Weaknesses:<br /> There are some minor issues that could enhance the clarity and completeness of the study:

(1) Statistical results should be visually presented in Figure 4 and Figure S1.

(2) Given the tumor heterogeneity and the identification of focal high expression of MCT1 in Figure 7 and Figure S5B, it is suggested that the authors include the results of immunohistochemical (IHC) analysis of MCT1 expression in both control and ME3BP-7 treated tumor tissues. This addition may offer insight into whether the remaining tumors are composed of PDAC cells with negative MCT1 expression, while the cells with relatively high levels of MCT1 expression were eliminated by ME3BP-7 treatment.

(3.)The authors are encouraged to discuss the future directions for improving the efficacy of this study. For example, exploring the combination of ME3BP-7 with a glutaminase-1 inhibitor (PMID 37891897) could be a valuable avenue for further research.

Reviewer #1 (Public Review):

Summary:

This work presents an in-depth characterization of the factors that influence the structural dynamics of the Clostridium botulinum guanidine-IV riboswitch (riboG). Using a single-molecule FRET, the authors demonstrate that riboG undergoes ligand and Mg2+ dependent conformational changes consistent with the dynamic formation of a kissing loop (KL) in the aptamer domain. Formation of the KL is attenuated by Mg2+ and Gua+ ligand at physiological concentrations as well as the length of the RNA. Interestingly, the KL is most stable in the context of just the aptamer domain compared to longer RNAs capable of forming the terminator stem. To attenuate transcription, binding of Gua+ and formation of the KL must occur rapidly after transcription of the aptamer domain but before transcription of the rest of the terminator stem.

Strengths:

(1) Single-molecule FRET microscopy is well suited to unveil the conformational dynamics of KL formation and the authors provide a wealth of data to examine the effect of the ligand and ions on riboswitch dynamics. The addition of complementary transcriptional readthrough assays provides further support for the author's proposed model of how the riboswitch dynamics contribute to function.

(2) The single-molecule data strongly support that the effect of Gua+ ligand and Mg2+ influence the RNA structure differently for varying lengths of the RNA. The authors also demonstrate that this is specific for Mg2+ as Na+ and K+ ions have little effect.

(3) The PLOR method utilized is clever and well adapted for both dual labeling of RNAs and examining RNA at various lengths to mimic co-transcriptional folding. Using PLOR, they demonstrate that a change in the structural dynamics and ligand binding can occur after the extension of the RNA transcript by a single nucleotide. Such a tight window of regulation has intriguing implications for kinetically controlled riboswitches.

Weaknesses:

(1) The authors use only one mutant to confirm that their FRET signal indicates the formation of the KL. Importantly, this mutation does not involve the nucleotides that are part of the KL interaction. It would be more convincing if the authors used mutations in both strands of the KL and performed compensatory mutations that restore base pairing. Experiments like this would solidify the structural interpretation of the work, particularly in the context of the full-length riboG RNA or in the co-transcriptional mimic experiments, which appear to have more conformational heterogeneity.

(2) The existence of the pre-folded state (intermediate FRET ~0.5) is not well supported in their data and could be explained by an acquisition artifact. The dwell times are very short often only a single frame indicating that there could be a very fast transition (< 0.1s) from low to high FRET that averages to a FRET efficiency of 0.5. To firmly demonstrate that this intermediate FRET state is metastable and not an artifact, the authors need to perform measurements with a faster frame rate and demonstrate that the state is still present.

(3) The PLOR method employs a non-biologically relevant polymerase (T7 RNAP) to mimic transcription elongation and folding near the elongation complex. T7 RNAP has a shorter exit channel than bacterial RNAPs and therefore, folding in the exit channel may be different between different RNAPs. Additionally, the nascent RNA may interact with bacterial RNAP differently. For these reasons, it is not clear how well the dynamics observed in the T7 ECs recapitulate riboswitch folding dynamics in bacterial ECs where they would occur in nature.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Zeng and Staley provide a valuable analysis of the molecular requirements for the export of a reporter mRNA that contains a lariat structure at its 5' end in the budding yeast S. cerevisiae. The authors provide evidence that this is regulated by the main mRNA export machinery (Yra1, Mex67, Nab2, Npl3, Tom1, and Mlp1). Of note, Mlp1 has been mainly implicated in the nuclear retention of unspliced pre-mRNA (i.e. quality control), and relatively little has been done to investigate its role in mRNA export in budding yeast.

Strengths:

There is relatively little information in the current literature about the nuclear export of splicing intermediates. This paper provides one of the first analyses of this process and dissects the molecular components that promote this form of RNA export. Overall, the strength of the data presented in the manuscript is solid. The paper is well written and the message is clear and of general interest to the mRNA community.

Weaknesses:

There are three problems with the paper, although these are not major and likely would not affect the final model as most aspects of the molecular details are confirmed by multiple complementary assays.

(1) The brG reporter produces both unspliced pre-mRNA and a lariat-containing intermediate RNA. Based on the primer extension assay the authors claim that only 33% of the final product is in pre-mRNA form and that this "is insufficient to account for the magnitude of the cytoplasmic signal from the brG reporter (83%)". Nevertheless, it is possible that primer extension is incomplete or that the lariat-containing RNA is inaccessible for smFISH. The authors could easily perform a dual smFISH experiment (similar to Adivarahan et l., Molecular Cell 2018) where exon 1 is labelled with probes of one color, and the region that overlaps the lariat-containing intermediate is labelled with probes of a second color. If the authors are correct, then one-third of the smFISH foci should have both labels and the rest would have only the second label. This would also confirm that the latter (i.e. the lariat-containing RNAs) are exported to the cytoplasm. Using this approach, the authors could then show that MLP1-depletion (or depletion of any of the other factors) affect(s) one pool of RNAs (i.e. those that are lariat-containing) but not the other (i.e. pre-mRNA). Including these experiments would make the evidence for their model more convincing.

(2) In some cases, the number of smFISH foci appears to change drastically depending on the genetic background. This could either be due to the stochastic nature of mRNA expression between cells or reflect real differences between the genetic backgrounds that could alter the interpretation of the other observations.

(3) The authors state in the discussion that "the general mRNA export pathway transports discarded lariat intermediates into the cytoplasm". Although this appears to be the case for the reporters that are investigated in this paper, I don't think that the authors should make such a broad sweeping claim. It may be that some discarded lariat intermediates are exported to the cytoplasm while others are targeted for nuclear retention and/or decay.

Reviewer #1 (Public Review):

Summary:

The major result in the manuscript is the observation of the higher order structures in a cryoET reconstruction that could be used for understanding the assembly of toroid structures. The cross-linking ability of ZapD dimers result in bending of FtsZ filaments to a constant curvature. Many such short filaments are stitched together to form a toroid like structure. The geometry of assembly of filaments - whether they form straight bundles or toroid like structures - depends on the relative concentrations of FtsZ and ZapD.

Strengths:

In addition to a clear picture of the FtsZ assembly into ring-like structures, the authors have carried out basic biochemistry and biophysical techniques to assay the GTPase activity, the kinetics of assembly, and the ZapD to FtsZ ratio.

Weaknesses:

The discussion does not provide an overall perspective that correlates the cryoET structural organisation of filaments with the biophysical data.

The crosslinking nature of ZapD is already established in the field. The work carried out is important to understand the ring assembly of FtsZ. However, the availability of the cryoET observations can be further analysed in detail to derive many measurements that will help validate the model, and obtain new insights.

Reviewer #1 (Public Review):

Summary:

Hippo pathway activity is required for pancreas morphogenesis, but its role in endocrine pancreas function remains elusive. The author aims to study the function of the TEAD1 gene in b-cells.

Strengths:

The authors generated TEAD1 conditional knockout animals by crossing the TEAD1f/f mice with three Cre strains (RIP-Cre, Ins1-Cre, and MIP-CreERT). In all of them, the KO animals showed progressive loss of insulin secretion with normal beta cell mass. Further characterization of the animals indicated glucose-induced insulin secretion defect and increased beta cell proliferation rate. RNA-Seq and ChIP-Seq experiments identified Pdx1, MafA, and Glut2, etc. as direct targets of TEAD1, which might be responsible for the insulin secretion defect in the animals. Of interest, the authors also uncovered the cell cycle-related gene p16 as a direct target of TEAD1. Reduction of p16 is likely to drive the beta cell proliferation in the TEAD1 knockout model. Thus, they proposed that TEAD1 is a regulator of the proliferative quiescence process in beta cells. Overall, the evidence provided by the authors is highly relevant and supports their conclusion.

Weaknesses:

(1) The authors don't explicitly mention that some results appeared in a previous publication (https://doi.org/10.1093/nar/gkac1063) from them.

(2) The authors begin their story by introducing TEAD1 as part of the Hippo pathway. They showed Taz expression data in Figure 1. Did they do any experiments to detect Taz in their TEAD1 model? Did the authors detect any expression changes in CTGF following TEAD1 knockout? I could not see this changed. The phenotype characterization data presented here contrasts with what has been shown in TAZ b-cell knockout mice (https://doi.org/10.1101/2022.05.31.494216). Based on the data presented here, Hippo is not involved, which should at least be discussed in length.

(3) Figure 1B - TAZ staining looks different in the three-month age group.

(4) TEAD ChIP-seq data doesn't look very convincing to me. It's hard to tell whether those highlighted regions in Figures 3A and 5J were signals or background noise. Although the authors also performed ChIP-qPCR in MIN6, it's unclear whether these binding events occur in vivo. The analysis of ChIP-seq dataset is limited as well. How many peaks called? What proportion of differentially expressed genes are bound by TEAD1? Was TEAD1 also detectable at NGN3 and NEUROD1 gene regions? If acquiring enough cells is not possible, the authors could try CUT&RUN or CUT&Tag to improve the data quality.

(5) The authors should perform RNA-seq or gene expression studies in MIP-CreERT to confirm, which could help narrow down the actual targets of TEAD1 as well.

(6) Figure 6 - the experiment lacks a control: Ezh2 beta cell KO. In addition to p16, Ezh2, and PRC2 have other targets in beta-cells, the authors could not rule out the contribution of those to the phenotype, so the implication of this experiment is vague.

Reviewer #1 (Public Review):

Summary:

Ewing sarcoma is an aggressive pediatric cancer driven by the EWS-FLI oncogene. Ewing sarcoma cells are addicted to this chimeric transcription factor, which represents a strong therapeutic vulnerability. Unfortunately, targeting EWS-FLI has proven to be very difficult, and a better understanding of how this chimeric transcription factor works is critical to achieving this goal. Towards this perspective, the group had previously identified a DBD-𝛼4 helix (DBD) in FLI that appears to be necessary to mediate EWS-FLI transcriptomic activity. Here, the authors used multi-omic approaches, including CUT&tag, RNAseq, and MicroC to investigate the impact of this DBD domain. Importantly, these experiments were performed in the A673 Ewing sarcoma model where endogenous EWS-FLI was silenced, and EWS-FLI-DBD proficient or deficient isoforms were re-expressed (isogenic context). They found that the DBD domain is key to mediating EWS-FLI cis activity (at msat) and to generating the formation of specific TADs. Furthermore, cells expressing DBD-deficient EWS-FLI display very poor colony-forming capacity, highlighting that targeting this domain may lead to therapeutic perspectives.

Strengths:

The group has strong expertise in Ewing sarcoma genetics and epigenetics and also in using and analyzing this model (Theisen et al., 2019; Boone et al., 2021; Showpnil et al., 2022).

They aim at better understanding how EWS-FLI mediated its oncogenic activity, which is critical to eventually identifying novel therapies against this aggressive cancer.

They use the most recent state-of-the-art omics methods to investigate transcriptome, epigenetics, and genome conformation methods. In particular, Micro-C enables achieving up to 1kb resolved 3D chromatin structures, making it possible to investigate a large number of TADs and sub-TADs structures where EWS-FLI1 mediates its oncogenic activity.

They performed all their experiments in an Ewing sarcoma genetic background (A673 cells) which circumvents bias from previously reported approaches when working in non-orthologous cell models using similar approaches.

Weaknesses:

The main weakness comes from the poor reproducibility of Micro-C data. Indeed, it appears that the distances/clustering observed between replicates are typically similar or even larger than between biological conditions. For instance, in Figure 1B, I do not see any clustering when considering DBD1, DBD2, DBD+1, DBD+2.

Lanes 80-83: "KD replicates clustered together with DBD replicate 1 on both axes and with DBD replicate 2 on the y-axis. DBD+ replicates, on the other hand, clustered away from both KD and DBD replicates. These observations suggest that the global chromatin structure of DBD replicates is more similar to KD than DBD+ replicates."

When replacing DBD replicate 1 with DBD replicate 2, their statement would not be true anymore.

Additional replicates to clarify this aspect seem absolutely necessary since those data are paving the way for the entire manuscript.

Similarly:<br /> - In Figure 1C, how would the result look when comparing DBD2/KD2/DBD+2? Same when comparing DBD 1 with KD1 and DBD+1. Would the difference go in the same direction?<br /> - Figure 1D-E. How would these plots look like when comparing each replicate to each other's? How much difference would be observed when comparing, for instance, DBD1/DBD2 ? or DBD1/DBD+1?<br /> - Figure 2: again, how would these analyses look like when performing the analysis with only DBD1/DBD+1/KD1 or DBD2/DBD+2/KD?

Another major question is the stability of EWS-FLI DBD vs EWS-FLI DBD+ proteins. Indeed, it seems that they have more FLAG (i.e., EWS-FLI) peaks in the DBD+ condition compared to the DBD condition (Figure 2B). In the WB, FLAG intensities seem also higher (2/3 replicates) in DBD+ condition compared to the DBD condition (Figure S1B).

Would it be possible that DBD+ is just more expressed or more stable than DBD? The higher stability of the re-expressed DBD+ could also partially explain their results independently of the 3D conformational change. In other words, can they exclude that DBD+ and DBD binding are not related to their respective protein stability or their global re-expression levels?

Surprisingly, WB FLI bands in DBD+ conditions are systematically (3/3 replicates) fainter than in DBD conditions (Figure S1B). How do the authors explain these opposite results between FLI and FALG in the WB?

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors provide strong evidence that the cell surface E3 ubiquitin ligases RNF43 and ZNRF3, which are well known for their role in regulating cell surface levels of WNT receptors encoded by FZD genes, also target EGFR for degradation. This is a newly identified function for these ubiquitin ligases beyond their role in regulating WNT signaling. Loss of RNF43/ZNRF3 expression leads to elevated EGFR levels and signaling, suggesting a potential new axis to drive tumorigenesis, whereas overexpression of RNF43 or ZNRF3 decreases EGFR levels and signaling. Furthermore, RNF43 and ZNRF3 directly interact with EGFR through their extracellular domains.

Strengths:

The data showing that RNF43 and ZNRF3 interact with EGFR and regulate its levels and activity are thorough and convincing, and the conclusions are largely supported.

Weaknesses:

While the data support that EGFR is a target for RNF43/ZNRF3, some of the authors' interpretations of the data on EGFR's role relative to WNT's roles downstream of RNF43/ZNRF3 are overstated. The authors, perhaps not intentionally, promote the effect of RNF43/ZNRF3 on EGFR while minimizing their role in WNT signaling. This is the case in most of the biological assays (cell and organoid growth and mouse tumor models). For example, the conclusion of "no substantial activation of Wnt signaling" (page 14) in the prostate cancer model is currently not supported by the data and requires further examination. In fact, examination of the data presented here indicates effects on WNT/b-catenin signaling, consistent with previous studies.<br /> Cancers in which RNF43 or ZNRF3 are deleted are often considered to be "WNT addicted", and inhibition of WNT signaling generally potently inhibits tumor growth. In particular, treatment of WNT-addicted tumors with Porcupine inhibitors leads to tumor regression. The authors should test to what extent PORCN inhibition affects tumor (and APC-min intestinal organoid) growth. If the biological effects of RNF43/ZNRF3 loss are mediated primarily or predominantly through EGFR, then PORCN inhibition should not affect tumor or organoid growth.

Reviewer #1 (Public Review):

Wang and colleagues conducted a study to determine the neurotransmitter identity of all neurons in C. elegans hermaphrodites and males. They used CRISPR technology to introduce fluorescent gene expression reporters into the genomic loci of NT pathway genes. This approach is expected to better reflect in vivo gene expression compared to other methods like promoter- or fosmid-based transgenes, or available scRNA datasets. The study presents several noteworthy findings, including sexual dimorphisms, patterns of NT co-transmission, neuronal classes that likely use NTs without direct synthesis, and potential identification of unconventional NTs (e.g. betaine releasing neurons). The data is well-described and critically discussed, including a comparison with alternative methods. Although many of the observations and proposals have been previously discussed by the Hobert lab, the current study is particularly valuable due to its comprehensiveness. This NT atlas is the most complete and comprehensive of any nervous system that I am aware of, making it an extremely useful tool for the community.

Reviewer #1 (Public Review):

Summary:

Dong et al here have studied the impact of the small Ras-like GTPase Rab10 on the exocytosis of dense core vesicles (DVC), which are important mediators of neuropeptide signaling in the brain. They use optical imaging to show that lentiviral depletion of Rab10 in mouse hippocampal neurons in culture independent of the established defects in neurite outgrowth hamper DCV exocytosis. They further demonstrate that such defects are paralleled by changes in ER morphology and defective ER-based calcium buffering as well as reduced ribosomal protein expression in Rab10-depleted neurons. Re-expression of Rab10 or supplementation of exogenous L-leucine to restore defective neuronal protein synthesis rescues impaired DCV secretion. Based on these results they propose that Rab10 regulates DCV release by maintaining ER calcium homeostasis and neuronal protein synthesis.

Strengths:

This work provides interesting and potentially important new insights into the connection between ER function and the regulated secretion of neuropeptides via DCVs. The authors combine advanced optical imaging with light and electron microscopy, biochemistry, and proteomics approaches to thoroughly assess the effects of Rab10 knockdown at the cellular level in primary neurons. The proteomic dataset provided may be valuable in facilitating future studies regarding Rab10 function. This work will thus be of interest to neuroscientists and cell biologists.

Weaknesses:

While the main conclusions of this study are comparably well supported by the data, I see three major weaknesses:

(1) For some of the data the statistical basis for analysis remains unclear. I.e. is the statistical assessment based on N= number of experiments or n = number of synapses, images, fields of view etc.? As the latter cannot be considered independent biological replicates, they should not form the basis of statistical testing.

(2) As it stands the paper reports on three partially independent phenotypic observations, the causal interrelationship of which remains unclear. Based on prior studies (e.g. Mercan et al 2013 Mol Cell Biol; Graves et al JBC 1997) it is conceivable that defective ER-based calcium signaling and the observed reduction in protein synthesis are causally related. For example, ER calcium release is known to promote pS6K1 phosphorylation, a major upstream regulator of protein synthesis and ribosome biogenesis. Conversely, L-leucine supplementation is known to trigger calcium release from ER stores via IP3Rs. Given the reported impact of Rab10 on axonal transport of autophagosomes and, possibly, lysosomes via JIP3/4 or other mediators (see e.g. Cason and Holzbaur JCB 2023) and the fact that mTORC1, the alleged target of leucine supplementation, is located on lysosomes, which in turn form membrane contacts with the ER, it seems worth analyzing whether the various phenotypes observed are linked at the level of mTORC1 signaling.

(3) The claimed lack of effect of Rab10 depletion on SV exocytosis is solely based on very strong train stimulation with 200 Aps, a condition not very well suited to analyze defects in SV fusion. The conclusion that Rab10 loss does not impact SV fusion thus seems premature.

Reviewer #1 (Public Review):

Summary:

Zhang et al., investigated the relationship between monocular and binocular responses of V1 superficial-layer neurons using two-photon calcium imaging. They found a strong relationship in their data: neurons that exhibited a greater preference for one eye or the other (high ocular dominance) were more likely to be suppressed under binocular stimulation, whereas neurons that are more equivalently driven by each other (low ocular dominance) were more likely to be enhanced by binocular stimulation. This result chiefly demonstrates the relationship between ocular dominance and binocular responses in V1, corroborating what has been shown previously using electrophysiological techniques with now much finer spatial resolution. The binocular responses were well-fitted by a model that institutes divisive normalization between the eyes that accounts for both the suppression and enhancement phenomena observed in the subpopulation of binocular neurons. In so doing, the authors reify the importance of incorporating ocular dominance in computational models of binocular combination.

The conclusions of this paper are well supported by the data. The authors deftly contextualize these important findings in the literature while also acknowledging the limitations of the methodology employed. Future work would do well to combine the spatial power of 2P imaging with the temporal power of electrophysiology to assess ocular dominance-dependent binocular combination across the V1 laminar microcircuit.

Strengths:

The two-photon imaging technique used to resolve the activity of individual neurons within intact brain tissue grants a host of advantages. Foremost, two-photon imaging confers considerably high spatial resolution. As a result, the authors were able to sample and analyze the activity from thousands of verified superficial-layer V1 neurons. The animal model used, awake macaques, is also highly relevant for the study of binocular combination. Macaques, like humans, are binocular animals, meaning they have forward-facing eyes that confer overlapping visual fields. Importantly, macaque V1 is organized into cortical columns that process specific visual features from the separate eyes just like in humans. In combination with a powerful imaging technique, this allowed the authors to evaluate the monocular and binocular response profiles of V1 neurons that are situated within neighboring ocular dominance columns, a novel feat. To this aim, the approach was well-executed and should instill confidence in the notion that V1 neurons combine monocular information in a manner that is dependent on the strength of their ocular dominance.

Weaknesses:

This study suffers no major weaknesses. The authors address the limitations of the methodology and have calibrated the interpretations accordingly.

Reviewer #1 (Public Review):

Summary:

This study examines lipid profiles in cancer patients treated with the neurotoxic chemotherapy paclitaxel. Multiple methods, including machine learning as well as more conventional statistical modelling, were used to classify lipid patterns before and after paclitaxel treatment and in conjunction with neuropathy status. Lipid profiles before and after paclitaxel therapy were analysed from 31 patients. The study aimed to characterize from the lipid profile if plasma samples were collected pre-paclitaxel or post-paclitaxel and their relevance to neuropathy status. Sphingolipids including sphinganine-1-phosphate (SA1P) differed between patients with and without neuropathy. To examine the potential role of SA1P, it was applied to murine primary sensory neuron cultures, and produced calcium transients in a proportion of neurons. This response was abolished by the application of a TRPV1 antagonist. The number of neurons responding to SA1P was partially reduced by the sphingosine 1-phosphate receptor (S1PR1) modulator fingolimod.

Strengths:

The strengths of this study include the use of multiple methods to classify lipid patterns and the attempt to validate findings from the clinical cohort in a preclinical model using primary sensory neurons.

Weaknesses:

There are a number of weaknesses in the study. The small sample size is a significant limitation of the study. Out of 31 patients, only 17 patients were reported to develop neuropathy, with significant neuropathy (grade 2/3) in only 5 patients. The authors acknowledge this limitation in the results and discussion sections of the manuscript, but it limits the interpretation of the results. Also acknowledged is the limited method used to assess neuropathy.

Potentially due to this small number of patients with neuropathy, the machine learning algorithms could not distinguish between samples with and without neuropathy. Only selected univariate analyses identified differences in lipid profiles potentially related to neuropathy.

Three sphingolipid mediators including SA1P differed between patients with and without neuropathy at the end of treatment. These sphingolipids were elevated at the end of treatment in the cohort with neuropathy, relative to those without neuropathy. However, across all samples from pre to post-paclitaxel treatment, there was a significant reduction in SA1P levels. It is unclear from the data presented what the underlying mechanism for this result would be. If elevated SA1P is associated with neuropathy development, it would be expected to increase in those who develop neuropathy from pre to post-treatment time points.

Primary sensory neuron cultures were used to examine the effects of SA1P application. SA1P application produced calcium transients in a small proportion of sensory neurons. It is not clear how this experimental model assists in validating the role of SA1P in neuropathy development as there is no assessment of sensory neuron damage or other hallmarks of peripheral neuropathy. These results demonstrate that some sensory neurons respond to SA1P and that this activity is linked to TRPV1 receptors. However, further studies will be required to determine if this is mechanistically related to neuropathy.

Impact:

Taken in total, the data presented do not provide sufficient evidence to support the contention that SA1P has an important role in paclitaxel-induced peripheral neuropathy. Further, the results do not provide evidence to support the use of S1PR1 receptor antagonists as a therapeutic strategy. It is important to be careful with language use in the discussion, as the significance of the present results is overstated.

However, based on the results of previous studies, it is likely that sphingolipid metabolism plays a role in chemotherapy-induced peripheral neuropathy. Based on this existing evidence, the S1PR1 receptor antagonist fingolimod has already been examined in experimental models and clinical trials. Further work is needed to examine the links between lipid mediators and neuropathy development and identify additional strategies for intervention.

Reviewer #2 (Public Review):

Summary:

Previous work has shown subjects can use a form of short-term sensory memory, known as 'iconic memory', to accurately remember stimuli over short periods of time (several hundred milliseconds). Working memory maintains representations for longer periods of time but is strictly limited in its capacity. While it has long been assumed that sensory information acts as the input to working memory, a process model of this transfer has been missing. To address this, Tomic and Bays present the Dynamic Neural Resource (DyNR) model. The DyNR model captures the dynamics of processing sensory stimuli, transferring that representation into working memory, the diffusion of representations within working memory, and the selection of a memory for report.

The DyNR model captures many of the effects observed in behavior. Most importantly, psychophysical experiments found the greater the delay between stimulus presentation and the selection of an item from working memory, the greater the error. This effect also depended on working memory load. In the model, these effects are captured by the exponential decay of sensory representations (i.e., iconic memory) following the offset of the stimulus. Once the selection cue is presented, residual information in iconic memory can be integrated into working memory, improving the strength of the representation and reducing error. This selection process takes time, and is slower for larger memory loads, explaining the observation that memory seems to decay instantly. The authors compare the DyNR model to several variants, demonstrating the importance of persistence of sensory information in iconic memory, normalization of representations with increasing memory load, and diffusion of memories over time.

Strengths:

The manuscript provides a convincing argument for the interaction of iconic memory and working memory, as captured by the DyNR model. The analyses are cutting-edge and the results are well captured by the DyNR model. In particular, a strength of the manuscript is the comparison of the DyNR model to several alternative variants.

The results provide a process model for interactions between iconic memory and working memory. This will be of interest to neuroscientists and psychologists studying working memory. I see this work as providing a foundation for understanding behavior in continuous working memory tasks, from either a mechanistic, neuroscience, perspective or as a high-water mark for comparison to other psychological process models.

Finally, the manuscript is well written. The DyNR model is nicely described and an intuition for the dynamics of the model are clearly shown in Figures 2 and 4.

Weaknesses:

The manuscript appropriately acknowledges and addresses several minor weaknesses that are due to the limited ability of the approach to disambiguate underlying neural mechanisms. Nevertheless, the manuscript adds significant value to the literature on working memory.

Reviewer #1 (Public Review):

Summary:

This study assumes but also demonstrates that auditory rhythm processing is produced by internal oscillating systems and evaluates the properties of internal oscillators across individuals. The authors designed an experiment and performed analyses that address individuals' preferred rate and flexibility, with a special focus on how much past rhythms influence subsequent trials. They find evidence for such historical dependence and show that we adapt less well to new rhythms as we age. While I have some doubts about the entrainment-based interpretation of the results, this work offers a useful contribution to our understanding of individual differences in rhythm processing regardless.

Strengths:

The inclusion of two tasks -- a tapping and a listening task -- complement each other methodologically. By analysing both the production and tracking of rhythms, the authors emphasize the importance of the characteristics of the receiver, the external world, and their interplay. The relationship between the two tasks and components within tasks are explored using a range of analyses. The visual presentation of the results is very clear. The age-related changes in flexibility are useful and compelling.

The paper includes a discussion of the study assumptions, and it contextualizes itself more explicitly as taking entrainment frameworks as a starting point. As such, even if the entrainment of oscillators cannot be decisively shown, it is now clear that this is nevertheless adopted as a useful theoretical lens.

Weaknesses:

The newly included analyses that justify an entrainment or oscillator-based interpretation of the result could be presented in a clearer manner so that readers can parse their validity better. For example, in line with an entrainment interpretation, the regression lines in Figure 2B show accuracy increases as the IOI moves towards the preferred rate -- but then beyond the preferred rate, accuracy appears to increase further still. Furthermore, the additional analyses on harmonic relationships could be enriched with justification and explanation of each of its steps.

Reviewer #1 (Public Review):

Summary:

The paper presents a nice study investigating the impairments of biological motion perception in individuals with ADHD in comparison with neurotypical controls. Motivated by the idea that there is a relationship between biological motion perception and social capabilities, the authors investigated the impairments of local and global (holistic) biological motion perception, the diagnosis status, and several additional behavioral variables that are affected in ADHS (IQ, social responsiveness, and attention / impulsivity). As well local as global biological motion perception is impaired in ADHD individuals. In addition, the study demonstrates a significant correlation between local biological motion perception skills and the social responsiveness score in the ADHD group, but not in controls. A path analysis in the ADHD group suggests that general performance in<br /> biological motion perception is influenced mainly by global biological motion perception performance and attentional and perceptual reasoning skills.

Strengths:

It is true that there exists not much work on biological motion perception and ADHD. Therefore, the presented study contributes an interesting new result to the biological motion literature, and adds potentially also new behavioral markers for this clinical group. The design of the study is straightforward and technically sound, and the drawn conclusions are supported by the presented results.

Weaknesses:

Some of the claims about the relationship between genetic factors and ADHD and the components of biological motion processing have to remain speculative at this point because genetic influences were not explicitly tested in this paper. Specifically, the hypothesis that the perception of human social interaction is critically based on a local mechanism for the detection of asymmetry in foot trajectories of walkers (this is what 'BL-local' really measures), or on the detection of live agents in cluttered scenes seems not very plausible.

Based on my last comments, now the discussion has been changed in a way that tries to justify the speculative claims by citing a lot of other speculative papers, which does not really address the problem. For example, the fact that chicks walk towards biological motion stimuli is interesting. To derive that this verifies a fundamental mechanism in human biological motion processing is extremely questionable, given that birds do not even have a cortex. Taking the argumentation of the authors serious, one would have to assume that the 'Local BM' mechanism is probably located in the mesencephalon in humans, and then would have to interact in some way with social perception differences of ADHD children. To me all this seems to make very strong (over-)claims. I suggest providing a much more modest interpretation of the interesting experimental result, based on what has been really experimentally shown by the authors and closely related other data, rather than providing lots of far-reaching speculations.

In the same direction, in my view, go claims like 'local BM is an intrinsic trait' (L. 448) , which is not only imprecise (maybe better 'mechanisms of processing of local BM cues') but also rather questionable. Likely, this' local processing of BM' is a lower level mechanisms, located probably in early and mid-levels of the visual cortex, with a possible influence of lower structures. It seems not really plausible that this is related to a classical trait variables in the sense of psychology, like personality, as seems to be suggested here. Also here I suggest a much more moderate and less speculative interpretation of the results.

Reviewer #1 (Public Review):

This paper presents a cognitive model of out-of-distribution generalisation, where the representational basis is grid-cell codes. In particular, the authors consider the tasks of analogies, addition, and multiplication, and the out-of-distribution tests are shifting or scaling the input domain. The authors utilise grid cell codes, which are multi-scale as well as translationally invariant due to their periodicity. To allow for domain adaptation, the authors use DPP-A which is, in this context, a mechanism of adapting to input scale changes. The authors present simulations results demonstrating this model can perform out-of-distribution generalisation to input translations and re-scaling, whereas other models fail.

This paper makes the point it sets out to - that there are some underlying representational bases, like grid cells, that when combined with a domain adaptation mechanism, like DPP-A, can facilitate out-of-generalisation. I don't have any issues with the technical details.

The paper nicely demonstrates how neural codes can be transformed into a common representational space so that analogies, and presumably other useful tasks/computations, can be performed.

Reviewer #1 (Public Review):

It is known that aberrant habit formation is a characteristic of obsessive-compulsive disorder (OCD). Habits can be defined according to the following features (Balleine and Dezfouli, 2019): rapid execution, invariant response topography, action 'chunking' and resistance to devaluation.

The extent to which OCD behavior is derived from enhanced habit formation relative to deficits in goal-directed behavior is a topic of debate in the current literature. This study examined habit-learning specifically (cf. deficits in goal-directed behavior) by regularly presenting, via smartphone, sequential learning tasks to patients with OCD and healthy controls. Participants engaged in the tasks every day over the course of a month. Automaticity, including the extent to which individual actions in the sequence become part of a unified 'chunk', was an important outcome variable. Following the 30 days of training, in-laboratory tasks were then administered to examine 1) if performing the learned sequences themselves had become rewarding 2) differences in goal-directed vs. habitual behavior.

Several hypotheses were tested, including:<br /> Patients would have impaired procedural learning vs. healthy volunteers (this was not supported, possibly because there were fewer demands on memory in the task used here)<br /> Once the task had been learned, patients would display automaticity faster (unexpectedly, patients were slower to display automaticity)<br /> Habits would form faster under a continuous (vs. variable) reinforcement schedule

Exploratory analyses were also conducted: an interesting finding was that OCD patients with higher self-reported symptoms voluntarily completed more sessions with the habit-training app and reported a reduction in symptoms.

Strengths

This paper is well situated theoretically within the habit learning/OCD literature.<br /> Daily training in a motor-learning task, delivered via smartphone, was innovative, ecologically valid and more likely to assay habitual behaviors specifically. Daily training is also more similar to studies with non-humans, making a better link with that literature. The use of a sequential-learning task (cf. tasks that require a single response) is also more ecologically valid.<br /> The in-laboratory tests (after the 1 month of training) allowed the researchers to test if the OCD group preferred familiar, but more difficult, sequences over newer, simpler sequences.

Weaknesses

The authors were not able to test one criterion of habits, namely resistance to devaluation, due to the nature of the task.<br /> The sample size was relatively small. Some potentially interesting individual differences within the OCD group could have been examined more thoroughly with a bigger sample (e.g., preference for familiar sequences). A larger sample may have allowed the statistical testing of any effects due to medication status.

The authors achieved their aims in that two groups of participants (patients with OCD and controls) engaged with the task over the course of 30 days. The repeated nature of the task meant that 'overtraining' was almost certainly established, and automaticity was demonstrated. This allowed the authors to test their hypotheses about habit learning. The results are supportive of the author's conclusions.

This article is likely to be impactful -- the delivery of a task across 30 days to a patient group is innovative and represents a new approach for the study of habit learning that is superior to an in-laboratory approach.

An interesting aspect of this manuscript is that it prompts a comparison with previous studies of goal-directed/habitual responding in OCD that used devaluation protocols, and which may have had their effects due to deficits in goal-directed behavior and not enhanced habit learning per se.

"Il résulte donc de ce qui précède, qu’en l’absence d’obstacle juridique, l’organe délibératif de l’EPLE est parfaitement libre d’adopter le principe d’une répartition de l’année scolaire en deux semestres, au lieu de trois trimestres. Une fois cette résolution arrêtée, il conviendra également de modifier en conséquence le règlement intérieur de l’établissement."

Reviewer #1 (Public Review):

Summary:

In this study, participants completed two different tasks. A perceptual choice task in which they compared the sizes of pairs of items and a value-different task in which they identified the higher value option among pairs of items with the two tasks involving the same stimuli. Based on previous fMRI research, the authors sought to determine whether the superior frontal sulcus (SFS) is involved in both perceptual and value-based decisions or just one or the other. Initial fMRI analyses were devised to isolate brain regions that were activated for both types of choices and also regions that were unique to each. Transcranial magnetic stimulation was applied to the SFS in between fMRI sessions and it was found to lead to a significant decrease in accuracy and RT on the perceptual choice task but only a decrease in RT on the value-different task. Hierarchical drift-diffusion modelling of the data indicated that the TMS had led to a lowering of decision boundaries in the perceptual task and a lower of non-decision times on the value-based task. Additional analyses show that SFS covaries with model-derived estimates of cumulative evidence and that this relationship is weakened by TMS.

Strengths:

The paper has many strengths including the rigorous multi-pronged approach of causal manipulation, fMRI and computational modelling which offers a fresh perspective on the neural drivers of decision making. Some additional strengths include the careful paradigm design which ensured that the two types of tasks were matched for their perceptual content while orthogonalizing trial-to-trial variations in choice difficulty. The paper also lays out a number of specific hypotheses at the outset regarding the behavioural outcomes that are tied to decision model parameters and are well justified.

Weaknesses:

Unless I have missed it, the SFS does not actually appear in the list of brain areas significantly activated by the perceptual and value tasks in Supplementary Tables 1 and 2. Its presence or absence from the list of significant activations is not mentioned by the authors when outlining these results in the main text. What are we to make of the fact that it is not showing significant activation in these initial analyses?

The value difference task also requires identification of the stimuli, and therefore perceptual decision-making. In light of this, the initial fMRI analyses do not seem terribly informative for the present purposes as areas that are activated for both types of tasks could conceivably be specifically supporting perceptual decision-making only. I would have thought brain areas that are playing a particular role in evidence accumulation would be best identified based on whether their BOLD response scaled with evidence strength in each condition which would make it more likely that areas particular to each type of choice can be identified. The rationale for the authors' approach could be better justified.

TMS led to reductions in RT in the value-difference as well as the perceptual choice task. DDM modelling indicated that in the case of the value task, the effect was attributable to reduced non-decision time which the authors attribute to task learning. The reasoning here is a little unclear. If task learning is the cause, then why are similar non-decision time effects not observed in the perceptual choice task? Given that the value-task actually requires perceptual decision-making, is it not possible that SFS disruption impacted the speed with which the items could be identified, hence delaying the onset of the value-comparison choice?

The sample size is relatively small. The authors state that 20 subjects is 'in the acceptable range' but it is not clear what is meant by this.

Reviewer #1 (Public Review):

Summary and strength:

The authors undertook to assemble and annotate the genome sequence of the Malabar grouper fish, with the aim of providing molecular resources for fundamental and applied research. Even though this is more mainstream, the task is still daunting and labor-intensive. Currently, high-quality and fully annotated genome sequences are of strategic importance in modern biology. The authors make use of the resource to address the endocrine control of an ecologically and developmentally relevant life cycle transition, metamorphosis. As opposed to amphibian and flat fish where body plan changes, fish metamorphosis is anatomically more subtle and much less known, although it is clear that thyroid hormone (TH) signaling is a key player. The authors thus provide a repertoire of TH-relevant gene expression changes during development and across metamorphosis and correlate developmental stages with changes in gene expression. Overall, this work has a strong potential to meet its target.

Weaknesses:

The manuscript needs proper editing and is not complete. Some wordings lack precision and make it difficult to follow (e.g. line 98 "we assembled a chromosome-scale genome of ..." should read instead "we assembled a chromsome-scla genome sequence of ...". Also, panel Figure 2E is missing.

The shortcomings of the manuscripts are not limited to the writing style, and important technical and technological information is missing or not clear enough, thereby preventing a proper evaluation of the resolution of the genomic resources provided:

- Several RNASeq libraries from different tissues have been built to help annotate the genome and identify transcribed regions. This is fine. But all along the manuscript, gene expression changes are summarized into a single panel where it is not clear at all which tissue this comes from (whole embryo or a specific tissue ?), or whether it is a cumulative expression level computed across several tissues (and how it was computed) etc. This is essential information needed for data interpretation.

- The bioinformatic processing, especially of the assemble and annotation, is very poorly described. This is also a sensitive topic, as illustrated by the numerous "assemblathon" and "annotathon" initiatives to evaluate tools and workflows. Importantly, providing configuration files and in-depth description of workflows and parameter settings is highly recommended. This can be made available through data store services and documents even benefit from DOIs. This provides others with more information to evaluate the resolution of this work. No doubt that it is well done,<br /> but especially in the field of genome assembly and annotation, high resolution is VERY cost and time-intensive. Not surprisingly, most projects are conditioned by trade-offs between cost, time, and labor. The authors should provide others with the information needed to evaluate this.

- Quantifications of T3 and T4 levels look fairly low and not so convincing. The work would clearly benefit from a discussion about why the signal is so low and what are the current technological limitations of these quantifications. This would really help (general) readers.

- Differential analysis highlights up to ~ 15,000 differentially expressed genes (DEG), out of a predicted 26k genes. This corresponds to more than half of all genes. ANOVA-based differential analysis relies on the simple fact that only a minority of genes are DEG. Having >50% DEG is well beyond the validity of the method. This should be addressed, or at least discussed.

Reviewer #1 (Public Review):

Summary:

In their manuscript, "Nicotine enhances the stemness and tumorigenicity in intestinal stem cells via Hippo-YAP/TAZ and Notch signal pathway", authors Isotani et al claimed that this study identifies a NIC-triggered pathway regulating the stemness and tumorigenicity of ISCs and suggest the use of DBZ as a potential therapeutic strategy for treating intestinal tumors. However, the presented data do not support the primary claims.

Weaknesses:

My main reservation is that the quality of the results presented in the manuscript may not fully substantiate their conclusions. For instance, in Figure 2 A and B, it is challenging to discern a healthy organoid. This is significant, as the entirety of Figure 2 and several panels in Figures 3 - 5 are based on these organoid assays. Additionally, there seems to be a discrepancy in the quality of results from the western blot, as the lanes of actin do not align with other proteins (Figure 6B).

Reviewer #1 (Public Review):

Summary:

Cognitive and brain development during the first two years of life is vast and determinant for later development. However, longitudinal infant studies are complicated and restricted to occidental high-income countries. This study uses fNIRS to investigate the developmental trajectories of functional connectivity networks in infants from a rural community in Gambia. In addition to resting-state data collected from 5 to 24 months, the authors collected growing measures from birth until 24 months and administrated an executive functioning task at 3 or 5 years old.

The results show left and right frontal-middle and right frontal-posterior negative connections at 5 months that increase with age (i.e., become less negative). Interestingly, contrary to previous findings in high-income countries, there was a decrease in frontal interhemispheric connectivity. Restricted growth during the first months of life was associated with stronger frontal interhemispheric connectivity and weaker right frontal-posterior connectivity at 24 months. Additionally, the study describes that some connectivity patterns related to better cognitive flexibility at pre-school age.

Strengths:

- The authors analyze data from 204 infants from a rural area of Gambia, already a big sample for most infant studies. The study might encourage more research on different underrepresented infant populations (i.e., infants not living in occidental high-income countries).

- The study shows that fNIRS is a feasible instrument to investigate cognitive development when access to fMRI is not possible or outside a lab setting.

- The fNIRS data preprocessing and analysis are well-planned, implemented, and carefully described. For example, the authors report how the choices in the parameters for the motion artifacts detection algorithm affect data rejection and show how connectivity stability varies with the length of the data segment to justify the threshold of at least 250 seconds free of artifacts for inclusion.

- The authors use proper statistical methods for analysis, considering the complexity of the dataset.

Weaknesses:

- No co-registration of the optodes is implemented. The authors checked for correct placement by looking at pictures taken during the testing session. However, head shape and size differences might affect the results, especially considering that the study involves infants from 5 months to 24 months and that the same fNIRS array was used at all ages.

- The authors regress the global signal to remove systemic physiological noise. While the authors also report the changes in connectivity without global signal regression, there are some critical differences. In particular, the apparent decrease in frontal inter-hemispheric connections is not present when global signal regression is omitted, even though it is present for deoxy-Hb. The authors use connectivity results obtained after applying global signal regression for further analysis. The choice of regressing the global signal is questionable since it has been shown to introduce anti-correlations in fMRI data (Murphy et al., 2009), and fNIRS in young infants does not seem to be highly affected by physiological noise (Emberson et al., 2016). Systemic physiological noise might change at different ages, which makes its remotion critical to investigate functional network development. However, global signal regression might also affect the data differently. The study would have benefited from having short separation channels to measure the systemic psychological component in the data.

- I believe the authors bypass a fundamental point in their framing. When discussing the results, the authors compare the developmental trajectories of the infants tested in a rural area of Gambia with the trajectories reported in previous studies on infants growing in occidental high-income countries (likely in urban contexts) and attribute the differences to adverse effects (i.e., nutritional deficits). Differences in developmental trajectories might also derive from other environmental and cultural differences that do not necessarily lead to poor cognitive development.

- While the study provides a solid description of the functional connectivity changes in the first two years of life at the group level, the evidence regarding the links between adverse situations, developmental trajectories, and later cognitive capacities is weaker. The authors find that early restricted growth predicts specific connectivity patterns at 24 months and that certain connectivity patterns at specific ages predict cognitive flexibility. However, the link between development trajectories (individual changes in connectivity) with growth and later cognitive capacities is missing. To address this question adequately, the study should have compared infants with different growing profiles or those who suffered or did not from undernutrition. However, as the authors discussed, they lacked statistical power.

Reviewer #1 (Public Review):

The authors sought to test whether anterior insular cortex neurons increase or decrease firing during fear behavior and freezing, bi-directionally control fear via separate, anatomically defined outputs. Using a fairly simple behavior where mice were exposed to tone-shock pairings, they found roughly equal populations that do indeed either increase or decrease firing during freezing. Next, they sought to test whether these distinct populations may also have distinct outputs. Using retrograde tracers they found that the anterior insular cortex contains non-overlapping neurons which project to the mediodorsal thalamus or amygdala. Mediodorsal thalamus-projecting neurons tended to cluster in deep cortical layers while amygdala-projecting neurons were primarily in more superficial layers. Stimulation of insula-thalamus projection decreased freezing behavior, and stimulation of insula-amygdala projections increased fear behavior. Given that the neurons that increased firing were located in deep layers, that thalamus projections occurred in deep layers, and that stimulation of insula-thalamus neurons decreased freezing, the authors concluded that the increased firing neurons may be thalamus projections. Similarly, given that decreased-firing neurons tended to occur in more superficial layers, that insula-amygdala projections were primarily superficial, and that insula-amygdala stimulation increased freezing behavior, authors concluded that the decreased firing cells may be amygdala projections. The study has several strengths though also some caveats.

Strengths:

The potential link between physiological activity, anatomy, and behavior is well laid out and is an interesting question. The activity contrast between the units that increase/decrease firing during freezing is clear.

It is nice to see the recording of extracellular spiking activity, which provides a clear measure of neural output, whereas similar studies often use bulk calcium imaging, a signal that rarely matches real neural activity even when anatomy suggests it might (see London et al 2018 J Neuro - there are increased/decreased spiking striatal populations, but both D1 and D2 striatal neurons increase bulk calcium).

Weaknesses:

The link between spiking, anatomy, and behavior requires assumptions/inferences: the anatomically/genetically defined neurons which had distinct outputs and opposite behavioral effects can only be assumed the increased/decreased spiking neurons, based on the rough area of the cortical layer they were recorded.

The behavior would require more control to fully support claims about the associative nature of the fear response (see Trott et al 2022 eLife) - freezing, in this case, could just as well be nonassociative. In a similar vein, fixed intertrial intervals, though common practice in the fear literature, pose a problem for neurophysiological studies. The first is that animals learn the timing of events, and the second is that neural activity is dynamic and changes over time. Thus it is very difficult to determine whether changes in neural activity are due to learning about the tone-shock contingency, timing of the task, simply occur because of time and independently of external events, or some combination of the above.

Reviewer #1 (Public Review):

Summary:

Cheong et al. use a synapse-resolution wiring map of the fruit fly nerve cord to comprehensively investigate circuitry between descending neurons (DNs) from the brain and motor neurons (MNs) that enact different behaviours. These neurons were painstakingly identified, categorised, and linked to existing genetic driver lines; this allows the investigation of circuitry to be informed by the extensive literature on how flights walk, fly, and escape from looming stimuli. New motifs and hypotheses of circuit function were presented. This work will be a lasting resource for those studying nerve cord function.

Strengths:

The authors present an impressive amount of work in reconstructing and categorising the neurons in the DN to MN pathways. There is always a strong link between the circuitry identified and what is known in the literature, making this an excellent resource for those interested in connectomics analysis or experimental circuits neuroscience. Because of this, there are many testable hypotheses presented with clear predictions, which I expect will result in many follow-up publications. Most MNs were mapped to the individual muscles that they innervate by linking this connectome to pre-existing light microscopy datasets. When combined with past fly brain connectome datasets (Hemibrain, FAFB) or future ones, there is now a tantalising possibility of following neural pathways from sensory inputs to motor neurons and muscle.

Weaknesses:

As with all connectome datasets, the sample size is low, limiting statistical analyses. Readers should keep this in mind, but note that this is the current state-of-the-art. Some figures are weakened by relying too much on depictions of wiring diagrams as evidence of circuit function, similarity between neuropils, etc. without additional quantitative justification.

Reviewer #1 (Public Review):

Summary:

This paper reports the first results on the effects of a novel waveform for weak transcranial magnetic stimulation, which they refer to as "perturbation" (kTMP). The waveform is sinusoidal at kHz frequency with subthreshold intensities of 2V/m, instead of the suprathreshold pulses used in conventional TMS (~100V/m). The effect reported here concerns motor-evoked potentials (MEPs) elicited on the hand with single-pulse TMS. These MEPs are considered a marker of "corotico-spinal excitability. The manuscripts report that kTMP at 3.5kHz enhances MEPs with a medium effect size, and reports independent replications of this fining on 3 separate cohorts of subjects (N=16, 15, 16). This result is important for the field of non-invasive brain stimulation. The evidence in support of this claim is compelling.

Strengths:

• This is a novel modality for non-invasive brain stimulation.

• Knowing the history in this field, is likely to lead to a large number of follow-up studies in basic and clinical research.

• The modality cases practically no sensation which makes it perfectly suitable for control conditions. Indeed, the study itself used a persuasive double-blinding procedure.

• The replication of the main result in two subsequent experiments is very compelling.

• The effect size of Cohen's d=0.5 is very promising.

• It is nice the E-fields were actually measured on a phantom, not just modeled.

Weakness:

• The within-subject design may have carry-over effects, although a 2-day gap is probably enough for washout.

• It would have been nice to assess washout by comparing the per-conditions between days. Particularly problematic are the paired-pulse effects that are done within sessions in experiments 2 and 3 which could have carried over to the main metric of interest, which was the single pulse MEP.

• Statistical analysis combining Experiments 1, 2, and 3 is a little muddled.

• Related, the biorxiv version history of this work as experiments 1-3 came together to point to diverging results, and changing analysis methods. Specifically, an earlier version of the work claims that modulated kHz sinusoids are more effective than un-modulated sinusoids, yet the current version says that no differences were detected - which seems consistent with the data presented in this version. However, it does raise concerns about analytic methods, which seem to have shifted over time.

• While sensation has been documented nicely, it does not seem like blinding has been directly assessed, by asking participants at the end which group they thought to be in.

Reviewer #1 (Public Review):

Summary:

The work by Zeng et al. comprehensively explored the differences in the effects of leaf and soil microbes on the seed germination, seedling survival, and seedling growth of an invasive forb, Ageratina Adenophora, and found evidence of stronger effects of leaf microbes on Ageratina compared with soil microbes, which were negative for seed germination and seedling survival but positive for seedling growth. By further DNA sequencing and fungal strain cultivation, the authors were able to identify some of the key microbial guilds that may facilitate such negative and positive feedback.

Strengths:

(1) The theoretic framework is well-established.

(2) Relating the direction of plant-microbe feedback to certain microbial guilds is always hard, but the authors have done a great job of identifying and interpreting such relationships.

Weaknesses:

(1) In the G0 and G21 inoculation experiments, allelopathic effects from leaf litters had not been accounted for, while these two experiments happened to be the ones where negative feedback was detected.

(2) The authors did not compare the fungal strains accumulated in dead seedlings to those accumulated in live seedlings to prove that the live seedlings indeed accumulated lower abundances of the strains that were identified to increase seedling mortality.

(3) The data of seed germination and seedling mortality could have been analyzed in the same manner as that of seedling growth, which makes the whole result section more coherent. I don't understand why the authors had not calculated the response index (RI) for germination/mortality rate and conducted analyses on the correlation between these RIs with microbial compositions.

(4) The language of the manuscript could be improved to increase clarity.

Reviewer #1 (Public Review):

Summary:

This finding shows a connection between cancer-associated beta-catenin mutations and extracellular vesicle secretion. A link between the beta-catenin mutation and expression of trafficking and exocytosis machinery. They used a multidisciplinary approach to explore expression levels of relevant proteins and single-particle imaging to directly explore the release of extracellular vesicles. These results suggest a role of extracellular vesicles in immune evasion in liver cancer with the role needing to be further explored in other forms of cancer. I find this work to be compelling and of strong significance.

Strengths:

This paper uses multidisciplinary methods to demonstrate the compelling role of beta-catenin mutations in suppressing EV secretion in tumors. The results and imaging are extremely convincing and compelling.

Weaknesses:

There is no major weakness in this work. There are only things that left me more intrigued about this work. While the role of Rab27 was strongly examined, the hits of the VAMP proteins were not explored in detail. I was wondering if the decrease in the presence of VAMPS directly suggests the final step of membrane fusion in the exocytosis of EVs is what is being impaired. Or if it is other trafficking steps along the EV secretion pathway.

Reviewer #1 (Public Review):

Summary:

The present study's main aim is to investigate the mechanism of how VirR controls the magnitude of MEV release in Mtb. The authors used various techniques, including genetics, transcriptomics, proteomics, and ultrastructural and biochemical methods. Several observations were made to link VirR-mediated vesiculogenesis with PG metabolism, lipid metabolism, and cell wall permeability. Finally, the authors presented evidence of a direct physical interaction of VirR with the LCP proteins involved in linking PG with AG, providing clues that VirR might act as a scaffold for LCP proteins and remodel the cell wall of Mtb. Since the Mtb cell wall provides a formidable anatomical barrier for the entry of antibiotics, targeting VirR might weaken the permeability of the pathogen along with the stimulation of the immune system due to enhanced vesiculogenesis. Therefore, VirR could be an excellent drug target. Overall, the study is an essential area of TB biology.

Strengths:

The authors have done a commendable job of comprehensively examining the phenotypes associated with the VirR mutant using various techniques. Application of Cryo-EM technology confirmed increased thickness and altered arrangement of CM-L1 layer. The authors also confirmed that increased vesicle release in the mutant was not due to cell lysis, which contrasts with studies in other bacterial species.

Another strength of the manuscript is that biochemical experiments show altered permeability and PG turnover in the mutant, which fits with later experiments where authors provide evidence of a direct physical interaction of VirR with LCP proteins.

Transcriptomics and proteomics data were helpful in making connections with lipid metabolism, which the authors confirmed by analyzing the lipids and metabolites of the mutant.

Lastly, using three approaches, the authors confirm that VirR interacts with LCP proteins in Mtb via the LytR_C terminal domain.

Altogether, the work is comprehensive, experiments are designed well, and conclusions are made based on the data generated after verification using multiple complementary approaches.

Weaknesses:

The major weakness is that the mechanism of VirR-mediated EV release remains enigmatic. Most of the findings are observational and only associate enhanced vesiculogenesis observed in the VirR mutant with cell wall permeability and PG metabolism. The authors suggest that EV release occurs during cell division when PG is most fragile. However, this has yet to be tested in the manuscript - the AFM of the VirR mutant, which produces thicker PG with more pore density, displays enhanced vesiculogenesis. No evidence was presented to show that the PG of the mutant is fragile, and there are differences in cell division to explain increased vesiculogenesis. These observations, counterintuitive to the authors' hypothesis, need detailed experimental verification.

Transcriptomic data only adds a little substantial. Transcriptomic data do not correlate with the proteomics data. It remains unclear how VirR deregulates transcription. TLCs of lipids are not quantitative. For example, the TLC image of PDIM is poor; quantitative estimation needs metabolic labeling of lipids with radioactive precursors. Further, change in PDIMs is likely to affect other lipids (SL-1, PAT/DAT) that share a common precursor (propionyl- CoA).

The connection of cholesterol with cell wall permeability is tenuous. Cholesterol will serve as a carbon source and contribute to the biosynthesis of methyl-branched lipids such as PDIM, SL-1, and PAD/DAT. Carbon sources also affect other aspects of physiology (redox, respiration, ATP), which can directly affect permeability and import/export of drugs. Authors should investigate whether restoration of the normal level of permeability and EV release is not due to the maintenance of cell wall lipid balance upon cholesterol exposure of the VirR mutant.

Finally, protein interaction data is based on experiments done once without statistical analysis. If the interaction between VirR and LCP protein is expected on the mycobacterial membrane, how the SPLIT_GFP system expressed in the cytoplasm is physiologically relevant. No explanation was provided as to why VirR interacts with the truncated version of LCP proteins and not with the full-length proteins.

Reviewer #1 (Public Review):

In this work, the authors provide a comprehensive description of transcriptional regulation in Pseudomonas syringae by investigating the binding characteristics of various transcription factors. They uncover the hierarchical network structure of the transcriptome by identifying top-, middle-, and bottom-level transcription factors that govern the flow of information in the network. Additionally, they assess the functional variability and conservation of transcription factors across different strains of P. syringae by studying DNA-binding characteristics. These findings notably expand our current knowledge of the P. syringae transcriptome.

The findings associated with crosstalk between transcription factors and pathways, and the diversity of transcription factor functions across strains provide valuable insights into the transcriptional regulatory network of P. syringae. However, these results are at times underwhelming as their significance is unclear. This study would benefit from a discussion of the implications of transcription factor crosstalk on the functioning of the organism as a whole. Additionally, the implications of variability in transcription factor functions on the phenotype of the strains studied would further this analysis.

Overall, this manuscript serves as a key resource for researchers studying the transcriptional regulatory network of P. syringae.

Reviewer #1 (Public Review):

Summary:

The article written by Kazdaghli et al. proposes a modification of imputation methods, to better account and exploit the variability of the data. The aim is to reduce the variability of the imputation results.<br /> The authors propose two methods, one that still includes some imputation variability, but accounts for the distribution of the data points to improve the imputation. The other one proposes a determinantal sampling, that presents no variation in the imputation data, but it seems to be, that they measure the variation in the classification task, instead. As these methods grow easily in computation requirements and time, they also propose an algorithm to run these methods in quantum processors.

Strengths:

The sampling method for imputing missing values that account for the variability of the data seems to be accurate.

Weaknesses:

The authors state "Ultimately, the quality and reliability of imputations can be measured by the performance of a downstream predictor, which is usually the AUC (area under the receiver operating curve) for a classification task." but there is no citation of other scientists doing this. I think the authors could have evaluated the imputations directly, as they mention in the introduction, I understand that the final goal in the task is to have a better classification. In a real situation, they would have data that would be used for training the algorithm, and then new data that needs to be imputed and classified. Is there any difference between imputing all the data together and training the algorithm, versus doing the imputation, training a classifier, then imputing new data (for the testing set), and then testing the classification?<br /> I wonder if there could be some spurious interaction between the imputation and the classification methods, that could bias the data in the sense of having a better classification, but not imputing the real values; in particular when the deterministic DPP is used.

Joint Public Review:

This papers performs fine-mapping of the silkworm mutants bd and its fertile allelic version, bdf, narrowing down the causal intervals to a small interval of a handful of genes. In this region, the gene orthologous to mamo is impaired by a large indel, and its function is later confirmed using expression profiling, RNAi, and CRISPR KO. All these experiments are convincingly showing that mamo is necessary for the suppression of melanic pigmentation in the silkworm larval integument.

The authors also use in silico and in vitro assays to probe the potential effector genes that mamo may regulate.

The genotype-to-phenotype workflow, combining forward (mapping) and reverse genetics (RNAi and CRISPR loss-of-function assays) linking mamo to pigmentation are extremely convincing.

Comments on latest version:

This second revision took into account all the reviewers' comments. The authors added an interesting analysis of nucleotide diversity at the Bm-mamo locus, using available sequence data from 51 wild silkworms and 171 domesticated silkworms.<br /> The last paragraph added to the discussion, starting with "It has often been believed that changes in CREs are caused by random mutations", is speculative. There is currently no evidence that the mutation rate is biased at the Bm-mamo locus.

Reviewer #1 (Public Review):

Summary:

The authors investigated how the presence of interspecific introgressions in the genome affects the recombination landscape. This research was intended to inform about genetic phenomena influencing the evolution of introgressed regions, although it should be noted that the research itself is based on examining only one generation, which limits the possibility of drawing far-reaching evolutionary conclusions. In this work, yeast hybrids with large (from several to several dozen percent of the chromosome length) introgressions from another yeast species were crossed. Then, the products of meiosis were isolated and sequenced, and on this basis, the genome-wide distribution of both crossovers (COs) and noncrossovers (NCOs) was examined. Carrying out the analysis at different levels of resolution, it was found that in the regions of introduction, there is a very significant reduction in the frequency of COs and a simultaneous increase in the frequency of NCOs. Moreover, it was confirmed that introgressions significantly limit the local shuffling of genetic information, and NCOs are only able to slightly contribute to the shuffling, thus they do not compensate for the loss of CO recombination.

Strengths:

- Previously, experiments examining the impact of SNP polymorphism on meiotic recombination were conducted either on the scale of single hotspots or the entire hybrid genome, but the impact of large introgressed regions from another species was not examined. Therefore, the strength of this work is its interesting research setup, which allows for providing data from a different perspective.

- Good quality genome-wide data on the distribution of CO and NCO were obtained, which could be related to local changes in the level of polymorphism.

Weaknesses:

- The research is based on examining only one generation, which limits the possibility of drawing far-reaching evolutionary conclusions. Moreover, meiosis is stimulated in hybrids in which introgressions occur in a heterozygous state, which is a very unlikely situation in nature. Therefore, I see the main value of the work in providing information on the CO/NCO decision in regions with high sequence diversification, but not in the context of evolution.

- The work requires greater care in preparing informative figures and, more importantly, re-analysis of some of the data (see comments below).

More specific comments:

- The authors themselves admit that the detection of NCO, due to the short size of conversion tracts, depends on the density of SNPs in a given region. Consequently, more NCOs will be detected in introgressed regions with a high density of polymorphisms compared to the rest of the genome. To investigate what impact this has on the analysis, the authors should demonstrate that the efficiency of detecting NCOs in introgressed regions is not significantly higher than the efficiency of detecting NCOs in the rest of the genome. If it turns out that this impact is significant, analyses should be presented proving that it does not entirely explain the increase in the frequency of NCOs in introgressed regions.

- CO and NCO analyses performed separately for individual regions rarely show statistical significance (Figures 3 and 4). I think that the authors, after dividing the introgressed regions into non-overlapping windows of 100 bp (I suggest also trying 200 bp, 500 bp, and 1kb windows), should combine the data for all regions and perform correlations to SNP density in each window for the whole set of data. Such an analysis has a greater chance of demonstrating statistically significant relationships. This could replace the analysis presented in Figure 3 (which can be moved to Supplement). Moreover, the analysis should also take into account indels.

- In Arabidopsis, it has been shown that crossover is stimulated in heterozygous regions that are adjacent to homozygous regions on the same chromosome (http://dx.doi.org/10.7554/eLife.03708.001, https://doi.org/10.1038/s41467- 022-35722-3). This effect applies only to class I crossovers, and is reversed for class II crossovers (https://doi.org/10.15252/embj.2020104858, https://doi.org/10.1038/s41467-023-42511-z). This research system is very similar to the system used by the authors, although it likely differs in the level of DNA sequence divergence. The authors could discuss their work in this context.

Reviewer #1 (Public Review):

Summary:<br /> The authors of this study developed a software application, which aims to identify images as either "friendly" or "unfriendly" for readers with deuteranopia, the most common color-vision deficiency. Using previously published algorithms that recolor images to approximate how they would appear to a deuteranope (someone with deuteranopia), authors first manually assessed a set of images from biology-oriented research articles published in eLife between 2012 and 2022. The researchers identified 636 out of 4964 images as difficult to interpret ("unfriendly") for deuteranopes. They claim that there was a decrease in "unfriendly" images over time and that articles from cell-oriented research fields were most likely to contain "unfriendly" images.<br /> The researchers used the manually classified images to develop, train, and validate an automated screening tool. They also created a user-friendly web application of the tool, where users can upload images and be informed about the status of each image as "friendly" or "unfriendly" for deuteranopes.

Strengths:<br /> The authors have identified an important accessibility issue in the scientific literature: the use of color combinations that make figures difficult to interpret for people with color-vision deficiency. The metrics proposed and evaluated in the study are a valuable theoretical contribution. The automated screening tool they provide is well-documented, open source, and relatively easy to install and use. It has the potential to provide a useful service to the scientists who want to make their figures more accessible. The data are open and freely accessible, well documented, and a valuable resource for further research. The manuscript is well written, logically structured, and easy to follow.

Weaknesses:<br /> (1) The authors themselves acknowledge the limitations that arise from the way they defined what constitutes an "unfriendly" image. There is a missed chance here to have engaged deuteranopes as stakeholders earlier in the experimental design. This would have allowed to determine to what extent spatial separation and labelling of problematic color combinations responds to their needs and whether setting the bar at a simulated severity of 80% is inclusive enough. A slightly lowered barrier is still a barrier to accessibility.

(2) The use of images from a single journal strongly limits the generalizability of the empirical findings as well as of the automated screening tool itself. Machine-learning algorithms are highly configurable but also notorious for their lack of transparency and for being easily biased by the training data set. A quick and unsystematic test of the web application shows that the classifier works well for electron microscopy images but fails at recognizing red-green scatter plots and even the classical diagnostic images for color-vision deficiency (Ishihara test images) as "unfriendly". A future iteration of the tool should be trained on a wider variety of images from different journals.

(3) Focusing the statistical analyses on individual images rather than articles (e.g. in figures 1 and 2) leads to pseudoreplication. Multiple images from the same article should not be treated as statistically independent measures, because they are produced by the same authors. A simple alternative is to instead use articles as the unit of analysis and score an article as "unfriendly" when it contains at least one "unfriendly" image. In addition, collapsing the counts of "unfriendly" images to proportions loses important information about the sample size. For example, the current analysis presented in Fig. 1 gives undue weight to the three images from 2012, two of which came from the same article. If we perform a logistic regression on articles coded as "friendly" and "unfriendly" (rather than the reported linear regression on the proportion of "unfriendly" images), there is still evidence for a decrease in the frequency of "unfriendly" eLife articles over time. Another issue concerns the large number of articles (>40%) that are classified as belonging to two subdisciplines, which further compounds the image pseudoreplication. Two alternatives are to either group articles with two subdisciplines into a "multidisciplinary" group or recode them to include both disciplines in the category name.

(4.)The low frequency of "unfriendly" images in the data (under 15%) calls for a different performance measure than the AUROC used by the authors. In such imbalanced classification cases the recommended performance measure is precision-recall area under the curve (PR AUC: https://doi.org/10.1371%2Fjournal.pone.0118432) that gives more weight to the classification of the rare class ("unfriendly" images).

Reviewer #1 (Public Review):

In this study, the authors use prospective sorting and microarray analyses, extended by single-cell RNA sequencing, in the neural stem cell niche of the subventricular zone (SVZ) to identify and refine a series of states along the continuum from quiescent neural stem cells to mature progeny. Of note, changes in the levels and subgroups of RNA splicing regulators are detailed across this continuum. Using in vitro proliferation and differentiation assays, coupled with in vivo engraftment of some prospectively sorted subsets, the authors argue that a stage they define as immature neuroblasts (iNBs) retain proliferative and multilineage differentiation capacity that is not seen in the mature neuroblast population, and is unexpected based on prior models for lineage progression in this system. This iNB stage is accompanied by a change in RNA splicing regulator expression, which is of interest due to the emerging roles for RNA processing and preferential translation within this niche.

The central tension driving the discussion between authors and reviewers, in my view, is what is required to define cells as a "molecularly distinct population" in a lineage. Is it transcript expression, in vitro potential, or more? The authors argue that sorted immature neuroblasts are a defined, separate step in the neurogenic lineage. An alternative possibility is that this population is simply cycling transit-amplifying progenitors that have initiated a transcriptional program associated with neuroblast fates - that these cells are an intermediate point on a continuum between stem cells, transit-amplifying progeny, and commitment to a neuronal (or other) fate. Despite some additions in response to initial reviews, it is still the case that much of the data presented would be equally or more effective in supporting the second model. For example, the differentially spliced gene sets in Figure S4, which are put forward by the authors to support a different molecular identity for immature neuroblasts, show that the terms enriched for immature neuroblasts are largely also found in transit amplifying progenitors (generation of neurons, neurogenesis, cell projection organization, neuron development) and/or mature neuroblasts (cell projection organization, generation of neurons), suggesting that "immature neuroblasts" are transiting between these two states and that one of their most relevant features is that they are still cycling.

These data complement several additional sc-RNAseq studies of this stem cell niche, and use a different, but similar, sorting strategy to isolate and profile subpopulations of stem/progenitor cells and neuroblast progeny. The claim that immature neuroblasts retain multipotency - the ability to generate glia and neurons - is surprising and somewhat controversial given that this has largely not been reported before under homeostatic conditions. Some factors to consider when interpreting these data are that the "immature neuroblast" populations are studied in some experiments using a transcriptional signature and a functional assay, namely the timing of reappearance of these cells after use of agents that kill rapidly dividing cells (in this case, radiation), leading to reconstitution of the lineage by previously quiescent stem cells. In a separate set of experiments, a tamoxifen-inducible labeling system is used in combination with cell-surface markers to prospectively isolate and study the differentiation potential of neuroblast populations that are assumed to be equivalent to those found in transcriptional experiments. It would be of interest in the future to confirm that the exact sorted populations (using CD24/EGFR/DCX-CreERT2::CAG) have the same transcriptional profile as those studied in earlier experiments within the paper and to confirm the purity of the sorted populations. Finally, while use is made of engraftment of sorted populations to study the differentiation and lineage potential of these immature neuroblasts, a remaining question is the relative abundance of each lineage (neurons/astrocytes/oligodendrocytes) produced by the engrafted cells - is production of glia rare, or common? Could this be due to factors such as alteration of lineage potential due to culture conditions, a disconnect between transcript expression and protein expression, or an incompletely purified starter population?

Overall, this manuscript presents an intriguing possible refinement of models for SVZ neurogenesis, and highlights the role of RNA splicing at specific stages in the lineage. It will be of interest to see if additional groups confirm these findings and whether multiplexed immunostaining, highly multiplexed flow cytometry, or other approaches focused at the proteomic level extend these findings, particularly given recent data in the developing brain that suggest transcript and protein levels are relatively poorly correlated in stem/progenitor populations.

Reviewer #1 (Public Review):

In this manuscript, authors have performed extensive imaging analysis of six human histone H1 variants, their enrichment and localization, their differential dynamics during interphase and mitosis, and their association with lamina-associated domains (LADs) or nucleolus-associated domains. The manuscript is well-written with high-quality confocal and super-resolution images. Various interesting observations are made on distribution patterns of H1 variants. H1.2, H1.3, and H1.5 are shown to be universally enriched at the nuclear periphery whereas H1.4 and H1X are found to be distributed throughout the nucleus. Interestingly, H1X was the only H1 variant found to be abundant in nucleoli. Depletion of H1 variants has been shown to affect chromatin structure in a variant-specific manner, with H1.2 knock-down resulting in global chromatin decompaction. Overall, the study presents several interesting insights on H1 variants conducted in a large number of cell lines.

Reviewer #1 (Public Review):

Summary:

The authors combined high-speed video tracking of the limbs of freely moving mice with in vivo electrophysiology to demonstrate how striatal neurons encode single-limb gait. They also examine encoding other well-known aspects of locomotion, such as movement velocity and the initiation/termination of movement. The authors show that striatal neurons exhibit firing phase-locked with mouse gait at the single limb but also multi-limb level. Moreover, they describe gait deficits induced by severe unilateral dopamine neuron degeneration, and associate these deficits with a relative strengthening of gait-modulation in the firing of D2-expressing MSNs. Although the source and function of this gait-modulation remain unclear, this manuscript uncovers an important physiological correlate of striatal activity with gait, which may have implications for gait deficits in Parkinson's Disease.

Strengths:

While some previous work has looked at the encoding of gait variables in the striatum and other basal ganglia nuclei, this paper uses more careful quantification of gait with video tracking, comparing healthy and 6-OHDA-treated mice in the open field. The authors have collected a relatively large dataset of optically-identified striatal recordings to shed light on similarities and differences in the encoding of gait by striatal direct and indirect pathway neurons

Weaknesses:

There are some caveats to the interpretation of the analyses presented here, including how to compare encoding of gait variables when animals have markedly different behaviors (eg comparing sham and unilaterally 6-OHDA treated mice). The authors now address this caveat in the Discussion.

In an effort to causally link striatal firing to gait, the authors have added data from N=4 mice in which D2-expressing MSNs are optogenetically activated, and measured the resulting changes in gait parameters. As the authors note, this experiment does not directly get at the question of whether gait modulation of firing in the striatum contributes to the kinematics of gait (an experiment in which they altered the pattern of firing, to reduce modulation, would likely be needed). Given that this experiment has very low N and there are no included controls (eg mice expressing a control construct with optical stimulation), I do not think this data should be included in the manuscript. I think commenting in the Discussion that causal experiments will be needed in the future is adequate.

Many of the examples, as well as the average firing rates shown, are higher than typical for MSNs as reported in the literature. This is true even of the optically identified units that are shown in Figure 4. This may reflect the inclusion of neurons with interneuron-type properties (the authors report that there were some optically identified units with interneuron properties), the inclusion of some multi-unit activity in some recordings, or differences in recording/spike sorting techniques.

Reviewer #1 (Public Review):

Summary:

In their article, the authors delve into the therapeutic potential of a newly identified liver-specific lncRNA, FincoR, regulated by the Farnesoid X Receptor (FXR) and induced by the agonist tropifexor, in treating nonalcoholic steatohepatitis (NASH). They demonstrate that FincoR significantly enhances tropifexor's effectiveness in reducing liver fibrosis and inflammation in NASH, presenting it as a promising therapeutic target. The manuscript revisions broaden the study to include both mouse and human data, showing elevated FincoR levels in various mouse models of liver disease and identifying a similar lncRNA in humans, potentially indicating a conserved therapeutic mechanism. This research offers valuable insights into FincoR's role in NASH and suggests further exploration into its functions and mechanisms in liver disease treatment.

Strengths:

This study enhances our understanding of FincoR, a liver-specific lncRNA, and its therapeutic potential in treating NASH through a multifaceted research approach. The revised manuscript further strengthens this contribution by incorporating additional experiments and human relevance, summarized as follows: 1) The use of GRO-seq and RNA-seq technologies has provided an in-depth and unbiased view of the transcriptional alterations driven by the FXR agonist tropifexor, especially emphasizing FincoR's pivotal role. 2) The research expands on the original findings by including diverse mouse models of NAFLD/NASH and cholestatic liver injury. These models demonstrate significant increases in hepatic FincoR levels across various conditions, such as diets high in fat and fructose, chemical induction of liver cholestasis with ANIT, and surgical induction via bile duct ligation. This broadened scope underscores FincoR's involvement in liver disease mechanisms beyond the initial models of FXR knockout (KO) and FincoR liver-specific knockdown (FincoR-LKD). 3) Incorporation of tropifexor, an FDA-approved FXR agonist, alongside these experimental models bridges experimental findings to potential therapeutic applications for NASH patients. 2) The manuscript revision includes promising data on the sequence similarity between mouse FincoR and a human locus, identifying a partially conserved human lncRNA (XR_007061585.1) with elevated levels in NAFLD and PBC patients. This addition enhances the study's relevance to human health. 3) The study's design, with the inclusion of both negative and positive controls and now enriched with a wider array of mouse models and human data, ensures that the observed therapeutic effects can be confidently attributed to FincoR's modulation by tropifexor.

Weaknesses:

The authors acknowledge that certain questions remain unanswered within the scope of this study on FincoR, due to feasibility and technical challenges. While it's important to note that such limitations are rooted in the practical and technical complexities, these unresolved issues might limit the study's immediate impact. The decision to focus on the discovery and initial characterization of FincoR, is strategically but not scientifically justified.

Reviewer #3 (Public Review):

Summary:

In their paper Li et al. investigate the transcriptome of satellite cells obtained from different muscle types including hindlimb, diaphragm and extraocular muscles (EOM) from wild type and G93A transgenic mice (end stage ALS) in order to identify potential factors involved in the maintenance of the neuromuscular junction. The underlying hypothesis being that since EOMs are largely spared from this debilitating disease, they may secrete NMJ-protective factors. The results of their transcriptome analysis identified several axon guidance molecules including the chemokine Cxcl12, which are particularly enriched in EOM-derived satellite cells. Transduction of hindlimb-derived satellite cells with AAV encoding Cxcl12 reverted hindlimb-derived myotubes from the G93A mice into myotubes sharing phenotypic characteristics similar to those of EOM-derived satellite cells. Additionally, the authors were able to demonstrate that EOM-derived satellite cell myotube cultures are capable of enhancing axon extensions and innervation in co-culture experiments.

Strengths:

The strength of the paper is that the authors successfully isolated and purified different populations of satellite cells, compared their transcriptomes, identified specific factors release by EOM-derived satellite cells, overexpressed one of these factors (the chemokine Cxcl12) by AAV-mediated transduction of hindlimb-derived satellite cells. The transduced cells were then able to support axon guidance and NMJ integrity. They also show that administration of Na butyrate to mice decreased NMJ denervation and satellite cell-depletion of hind limbs. Furthermore, addition of Na Butyrate to hindlimb derived satellite cell myotube cultures increased Cxcl12 expression. These are impressive results providing important insights for the development of therapeutic targets to slow the loss on neuromuscular function characterizing ALS.

Weaknesses:

Several important aspects have not been addressed by the authors, these include the following points which weaken the conclusions and interpretation of the results.<br /> (a) Na Butyrate was shown to extend the survival of G93A mice by Zhang et al. Na butyrate has a variety of biological effects. For example, anti-inflammatory effects, inhibits mitochondrial oxidative stress, positively influences mitochondrial function, is a class I / II HDAC inhibitor etc. What is the mechanism underlying its beneficial effects both in the context of mouse muscle function in the ALS G93A mice and in the in vitro myotube assay? Cytokine quantification as well as histone acetylation/methylation can be assessed experimentally and this is an important point that has not been appropriately investigated.<br /> (b) In the context of satellite cell characterization, on line 151-152 the authors state that soleus muscles were excluded from further studies since they have a higher content of slow twitch fibers and are more similar to diaphragm. This justification is not valid in the context of ALS as well as many other muscle disorders. Indeed, soleus and diaphragm muscles contain a high proportion of slow twitch fibers (up to 80% and 50% respectively) but soleus muscles are more spared than diaphragm muscles. What makes soleus muscles (and EOMs) more resistant to ALS NMJ injury? Satellite cells from soleus muscles need to be characterized in detail as well.<br /> Furthermore, EOMs are complex muscles, containing many types of fibers and expressing different myosin heavy chain isoforms and muscle proteins. The fact that in mouse both the globular layer and orbital layers of EOMs express slow myosin heavy chain isoform as well as myosin heavy chain 2X, 2A and 2B (Zhou et al., 2010 IOVIS 51:6355-6363) also indicates that the sparing is not directly linked to the fast or slow twitch nature of the muscle fiber. This needs to be considered.<br /> (c) In the context of myotube formation from cultured satellite cells on line 178-179 the authors stained the myotubes for myosin heavy chain. Because of the diversity of myosin heavy chain isoforms and different muscle origin of the satellite cells investigated, the isoform of myosin heavy chain expressed by the myotubes needs to be tested and described. It is not sufficient to state anti-MYH.<br /> (d) The original RNAseq results have not been deposited and while it is true that the authors have analyzed the results and described them in Figures 6 and 7 and relative supplements, the original data needs to be shown both as an xls list as a Volcano plots (q value versus log2 fold change). This will facilitate the independent interpretation of the results by the readers as some transcripts may not be listed. As presented it is rather difficult to identify which transcripts aside Cxcl12 are commonly upregulated. Can the data be presented in a more visual way?<br /> (e) There is no section describing the statistical analysis methods used. In many figures more than 2 groups are compared so the authors need to use an ANOVA followed by a post hoc test.

The authors have achieved their aim in showing that satellite cells derived from EOMs have a distinct transcriptome and that this may be the basis of their sparing in ALS. Furthermore, this work may help develop future therapeutic interventions for patients with ALS.

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors set up a pipeline to predict insect repellents that are pleasant and safe for humans. This is done by daisy-chaining a new classification model based on predicting repellents with a published model on predicting human perception. Models use a feature-engineered selection of chemical features to make their predictions. The predicted molecules are then validated against a proxy humanoid (heated brick) and its safety is tested by molecular assays of human cells. The humanistic approach to modeling these authors have taken (which considers cosmetic/aesthetic appeal and safety) is novel and a necessary step for consumer usage. However, the importance of pleasantness over effectiveness is still up for debate (DEET is unpleasant but still used often) and the generalization of safety tests is unknown and assumed. The effectiveness of the prediction models is also still warranted. They pass the authors' own behavioral tests, but their contribution to the field is unknown as both models (new and published) have not been rigorously benchmarked to previous models. Moreover, the author's breadth of literature in this field is sparse, ignoring directly related studies.

Strengths:

Humanistic approach to modeling considers pleasantness and safety. Chaining models can help limit the candidate odorants from the vastness of odor space.

Weaknesses:

The current models need to be bench-marked against leading models predicting similar outcomes. Similarly, many of these papers need to be addressed and discussed in the introduction. The authors might even consider their data sources for model training to increase performance and lexical categorization for interoperability. For instance, the Dravnikes data lexicon, currently used in the human perception lexicon, has been highly criticized for its overlapping and hard-to-interpret descriptive terms ("FRAGRANT", "AROMATIC").

Human Perception

Khan, R. M., Luk, C. H., Flinker, A., Aggarwal, A., Lapid, H., Haddad, R., & Sobel, N. (2007). Predicting odor pleasantness from odorant structure: pleasantness as a reflection of the physical world. Journal of Neuroscience, 27(37), 10015-10023.

Keller, A., Gerkin, R. C., Guan, Y., Dhurandhar, A., Turu, G., Szalai, B., ... & Meyer, P. (2017). Predicting human olfactory perception from chemical features of odor molecules. Science, 355(6327), 820-826.

Gutiérrez, E. D., Dhurandhar, A., Keller, A., Meyer, P., & Cecchi, G. A. (2018). Predicting natural language descriptions of mono-molecular odorants. Nature communications, 9(1), 4979.

Lee, B. K., Mayhew, E. J., Sanchez-Lengeling, B., Wei, J. N., Qian, W. W., Little, K. A., ... & Wiltschko, A. B. (2023). A principal odor map unifies diverse tasks in olfactory perception. Science, 381(6661), 999-1006.<br /> Related cleaned data: https://github.com/BioMachineLearning/openpom

Insect Repellents:

Wright, R. H. (1956). Physical basis of insect repellency. Nature, 178(4534), 638-638.

Katritzky, A. R., Wang, Z., Slavov, S., Tsikolia, M., Dobchev, D., Akhmedov, N. G., ... & Linthicum, K. J. (2008). Synthesis and bioassay of improved mosquito repellents predicted from chemical structure. Proceedings of the National Academy of Sciences, 105(21), 7359-7364.

Bernier, U. R., & Tsikolia, M. (2011). Development of Novel Repellents Using Structure− Activity Modeling of Compounds in the USDA Archival Database. In Recent Developments in Invertebrate Repellents (pp. 21-46). American Chemical Society.

Wei, J. N., Vlot, M., Sanchez-Lengeling, B., Lee, B. K., Berning, L., Vos, M. W., ... & Dechering, K. J. (2022). A deep learning and digital archaeology approach for mosquito repellent discovery. bioRxiv, 2022-09.

The current study assumes that insect repellents repel via their odor valence to the insect, but this is not accurate. Insect repellents also mask the body odor of humans making them hard to locate. The authors need to consult the literature to understand the localization and landing mechanisms of insects to their hosts. Here, they will understand that heat alone is not the attractant as their behavioral assay would have you believe. I suggest the authors test other behaviour assays to show more convincing evidence of effectiveness. See the following studies:

De Obaldia, M. E., Morita, T., Dedmon, L. C., Boehmler, D. J., Jiang, C. S., Zeledon, E. V., ... & Vosshall, L. B. (2022). Differential mosquito attraction to humans is associated with skin-derived carboxylic acid levels. Cell, 185(22), 4099-4116.

McBride, C. S., Baier, F., Omondi, A. B., Spitzer, S. A., Lutomiah, J., Sang, R., ... & Vosshall, L. B. (2014). Evolution of mosquito preference for humans linked to an odorant receptor. Nature, 515(7526), 222-227.

Wei, J. N., Vlot, M., Sanchez-Lengeling, B., Lee, B. K., Berning, L., Vos, M. W., ... & Dechering, K. J. (2022). A deep learning and digital archaeology approach for mosquito repellent discovery. bioRxiv, 2022-09.

Reviewer #1 (Public Review):

Summary:

In this report, the authors investigated the effects of reproductive secretions on sperm function in mice. The authors attempt to weave together an interesting mechanism whereby a testosterone-dependent shift in metabolic flux patterns in the seminal vesicle epithelium supports fatty acid synthesis, which they suggest is an essential component of seminal plasma that modulates sperm function by supporting linear motility patterns.

Strengths:

The topic is interesting and of general interest to the field. The study employs an impressive array of approaches to explore the relationship between mouse endocrine physiology and sperm function mediated by seminal components from various glandular secretions of the male reproductive tract.

Weaknesses:

Unfortunately, support for the proposed mechanism is not convincingly supported by the data, and the experimental design and methodology need more rigor and details, and the presence of numerous (uncontrolled) confounding variables in almost every experimental group significantly reduce confidence in the overall conclusions of the study.

The methodological detail as described is insufficient to support replication of the work. Many of the statistical analyses are not appropriate for the apparent designs (e.g. t-tests without corrections for multiple comparisons). This is important because the notion that different seminal secretions will affect sperm function would likely have a different conclusion if the correct controls were selected for post hoc comparison. In addition, the HTF condition was not adjusted to match the protein concentrations of the secretion-containing media, likely resulting in viscosity differences as a major confounding factor on sperm motility patterns.

There is ambiguity in many of the measurements due to the lack of normalization (e.g. all Seahorse Analyzer measurements are unnormalized, making cell mass and uniformity a major confounder in these measurements). This would be less of a concern if basal respiration rates were consistently similar across conditions and there were sufficient independent samples, but this was not the case in most of the experiments.

The observation that oleic acid is physiologically relevant to sperm function is not strongly supported. The cellular uptake of 10-100uM labeled oleic acid is presumably due to the detergent effects of the oleic acid, and the authors only show functional data for nM concentrations of exogenous oleic acid. In addition, the effect sizes in the supporting data were not large enough to provide a high degree of confidence given the small sample sizes and ambiguity of the design regarding the number of biological and technical replicates in the extracellular flux analysis experiments.

Overall, the most confident conclusion of the study was that testosterone affects the distribution of metabolic fluxes in a cultured human seminal vesicle epithelial cell line, although the physiological relevance of this observation is not clear.

In the introduction, the authors suggest that their analyses "reveal the pathways by which seminal vesicles synthesize seminal plasma, ensure sperm fertility, and provide new therapeutic and preventive strategies for male infertility." These conclusions need stronger or more complete data to support them.

Reviewer #1 (Public Review):

The manuscript investigates the role of membrane contact sites (MCSs) and sphingolipid metabolism in regulating vacuolar morphology in the yeast Saccharomyces cerevisiae. The authors show that tricalbin (1-3) deletion leads to vacuolar fragmentation and the accumulation of the sphingolipid phytosphingosine (PHS). They propose that PHS triggers vacuole division through MCSs and the nuclear-vacuolar junction (NVJ). The study presents some solid data and proposes potential mechanisms underlying vacuolar fragmentation driven by this pathway. Although the manuscript is clear in what the data indicates and what is more hypothetical, the story would benefit from providing more conclusive evidence to support these hypothesis. Overall, the study provides valuable insights into the connection between MCSs, lipid metabolism, and vacuole dynamics.

Reviewer #1 (Public Review):

The authors investigate the alpha chain t cell receptor landscape in conventional vs regulatory CD4 T cells. Overall I think it is a very well thought out and executed study with interesting conclusions. Findings are valuable and are supported by convincing evidence. This work will be of interest for immunologists studying T cells.

Strengths:

- One of a kind evidence and dataset.

- State of the art analyses using well accepted in the literature tools.

- Interesting conclusions on the breadth of immune response to challenges across different types of challenges (tumor, viral and parasitic).

Reviewer #1 (Public Review):

In this manuscript, Shimonty and colleagues study the effects of FNDC5/irisin deletion on osteocytes in a sex-specific manner using models of lactation induced bone loss and bone loss due to low calcium diet (LCD). Consistent with the previous findings of Kim et al. (2018), the authors report 'protective' effects of irisin deficiency in lactating female FNDC5-null mice due to reduced osteocytic osteolysis. Interestingly, FNDC5 null mice show distinct changes when placed on LCD, with mutant females showing some protection from hyperparathyroidism-induced bone loss, while mutant males (which have more cortical bone at baseline) show increased LCD-induced bone loss. Furthermore, new insights into irisin's role in osteocytes regarding cellular energetic metabolism were provided by sex and gene-dependent transcriptomic datasets. Strengths of the well-written manuscript include clear description of sex-dependent effects, strong transcriptomic datasets, and focus on cortical bone changes using microCT, histomorphometry, BSEM, and serum analysis. Despite these strengths, important weaknesses are noted (below) which could be addressed to improve the impact of the work for a broad audience.

Major comments:

(1) Overall, the magnitude of the effect size due to FNDC5 deficiency in both male and female mice is rather modest at the level of bone mass. Looking at the data from a qualitative perspective, it is clear that knockout females still lose bone during lactation and on the low calcium diet (LCD). It is difficult to assess the physiologic consequence of the modest quantitative 'protection' seen in FNDC5 mutants since the mutants still show clear and robust effects of lactation and LCD on all parameters measured. Similarly, the magnitude of the 'increased' cortical bone loss in FNDC5 mutant males is also modest, and perhaps could be related to the fact that these mice are starting with slightly more cortical bone. Since the authors do not provide a convincing molecular explanation for why FNDC5 deficiency causes these somewhat subtle changes, I would like to offer a suggestion for the authors to consider (below, point #2) which might de-emphasize the focus of the manuscript on FNDC5. If the authors chose not to follow this suggestion, the manuscript could be strengthened by addressing the consequences of the modest changes observed in WT versus FNDC5 KO mice. I understand that the effects of FNDC5 are more obvious at the level of osteocyte morphology, and it is reasonable to emphasize these findings here.

(2) The bone RNA-seq findings reported in Figures 4-6 are quite interesting. Although Youlten et al previously reported that the osteocyte transcriptome is sex-dependent, the work here certainly advances that notion to a considerable degree, and likely will be of high interest to investigators studying skeletal biology and sexual dimorphism in general. To this end, one direction for the authors to consider might be to refocus their manuscript towards sexually-dimorphic gene expression patterns in osteocytes and the different effects of LCD on male versus female mice. This would allow the authors to better emphasize these major findings, and then to use FNDC5 deficiency as an illustrative example of how sexually-dimorphic osteocytic gene expression patterns might be affected by deletion of an osteocyte-acting endocrine factor. Ideally, the authors would confirm RNA-seq data comparing male versus female mice in osteocytes using in situ hybridization or immunostaining. Of course, this point is only a suggestion for the authors to consider.

(3) It would be appreciated if the authors could provide additional serum parameters (if possible) to clarify incomplete data in both lactation and low-calcium diet models: RANKL/OPG ratio, Ctx, PTHrP, and 1,25-dihydroxyvitamin D levels. I understand that this may not be possible due to lack of available material.

Reviewer #1 (Public Review):

The authors present a number of deep learning models to analyse the dynamics of epithelia. In this way they want to overcome the time-consuming manual analysis of such data and also remove a potential operator bias. Specifically, they set up models for identifying cell division events and cell division orientation. They apply these tools to the epithelium of the developing Drosophila pupal wing. They confirm a linear decrease of the division density with time and identify a burst of cell division after healing of a wound that they had induced earlier. These division events happen a characteristic time after and a characteristic distance away from the wound. These characteristic quantities depend on the size of the wound.

Strengths:

The methods developed in this work achieve the goals set by the authors and are a very helpful addition to the toolbox of developmental biologists. They could potentially be used on various developing epithelia. The evidence for the impact of wounds on cell division is compelling.

The methods presented in this work should prove to be very helpful for quantifying cell proliferation in epithelial tissues.

Reviewer #1 (Public Review):

This is a clear account of some interesting work. The experiments and analyses seem well done and the data are useful. It is nice to see that VSDI results square well with those from prior extracellular recordings.

The authors have done a good job responding to the main points of my previous review. One important question remains, as stated in that review:

"My reading is that this is primarily a study of surround suppression with results that follow pretty directly from what we already know from that literature, and although they engage with some of the literature they do not directly mention surround suppression in the text. Their major effect - what they repeatedly describe as a "paradoxical" result in which the responses initially show a stronger response to matched targets and backgrounds and then reverse - seems to pretty clearly match the expected outcome of a stimulus that initially evokes additional excitation due to increased center contrast followed by slightly delayed surround suppression tuned to the same peak orientation. Their dynamics result seems entirely consistent with previous work, e.g. Henry at al 2020, particularly their Fig. 3 https://elifesciences.org/articles/54264, so it seems like a major oversight to not engage with that work at all, and to explain what exactly is new here."

Their rebuttal of my first review is not convincing -- I still believe that surround influences are important and perhaps predominant in determining the outcome of the experiments. This is particularly clear for the "paradoxical" dynamics that they observe, which seem exactly to reflect the behavior of the surround.

The authors' arguments to the contrary are based on three main points. First, their stimuli cover the center and surround, unlike those of many previous experiments, so they argue that this somehow diminishes the impact of the surround. But the argument is not accompanied by data showing the effects of center stimuli alone or surround stimuli alone. Second, their model -- a normalization model -- does not need surround influences to account for the masking effect. Third, they cite human psychophysical masking results from their collaborators (Sebastian et al 2017), but do not cite an equally convincing demonstration that surround contrast creates potent orientation selective masking when presented alone (Petrov et al 2005, https://doi.org/10.1523/JNEUROSCI.2871-05.2005).

At the end of the day, these issues will be resolved by further experiments, not argumentation. The paper stands as an excellent contribution, but it might be wise for the authors to be less doctrinaire in their interpretations.

Reviewer #1 (Public Review):

Summary:

In this work, the authors utilize recurrent neural networks (RNNs) to explore the question of when and how neural dynamics and the network's output are related from a geometrical point of view. The authors found that RNNs operate between two extremes: an 'aligned' regime in which the weights and the largest PCs are strongly correlated and an 'oblique' regime where the output weights and the largest PCs are poorly correlated. Large output weights led to oblique dynamics, and small output weights to aligned dynamics. This feature impacts whether networks are robust to perturbation along output directions. Results were linked to experimental data by showing that these different regimes can be identified in neural recordings from several experiments.

Strengths:

A diverse set of relevant tasks.

A well-chosen similarity measure.

Exploration of various hyperparameter settings.

Weaknesses:

One of the major connections found BCI data with neural variance aligned to the outputs. Maybe I was confused about something, but doesn't this have to be the case based on the design of the experiment? The outputs of the BCI are chosen to align with the largest principal components of the data.

Proposed experiments may have already been done (new neural activity patterns emerge with long-term learning, Oby et al. 2019). My understanding of these results is that activity moved to be aligned as the manifold changed, but more analyses could be done to more fully understand the relationship between those experiments and this work.

Analysis of networks was thorough, but connections to neural data were weak. I am thoroughly convinced of the reported effect of large or small output weights in networks. I also think this framing could aid in future studies of interactions between brain regions.

This is an interesting framing to consider the relationship between upstream activity and downstream outputs. As more labs record from several brain regions simultaneously, this work will provide an important theoretical framework for thinking about the relative geometries of neural representations between brain regions.

It will be interesting to compare the relationship between geometries of representations and neural dynamics across connected different brain areas that are closer to the periphery vs. more central.

It is exciting to think about the versatility of the oblique regime for shared representations and network dynamics across different computations.

The versatility of the oblique regime could lead to differences between subjects in neural data.

Reviewer #1 (Public Review):

Summary:

The pioneering work of Eve Marder on central pattern generators in the stomatogastric ganglion (STG) has made a strong case for redundancy as a biological mechanism for ensuring functional robustness, where multiple configurations of biophysical parameters are equivalent in terms of their ability to generate desired patterns of periodic circuit activity. In parallel, normative theories of synaptic plasticity have argued for functional equivalences between learning objectives and corresponding plasticity rules in implementing simple unsupervised learning (see Brito & Gerstner 2016, although similar arguments have been made long before e.g. in Aapo Hyvarinen's ICA book). This manuscript argues that similar notions of redundancy need to be taken into account in the study of synaptic plasticity rules in the brain, more specifically in the context of data-driven approaches to extract the "true" synaptic plasticity rule operating in a neural circuit from neural activity recordings. Concretely, the modeling approach takes a set of empirical measurements of the evolution of neural activity and trains a flexibly parametrized model to match that in statistical terms. Instead of being predefined by the experimenter, the features that determine this match are themselves extracted from data using a generative adversarial network framework (GAN). They show that the flexible models manage to reproduce the neural activity to a reasonable degree (though not perfectly), but lead to very different synaptic trajectories.

Strengths:

The idea of learning rule redundancy is a good one, and the use of GANs for the learning rule estimation is a good complement to other data-driven approaches to extract synaptic plasticity ruled from neural data.

Weaknesses:

(1) Numerics provide only partial support to the statements describing the results.

(2) Even if believing the results, I don't necessarily agree with the interpretation. First: unlike the Marder example where there is complementary evidence to argue that the parameter variations actually reflect across animal biophysical variations, here the statements are really about uncertainty that the experimenter has about what is going on in a circuit observed through a certain measurement lens. Second, while taking into account this uncertainty when using the outcomes of this analysis for subsequent scientific goals is certainly sensible, the biggest punchline for me is that simply observing neural activity in a simple and very restricted context does not provide enough information about the underlying learning mechanism, especially when the hypothesis space is very large (as is the case for the MLP). So it seems more useful to use this framework to think about how to enrich the experimental design/ learning paradigms/ or the measurements themselves to make the set of hypotheses more discriminable (in the spirit of the work by Jacob Portes et al, 2022 for instance). Conversely, one should perhaps think about other ways in which to use other forms of experimental data to reasonably constrain the hypothesis space in the first place.

Reviewer #2 (Public Review):

Summary:

This study from Bamgbose et al. identifies a new and important interaction between H4K20me and Parp1 that regulates inducible genes during development and heat stress. The authors present convincing experiments that form a mostly complete manuscript that significantly contributes to our understanding of how Parp1 associates with target genes to regulate their expression.

Strengths:

The authors present 3 compelling experiments to support the interaction between Parp1 and H4K20me, including:

(1) PR-Set7 mutants remove all K4K20me and phenocopy Parp mutant developmental arrest and defective heat shock protein induction.

(2) PR-Set7 mutants have dramatically reduced Parp1 association with chromatin and reduced poly-ADP ribosylation.

(3) Parp1 directly binds H4K20me in vitro.

Weaknesses:

(1) The RNAseq analysis of Parp1/PR-Set7 mutants is reasonable, but there is a caveat to the author's conclusion (Line 251): "our results indicate H4K20me1 may be required for PARP-1 binding to preferentially repress metabolic genes and activate genes involved in neuron development at co-enriched genes." An alternative possibility is that many of the gene expression changes are indirect consequences of altered development induced by Parp1 or PR-Set7 mutants. For example, Parp1 could activate a transcription factor that represses metabolic genes. The authors counter this model by stating that Parp1 directly binds to "repressed" metabolic genes. While this argument supports their model, it does not rule out the competing indirect transcription factor model. Therefore, they should still mention the competing model as a possibility.

(2) The section on inducibility of heat shock genes is interesting but missing an important control that might significantly alter the author's conclusions. Hsp23 and Hsp83 (group B genes) are transcribed without heat shock, which likely explains why they have H4K20me without heat shock. The authors made the reasonable hypothesis that this H4K20me would recruit Parp-1 upon heat shock (line 270). However, they observed a decrease of H4K20me upon heat shock, which led them to conclude that "H4K20me may not be necessary for Parp1 binding/activation" (line 275). However, their RNA expression data (Fig4A) argues that both Parp1 and H40K20me are important for activation. An alternative possibility is that group B genes indeed recruit Parp1 (through H4K20me) upon heat shock, but then Parp1 promotes H3/H4 dissociation from group B genes. If Parp1 depletes H4, it will also deplete H4K20me1. To address this possibility, the authors should also do a ChIP for total H4 and plot both the raw signal of H4K20me1 and total H4 as well as the ratio of these signals. The authors could also note that Group A genes may similarly recruit Parp1 and deplete H3/H4 but with different kinetics than Group B genes because their basal state lacks H4K20me/Parp1. To test this possibility, the authors could measure Parp association, H4K20methylation, and H4 depletion at more time points after heat shock at both classes of genes.

Reviewer #1 (Public Review):

Summary:

Knudstrup et al. use two-photon calcium imaging to measure neural responses in the mouse primary visual cortex (V1) in response to image sequences. The authors presented mice with many repetitions of the same four-image sequence (ABCD) for four days. Then on the fifth day, they presented unexpected stimulus orderings where one stimulus was either omitted (ABBD) or substituted (ACBD). After analyzing trial-averaged responses of neurons pooled across multiple mice, they observed that stimulus omission (ABBD) caused a small, but significant, strengthening of neural responses but observed no significant change in the response to stimulus substitution (ACBD). Next, they performed population analyses of this dataset. They showed that there were changes in the correlation structure of activity and that many features of sequence ordering could be reliably decoded. This second set of analyses is interesting and exhibited larger effect sizes than the first results about predictive coding. However, concerns about the design of the experiment temper my enthusiasm.

Strengths:

(1) The topic of predictive coding in the visual cortex is exciting, and this task builds on previous important work by the senior author (Gavornik and Bear 2014) where unexpectedly shuffling sequence order caused changes in LFPs recorded from the visual cortex.

(2) Deconvolved calcium responses were used appropriately here to look at the timing of the neural responses.

(3) Neural decoding results showing that the context of the stimuli could be reliably decoded from trial-averaged responses were interesting. However I have concerns about how the data was formatted for performing these analyses.

Weaknesses:

(1) All analyses were performed on trial-averaged neural responses that were pooled across mice. Owing to differences between subjects in behavior, experimental preparation quality, and biological variability, it seems important to perform at least some analyses on individual analyses to assess how behavioral training might differently affect each animal.

(2) The correlation analyses presented in Figure 3 (labeled the second Figure 2 in the text) should be conducted on a single-animal basis. Studying population codes constructed by pooling across mice, particularly when there is no behavioral readout to assess whether learning has had similar effects on all animals, appears inappropriate to me. If the results in Figure 3 hold up on single animals, I think that is definitely an interesting result.

(3) On Day 0 and Day 5, the reordered stimuli are presented in trial blocks where each image sequence is shown 100 times. Why wasn't the trial ordering randomized as was done in previous studies (e.g. Gavornik and Bear 2014)? Given this lack of reordering, did neurons show reduced predictive responses because the unexpected sequence was shown so many times in quick succession? This might change the results seen in Figure 2, as well as the decoder results where there is a neural encoding of sequence order (Figure 4). It would be interesting if the Figure 4 decoder stopped working when the higher-order block structure of the task was disrupted.

(4) A primary advantage of using two-photon calcium imaging over other techniques like extracellular electrophysiology is that the same neurons can be tracked over many days. This is a standard approach that can be accomplished by using many software packages-including Suite2P (Pachitariu et al. 2017), which is what the authors already used for the rest of their data preprocessing. The authors of this paper did not appear to do this. Instead, it appears that different neurons were imaged on Day 0 (baseline) and Day 5 (test). This is a significant weakness of the current dataset.

Reviewer #1 (Public Review):

Summary:

The authors show that SVZ-derived astrocytes respond to a middle carotid artery occlusion (MCAO) hypoxia lesion by secreting and modulating hyaluronan at the edge of the lesion (penumbra) and that hyaluronan is a chemoattractant to SVZ astrocytes. They use lineage tracing of SVZ cells to determine their origin. They also find that SVZ-derived astrocytes express Thbs-4 but astrocytes at the MCAO-induced scar do not. Also, they demonstrate that decreased HA in the SVZ is correlated with gliogenesis. While much of the paper is descriptive/correlative they do overexpress Hyaluronan synthase 2 via viral vectors and show this is sufficient to recruit astrocytes to the injury. Interestingly, astrocytes preferred to migrate to the MCAO than to the region of overexpressed HAS2.

Strengths:

The field has largely ignored the gliogenic response of the SVZ, especially with regard to astrocytic function. These cells and especially newborn cells may provide support for regeneration. Emigrated cells from the SVZ have been shown to be neuroprotective via creating pro-survival environments, but their expression and deposition of beneficial extracellular matrix molecules are poorly understood. Therefore, this study is timely and important. The paper is very well written and the flow of results is logical.

Weaknesses:

The main problem is that they do not show that Hyaluronan is necessary for SVZ astrogenesis and or migration to MCAO lesions. Such loss of function studies have been carried out by studies they cite (e.g. Girard et al., 2014 and Benner et al., 2013). Similar approaches seem to be necessary in this work.

Major points:

(1) How good of a marker for newborn astrocytes is Thbs4? Did you co-label with B cell markers like EGFr? Is the Thbs4 gene expressed in B cells? Do scRNAseq papers show it is expressed in B cells? Are they B1 or B2 cells?

(2) It is curious that there was no increase in Type C cells after MCAO - do the authors propose a direct NSC-astrocyte differentiation?

(3) The paper would be strengthened with orthogonal views of z projections to show co-localization.

(4) It is not clear why the dorsal SVZ is analysed and focused on in Figure 4. This region emanates from the developmental pallium (cerebral cortex anlagen). It generates some excitatory neurons early postnatally and is thought to have differential signalling such as Wnt (Raineteau group).

(5) Several of the images show the lesion and penumbra as being quite close to the SVZ. Did any of the lesions contact the SVZ? If so, I would strongly recommend excluding them from the analysis as such contact is known to hyperactivate the SVZ.

(6) The authors switch to a rat in vitro analysis towards the end of the study. This needs to be better justified. How similar are the molecules involved between mouse and rat?

(7) Similar comment for overexpression of naked mole rat HA.

Reviewer #1 (Public Review):

The present study examines whether one can identify kinematic signatures of different motor strategies in both humans and non-human primates (NHP). The Critical Stability Task (CST) requires a participant to control a cursor with complex dynamics based on hand motion. The manuscript includes datasets on performance of NHPs collected from a previous study, as well as new data on humans performing the same task. Further human experiments and optimal control models highlight how different strategies lead to different patterns of hand motion. Finally, classifiers were developed to predict which strategy individuals were using on a given trial.

There are several strengths to this manuscript. I think the CST task provides a very useful behavioural task to explore the neural basis of voluntary control. While reaching is an important basic motor skill and commonly studied, there is much to learn by looking at other motor actions to address many fundamental issues on the neural basis of voluntary control.

I also think the comparison between human and NHP performance is important as there is a common concern that NHPs can be overtrained in performing motor tasks leading to differences in their performance as compared to humans. The present study highlights that there are clear similarities in motor strategies of humans and NHPs. While the results are promising, I would suggest that the actual use of these paradigms and techniques likely need some improvement/refinement. Notably, the threshold or technique to identify which strategy an individual is using on a given trial needs to be more stringent given the substantial overlap in hand kinematics between different strategies.

The most important goal of this study is to set up future studies to examine how changes in motor strategies impact neural processing. The revised manuscript has improved the technique for identifying which strategy appears to be performed by the individual. A pivotal assumption is that one can identify control strategies from differences in behaviour. As I'm sure the authors know, this inversion of the control problem is not trivial and so success requires that there are only a few 'reasonable' strategies to solve the control problem, and that these strategies lead to distinct patterns of behavior. Many of the concerns raised by myself and the other reviewers relate to this challenge. The revised manuscript now uses a more strict criteria which is good improvement.

One of the values of this paper is to start to develop the tools and approaches to address neural basis of control. The strength of the present manuscript is that it includes modelling, explicit strategy instructions in humans, and then analysis of free-form performance in humans and non-human primates. Given the novelty of this question and approach, there likely are many ways that the techniques and approaches could be improved, but I think they've done a great start. Their approach is quite clever and provides an important blueprint for future studies.

One weakness at this point is that there is still substantial overlap in behavoural performance predicted between strategies, as some human participants given an explicit strategy were almost equally categorized as reflecting the other strategy. I'm glad to see the addition of the model performance on perturbation trials as this additional figure clearly highlights much greater separation in performance than when observing natural behavior. While it is not reasonable to expand beyond this for the present manuscript, I think it is essential for this group to develop the perturbation paradigm (and potentially other approaches) that can better isolate behavioral signatures of different control strategies. I think future work will be strengthened by having multiple experimental angles to interpret the neural activity.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, Fister et. al. investigate how amputational and burn wounds affect sensory axonal damage and regeneration in a zebrafish model system. The authors discovered that burn injury results in increased peripheral axon damage and impaired regeneration. Convincing experiments show altered axonal morphology and increased Ca2+ fluxes as a result of burn damage. Further experimental proof supports that early removal of the burnt tissue by amputation rescues axonal damage. Burn damage was also shown to markedly increase keratinocyte migration and increase localized ROS production as measured by the dye Pfbsf. These responses could be inhibited by Arp 2/3 inhibition and isotonic treatment.

Strengths:<br /> The authors use state-of-the-art methods to study and compare transection and burn-induced tissue damage. Multiple experimental approaches (morphology, Ca2+ fluxing, cell membrane labeling) confirm axonal damage and impaired regeneration time. Furthermore, the results are also accompanied by functional response tests of touch sensitivity. This is the first study to extend the role of tissue-damage-related osmotic exposure beyond wound closure and leukocyte migration to a novel layer of pathology: axonal damage and regeneration.

Weaknesses:<br /> The conclusions of the paper claiming a link between burn-induced epithelial cell migration, spatial redox signaling, and sensory axon regeneration are mainly based on correlative observations. Arp 2/3 inhibition impairs cell migration but has no significant effect on axon regeneration and restoration of touch sensitivity.

Pharmacological or genetic approaches should be used to prove the role of ROS production by directly targeting the known H2O2 source in the system: DUOX.

While the authors provide clear and compelling proof that osmotic responses lie at the heart of the burn-induced axonal damage responses, they did not consider the option of further exploring any biology related to osmotic cell swelling. Could osmotic ATP release maybe play a role through excitotoxicity? Could cPLA2 activation-dependent eicosanoid production relate to the process? Pharmacological tests using purinergic receptor inhibition or blockage of eicosanoid production could answer these questions.

The authors provide elegant experiments showing that early removal of the burnt tissue can rescue damage-induced axonal damage, which could also be interpreted in an osmotic manner: tail fin transections could close faster than burn wounds, allowing for lower hypotonic exposure time. Axonal damage and slow regeneration in tail fin burn wounds could be a direct consequence of extended exposure time to hypotonic water.

Reviewer #1 (Public Review):

This manuscript proposes a new bioinformatics approach identifying several hundreds of previously unknown inhibitory immunoreceptors. When expressed in immune cells (such as neutrophils, monocytes, CD8+, CD4+, and T-cells), such receptors inhibit the functional activity of these cells. Blocking inhibitory receptors represents a promising therapeutic strategy for cancer treatment.

As such, this is a high-quality and important bioinformatics study. One general concern is the absence of direct experimental validation of the results. In addition to the fact that the authors bioinformatically identified 51 known receptors, providing such experimental evaluation (of at least one, or better few identified receptors) would, in my opinion, significantly strengthen the presented evidence.

I will now briefly summarize the results and give my comments.

First, using sequence comparison analysis, the authors identify a large set of putative receptors based on the presence of immunoreceptor tyrosine-based inhibitory motifs (ITIMs), or immunoreceptor tyrosine-based switch motifs (ITSMs). They further filter the identified set of receptors for the presence of the ITIMs or ITSMs in an intracellular domain of the protein. Second, using AlphaFold structure modeling, the authors select only receptors containing ITIMs/ITSMs in structurally disordered regions. Third, the evaluation of gene expression profiles of known and putative receptors in several immune cell types was performed. Fourth, the authors classified putative receptors into functional categories, such as negative feedback receptors, threshold receptors, threshold disinhibition, and threshold-negative feedback. The latter classification was based on the available data from Nat Rev Immunol 2020. Fifth, using publicly available single-cell RNA sequencing data of tumor-infiltrating CD4+ and CD8+ cells from nearly twenty types of cancer, the authors demonstrate that a significant fraction of putative receptors are indeed expressed in these datasets.

In summary, in my opinion, this is an interesting, important, high-quality bioinformatics work. The manuscript is clearly written and all technical details are carefully explained.

One comment/suggestion regarding the methodology of evaluating gene expression profiles of putative receptors: perhaps it might be important to look at clusters of genes that are co-expressed with putative inhibitory receptors.

Reviewer #1 (Public Review):

Summary:

In the paper entitled "PI3K/HSCB axis facilitates FOG1 nuclear translocation to promote erythropoiesis and megakaryopoiesis", the authors sought to determine the role of HSCB, a known regulator of iron-sulfur cluster transfer, in the generation of erythrocytes and megakaryocytes. They utilized a human primary cell model of hematopoietic differentiation to identify a novel mechanism whereby HSCB is necessary for the activation of erythroid and megakaryocytic gene expression through regulation of the nuclear localization of FOG-1, an essential transcription co-regulator of the GATA transcription factors. Their work establishes this novel regulatory axis as a mechanism by which cytokine signaling through EPO-R and MPL drives the lineage-specification of hematopoietic progenitors to erythrocytes and megakaryocytes, respectively.

Impact:

The major impact of this work is in a greater understanding of how cytokine signaling through EPO/TPO functions to promote lineage specification of hematopoietic stem/progenitor cells. While the major kinase cascades downstream of the EPO/TPO receptors have been elucidated, how those cascades affect gene expression to promote a specific differentiation program is poorly understood. For this work, we now understand that nuclear localization of FOG is a critical regulatory node by which EPO/TPO signaling is required to launch FOG-dependent gene expression. However, these cytokine receptors have many overlapping and redundant targets, so it still remains to be elucidated how signaling through the different receptors promotes divergent gene expression programs. Perhaps similar regulatory mechanisms exist for other lineage-specifying transcription factors.

Strengths:

The authors use two different cellular models of erythroid differentiation (K562 and human primary CD34+ cells) to elucidate the multi-factorial mechanism controlling FOG-1 nuclear localization. The studies are well-controlled and rigorously establish their mechanism through complementary approaches. The differentiation effects are established through cell surface marker expression, protein expression, and gene expression analyses. Novel protein interactions discovered by proteomics analyses were validated through bi-directional co-IP experiments in multiple experimental systems. Protein cellular localization findings are supported by both immunofluorescence and cell fractionation immunoblot analyses. The robustness of their experimental findings gives great confidence in the likelihood that the methods and findings can be reproduced in future work based on their conclusions.

Weaknesses:

The one unexplained step in this intricately described mechanism is how HSCB functions to promote TACC3 degradation. It appears that the proteasome is involved since MG-132 reverses the effect of HSCB deficiency, but no other details are provided. Does HSCB target TACC3 for ubiquitination somehow? Future studies will be required to understand this portion of the mechanism.

One weakness of the study design is that no in vivo experiments are conducted. The authors comment that the HSCB mouse phenotype is too dramatic to permit studies of erythropoiesis in vivo; however, a conditional approach could have been pursued.

It should also be noted that a previous study had already shown that TACC3 regulates the nuclear localization of FOG-1, so this portion of the mechanism is not entirely novel. However, the role of HSCB and the proteasomal degradation of TACC3 is entirely novel to my knowledge.

Reviewer #1 (Public Review):

Summary:

The authors developed a new viral 'gene drive' based on an alternate CRISPR Cas system: UNCas12f1. They show in HSV-1 that the gene drive virus can transmit as hypothesized and is superior to Cas9 in terms of evolutionary robustness.

Strengths:

No doubt this is an impressive technological achievement and UNCas12f1 does appear superior to Cas9 in terms of taking longer to develop resistance. This is a strong body of work and Fig 3B is the crux of the paper for me showing that resistance does take longer in terms of % of viruses that are wildtype versus UNCas12f1 gene drive. I applaud the authors and I think this is a nice technological contribution.

Weaknesses:

I will focus on major conceptual issues.

(1) Mechanism. It is not really that clear to me why the UNCas12f1 has a higher barrier to the evolution of resistance. Is this simply a temporal delay or is there something intrinsic about UNCas12f1 that does not allow resistance to arise? There is a some discussion about this but it is speculative and I could not understand why resistance would not develop.

(2) Evolution. Fig 3B is the crux of the paper for me showing that resistance does take longer in terms of % of viruses that are wildtype versus UNCas12f1 gene drive. The authors did a nice job, however, I think they need to temper the claims somewhat as longer studies (other studies typically go out to >40 days) might show resistance arising. Also, I think absolute viral titers need to be shown in addition to percentage of viruses.

(3) Therapeutic Utility. Is this proposed as a therapeutic strategy? If so, how would it work? Could it lower overall total viral burden (i.e., wt + gene drive)? Another issue that I think needs to be specifically addressed is the issue of MOI as typically HSV-1 is thought to be (i.e. shown to be) a low MOI infection in vivo and in patients, whereas this strategy appears to rely on high MOI. Overall, to me, this is probably the major weakness: i.e., whether this strategy has therapeutic potential.

(4) Title. I don't think the subordinate clause of the title "virus that 'infect' viruses" is quite correct. This needs to be be reworded. This strategy converts the viral population from wild type to a gene drive virus but "infect" does not seem accurate.

Reviewer #2 (Public Review):

Summary:

Here the authors examine how increased temperature affects pollen production and fertility of Arabidopsis thaliana plants grown at selected temperature conditions ranging from 16C to 30C. They show that pollen production and fertility decline with increasing temperature. To identify the cause of reduced pollen and fertility, they resort to living cell imaging of male meiotic cells to identify that duration of meiosis increases with an increase in temperature. They also show that pollen sterility is associated with the increased presence of micronuclei likely originating from heat stress-induced impaired meiotic chromosome segregation. They correlate abnormal meiosis to weakened centromere caused by meiosis-specific defective loading of the centromere-specific histone H3 variant (CenH3) to the meiotic centromeres. Similar is the case with kinetochore-associated spindle assembly checkpoint(SAC) protein BMF1. Intriguingly, they observe a reverse trend of strong CENH3 presence in the somatic cells of the tapetum in contrast to reduced loading of CENH3 in male meiocytes with increasing temperature. In contrast to CENH3 and BMF1, the SAC protein BMF3 persists for longer periods than the WT control, based on which authors conclude that the heat stress prolongs the duration of SAC at metaphase I, which in turn extends the time of chromosome biorientation during meiosis I. This study provides insights onto the processes that affect plant reproduction with increasing temperatures which may be relevant to develop climate-resilient cultivars.

Strengths:

This study shows that the centromere function is affected under heat stress in meiotic cells by modulating the dynamics of the centromere specific histone H3 (CENH3) that in turn compromises the assembly of kinetochore complex proteins. This they have demonstrated by the way of live cell imaging of male meiocytes by tracking the loading dynamics and resident time of fluorescently tagged centromere/kinetochore proteins and spindle assembly checkpoint proteins.

Weaknesses:

Though the results presented here are interesting and solid, the current study lacks a deeper mechanistic understanding of what causes the defective loading of CenH3 to the centromeres, and why the SAC protein BMF3 persists only at meiotic centromeres to prolong the spindle assembly checkpoint, which will be interesting to delve further to completely understand the process.

Here the authors monitor one representative centromere protein CENH3, one kinetochore-associated SAC protein BMF1, and the SAC protein BMF3 to conclude that heat stress impairs centromere/kinetochore function and prolongs SAC with increased temperatures. Centromere and its associated protein complex the kinetochores and the SAC contains a multitude of proteins, some of which are well characterized in Arabidopsis thaliana. Hence the authors could have used additional such tagged proteins to further strengthen their claim.

Reviewer #1 (Public Review):

The authors aim to develop an easy-to-use image analysis tool for the mother machine that is used for single-cell time-lapse imaging. Compared with related software, they tried to make this software more user-friendly for non-experts with a design of "What You Put Is What You Get". This software is implemented as a plugin of Napari, which is an emerging microscopy image analysis platform. The users can interactively adjust the parameters in the pipeline with good visualization and interaction interface.

Strengths:

- Updated platform with great 2D/3D visualization and annotation support.<br /> - Integrated one-stop pipeline for mather machine image processing.<br /> - Interactive user-friendly interface.<br /> - The users can have a visualization of intermediate results and adjust the parameters.

Weaknesses:

- Based on the presentation of the manuscript, it is not clear that the goals are fully achieved.<br /> - Although there is great potential, there is little evidence that this tool has been adopted by other labs.<br /> - the diversity of datasets used in this study is limited.<br /> - Some paragraphs in the Discussion section are like blogs with general recommendations. Although the suggestions look pretty useful, it is not the focus of this manuscript. It might be more appropriate to put it in the GitHub repo or a documentation page. The discussion should still focus on the software, such as features, software maintenance, software development roadmap, and community adoption.

A discussion of the likely impact of the work on the field, and the utility of the methods and data to the community.<br /> - The impact of this work depends on the adoption of the software MM3. Napari is a promising platform with an expanding community. With good software user experience and long-term support, there is a good chance that this tool could be widely adopted in the mother machine image analysis community.<br /> - The data analysis in this manuscript is used as a demo of MM3 features, rather than scientific research.

Reviewer #1 (Public Review):

Zhang et al. investigate the hypothesis that tRNA methyl transferase 1 (TRMT1) is cleaved by NSP5 (nonstructural protein 5 or MPro), the SARS-CoV-2 main protease, during SARS-CoV-2 infection. They provide solid evidence that TRMT1 is a substrate of Nsp5, revealing an Nsp5 target consensus sequence and evidence of TRMT1 cleavage in cells. Their conclusions are exceptionally strong given the co-submission by D'Oliveira et al showing cleavage of TRMT1 in vitro by Nsp5. The detection of the N-terminal TRMT1 fragment by western blot is not robust; however, the authors provide corroborating assays and detailed densitometry methods, providing confidence to this reviewer that a TRMT1 fragment is produced under some conditions. Separately, the authors convincingly demonstrate widespread downregulation of RNA modifications during CoV-2 infection, including a requirement for TRMT1 in efficient viral replication. This finding is congruent with the authors' previous work defining the impact of TRMT1 and m2,2g on global translation, which is most likely necessary to support infection and virion production. Based on the data provided here, TRMT1 cleavage may be an act by CoV-2 to self-limit replication, as expression of a non-cleavable TRMT1 (versus wild type TRMT1) supports enhanced viral RNA expression at certain MOIs. The authors propose a few fascinating ideas to why this may be so in "Ideas and Speculation." Theoretically, TRMT1 cleavage should inactivate the modification activity of TRMT1, which the authors thoroughly and elegantly investigate with rigorous biochemical assays. However, only a minority of TRMT1 undergoes cleavage during infection at low MOIs and thus whether TRMT1 cleavage serves an important functional role during CoV-2 replication will be an important topic for future work. The authors fairly assess their work in this regard. In summary, this study demonstrates an important finding that the tRNA modification landscape is altered during CoV-2 infection, and that TRMT1 is an important host factor supporting CoV-2 replication. Their data pushes forward the idea that control of tRNA expression and functionality is an important and understudied area of host-pathogen interaction.

Reviewer #1 (Public Review):

The study by Vengayil et al. presented a role for Ubp3 for mediating inorganic phosphate (Pi) compartmentalization in cytosol and mitochondria, which regulates metabolic flux between cytosolic glycolysis and mitochondrial processes. Although the exact function of increased Pi in mitochondria is not investigated, findings have valuable implications for understanding the metabolic interplay between glycolysis and respiration under glucose-rich conditions. They showed that UBP3 KO cells regulated decreased glycolytic flux by reducing the key Pi-dependent-glycolytic enzyme abundances, consequently increasing Pi compartmentalization to mitochondria. Increased mitochondria Pi increases oxygen consumption and mitochondrial membrane potential, indicative of increased oxidative phosphorylation. In conclusion, the authors reported that the Pi utilization by cytosolic glycolytic enzymes is a key process for mitochondrial repression under glucose conditions.

Comments on revised version:

This reviewer appreciates the author's responses addressing some of the concerns.

However, the concern of reproducibility and experimental methods applied to the study is still valid, particularly considering that many conclusions were drawn from western blot analysis. The authors used separate gel loading controls for western blot analysis, which is not a valid method. Considering loading and other errors/discrepancies during the transfer phase of the assay, the direct control should be analyzing the membrane after transfer or using an internal control antibody on the same membrane. None of the western blots are indicated with marker sizes, and it isn't very clear how many repeats there are and whether those repeats are biological or technical repeats.

Concern regarding citing the Ouyang et al. paper is still valid. This paper is an essential implication in phosphate metabolism and is directly related to some of the findings associated with mitochondrial function, along with conflicting results, which should be discussed in the discussion section. As a reviewer, I do not request citing any paper from the authors in general; however, considering some of the conflicting results here, citing and discussing paper from Ouyang et al. will improve the interoperation/value of their findings.

Considering these factors, the presented results do not fully support the findings.

Reviewer #1 (Public Review):

This study explores whether the extreme polygenicity of common traits (the fact that variation in such traits is explained by a very large number of genetic variants) could be explained in part by competition among genes for limiting molecular resources involved in gene regulation, which would cause the expression of most genes to be correlated. While the hypothesis is interesting, I still have some concerns about the analysis and interpretation.

As the authors say in their rebuttal, assuming extreme resource limitation, i.e., going from equation 2 to 5 essentially assumes assuming that 1/(gtot [G] ) <<1 and that terms that are order [ 1/(gtot [G] ) ] can neglected. However, then the authors derive so-called resource competition terms that are order (1/m) where m is the number of genes, so that gtot is proportional to m. My main criticism (which I am not sure was addressed) is thus: can we reliably derive small order (1/m) effects while neglecting order [ 1/(gtot [G] ) ] terms, when both are presumably similar in order of magnitude? Is this mathematically sound?

I do not think the supplement that the authors have added actually gets to this. For example, section 7.1 just gives the textbook derivation of Michelis-Menten kinetics, and does not address my earlier criticism that the terms neglected in going from eq. 16 to eq. 17 (or from eq. 2 to 3) may be similar in magnitude to the terms being derived and interpreted in eqs. 6 and 7.<br /> Similarly, it is unclear from section 7.2 how the authors are doing the simulations. Are these true Michelis-Menten simulations involving equation 2? If yes, then what is the value of [G] and [P_0] in the simulations? If these are not true Michelis-Menten simulations, but instead something that already uses equation 5, then this still does not address my earlier criticism.

Reviewer #2 (Public Review):

Summary:

Two early Cambrian taxa of linguliform brachiopods are assigned to the family Eoobolidae. The taxa exhibit a columnar shell structure and the phylogenetic implications of this shell structure in relation to other early Cambrian families is outlined.

Strengths:

Interesting idea regarding the evolution of shell structure.

Weaknesses:

The early record of shell structures of linguliform brachiopods is incomplete and partly contradictory. The authors maintain silence regarding contradictory information throughout the article to an extend that information is cited wrongly. The article is written under the assumption that all eoobolids have a columnar shell structure. Thus, the previously claimed columnar structure of Eoobolus incipiens which has been re-illustrated in the paper is not convincing and could be interpreted in other ways.

The article still needs a proper results section. The Discussion is mainly a review of published data. Other potential results are hidden in this "discussion". Large sections of the paper appear irrelevant and can be deleted.

A critical revision of the family Eoobolidae and Lingulellotretidae including a revision of the type species of Eoobolus and Lingulellotreta is needed first.

The potential evolutionary patterns that are presented towards the end (summarized in Fig 6) are interesting but rather unconvincing. The stated numbers of shell laminae, whose origin has now been clarified in a still rather short Methods section, represent a mix of data and are not comparable. Achieved numbers of laminae based on literature data include laminae from the secondary and tertiary shell layer, a distinction between the two would be crucial for the proposed claims.<br /> The obtained evolutionary patterns as presented in Fig. 6 must, after the second revision and clarification of the methods used, be regarded as misleading and reflects a limited understanding of shell growths in linguliform brachiopods (despite the extensive review of the literature).

Reviewer #1 (Public Review):

Summary:

This study by Lee et al. is a direct follow-up on their previous study that described an evolutionary conservancy among placental mammals of two motifs (a transmembrane motif and a juxtamembrane palmitoylation site) in CD4, an antigen co-receptor, and showed their relevance for T-cell antigen signaling. In this study, they describe the contribution of these two motifs to the CD4-mediated antigen signaling in the absence of CD4-LCK binding. Their approach was the comparison of antigen-induced proximal TCR signaling and distal IL-2 production in 58-/- T-cell hybridoma expressing exogenous truncated version of CD4 (without the interaction with LCK), called T1 and T1 version with the mutations in either or both of the conserved motifs. They show that the T1 CD4 can support signaling to extend similar to WT CD4, but the mutation of the conserved motifs substantially reduced the signaling. The authors conclude that the role of these motifs is independent of the LCK-binding.

Strengths:

The authors convincingly show that CD4 is capable of contributing to TCR signaling in a manner independent of LCK, but dependent on the two studied motifs in CD4.

Weaknesses:

(1) Experiments in primary T cells are required to estimate the relative contribution of LCK-dependent and LCK-independent mechanisms of CD4 signaling.

(2) The mechanistic explanation (beyond the independence of LCK binding) of the role of these motifs is unclear at the moment.

Reviewer #1 (Public Review):

The authors have addressed most of the concerns I had about the original version in this revised version.

Reviewer #1 (Public Review):

Caprylic acid (CAP), i.e., octanoic acid, is a saturated fatty acid. CAP is commonly used as a food contact surface sanitizer. In mammals, caprylic acid is related to hunger sensation (i.e., food consumption). serine hydroxymethyl transferase (SHMT) has been previously known as a potential herbicidal target. The present study involves a huge amount of work. The results are useful and contribute well to the literature. The data does support the conclusion. It does not seem that SHMT is the only target of CAP though (CAP may act on other proteins as well). A major deficiency of this manuscript is that there are many unclear, inaccurate, or unconcise descriptions.

Reviewer #1 (Public Review):

Summary:

This study used a unique acute HIV-1 infection cohort, RV217, to study the evolution of transmitted founder viral Envelope sequences under nascent immune pressure. The striking feature of the RV217 cohort is the ability to detect viremia in the first week of infection, which can be followed at discrete Fiebig stages over long time intervals. This study evaluated Env sequences at 1 week, 4 weeks, and 24 weeks to provide a picture of viral and immunological co-evolution from Fiebig Stage I (1 week), Fiebig Stages IV (4 weeks), and Fiebig Stage VI (>24 weeks). This study design enabled lineage tracing of viral variants from a single transmitted founder (T/F) over the Fiebig Stages I, IV, and VI under nascent immune pressure generated in response to the T/F virus and its subsequent mutants.

Strengths:

As expected, there were temporal differences in the appearance of virus quasispecies among the individuals, which were located predominantly in solvent-exposed residues of Env, which is consistent with prior literature. Interestingly, two waves of antibody reactivity were observed for variants with mutations in the V2 region that harbors V2i and V2p epitopes correlated with protection in the RV144 clinical trial. Two waves of antibody response, detected by SPR, were observed, with the first wave being predominated by antibodies specific for the T/F07 V2 epitope associated with H173 located on the C -strand in the V2 region. The second wave was dominated by antibodies specific for an H to Y mutation at 173 that emerged due to antibody-mediated pressure to the original H173 virus. This is a remarkable finding in three ways.

First, the mutation is in the C β-strand, an unlikely paratope contact residue, as this region of the V2 loop is shielded by glycans in Env trimer structures with full glycan representation (see PDB:5t3x). The structure used for modeling in the current study was an earlier structure, PDB:4TVP, that had many truncated glycans. This does not detract from the finding that the H173Y mutation likely causes a conformational shift from a more rigid helical/coil conformation to a more dynamic conformation with a β-stranded and -sheet core preference as indicated by the literature and by the MD simulations carried out by the authors. This observation suggests that using V2 scaffolds with both the H173 and H173Y variants will increase the breadth of potentially protective antibody responses to HIV-1, as indicated in reference 42, cited by the authors. Interestingly, the H173Y mutation abrogates reactivity to mAb CH58 and attenuates reactivity to mAb CH59 isolated from RV144 volunteers. These mAbs recognize conformationally distinct V2 epitopes, adding further credence to the conclusion that the H173Y mutation results in a conformational switch of the V2 region.

Second, the H173Y mutation affects the conformation of V2 epitopes recognized by mAbs that do not neutralize T/F HIV-1 while mediating potent ADCC. The ADCC data in the manuscript provides strong support for this hypothesis and augers for further exploration of the V2 epitopes as HIV-1 vaccine targets.

Third, it is striking that immunogens based on the H173Y mutation successfully recapitulated the observed human antibody responses in wild-type Balb/c mice. The investigators used their extensive knowledge of V2 structures and scaffold-immunogens to create the library of constructs used for this study. In this case, the ΔDSV mutation increased the breadth and magnitude of the murine antibody responses.

Reviewer #2 (Public Review):

Summary:

Liao and colleagues generated tagged SMAD1 and SMAD5 mouse models and identified genome occupancy of these two factors in the uterus of these mice using the CUT&RUN assay. The authors used integrative bioinformatic approaches to identify putative SMAD1/5 direct downstream target genes and to catalog the SMAD1/5 and PGR genome co-localization pattern. The role of SMAD1/5 on stromal decidualization was assayed in vitro on primary human endometrial stromal cells. The new mouse models offer opportunities to further dissect SMAD1 and SMAD5 functions without the limitation from SMAD antibodies, which is significant. The CUT&RUN data further support the usefulness of these mouse models for this purpose.

Strengths:

The strength of this study is the novelty of new mouse models and the valuable cistromic data derived from these mice. This revised manuscript provides lots of food for thought inside and outside of the field of reproductive biology.

Weaknesses:

Causal effects of SMAD1/5 on the genome occupancy of other major uterine transcription factors were discussed but not experimentally examined in the present manuscript, which is understandable.

Reviewer #1 (Public Review):

Summary:

Wang and colleagues presented an investigation of pig-origin bacteria Bacillus velezensis HBXN2020, for its released genome sequence, in vivo safety issue, probiotic effects in vitro, and protection against Salmonella infection in a murine model. Various techniques and assays are performed.

Strengths:

An extensive study on the probiotic properties of the Bacillus velezensis strain HBXN2020.

Weaknesses:

- The main results are all descriptive, without new insight advancing the field or a mechanistic understanding of the observed protection.

- Most of the results and analysis parts are separated without a link or any story-telling to deliver a concise message.

- For the Salmonella Typhimurium-induced mouse model of colitis, it is not clear how an oral infection of C57BL/6 would lead to colitis. Streptomycin is always pretreated (https://link.springer.com/protocol/10.1007/978-1-0716-1971-1_17).

Reviewer #1 (Public Review):

Summary:

In this paper, Hackwell and colleagues performed technically impressive, long-term, GCaMP fiber photometry recordings from Kiss1 neurons in the arcuate nucleus of mice during multiple reproductive states. The data show an immediate suppression of activity of arc Kiss1 neuronal activity during pregnancy that is maintained during lactation. In the absence of any apparent change in suckling stimulus or milk production, mice lacking prolactin receptors in arcuate Kiss1 neurons regained Kiss1 episodic activity and estrous cyclicity faster than control mice, demonstrating that direct prolactin action on Kiss1 neurons is at least partially responsible for suppressing fertility in this species. The effect of loss of prolactin receptors from CamK2a expressing neurons was even greater, indicating either that prolactin sensitivity in Kiss1 neurons of the RP3V contributes to lactational infertility or that other prolactin-sensitive neurons are involved. These data demonstrate the important role of prolactin in suppressing Kiss1 neuron activity and thereby fertility during the lactational period in the mouse.

Strengths:

This is the first study to monitor the activity of the GnRH pulse-generating system across different reproductive states in the same animal. Another strength in the study design is that it isolated the effects of prolactin by maintaining normal lactation and suckling (assessed indirectly using pup growth curves). The study also offers insight into the phenomenon of postpartum ovulation in mice. The results showed a brief reactivation of arcuate Kiss1 activity immediately prior to parturition, attributed to falling progesterone levels at the end of pregnancy. This hypothesis will be of interest to the field and is likely to inspire testing in future studies. With the exceptions mentioned below, the conclusions of the paper are well supported by the data, and the aims of the study were achieved. This paper is likely to raise the standard for technical expectations in the field and spark new interest in the direct impact of prolactin on Kiss1 neurons during lactation in other species.

Weaknesses:

A weakness in the approach is the use of genetic models that do not offer complete deletion of the prolactin receptor from targeted neuronal populations. A substantial proportion of Kiss1 neurons in both models retain the receptor. As a result, it is not clear whether the partial maintenance of cyclicity during lactation in the genetic models is due to incomplete deletion or to the involvement of other factors. This weakness should be more fully discussed in the text. In addition, results showing no impact of progesterone on LH secretion during lactation are surprising, given the effectiveness of progesterone-containing birth control in lactating women. The progesterone-related experiments were not well justified or discussed in the text. While the authors assert their findings may reflect an important role for prolactin in lactational infertility in other mammalian species, that remains to be seen. Hyperprolactinemia is known to suppress GnRH release, but its importance in the suppression of cyclicity during lactation is controversial. Indeed, in several species, the stimulus of suckling is considered to be the main driver of lactational fertility suppression. Data from rats shows that exogenous prolactin was unable to suppress LH release in dams deprived of their pups shortly after birth; both suckling and prolactin were necessary to suppress a post ovariectomy rise in LH levels. The duration of amenorrhea does not correlate with average prolactin levels in humans, and suckling but not prolactin was required to suppress the postpartum rise in LH in the rhesus monkey. The authors should discuss more thoroughly whether the protocol of this or other studies might result in discordant results and whether mice are likely to be an outlier in their mechanism of cycle suppression.

Reviewer #1 (Public Review):

Summary:

The study investigates the role of cylicin-1 (CYLC1) in sperm acrosome-nucleus connections and its clinical relevance to male infertility. Using mouse models, the researchers demonstrate that cylicin-1 is specifically expressed in the post acrosomal sheath-like region in spermatids and plays a crucial role in mediating acrosome-nucleus connections. Loss of CYLC1 results in severe male subfertility, characterized by acrosome detachment and aberrant head morphology in sperm. Further analysis of a large cohort of infertile men reveals CYLC1 variants in patients with sperm head deformities. The study provides valuable insights into the role of CYLC1 in male fertility and proposes CYLC1 variants as potential risk factors for human male infertility, emphasizing the importance of mouse models in understanding the pathogenicity of such variants.

Strengths:

This article demonstrates notable strengths in various aspects. Firstly, the clarity and excellent writing style contribute to the accessibility of the content. Secondly, the employed techniques are not only relevant but also complementary, enhancing the robustness of the study. The precision in their experimental design and the meticulous interpretation of results reflect the scientific rigor maintained throughout the study. Furthermore, the decision to create a second mouse model with the exact CYLC1 mutation found in humans adds significant qualitative value to the research. This approach not only validates the clinical relevance of the identified variant but also strengthens the translational impact of the findings.

Weaknesses:

There are no obvious weaknesses. While a few minor refinements, as suggested in the recommendations to authors, could enhance the overall support for the data and the authors' messages, these suggested improvements in no way diminish the robustness of the already presented data.

Reviewer #1 (Public Review):

Summary:

In this study, Nishi et al. claim that the ratio of long-term hematopoietic stem cell (LT-HSC) versus short-term HSC (ST-HSC) determines the lineage output of HSCs and reduced ratio of ST-HSC in aged mice causes myeloid-biased hematopoiesis. The authors used Hoxb5 reporter mice to isolate LT-HSC and ST-HSC and performed molecular analyses and transplantation assays to support their arguments. How the hematopoietic system becomes myeloid-biased upon aging is an important question with many implications in the disease context as well. However, their study is descriptive with remaining questions.

Weaknesses:

(1) The authors may need conceptual re-framing of their main argument because whether the ST-HSCs used in this study are functionally indeed short-term "HSCs" is questionable. The data presented in this study and their immunophenotypic definition of ST-HSCs (Lineage negative/Sca-1+/c-Kit+/Flk2-/CD34-/CD150+/Hoxb5-) suggest that authors may find hematopoietic stem cell-like lymphoid progenitors as previously shown for megakaryocyte lineage (Haas et al., Cell stem cell. 2015) or, as the authors briefly mentioned in the discussion, Hoxb5- HSCs could be lymphoid-biased HSCs. The authors disputed the idea that Hoxb5- HSCs as lymphoid-biased HSCs based on their previous 4 weeks post-transplantation data (Chen et al., 2016). However, they overlooked the possibility of myeloid reprogramming of lymphoid-biased population during regenerative conditions (Pietras et al., Cell stem cell., 2015). In other words, early post-transplant ST-HSCs (Hoxb5- HSCs) can be seen as lacking the phenotypic lymphoid-biased HSCs. Thinking of their ST-HSCs as hematopoietic stem cell-like lymphoid progenitors or lymphoid-biased HSCs makes more sense conceptually as well. ST-HSCs come from LT-HSCs and further differentiate into lineage-biased multipotent progenitor (MPP) populations including myeloid-biased MPP2 and MPP3. Based on the authors' claim, LT-HSCs (Hoxb5- HSCs) have no lineage bias even in aged mice. Then these LT-HSCs make ST-HSCs, which produce mostly memory T cells. These memory T cell-producing ST-HSCs then produce MPPs including myeloid-biased MPP2 and MPP3. This differentiation trajectory is hard to accept. If we think Hoxb5- HSCs (ST-HSCs by authors) as a sub-population of immunophenotypic HSCs with lymphoid lineage bias or hematopoietic stem cell-like lymphoid progenitors, the differentiation trajectory has no flaw.

(2) Authors' experimental designs have some caveats to support their claims. Authors claimed that aged LT-HSCs have no myeloid-biased clone expansion using transplantation assays. In these experiments, authors used 10 HSCs and young mice as recipients. Given the huge expansion of old HSC by number and known heterogeneity in immunophenotypically defined HSC populations, it is questionable how 10 out of so many old HSCs can faithfully represent the old HSC population. The Hoxb5+ old HSC primary and secondary recipient mice data (Figure 2C and D) support this concern. In addition, they only used young recipients. Considering the importance of the inflammatory aged niche in the myeloid-biased lineage output, transplanting young vs old LT-HSCs into aged mice will complete the whole picture.

(3) The authors' molecular data analyses need more rigor with unbiased approaches. They claimed that neither aged LT-HSCs nor aged ST-HSCs exhibited myeloid or lymphoid gene set enrichment but aged bulk HSCs, which are just a sum of LT-HSCs and ST-HSCs by their gating scheme (Figure 4A), showed the "tendency" of enrichment of myeloid-related genes based on the selected gene set (Figure 4D). Although the proportion of ST-HSCs is reduced in bulk HSCs upon aging, since ST-HSCs do not exhibit lymphoid gene set enrichment based on their data, it is hard to understand how aged bulk HSCs have more myeloid gene set enrichment compared to young bulk HSCs. This bulk HSC data rather suggests that there could be a trend toward certain lineage bias (although not significant) in aged LT-HSCs or ST-HSCs. The authors need to verify the molecular lineage priming of LT-HSCs and ST-HSCs using another comprehensive dataset.

(4) Some data are too weak to fully support their claims. The authors claimed that age-associated extramedullary changes are the main driver of myeloid-biased hematopoiesis based on no major differences in progenitor populations upon transplantation of 10 young HSCs into young or old recipient mice (Figure 7F) and relatively low donor-derived cells in thymus and spleen in aged recipient mice (Figure 7G-J). However, they used selected mice to calculate the progenitor populations in recipient mice (8 out of 17 from young recipients denoted by * and 8 out of 10 from aged recipients denoted by * in Figure 7C). In addition, they calculated the progenitor populations as frequency in c-kit positive cells. Given that they transplanted 10 LT-HSCs into "sub-lethally" irradiated mice and 8.7 Gy irradiation can have different effects on bone marrow clearance in young vs old mice, it is not clear whether this data is reliable enough to support their claims. The same concern applies to the data Figure 7G-J. Authors need to provide alternative data to support their claims.

Reviewer #1 (Public Review):

Summary:

Given knowledge of the amino acid sequence and of some version of the 3D structure of two monomers that are expected to form a complex, the authors investigate whether it is possible to accurately predict which residues will be in contact in the 3D structure of the expected complex. To this effect, they train a deep learning model which takes as inputs the geometric structures of the individual monomers, per-residue features (PSSMs) extracted from MSAs for each monomer, and rich representations of the amino acid sequences computed with the pre-trained protein language models ESM-1b, MSA Transformer, and ESM-IF. Predicting inter-protein contacts in complexes is an important problem. Multimer variants of AlphaFold, such as AlphaFold-Multimer, are the current state of the art for full protein complex structure prediction, and if the three-dimensional structure of a complex can be accurately predicted then the inter-protein contacts can also be accurately determined. By contrast, the method presented here seeks state-of-the-art performance among models that have been trained end-to-end for inter-protein contact prediction.

Strengths:

The paper is carefully written and the method is very well detailed. The model works both for homodimers and heterodimers. The ablation studies convincingly demonstrate that the chosen model architecture is appropriate for the task. Various comparisons suggest that PLMGraph-Inter performs substantially better, given the same input, than DeepHomo, GLINTER, CDPred, DeepHomo2, and DRN-1D2D_Inter.<br /> The authors control for some degree of redundancy between their training and test sets, both using sequence and structural similarity criteria. This is more careful than can be said of most works in the field of PPI prediction.<br /> As a byproduct of the analysis, a potentially useful heuristic criterion for acceptable contact prediction quality is found by the authors: namely, to have at least 50% precision in the prediction of the top 50 contacts.

Weaknesses:

The authors check for performance drops when the test set is restricted to pairs of interacting proteins such that the chain pair is not similar *as a pair* (in sequence or structure) to a pair present in the training set. A more challenging test would be to restrict the test set to pairs of interacting proteins such that *none* of the chains are separately similar to monomers present in the training set. In the case of structural similarity (TM-scores), this would amount to replacing the two "min"s with "max"s in Eq. (4). In the case of sequence similarity, one would simply require that no monomer in the test set is in any MMSeqs2 cluster observed in the training set. This may be an important check to make, because a protein may interact with several partners, and/or may use the same sites for several distinct interactions, contributing to residual data leakage in the test set.

The training set of AFM with v2 weights has a global cutoff of 30 April 2018, while that of PLMGraph-Inter has a cutoff of March 7 2022. So there may be structures in the test set for PLMGraph-Inter that are not in the training set of AFM with v2 weights (released between May 2018 and March 2022). The "Benchmark 2" dataset from the AFM paper may have a few additional structures not in the training or test set for PLMGraph-Inter. I realize there may be only few structures that are in neither training set, but still think that showing the comparison between PLMGraph-Inter and AFM there would be important, even if no statistically significant conclusions can be drawn.

Finally, the inclusion of AFM confidence scores is very good. A user would likely trust AFM predictions when the confidence score is high, but look for alternative predictions when it is low. The authors' analysis (Figure 6, panels c and d) seems to suggest that, in the case of heterodimers, when AFM has low confidence, PLMGraph-Inter improves precision by (only) about 3% on average. By comparison, the reported gains in the "DockQ-failed" and "precision-failed" bins are based on knowledge of the ground truth final structure, and thus are not actionable in a real use-case.

Reviewer #1 (Public Review):

Summary:

In this paper, Li and colleagues overcome solubility problems to determine the structure of FtsEX bound to EnvC from E. coli.

Strengths:

The structural work is well done and the work is consistent with previous work on the structure of this complex from P. aerugionsa.

Weaknesses:

The model does not take into account all information that the authors obtained as well as known in vivo data.

The work lacks a clear comparison to the Pseudomonas structure highlighting new information that was obtained so that it is readily available to the reader.

The authors set out to obtain the structure of FtsEX-EnvC complex from E. coli. Previously, they were unable to do so but were able to determine the structure of the complex from P. aeruginosa. Here they persisted in attacking the E. coli complex since more is known about its involvement in cell division and there is a wealth of mutants in E. coli. The structural work is well done and recapitulates the results this lab obtained with this complex from P. aeruginosa. It would be helpful to compare more directly the results obtained here with the E. coli complex with the previously reported P. aeruginosa complex - are they largely the same or has some insight been obtained from the work that was not present in the previous complex from P. aeruginosa. This is particularly the case in discussing the symmetrical FtsX dimer binding to the asymmetrical EnvC, since this is emphasized in the paper. However, Figures 3C & D of this paper appear similar to Figures 2D & E of the P. aeruginosa structure. Presumably, the additional information obtained and presented in Figure 4 is due to the higher resolution, but this needs to be highlighted and discussed to make it clear to a general audience.

The main issue is the model (Figure 6). In the model ATP is shown to bind to FtsEX before EnvC, however, in Figure 1c it is shown that ADP is sufficient to promote binding of FtsEX to EnvC.

The work here is all done in vitro, however, information from in vivo needs to be considered. In vivo results reveal that the ATP-binding mutant FtsE(D162N)X promotes the recruitment of EnvC (Proc Natl Acad Sci U S A 2011 108:E1052-60). Thus, even FtsEX in vivo can bind EnvC without ATP (not sure if this mutant can bind ADP).

Perhaps the FtsE protein from E. coli has to have bound nucleotides to maintain its 3D structure.

Reviewer #1 (Public Review):

Summary:

The authors present a new application of the high-content image-based morphological profiling Cell Painting (CP) to single cell type classification in mixed heterogeneous induced pluripotent stem cell-derived mixed neural cultures. Machine learning models were trained to classify single cell types according to either "engineered" features derived from the image or from the raw CP multiplexed image. The authors systematically evaluated experimental (e.g., cell density, cell types, fluorescent channels) and computational (e.g., different models, different cell regions) parameters and convincingly demonstrated that focusing on the nucleus and its surroundings contains sufficient information for robust and accurate cell type classification. Models that were trained on mono-cultures (i.e., containing a single cell type) could generalize for cell type prediction in mixed co-cultures, and describe intermediate states of the maturation process of iPSC-derived neural progenitors to differentiation neurons.

Strengths:

Automatically identifying single-cell types in heterogeneous mixed-cell populations holds great promise to characterize mixed-cell populations and to discover new rules of spatial organization and cell-cell communication. Although the current manuscript focuses on the application of quality control of iPSC cultures, the same approach can be extended to a wealth of other applications including an in-depth study of the spatial context. The simple and high-content assay democratizes use and enables adoption by other labs.

The manuscript is supported by comprehensive experimental and computational validations that raise the bar beyond the current state of the art in the field of high-content phenotyping and make this manuscript especially compelling. These include (i) Explicitly assessing replication biases (batch effects); (ii) Direct comparison of feature-based (a la cell profiling) versus deep-learning-based classification (which is not trivial/obvious for the application of cell profiling); (iii) Systematic assessment of the contribution of each fluorescent channel; (iv) Evaluation of cell-density dependency; (v) Explicit examination of mistakes in classification; (vi) Evaluating the performance of different spatial contexts around the cell/nucleus; (vii) Generalization of models trained on cultures containing a single cell type (mono-cultures) to mixed co-cultures; (viii) Application to multiple classification tasks.

I especially liked the generalization of classification from mono- to co-cultures (Figure 4C), and quantitatively following the gradual transition from NPC to Neurons (Figure 5H).

The manuscript is well-written and easy to follow.

Weaknesses:

I am not certain how useful/important the specific application demonstrated in this study is (quality control of iPSC cultures), this could be better explained in the manuscript. Another issue that I feel should be discussed more explicitly is how far can this application go - how sensitively can the combination of cell painting and machine learning discriminate between cell types that are more subtly morphologically different from one another?

Regarding evaluations, the use of accuracy, which is a measure that can be biased by class imbalance, is not the most appropriate measurement in my opinion. The confusion matrices are a great help, but I would recommend using a measurement that is less sensitive for class imbalance for cell-type classification performance evaluations. Another issue is that the performance evaluation is calculated on a subset of the full cell population - after exclusion/filtering. Could there be a bias toward specific cell types in the exclusion criteria? How would it affect our ability to measure the cell type composition of the population?

I am not entirely convinced by the arguments regarding the superiority of the nucleocentric vs. the nuclear representations. Could it be that this improvement is due to not being sensitive/ influenced by nucleus segmentation errors?

GRADCAM shows cherry-picked examples and is not very convincing.

There are many missing details in the figure panels, figure legend, and text that would help the reader to better appreciate some of the technical details, see details in the section on recommendations for the authors.

Reviewer #1 (Public Review):

Summary:

SUMO proteins are processed and then conjugated to other proteins via a C-terminal di-glycine motif. In contrast, the N-terminus of some SUMO proteins (SUMO2/3) contains lysine residues that are important for the formation of SUMO chains. Using NMR studies, the N-terminus of SUMO was previously reported to be flexible (Bayer et al., 1998). The authors are investigating the role of the flexible (referred to as intrinsically disordered) N-terminus of several SUMO proteins. They report their findings and modeling data that this intrinsically disordered N-terminus of SUMO1 (and the C. elegans Smo1) regulates the interaction of SUMO with SUMO interacting motifs (SIMs).

Strengths:

Among the strongest experimental data suggesting that the N-terminus plays an inhibitory function are their observations that<br /> (1) SUMO1∆N19 binds more efficiently to SIM-containing Usp25, Tdp2, and RanBp2,<br /> (2) SUMO1∆N19 shows improved sumoylation of Usp25,<br /> (3) changing negatively-charged residues, ED11,12KK in the SUMO1 N-terminus increased the interaction and sumoylation with/of USP25.

The paper is very well-organized, clearly written, and the experimental data are of high quality. There is good evidence that the N-terminus of SUMO1 plays a role in regulating its binding and conjugation to SIM-containing proteins. Therefore, the authors are presenting a new twist in the ever-evolving saga of SUMO, SIMs, and sumoylation.

Weaknesses:

Much has been learned about SUMO through structure-function analyses and this study is another excellent example. I would like to suggest that the authors take some extra time to place their findings into the context of previous SUMO structure-function analyses. Furthermore, it would be fitting to place their finding of a potential role of N-terminally truncated Smo1 into the context of the many prior findings that have been made with regard to the C. elegans SUMO field. Finally, regarding their data modeling/simulation, there are questions regarding the data comparisons and whether manipulations of the N-terminus also have an effect on the 70/80 region of the core.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Ngo et al. report a peculiar effect where a single base mismatch (CC) can enhance the mechanical stability of a nucleosome. In previous studies, the same group used a similar state-of-the-art fluorescence-force assay to study the unwrapping dynamics of 601-DNA from the nucleosome and observed that force-induced unwrapping happens more slowly for DNA that is more bendable because of changes in sequence or chemical modification. This manuscript appears to be a sequel to this line of projects, where the effect of CC is tested. The authors confirmed that CC is the most flexible mismatch using the FRET-based cyclization assay and found that unwrapping becomes slower when CC is introduced at three different positions in the 601 sequence. The CC mismatch only affects the local unwrapping dynamics of the outer turn of nucleosomal DNA.

Strengths:

These results are in good agreement with the previously established correlation between DNA bendability and nucleosome mechanical stability by the same group. This well-executed, technically sound, and well-written experimental study contains novel nucleosome unwrapping data specific to the CC mismatch and 601 sequence, the cyclizability of DNA containing all base pair mismatches, and the unwrapping of 601-DNA from xenophus and yeast histones. Overall, this work will be received with great interest by the biophysics community and is definitely worth attention.

Weaknesses:

The scope and impact of this study are somewhat limited due to the lack of sequence variation. Whether the conclusion from this study can be generalized to other sequences and other bendability-enhancing mismatches needs further investigation.

Major questions:

(1) As pointed out by the authors, the FRET signal is not sensitive to nucleosome position; therefore, the increasing unwrapping force in the presence of CC can be interpreted as the repositioning of the nucleosome upon perturbation. It is then also possible that CC-containing DNA is not positioned exactly the same as normal DNA from the start upon nucleosome assembly, leading to different unwrapping trajectories. What is the experimental evidence that supports identical positioning of the nucleosomes before the first stretch?

(2) The authors chose a constant stretching rate in this study. Can the authors provide a more detailed explanation or rationale for why this rate was chosen? At this rate, the authors found hysteresis, which indicates that stretching is faster than quasi-static. But it must have been slow and weak enough to allow for reversible unwrapping and wrapping of a CC-containing DNA stretch longer than one helical turn. Otherwise, such a strong effect of CC at a single location would not be seen. I am also curious about the biological relevance of the magnitude of the force. Can such force arise during nucleosome assembly in vivo?

(3) In this study, the CC mismatch is the only change made to the 601 sequence. For readers to truly appreciate its unique effect on unwrapping dynamics as a base pair defect, it would be nice to include the baseline effects of other minor changes to the sequence. For example, how robust is the unwrapping force or dynamics against a single-bp change (e.g., AT to GC) at the three chosen positions?

(4) The last section introduces yeast histones. Based on the theme of the paper, I was expecting to see how the effect of CC is or is not preserved with a different histone source. Instead, the experiment only focuses on differences in the unwrapping dynamics. Although the data presented are important, it is not clear how they fit or support the narrative of the paper without the effect of CC.

(5) It is stated that tRNA was excluded in experiments with yeast-expressed nucleosomes. What is the reason for excluding it for yeast nucleosomes? Did the authors rule out the possibility that tRNA causes the measured difference between the two nucleosome types?

Reviewer #1 (Public Review):

Summary:<br /> TMC7 knockout mice were generated by the authors and the phenotype was analyzed. They found that Tmc7 is localized to Golgi and is needed for acrosome biogenesis.

Strengths:<br /> The phenotype of infertility is clear, and the results of TMC7 localization and the failed acrosome formation are highly reliable. In this respect, they made a significant discovery regarding spermatogenesis.

Weaknesses:<br /> There are also some concerns, which are mainly related to the molecular function of TMC7 and Figure 5. It is understandable that TMC7 exhibits some channel activity in the Golgi and somehow affects luminal pH or Ca2+, leading to the failure of acrosome formation. On the other hand, since they are conducting the pH and calcium imaging from the cytoplasm, I do not think that the effect of TMC7 channel function in Golgi is detectable with their methods. Rather, it is more likely that they are detecting apoptotic cells that have no longer normal ion homeostasis. Another concern is that n is only 3 for these imaging experiments.

Reviewer #1 (Public Review):

Among the many challenges in the cilia field, is the question of how multicellular organisms assemble a variety of structurally and functionally specialized cilia, including cilia of different lengths. This study addresses the important question of how ciliary length differences are established in vertebrates. Specifically, the authors analyzed the role of intraflagellar transport (IFT) in ciliary length regulation in zebrafish, exploiting the transparency of the embryos. Zebrafish possess functionally specialized motile and non-motile cilia in a variety of tissues. Expression of GFP-tagged IFT88, a component of the IFT-B subcomplex, in a corresponding mutant, allowed the authors to image IFT in five distinct types of cilia. They note that IFT moves faster in longer cilia. Tagging and imaging of the IFT-A protein IFT43 further support this observation. IFT speed was largely unaffected in knock-out and morphants targeting the BBSome, various kinesin-2 motors, and the posttranslational modifications of tubulin polyglycylation and polyglutamylation. Using high-resolution STED imaging, the authors observe that IFT signals (likely, corresponding to IFT trains) are smaller in the shorter spinal cord cilia compared to the long cristae cilia. Based on these observations, the authors test the hypothesis that larger IFT trains recruit more motors or coordinate the motors better, resulting in faster trains, and causing cilia to be longer. This is further tested using partial knock-down of IFT88-GFP, which resulted in shorter crista cilia, reduced IFT particle number, size, and velocity. Some parts of the manuscript show "negative" data (e.g., ciliary length and IFT are not affected by the loss of BBS4) but these add beautifully to the overall story and allow for additional conclusions such as the minor role of ttll3 and ccp knockouts on ciliary length in this model. This is an excellent study, which documents IFT in a vertebrate species and explores its regulation. The data are of high quality and support most of the conclusions.

(1) The main hypothesis/conclusion is summarized in the abstract: "Our study presents an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex." The data clearly document the remarkable correlation between IFT velocity and ciliary length in the different cells/tissues/organs analyzed. The experimental test of this idea, i.e., the knock-down of GFP-IFT88, further supports the conclusion but needs to be interpreted more carefully. While IFT particle size and train velocity were reduced in the IFT88 morphants, the number of IFT particles is even more decreased. Thus, the contributions of the reduction in train size and velocity to ciliary length are, in my opinion, not unambiguous. Also, the concept that larger trains move faster, likely because they dock more motors and/or better coordinating kinesin-2 and that faster IFT causes cilia to be loner, is to my knowledge, not further supported by observations in other systems (see below).

(2) I think the manuscript would be strengthened if the IFT frequency would also be analyzed in the five types of cilia. This could be done based on the existing kymographs from the spinning disk videos. As mentioned above, transport frequency in addition to train size and velocity is an important part of estimating the total number of IFT particles, which bind the actual cargoes, entering/moving in cilia.

(3) Here, the variation in IFT velocity in cilia of different lengths within one species is documented - the results document a remarkable correlation between IFT velocity and ciliary length. These data need to be compared to observations from the literature. For example, the velocity of IFT in the quite long (~ 100 um) olfactory cilia of mice is similar to that observed in the rather short cilia of fibroblasts (~0.6 um/s). In Chlamydomonas, IFT velocity is not different in long flagella mutants compared to controls. Probably data are also available for C. elegans or other systems. Discussing these data would provide a broader perspective on the applicability of the model outside of zebrafish.

Reviewer #1 (Public Review):

Summary:

The study "Effect of alpha-tubulin acetylation on the doublet microtubule structure" by S. Yang et al employs a multi-disciplinary approach, including cryo-electron microscopy (cryo-EM), molecular dynamics, and mass spectrometry, to investigate the impact of α-tubulin acetylation at the lysine 40 residue (αK40) on the structure and stability of doublet microtubules in cilia. The work reveals that αK40 acetylation exerts a small-scale, but significant, effect by influencing the lateral rotational angle of the microtubules, thereby affecting their stability. Additionally, the study provided an explanation of the relationship between αK40 acetylation and phosphorylation within cilia, despite that the details still remain elusive. Overall, these findings contribute to our understanding of how post-translational modifications can influence the structure, composition, stability, and functional properties of important cellular components like cilia.

Strengths:

(1) Multi-Disciplinary Approach: The study employs a robust combination of cryo-electron microscopy (cryo-EM), molecular dynamics, and mass spectrometry, providing a comprehensive analysis of the subject matter.<br /> (2) Significant Findings: The paper successfully demonstrates the impact of αK40 acetylation on the lateral rotational angles between protofilaments (inter-PF angles) of doublet microtubules in cilia, thereby affecting their stability. This adds valuable insights into the role of post-translational modifications in cellular components.<br /> (3) Exploration of Acetylation-Phosphorylation Relationship: The study also delves into the relationship between αK40 acetylation and phosphorylation within cilia, contributing to a broader understanding of post-translational modifications.<br /> (4) High-quality data: The authors are cryo-EM experts in the field and the data quality presented in the manuscript is excellent.<br /> (5) Depth of analysis: The authors analyzed the effects of αK40 acetylation in excellent depth which significantly improved our understanding of this system.

Weaknesses:

I have no major concerns about this paper.

Reviewer #1 (Public Review):

Summary:<br /> In the present study, authors found the ternary complex formed by NCAN, TNC, and HA as an important factor facilitating the multipolar to bipolar transition in the intermediate zone (IZ) of the developing cortex. NCAM binds HA via the N-terminal Link modules, meanwhile, TNC cross-links NCAN through the CDL domain at the C-terminal. The expression and right localization of these three factors facilitate the multipolar-bipolar transition necessary for immature neurons to migrate radially. TNC and NCAM are also involved in neuronal morphology. The authors used a wide range of techniques to study the interaction between these three molecules in the developing cortex. In addition, single and double KO mice for NCAN and TNC were analyzed to decipher the role of these molecules in neuronal migration and morphology.

Strengths:<br /> The study of the formation of the cerebral cortex is crucial to understanding the pathophysiology of many neurodevelopmental disorders associated with malformation of the cerebral cortex. In this study, the authors showed, for the first time, that the ternary complex formed by NCAN, TNC, and HA promotes neuronal migration. The results regarding the interaction between the three factors forming the ternary complex are convincing.

Reviewer #1 (Public Review):

Summary:

The manuscript by Sztangierska et al explores how the Hsp70 chaperone together with its JDP-NEF cofactors and Hsp104 disentangle aggregated proteins. Specifically, the study provides mechanistic findings that explain what role the NEF class Hsp110 has in protein disaggregation. The results explain several previous observations related to Hsp110 in protein disaggregation. Importantly, the study provides compelling evidence that Hsp110 acts early in the disaggregation process.

Strengths:<br /> (1) This is a very well-performed study with multiple in vitro experiments that provide convincing support for the claims.

(2) An important finding is that the study places the Hsp110 function early in the disaggregation process.

(3) The study has an important value in that it picks up on a number of observations in the field that have not been explored or directly tested by experiment. The presented results settle questions and controversy regarding Hsp110 function in disaggregation.

Weaknesses:

(1) While the key finding of this manuscript is that it places Hsp110 early in the disaggregation process, the other findings are advancing the field less.

(2) A claim in the paper is that Hsp110 NEFs improve disaggregation by Hsp70 in a manner dependent on the class of JDP (class A vs class B). However, it rather appears that in the experiments class B JDPs support robust disaggregation, while class A JDPs are not as effective. This simple fact may very well underly the differences and questions if class specificity should be in focus in the interpretation of the data.

(3) The experiments differ somewhat in regard to the aggregated protein used. For example, in Figure 1A, FFL is used with only limited reactivation (10% reactivated at the last timepoint and the curve is flattening), while in Figure 2B FFL-EGFP is used to monitor microscopically what appears to be complete disaggregation. Does FFL-EGFP behave the same as FFL in assays such as the one in Figure 1A or are there major differences that may impact how the data should be interpreted?

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors show compelling data indicating that ExoIII has significant ssDNA nuclease activity that is posited to interfere with biosensor assays. This does not come as a surprise as other published works have indeed shown the same, but in this work, the authors provide a deeper analysis of this underestimated activity.

Strengths:

The authors used a variety of assays to examine the ssDNA nuclease activity of ExoIII and its origin. Fluorescence-based assays and native gel electrophoresis, combined with MS analysis clearly indicate that both commercial and laboratory purified ExoIII contain ssDNA nuclease activity. Mutational analysis identifies the residues responsible for this activity. Of note is the observation in this submitted work that the sites of ssDNA and dsDNA exonuclease activity overlap, suggesting that it may be difficult to identify mutations that affect one activity but not the other. In this regard, it is of interest the observation by the authors that the ssDNA nuclease activity depends on the sequence composition of the ssDNA, and this may be used as a strategy to suppress this activity when necessary. For example, the authors point out that a 3′ A4-protruding ssDNA could be employed in ExoIII-based assays due to its resistance to digestion. However, this remains an interesting suggestion that the authors do not test, but that would have strengthened their conclusion.

Weaknesses:

The authors provide a wealth of experimental data showing that E. coli ExoIII has ssDNA nuclease activities, both exo- and endo-, however this work falls short in showing that indeed this activity practically interferes with ExoIII-driven biosensor assays, as suggested by the authors. Furthermore, it is not clear what new information is gained compared to the one already gathered in previously published works (e.g. references 20 and 21). Also, the authors show that ssDNA nuclease activity has sequence dependence, but in the context of the observation that this activity is driven by the same site as dsDNA Exo, how does this differ from similar sequence effects observed for the dsDNA Exo? (e.g. see Linxweiler, W. and Horz, W. (1982). Nucl. Acids Res. 10, 4845-4859).

Because of the claim that the underestimated ssDNA nuclease activity can interfere with commercially available assays, it would have been appropriate to test this. The authors only show that ssDNA activity can be identified in commercial ExoIII-based kits, but they do not assess how this affects the efficiency of a full reaction of the kit. This could have been achieved by exploiting the observed ssDNA sequence dependence of the nuclease activity. In this regard, the work cited in Ref. 20 showed that indeed ExoIII has ssDNA nuclease activity at concentrations as low as 50-fold less than what test in this work. Ref 20 also tested the effect of the ssDNA nuclease activity in Targeted Recycle Assays, rather than just testing for its presence in a kit.

Because of the implication that the presence of ssDNA exonuclease activity may have in reactions that are supposed to only use ExoIII dsDNA exonuclease, it is surprising that in this submitted work no direct comparison of these two activities is done. Please provide an experimental determination of how different the specific activities for ssDNA and dsDNA are.

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors set out to determine whether colorectal cancer surgery site (right, left, rectal) and chemotherapy impact the subsequent risk of developing T2DM in the Danish national health register.

Strengths:<br /> - The research question is conceptually interesting<br /> - The Danish national health register is a comprehensive health database<br /> - The data analysis was thorough and appropriate<br /> -The findings are interesting, and a little surprising that there was no impact of chemotherapy on the development of T2DM<br /> - The authors have addressed my previous clarifications and questions.

- Regarding the generalizability of this study, as the authors discuss the prevalence of T2DM and obesity are lower in Denmark than in a number of other high income countries. Therefore, similar studies in other populations would be of interest.<br /> - The study includes individuals who filled a prescription for diabetes medication, so likely includes some individuals with transient hyperglycemia/steroid induced diabetes during chemotherapy, rather than those with new onset longterm T2DM.

Overall, the authors achieved their aims, and the conclusions are supported by their results as reported.<br /> The results are unlikely to significantly impact clinical practice or T2DM screening in this population, however are of interest to the community.

Reviewer #2 (Public Review):

Yanagihara and colleagues investigated the immune cell composition of bronchoalveolar lavage fluid (BALF) samples in a cohort of patients with malignancy undergoing chemotherapy and with lung adverse reactions including Pneumocystis jirovecii pneumonia (PCP) and immune-checkpoint inhibitors (ICIs) or cytotoxic drug induced interstitial lung diseases (ILDs). Using mass cytometry, their aim was to characterize the cellular and molecular changes in BAL to improve our understanding of their pathogenesis and identify potential biomarkers and therapeutic targets. In this regard, the authors identify a correlation between CD16 expression in T cells and the severity of PCP and an increased infiltration of CD57+ CD8+ T cells expressing immune checkpoints and FCLR5+ B cells in ICI-ILD patients.

The conclusions of this paper are mostly well supported by data, but some aspects of the data analysis need to be clarified and extended.

The authors should elaborate on why different sets of markers were selected for each analysis step. E.g., Different sets of markers were used for UMAP, CITRUS and viSNE in the T cell and myeloid analysis.

Reviewer #1 (Public Review):

When writing a short review on the function of Pin1 some 15 years ago (Lippens et al., Febs J 2007), we concluded the introduction by the following sentence: "..., it seems that further analysis is required to determine whether binding or catalysis is the primary mechanism through which Pin1 affects cell cycle progression." In the present manuscript, the authors provide experimental evidence for the Pin1/PKC interaction that tips the balance towards interaction and not catalysis.

Their main data concern the interaction between the V5 domains of two PKC isoenzymes (alpha and betaII) and Pin1. This V5 domain can be further separated into a Turn Motif (TM) and a Hydrophobic Motif (HM), that both can be phosphorylated on specific positions. Phosphorylation in the TM occurs on a TPP motif, and in agreement with previous results on the same motif in Tau, Pin1 cannot isomerize efficiently the TP amide bond when the residue following the proline is another proline. Phosphorylation of the HM is not proline directed but occurs on a serine flanked by 2 aromatic residues (FSF or FSY, according to the isoenzyme). They dissect in detail the interaction of both motifs with the WW and PPIase domains and conclude that the fully phosphorylated V5 peptide binds Pin1 in a directional mode, with the TM binding to the WW domain and the HM to the PPIase domain.

In the absence of crystals of the complex, they solve a structure by NMR, and use selectively labeled peptides (and probably a lot of NMR time) to obtain a structural model. Finally, they provide functional data by silencing/overepxressing Pin1 and inactive mutants (both at the level of its WW domain and the PPIase domain) in HEK293T cells and evaluating the PKCalpha homeostasis.

The structural part of this work is interesting, as it is the first structure of Pin1 with a ligand that bridges both domains. They might want to underline this - all other structures in the PDB have a single domain complex, but never both domains by a single longer peptide. I would however question the static representation of this structure - the 90{degree sign} kink in the peptide when complexed is probably one single snapshot, but I hardly believe the PPIase/WW domain orientation to be static. Unless the authors have additional information to stand by this static structure, this point merits being commented on in the manuscript.

I would like to point out to literature that described for example the non-canonical binding (Yeh ES, Lew BO & Means AR (2006) The loss of PIN1 deregulates cyclin E and sensitizes mouse embryo fibroblasts to genomic instability. J Biol Chem 281, 241-251. Pin1 recognizes cyclin E via a noncanonical pThr384- Gly385 motif [33] rather than the pThr380-Pro381 motif.). They mention briefly the absence of isomerase activity in similar TPP motifs, but this information might already come in the Results section.

The weakest part seems the in vivo data. Although this is not the main focus of this lab, there is some issues that could be addressed. The expression levels of Pin1 and PKCa are amazingly linear (Fig 7A), but when they overexpress WT Pin1 in a KO line, with 3-4 times higher overexpression, the PKCa levels are hardly higher than in the original WT cell line. Also, the levels in the W34A/R68A/R69A (abolishing both WW and PPIase binding functions) are surprising, why would PKCa levels rise above the level found in the Pin1 KO cells? Finally, if even slight overexpression of the C113S catalytically inactive mutant leads to more efficient PKCa degradation than overexpression of the WT Pin1 (Figure 7C), it is hard to interpret. The conclusion that Pin1-mediated regulation of PKCa requires a bivalent interaction mode of Pin1 with PKCa independent of its catalytic activity do depend on these data, so they merit further analysis.

Reviewer #1 (Public Review):

By using deep convolutional neural networks (CNNs) as model for the visual system, this study aims at understanding and explaining the emergence of mirror-symmetric viewpoint tuning in the brain.

Major strengths of the methods and results:

(1) The paper presents comprehensive, insightful and detailed analyses investigating how mirror-symmetric viewpoint tuning emergence in artificial neural networks, providing significant and novel insights into this complex process.<br /> (2) The authors analyze reflection equivariance and invariance in both trained and untrained CNNs' convolutional layers. This elucidates how object categorization training gives rise to mirror-symmetric invariance in the fully-connected layers.<br /> (3) By training CNNs on small datasets of numbers and a small object set excluding faces, the authors demonstrate mirror-symmetric tuning's potential to generalize to untrained categories and the necessity of view-invariant category training for its emergence.<br /> (4) A further analysis probes the contribution of local versus global features to mirror-symmetric units in the first fully-connected layer of a network. This innovative analysis convincingly shows that local features alone suffice for the emergence of mirror-symmetric tuning in networks.<br /> (5) The results make a clear prediction that mirror-symmetric tuning should also emerge for other bilaterally symmetric categories, opening avenues for future neural studies.

Major weaknesses of the methods and results:

(1) The authors propose a mirror-symmetric viewpoint tuning index, which, although innovative, complicates comparison with previous work and this choice is not well motivated. This index is based on correlating representational dissimilarity matrices (RDMs) with their flipped versions, a method differing from previous approaches.<br /> (2) Faces exhibit unique behavior in terms of the progression of mirror-symmetric viewpoint tuning and their training task and dataset dependency. Given that mirror-symmetric tuning has been identified in the brain for faces, it would be beneficial to discuss this observation and provide potential explanations.<br /> (3) Previous work reported critical differences between CNNs and neural representations in area AL indicating that mirror-symmetric viewpoint tuning is less present than view invariance in CNNs compared to area AL. While such findings could potentially limit the usefulness of CNNs as models for mirror-symmetric viewpoint tuning in the brain, they are not addressed in the study.<br /> (4) The study's results, while informative, are qualitative rather than quantitative, and lack direct comparison with neural data. This obscures the implications for neural mechanisms and their relevance to the broader field.

The study provides compelling evidence that learning to discriminate bilaterally symmetric objects (beyond faces) induces mirror-symmetric viewpoint tuning in the networks, qualitatively similar to the brain. Moreover, the results suggest that this tuning can, in principle, generalize beyond previously trained object categories. Overall, the study provides important conclusions regarding the emergence of mirror-symmetric viewpoint tuning in networks, and potentially the brain. However, the conducted analyses and results do not entirely address the question why mirror-symmetric viewpoint tuning emerges in networks or the brain. Specifically, the results leave open whether mirror-symmetric viewpoint tuning is indeed necessary to achieve view invariance for bilaterally symmetric objects.

Taken together, this study moves us a step closer to uncovering the origins of mirror-symmetric tuning in networks, and has implications for more comprehensive investigations into this neural phenomenon in the brain. The methods of probing CNNs are innovative and could be applied to other questions in the field. This work will be of broad interest to cognitive neuroscientists, psychologists, and computer scientists.

Reviewer #1 (Public Review):

In this manuscript, the authors perform a very thorough, extensive characterization of the impact of an iron-rich diet on multiple phenotypes in a wide range of inbred mouse strains. While a work of this type does not offer mechanistic insights, the value of the study lies not only in its immediate results but also in what it can offer to future researchers as they explore the genetic basis of iron levels and other related phenotypes in rodent studies. The creation of a web resource and the offer from the authors to share all available samples is particularly laudable, and helps to increase the accessibility of the work to other scientists. There is one shortcoming to the work however. To induce iron overload in mice in the main study in this work, mice were placed on an iron-rich diet that differed in its composition from the baseline diet in more than just iron. This could influence some of the phenotypes observed in this study.

Reviewer #1 (Public Review):

Summary:<br /> Cell-to-cell communication is essential for higher functions in bacterial biofilms. Electrical signals have proven effective in transmitting signals across biofilms. These signals are then used to coordinate cellular metabolisms or to increase antibiotic tolerance. Here, the authors have reported for the first time coordinated oscillation of membrane potential in E. coli biofilms that may have a functional role in photoprotection.

Strengths:<br /> - The authors report original data.<br /> - For the first time, they showed that coordinated oscillations in membrane potential occur in E. Coli biofilms.<br /> - The authors revealed a complex two-phase dynamic involving distinct molecular response mechanisms.<br /> - The authors developed two rigorous models inspired by 1) Hodgkin-Huxley model for the temporal dynamics of membrane potential and 2) Fire-Diffuse-Fire model for the propagation of the electric signal.<br /> - Since its discovery by comparative genomics, the Kch ion channel has not been associated with any specific phenotype in E. coli. Here, the authors proposed a functional role for the putative K+ Kch channel : enhancing survival under photo-toxic conditions.

Weaknesses:<br /> - Since the flow of fresh medium is stopped at the beginning of the acquisition, environmental parameters such as pH and RedOx potential are likely to vary significantly during the experiment. It is therefore important to exclude the contributions of these variations to ensure that the electrical response is only induced by light stimulation. Unfortunately, no control experiments were carried out to address this issue.<br /> - Furthermore, the control parameter of the experiment (light stimulation) is the same as that used to measure the electrical response, i.e. through fluorescence excitation. The use of the PROPS system could solve this problem.<br /> - Electrical signal propagation is an important aspect of the manuscript. However, a detailed quantitative analysis of the spatial dynamics within the biofilm is lacking. In addition, it is unclear if the electrical signal propagates within the biofilm during the second peak regime, which is mediated by the Kch channel. This is an important question, given that the fire-diffuse-fire model is presented with emphasis on the role of K+ ions.<br /> - Since deletion of the kch gene inhibits the long-term electrical response to light stimulation (regime II), the authors concluded that K+ ions play a role in the habituation response. However, Kch is a putative K+ ion channel. The use of specific drugs could help to clarify the role of K+ ions.<br /> - The manuscript as such does not allow us to properly conclude on the photo-protective role of the Kch ion channel.<br /> - The link between membrane potential dynamics and mechanosensitivity is not captured in the equation for the Q-channel opening dynamics in the Hodgkin-Huxley model (Supp Eq 2).<br /> - Given the large number of parameters used in the models, it is hard to distinguish between prediction and fitting.

Reviewer #1 (Public Review):

Summary:

Zheng et al. study the 'glass' transitions that occur in proteins at ca. 200K using neutron diffraction and differential isotopic labeling (hydrogen/deuterium) of the protein and solvent. To overcome limitations in previous studies, this work is conducted in parallel with 4 proteins (myoglobin, cytochrome P450, lysozyme, and green fluorescent protein) and experiments were performed at a range of instrument time resolutions (1ns - 10ps). The author's data looks compelling, and suggests that transitions in the protein and solvent behavior are not coupled and contrary to some previous reports, the apparent water transition temperature is a 'resolution effect'; i.e. instrument response is limited. This is likely to be important in the field, as a reassessment of solvent 'slaving' and the role of the hydration shell on protein dynamics should be reassessed in light of these findings.

Strengths:

The use of multiple proteins and instruments with a rate of energy resolution/ timescales.

Weaknesses:

The paper could be organised to better allow the comparison of the complete dataset collected.<br /> The extent of hydration clearly influences the protein transition temperature. The authors suggest that "water can be considered here as lubricant or plasticizer which facilitates the motion of the biomolecule." This may be the case, but the extent of hydration may also alter the protein structure.

Reviewer #1 (Public Review):

Summary:

This Research Advance is an extension of this group's prior eLife paper published in 2022 on the conserved roles of the Hippo pathway effector Yorkie in C. owczarzaki (PMID: 35659869). This species is an amoeba that holds an important phylogenetic position as a close relative of multicellular animals. The prior study used genome editing to delete the C. owczarzaki Yki (termed coYki) and found that Yki is not required for proliferation but instead regulates cell contractility and cell aggregation. In the current study, the authors wanted to address whether Hippo pathway kinases - coHippo (coHpo) and coWarts (coWts) - regulate coYki and whether they are dispensable for proliferation but instead regulate cell contractility and cell aggregation. They used genome editing to delete coHpo and coWts singly in C. owczarzaki. Both mutant strains had increased nuclear location of transfected coYki (tagged with Scarlet), suggesting that Hippo kinase pathway regulation of Yki is conserved in this organism. Neither kinase is required for proliferation. Either kinase mutant strain had a significantly increased percentage of cells that were elongated, which was relatively rare in a control population. The incident of elongation could be enhanced in both kinase-mutant and in control cells when myosin inhibitors were added to the media. coHpo and coWts-mutant aggregates were more tightly packed than control cell aggregates, which they hypothesize is due to the increased contractility seen in kinase-mutant cells. They could reduce the density of packing in kinase-mutant aggregates when they treated the cells with myosin or F-actin inhibitors. To test whether the effects observed in kinase-mutant strains were due to increased Yki activation, they generated a coYki with four S to A substitutions (termed coYki4SA), which should produce a dominant-active Yki impervious to phosphorylation and hence inactivation by Hippo kinases. Control C. owczarzaki cells transfected with coYki4SA had increased cell density in aggregates and elongation in adherent cells. These results support their conclusions that coHpo and coWts regulate cell contractility and cell packing through coYki.

Strengths:

The major strengths of the paper include high quality data, robust analyses of the data, and a well-written manuscript. The combination of genome editing in C. owczarzaki, transfection of C. owczarzaki, and time-lapse movies of adherent cells generally support the conclusions (1) that control of cell density is an ancient function of the Hippo pathway; (2) that Hippo pathway control of cytoskeletal properties and contractile behavior underlie its regulation of cell density, and (3) that Hippo kinase control of Yki localization is likely an ancient function of the pathway.

Weaknesses:

There are no weaknesses.

Reviewer #1 (Public Review):

Summary:

In "Prediction error determines how memories are organized in the brain: a study of Pavlovian fear 2 extinction in rats", Kennedy et al examine how new information is organized in memory. They tested an idea based on latent theory that suggests that a large prediction error leads to the formation of a new memory, whereas a small prediction error leads to memory updating. They directly tested the prediction by extinguishing fear-conditioned rats with gradual extinction. For their experiment, gradual extinction was carried out by progressively reducing the intensity of shocks that were co-terminated with the CS, until the CS was presented alone. Doing so resulted in diminished spontaneous recovery and reinstatement compared to Standard Extinction. The results are compelling, and have important implications for the field of fear learning and memory as well as translation to anxiety-related disorders.

The authors carried out the Spontaneous Recovery experiment in 2 separate experiments. In one, they found differences between the Gradual and Standard Extinction groups, but in the second, they did not. It seems that their reinstatement test was more robust, and showed significant differences between the Gradual and Standard Extinction groups.

The authors carried out important controls that enable proper contextualization of the findings. They included a "Home" group, in which rats received fear conditioning, but not extinction manipulation. Relative to this group, the Gradual and Standard extinction groups showed a reduction in freezing.

In Experiments 3 and 4, the authors essentially carried out clever controls that served to examine whether shock devaluation (Experiment 4) and reduction in shock intensity (rather than a gradual decrease in shock intensity) (Experiment 3) would also yield a decrease in the return of fear. In line with a latent-cause updating explanation for accounting for the Gradual Extinction, they did not.

In Experiment 5, the authors examined whether a prediction error produced by a change of context might contribute interference to the latent cause updating afforded by the Gradual Extinction. Such a prediction would align with a more flexible interpretation of a latent-cause model, such as those proposed by Redish (2007) and Gershman et al (2017), but not the latent-cause interpretation put forth by the Cochran-Cisler model (2019). Their findings showed that whereas Gradual Extinction carried out in the same context as acquisition resulted in less return of fear than Standard Extinction, it actually yielded a greater degree of return of fear when carried out in a different context, in support of the Redish and Gershman accounts, but not Cochran-Cisler.

Experiment 6 extended the findings from Experiment 5 in a different state-splitting modality: timing. In this experiment, the authors tested whether a shift in temporal context also influenced the gradual extinction effect. They thus carried out the extinction sessions 21 days after conditioning. They found that while Gradual Extinction was indeed effective when carried out one day after fear conditioning, it did not when conducted 21 days later.

The authors next carried out an omnibus analysis which included all the data from their 6 experiments, and found that overall, Gradual Extinction resulted in diminished return of fear relative to Standard Extinction. I thought the omnibus analysis was a great idea and an appropriate way to do their data justice.

Strengths:

Compelling findings. The data support the conclusions. 6 rigorous experiments were conducted which included clever controls. Data include male and female rats. I really liked the omnibus analysis.

Weaknesses:

None noted.

Reviewer #1 (Public Review):

Summary:

This is an interesting study that performs scRNA-Seq on infected and uninfected wounds. The authors sought to understand how infection with E. faecalis influences the transcriptional profile of healing wounds. The analysis demonstrated that there is a unique transcriptional profile in infected wounds with specific changes in macrophages, keratinocytes, and fibroblasts. They also speculated on potential crosstalk between macrophages and neutrophils and macrophages and endothelial cells using NicheNet analysis and CellChat. Overall the data suggest that infection causes keratinocytes to not fully transition which may impede their function in wound healing and that the infection greatly influenced the transcriptional profile of macrophages and how they interact with other cells.

Strengths:

It is a useful dataset to help understand the impact of wound infection on the transcription of specific cell types. The analysis is very thorough in terms of transcriptional analysis and uses a variety of techniques and metrics.

Weaknesses:

Some drawbacks of the study are the following. First, the fact that it only has two mice per group, and only looks at one time point after wounding decreases the impact of the study. Wound healing is a dynamic and variable process so understanding the full course of the wound healing response would be very important to understand the impact of infection on the healing wound. Including unwounded skin in the scRNA-Seq would also lend a lot more significance to this study. Another drawback of the study is that mouse punch biopsies are very different than human wounds as they heal primarily by contraction instead of re-epithelialization like human wounds. So while the conclusions are generally supported the scope of the work is limited.

Reviewer #1 (Public Review):

Abreo et al. performed a detailed multidisciplinary analysis of a pathogenic variant of the KCNQ2 ion channel subunit identified in a child with neonatal-onset epilepsy and neurodevelopmental disorders. These analyses revealed multiple molecular and cellular mechanisms associated with this variant and provided important insights into what distinguishes distinct pathogenic variants of KCNQ2 associated with self-limited familial neonatal epilepsy versus those leading to developmental and epileptic encephalopathy, and how they may mechanistically differ, to result in different extents of developmental impairment.

The authors first provide a detailed clinical description of the patient heterozygous for a novel pathogenic variant encoding KCNQ2 G256W. They then model the structure of the G256W variant based on recent cryo-EM structures of KCNQ2 and other ion channel subunits and find that while the affected position is quite distinct from the channel pore, it participates in a novel, evolutionarily conserved set of amino acids that form a network of hydrogen bonds that stabilize the structure of the pore domain.

They then undertake a series of rigorous and quantitative laboratory experiments in which the KCNQ2 G256W variant is coexpressed exogenously with WT KCNQ2 and KCNQ3 subunits in heterologous cells, and endogenously in novel gene-edited mice generated for this study. This includes detailed electrophysiological analyses in the transfected heterologous cells revealing the dominant-negative phenotype of KCNQ2 G256W. They found altered firing properties in hippocampal CA1 neurons in brain slices from the heterozygous KCNQ2 G256W mice.

They next showed that the expression and localization of KCNQ channels are altered in brain neurons from heterozygous KCNQ2 G256W mice, suggesting that this variant impacts KCNQ2 trafficking and stability.

Together, these laboratory studies reveal that the molecular and cellular mechanisms shaping KCNQ channel expression, localization, and function are impacted at multiple levels by the variant encoding KCNQ2 G256W, likely contributing to the clinical features of the child heterozygous for this variant relative to patients harboring distinct KCNQ2 pathogenic variants.

DOI: 10.1016/j.isci.2024.109337

Resource: (ZFIN Cat# ZDB-GENO-060207-1,RRID:ZFIN_ZDB-GENO-060207-1)

Curator: @abever99

SciCrunch record: RRID:ZFIN_ZDB-GENO-060207-1

What is this?

DOI: 10.1016/j.isci.2024.109272

Resource: (ZFIN Cat# ZDB-GENO-060207-1,RRID:ZFIN_ZDB-GENO-060207-1)

Curator: @abever99

SciCrunch record: RRID:ZFIN_ZDB-GENO-060207-1

What is this?

Reviewer #1 (Public Review):

Summary:

Thayer et al build upon their prior findings that ASAR long noncoding RNAs (lncRNAs) are chromatin-associated and are implicated in control of replication timing. To explore the mechanism of function of ASAR transcripts, they leveraged the ENCODE RNA binding protein eCLIP datasets to show that a 7kb region of ASAR6-141 is bound by multiple hnRNP proteins. Deletion of this 7kb region resulted in delayed chromosome 6 replication. Furthermore, ectopic integration of the ASAR6-141 7kb region into autosomes or the inactive X-chromosome also resulted in delayed chromosome replication. They then use RNA FISH experiments to show that the knockdown of these hnRNP proteins disrupts ASAR6-141 localization to chromatin and in turn replication timing.

Strengths:

Given prior publications showing HNRNPU to be important for chromatin retention of XIST and Firre, this work expands upon our understanding of the role of hnRNP proteins in lncRNA function.

Weaknesses:

The work presented is mechanistically interesting, however, one must be careful with the over-interpretation that hnRNP proteins can regular chromosome replication directly. Furthermore, the work could be strengthened by including a few controls and clarifications.

Reviewer #2 (Public Review):

This article is focused on investigating incremental speech processing, as it pertains to building higher order syntactic structure. This is an important question because speech processing in general is lesser studied as compared to reading, and syntactic processes are lesser studied than lower-level sensory processes. The authors claim to shed light on the neural processes that build structured linguistic interpretations. The authors apply modern analysis techniques, and use state-of-the-art large language models in order to facilitate this investigation. They apply this to a cleverly designed experimental paradigm of EMEG data, and compare neural responses of human participants to the activation profiles in different layers of the BERT language model.

Comments on revised version:

Similar to my original review, I find the paper hard to follow, and it is not clear to me that the use of the LLM is adding much to the findings. Using complex language models without substantial motivation dampens my enthusiasm significantly. This concern has not been alleviated since my original review.

Reviewer #1 (Public Review):

Summary:

Information transfer between the hippocampus and prefrontal cortex is thought to be critical for spatial working memory, but most of the prior evidence for this hypothesis is correlational. This study attempts to test this causally by linking trial start times to theta-band coherence between these two structures. The authors find that trials initiated during periods of high coherence led to a dramatic improvement in performance. This applied not only to a spatial working memory task, but also to a cue-guided navigation task, suggesting that coherence in these regions may be a signature of a heightened attentional or preparatory state. The authors supplement this behavioral result with electrophysiological recordings and optogenetic manipulations to test whether ventral midline thalamus is likely to mediate hippocampal-prefrontal coherence.

Strengths:

This study demonstrates a striking behavioral effect; by changing the moment at which a trial is initiated, performance on a spatial working memory task improves dramatically, from around 80% correct to over 90% correct. A smaller but nonetheless robust increase in accuracy was also seen in a texture discrimination task. Therefore, prefrontal-hippocampal synchronization in the theta band may not only be important for spatial navigation, but may also be associated with improved performance in a range of tasks. If these results can be replicated using noninvasive EEG, it would open up a powerful avenue for modulating human behavior.

Weaknesses:

Ventral midline thalamic nuclei, such as reuniens, have reciprocal projections to both prefrontal cortex and hippocampus and are therefore well-situated to mediate theta-band interactions between these structures. However, alternative mechanisms cannot be ruled out by the results of this study. For example, theta rhythms are globally coherent across the rodent hippocampus, and ventral hippocampus projects directly to prefrontal cortex. Theta propagation may depend on this pathway, and may only be passively inherited by VMT.

The optogenetic manipulations are intended to show that theta in VMT propagates to PFC and also affects HPC-PFC coherence. However, the "theta" induced by driving thalamic neurons at 7 Hz is extremely artificial. To demonstrate that VMT is causally involved in coordinating activity across HPC and PFC, it would have been better to optogenetically inhibit, rather than excite, these nuclei. If the authors were able to show that the natural occurrence of theta in PFC depends on activity in VMT, that would be much more convincing test of their hypothesis.

Reviewer #1 (Public Review):

In this study, Lin et al developed a protocol termed MOCAT, to perform tissue clearing and labelling on large-scale FFPE mouse brain specimens. They have optimised protocols for dewaxing and adequate delipidation of FFPE tissues to enable deep immunolabelling, even for whole mouse brains. This was useful for the study of disease models such as in an astrocytoma model to evaluate spatial architecture of the tumour and its surrounding microenvironment. It was also used in a traumatic brain injury model to quantify changes in vasculature density and differences in monoaminergic innervation. They have also demonstrated the potential of multi-round immunolabelling using photobleaching, as well as expansion microscopy with FFPE samples using MOCAT.

Comments on revised version:

The revised manuscript by Lin et al is much improved with a more detailed methods description. There are only a few minor comments for the authors:

- The new figures provided in Supplementary figure 5 did demonstrate a good level of transparency for the mouse brain tissue. However, quite marked tissue expansion can be seen following antigen retrieval and RI matching and this should be mentioned in the manuscript.<br /> - The authors have provided comparison between mouse and human brain samples in Figure S12. However, it is misleading to mention that the "fluorescent signals are comparable at varying depth" as the figure clearly showed a lack of continuous staining especially for SMI312 at 900um depth, and human brain tissue showed considerably increased background signal (likely due to endogenous lipofuscin which has autofluorescent properties).<br /> - It is understandable the authors cannot provide the full detail of the RI matching reagent as it is a commercialised product. However, it may still be useful if they can quote the refractive index +/- pH of the solution.

Reviewer #1 (Public Review):

Summary:

Mice can learn to associate sensory cues (sound and light) with a reward or activation of dopamine neurons in the ventral tegmental area (VTA), and then anticipate the reward from the sensory cue only. Using this paradigm, Harada et al. showed that after learning, the cue is able to induce dopamine release in the projection targets of the VTA, namely the nucleus accumbens and lateral hypothalamus (LH). Within the LH, dopamine release from VTA neurons (either by presentation of the cue or direct optical stimulation of VTA neurons) activates orexin neurons, measured as an increase in intracellular calcium levels.

Strengths:

This study utilized genetically encoded optical tools to selectively stimulate dopamine neurons and to monitor dopamine release in target brain areas and calcium response of orexin neurons. This allowed a direct assessment of the relationship between the behavioral response of the animals, release of a key neurotransmitter in select brain areas and its effect on target cells with the precision previously not possible. The results shed light onto the mechanism underlying reward-related learning and expectation.

Weaknesses:

Supplementary Fig.2: While the differences in time course are analyzed and extensively discussed, there is also a large discrepancy in the magnitude of change in DA levels in the two areas that is not mentioned. Specifically, DA increases is about 90-fold of baseline in NAc while it is about 2-fold in the LH. This could be because the DA level is either higher during baseline or lower during peak in the LH. Is there a known difference in the DA fiber density or extracellular DA levels in the two areas?

The DA antagonist i.p. study (Fig.5E and suppl fig 4) appears to be repeated measurements in same animals. If so, is it possible that repeated opto-sessions result in desensitization of the response, and therefore the smaller response is not due to the antagonist? Ideally, the order of experiments (i.e. vehicle, SCH23390 and raclopride) would be randomized, and a control group should be shown where DA terminal-stimulation induces consistent response in orexin neurons when applied three times without any antagonists. The result should be assessed using one-way repeated measures ANOVA.

Importantly, only 5 minutes were allowed for i.p. injected drugs to be absorbed and distributed to the brain before DA release was evoked and ORX neuron activity were monitored. Unfortunately, this is too short (In Ref 13, ip injection of SCH 23390 was 30 minutes prior to optogenetics/photometry experiments. In Ref 70, no effect on behavior was detected at 10 min post-i.p. injection of SCH 23390; In Ref 71, the effect of raclopride on behavior was measured 30 min post-ip injection).

Overall, it seems premature to make a conclusion about a role for D2 receptors or lack of involvement of D1 receptors in the observed phenomenon.

Reciprocal activation of VTA DA neurons and LH orexin neurons is an interesting idea. However, if this is the case, the activity of these two types of cells should show similar pattern and time course. This manuscript shows that extracellular DA levels decays quickly following the cessation of optical stimulation (Fig. 3B) whereas orexin neuron activity is long-lasting (Fig. 5). Thus, the hypothesis does not seem to be fully supported by experimental data.

Reviewer #1 (Public Review):

While I acknowledge the authors' effort in conducting Southern blot analysis to address my prior concern regarding the presence of dual copies of torA and tapA, I find their current resolution inadequate. Specifically, the simple deletion of the respective result sections for torA and tapA significantly impacts the overall significance of this study. The repeated unsuccessful attempts to generate correct mutants only offer circumstantial evidence, as technical issues may have been a contributing factor. Therefore, instead of merely removing these sections, it is essential for the authors to present more compelling experimental data demonstrating that torA and tapA are indeed vital for the viability of A. flavus. Such data would enhance the overall significance of this study.

Reviewer #1 (Public Review):

The authors have identified the predicted EBE of PthA4 in the promoter of Cs9g12620, which is induced by Xcc. The authors identified a homolog of Cs9g12620, which has variations in the promoter region. The authors show that PthA4 suppresses Cs9g12620 promoter activity independent of the binding action. The authors also show that CsLOB1 binds to the promoter of Cs9g12620. Interestingly, the authors show that PthA4 interacts with CsLOB1 at the protein level. Finally, it shows that Cs9g12620 is important for canker symptoms. Overall, this study has reported some interesting discoveries and the writing is generally well done. However, the discoveries are affected by the reliability of the data and some flaws in the experimental designs.

Here are some major issues:<br /> The authors have demonstrated that Cs9g12620 contains the EBE of PthA4 in the promoter region, to show that PthA4 controls Cs9g12620, the authors need to compare to the wild type Xcc and pthA4 mutant for Cs9g12620 expression. The data in Figure 1 is not enough.

The authors confirmed the interaction between PthA4 and the EBE in the promoter of Cs9g12620 using DNA electrophoretic mobility shift assay (EMSA). However, Figure 2B is not convincing. The lane without GST-PthA4 also clearly showed a mobility shift. For the EMSA assay, the authors need also to include a non-labeled probe as a competitor to verify the specificity. The description of the EMSA in this paper suggests that it was not done properly. It is suggested the authors redo this EMSA assay following the protocol: Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions PMID: 17703195.

The authors also claimed that PthA4 suppresses the promote activity of Cs9g12620. The data is not convincing and also contradicts with their own data that overexpression of Cs9g12620 causes canker and silencing of it reduces canker considering PthA4 is required for canker development. The authors conducted the assays using transient expression of PthA4. It should be done with Xcc wild type, pthA4 mutant, and negative control to inoculate citrus plants to check the expression of Cs9g12620.

Figure 6 AB is not convincing. There are no apparent differences. The variations shown in B are common in different wild-type samples. It is suggested that the authors conduct transgenic instead of transient overexpression.

Gene silencing data needs more appropriate controls. Figure D seems to suggest canker symptoms actually happen for the RNAi treated. The authors need to make sure the same amount of Xcc was used for both CTV empty vector and the RNAi. It is suggested a blink test is needed here.

Reviewer #1 (Public Review):

Summary:

Doxorubincin has long been known to cause bone loss by increasing osteoclast and suppressing osteoblast activities. The study by Wang et al. reports a comprehensive investigation into the off-target effects of doxorubicin on bone tissues and potential mechanisms.. They used a tumor-free model with wild type mice and found that even a single dose of doxorubicin has a major influence by increasing leukopenia and DAMPs and inflammasomes in macrophages and neutrophils, and inflammation-related cell death (pyroptosis and NETosis). The gene knockout study shows that AIM2 and NLRP3 are the major contributors to bone loss. Overall, the study confirmed previous findings regarding the impact of doxorubicin on tissue inflammation and expands the research further into bone tissue. The presented data presented are consistent; however, a major question remains regarding whether doxorubicin drives inflammation and its related events. Most in vitro study showed that the effect of doxorubincin cannot be demonstrated without LPS priming. This observation raises the question of whether doxorubincin itself could activate the inflammasome and the related events. In vivo study, on the other hand, suggested that it doesn't require LPS. The inconsistency here was not explained further. Moreover, a tumor-free mouse model was used for the study; however, immune responses in tumor bearing models would likely be distinct from tumor-free ones. The justification for using tumor-free models is not well-established.

Strengths:<br /> The paper includes a comprehensive study that shows the effects of doxorubincin on cytokine levels in serum, release of DAMPs and NETosis, and leukopenia using both in vivo and in vitro models. Bone marrow cells, macrophages and neutrophils were isolated from the bone marrow, and the levels of cytokines in serum were also determined.

They employed multiple knockout models with deficiency in Aim 2, Nlirp3, and double deficiencies to dissect the functional involvement of these two inflammasomes.

The experiments in general are well designed. The paper is also logically written, and figures were clearly labeled.

Weaknesses:<br /> Most of the data presented are correlative, and there is not much effort to dissect the underlying molecular mechanism.

It is not entirely clear why a tumor free model is chosen to study immune responses, as immune responses can differ significantly with or without tumor-bearing.

Immune responses in isolated macrophages, neutrophils and bone marrow cells require priming with LPS, while such responses are not observed in vivo. There is no explanation for these differences.

The band intensities on Western blots in Fig. 4 and Fig. 5 are not quantified, and the numbers of repeats are also not provided.

Many abbreviations are used throughout the text, and some of the full names are not provided.

Fig. 5B needs a label on X axis.