Reviewer #1 (Public review):

Summary:

The authors use analysis of existing data, mathematical modelling, and new experiments, to explore the relationship between protein expression noise, translation efficiency, and transcriptional bursting.

Strengths:

The analysis of the old data and the new data presented is interesting and mostly convincing.

Weaknesses:

(1) My main concern is the analysis presented in Figure 4. This is the core of mechanistic analysis that suggests ribosomal demand can explain the observed phenomenon. I am both confused by the assumptions used here and the details of the mathematical modelling used in this section. Firstly, the authors' assumption that the fluctuations of a single gene mRNA levels will significantly affect ribosome demand is puzzling. On average the total level of mRNA across all genes would stay very constant and therefore there are no big fluctuations in the ribosome demand due to the burstiness of transcription of individual genes. Secondly, the analysis uses 19 mathematical functions that are in Table S1, but there are not really enough details for me to understand how this is used, are these included in a TASEP simulation? In what way are mRNA-prev and mRNA-curr used? What is the mechanistic meaning of different terms and exponents? As the authors use this analysis to argue ribosomal demand is at play, I would like this section to be very much clarified.

(2) Overall, the paper is very long and as there are analytical expressions for protein noise (e.g. see Paulsson Nature 2004), some of these results do not need to rely on Gillespie simulations. Protein CV (noise) can be written as three terms representing protein noise contribution, mRNA expression contribution, and bursty transcription contribution. For example, the results in panel 1 are fully consistent with the parameter regime, protein noise is negligible compared to transcriptional noise.

Reviewer #1 (Public review):

Summary:

Numerous mechanism and structural studies reported the cooperative role of Oct4 and Sox2 during the establishment of pluripotency during reprogramming. Due to the difficulty in sample collection and RNA-seq with low-number cells, the precise mechanisms remain in early embryos. This manuscript reported the role of OCT4 and SOX2 in mouse early embryos using knockout models with low-input ATAC-seq and RNA-seq. Compared to the control, chromatin accessibility and transcriptome were affected when Oct4 and Sox2 were deleted in early ICM. Specifically, decreased ATAC-seq peaks showed enrichment of Motifs of TF such as OCT, SOX, and OCT-SOX, indicating their importance during early development. Moreover, by deep analysis of ATAC-seq and RNA-seq data, they found Oct4 and Sox2 target enhancer to activate their downstream genes. In addition, they also uncovered the role of OS during development from the morula to ICM, which provided the scientific community with a more comprehensive understanding.

Strengths:

On the whole, the manuscript is innovative, and the conclusions of this paper are mostly well supported by data, however, there are some issues that need to be addressed.

Weaknesses:

Major Points:

(1) In Figure 1, a more detailed description of the knockout strategy should be provided to clarify itself. The knockout strategy in Fig1 is somewhat obscure, such as how is OCT4 inactivated in Oct4mKO2 heterozygotes. As shown in Figure 1, the exon of OCT4 is not deleted, and its promoter is not destroyed. Therefore, how does OCT4 inactivate to form heterozygotes?

(2) Is ZP 3-Cre expressed in the zygotes? Is there any residual protein?

(3) What motifs are enriched in the rising ATAC-seq peaks after knocking out of OCT4 and SOX2?

(4) The ordinate of Fig4c is lost.

(5) Signals of H3K4me1, H3K27ac, and so on are usually used to define enhancers, and the loci of enhancers vary greatly in different cells. In the manuscript, the authors defined ATAC-seq peaks far from the TSS as enhancers. The definition in this manuscript is not strictly an enhancer.

(6) If Oct4 and Sox2 truly activate sap 30 and Uhrf 1, what effect does interfering with both genes have on gene expression and chromatin accessibility？

Reviewer #1 (Public review):

Summary:

This study makes use of the EM reconstruction of the fly brain to investigate the morphology and topography of the synapses between retinotopic, loom-sensitive visual projection neurons (VPNs) and downstream descending neurons (DNs). The authors analyzed the distribution of synapses on the dendritic trees of DNs and performed multi-compartmental modelling to study the implications of the synaptic arrangements for neuronal integration of input signals.

Until recently, it has been unclear how spatial information is passed from retinotopic loom-sensitive neurons to descending neurons because the axons of the VPNs terminate in small optic glomeruli with no apparent topographic organization. It has recently been shown that synaptic weight gradients of VPNs connecting to DNs are the main mechanisms that allow for directed behavioral output (Dombrovski et al.). This study now goes one step further to determine if precise synapse location on the dendritic tree contributes further to the information processing. The study suggests that (1) none of the VPNs investigated show a retinotopic organization of synapses on DN dendrites. (2) Synapses of single VPNs are locally clustered. (3) Initial EPSPs at the synaptic location have, as expected, varying amplitudes but the amplitudes are passively normalized and only cover a small range when measured at the SIZ. (4) A near random distribution of synapses allows for linear integration of synaptic inputs when only a few VPNs are activated.

Strengths:

This study provides a detailed picture of the synapse distribution for a set of VPN and DN pairs, in combination with multi-compartmental modelling fitted to electrophysiological data. The data and methods are clear. The findings are overall interesting. The computational pipeline, which should ideally be made publicly available, will allow the community to make similar analyses on different neuronal classes, which will facilitate the detection of more general mechanisms of dendritic computation.

Weaknesses:

- In my opinion, we need more detail on the electrophysiological data and the fitting of the multi-compartmental model, which is the foundation of large parts of the study.<br /> - The study shows that the synapses of an individual VPN are locally clustered and suggests this as evidence for clustering of synapses of similar tuning (as has been shown previously in other systems). I am not fully convinced by the arguments here, since synapses of a single neuron are by necessity not randomly distributed in space.<br /> - As written, it was in parts unclear to me what the main hypotheses and conclusions were - e.g., how would a retinotopic distribution of synapses on dendritic trees contribute to information processing? Are the model predictions in line with the presumed behavioural role of these neurons?

Reviewer #1 (Public review):

In the manuscript entitled "A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome", Qian et al. found an activation of the non-canonical inflammasome, but not the downstream NLRP3 inflammasome, during the infection of macrophage by P. aeruginosa, which is in sharp contrast to that by E. coli (Figure 1). In realizing that the suppression of the NLRP3 inflammasome is Caspase-11 dependent, the authors performed a screening among P. aeruginosa proteins and identified VgrG2b being a major substrate of Caspase-11 (Figure 2). Next, the authors mapped the cleavage site on VgrG2b to D883, and demonstrated that cleavage of VgrG2b by Caspase-11 is essential for the suppression of the NLRP3 inflammasome (Figure 3). Furthermore, they found that a binding between the C-terminal fragment of the cleaved VgrG2b and NLRP3 existed (Figure 4), which was then proved to block the association of NLRP3 with NEK7 (Figure 5). Finally, the authors demonstrated that blocking of VgrG2b cleavage, by either mutation of the D883 or administration of a designed peptide, effectively improved the survival rate of the P. aeruginosa-infected mice (Figure 6). This is a well-designed and executed study, with the results clearly presented and stated.

Reviewer #1 (Public review):

Summary:

Wang, Po-Kai, et al., utilized the de novo polarization of MDCK cells cultured in Matrigel to assess the interdependence between polarity protein localization, centrosome positioning, and apical membrane formation. They show that the inhibition of Plk4 with Centrinone does not prevent apical membrane formation, but does result in its delay, a phenotype the authors attribute to the loss of centrosomes due to the inhibition of centriole duplication. However, the targeted mutagenesis of specific centrosome proteins implicated in the positioning of centrosomes in other cell types (CEP164, ODF2, PCNT, and CEP120) did not affect centrosome positioning in 3D cultured MDCK cells. A screen of proteins previously implicated in MDCK polarization revealed that the polarity protein Par-3 was upstream of centrosome positioning, similar to other cell types.

Strengths:

The investigation into the temporal requirement and interdependence of previously proposed regulators of cell polarization and lumen formation is valuable to the community. Wang et al., have provided a detailed analysis of many of these components at defined stages of polarity establishment. Furthermore, the generation of PCNT, p53, ODF2, Cep120, and Cep164 knockout MDCK cell lines is likely valuable to the community.

Weaknesses:

Additional quantifications would highly improve this manuscript, for example it is unclear whether the centrosome perturbation affects gamma tubulin levels and therefore microtubule nucleation, it is also not clear how they affect the localization of the trafficking machinery/polarity proteins. For example, in Figure 4, the authors measure the intensity of Gp134 at the apical membrane initiation site following cytokinesis, but there is no measure of Gp134 at the centrosome prior to this.

Reviewer #1 (Public review):

Previous studies have highlighted some of these paracrine activities of Toxoplasma - and Rasogi et al (mBio, 2020) used a single cell sequencing approach of cells infected in vitro with the WT or MYR KO parasites - and one of their conclusions was that MYR-1 dependent paracrine activities counteract ROP-dependent processes. Similarly, Chen et al (JEM 2020) highlighted that a particular rhoptry protein (ROP16) could be injected into uninfected macrophages and move them to an anti-inflammatory state that might benefit the parasite.

There are caveats around immunity and as yet no insight into how this works. In Figure 2 there is a marked defect in the ability of the parasites to expand at day 2 and day 5. Together, these data sets suggest that this paracrine effect mediated by MYR-1 works early - well before the development of adaptive responses.

Reviewer #1 (Public review):

Hotinger et al. explore the population dynamics of Salmonella enterica serovar Typhimurium in mice using genetically tagged bacteria. In addition to physiological observations, pathology assessments, and CFU measurements, the study emphasizes quantifying host bottleneck sizes that limit Salmonella colonization and dissemination. The authors also investigate the genetic distances between bacterial populations at various infection sites within the host.

Initially, the study confirms that pretreatment with the antibiotic streptomycin before inoculation via orogastric gavage increases the bacterial burden in the gastrointestinal (GI) tract, leading to more severe symptoms and heightened fecal shedding of bacteria. This pretreatment also significantly reduces between-animal variation in bacterial burden and fecal shedding. The authors then calculate founding population sizes across different organs, discovering a severe bottleneck in the intestine, with founding populations reduced by approximately 10^6-fold compared to the inoculum size. Streptomycin pretreatment increases the founding population size and bacterial replication in the GI tract. Moreover, by calculating genetic distances between populations, the authors demonstrate that, in untreated mice, Salmonella populations within the GI tract are genetically dissimilar, suggesting limited exchange between colonization sites. In contrast, streptomycin pretreatment reduces genetic distances, indicating increased exchange.

In extraintestinal organs, the bacterial burden is generally not substantially increased by streptomycin pretreatment, with significant differences observed only in the mesenteric lymph nodes and bile. However, the founding population sizes in these organs are increased. By comparing genetic distances between organs, the authors provide evidence that subpopulations colonizing extraintestinal organs diverge early after infection from those in the GI tract. This hypothesis is further tested by measuring bacterial burden and founding population sizes in the liver and GI tract at 5 and 120 hours post-infection. Additionally, they compare orogastric gavage infection with the less injurious method of infection via drinking, finding similar results for CFUs, founding populations, and genetic distances. These results argue against injuries during gavage as a route of direct infection.

To bypass bottlenecks associated with the GI tract, the authors compare intravenous (IV) and intraperitoneal (IP) routes of infection. They find approximately a 10-fold increase in bacterial burden and founding population size in immune-rich organs with IV/IP routes compared to orogastric gavage in streptomycin-pretreated animals. This difference is interpreted as a result of "extra steps required to reach systemic organs."

While IP and IV routes yield similar results in immune-rich organs, IP infections lead to higher bacterial burdens in nearby sites, such as the pancreas, adipose tissue, and intraperitoneal wash, as well as somewhat increased founding population sizes. The authors correlate these findings with the presence of white lesions in adipose tissue. Genetic distance comparisons reveal that, apart from the spleen and liver, IP infections lead to genetically distinct populations in infected organs, whereas IV infections generally result in higher genetic similarity.

Finally, the authors investigate GI tract reseeding, identifying two distinct routes. They observe that the GI tracts of IP/IV-infected mice are colonized either by a clonal or a diversely tagged bacterial population. In clonally reseeded animals, the genetic distance within the GI tract is very low (often zero) compared to the bile population, which is predominantly clonal or pauciclonal. These animals also display pathological signs, such as cloudy/hardened bile and increased bacterial burden, leading the authors to conclude that the GI tract was reseeded by bacteria from the gallbladder bile. In contrast, animals reseeded by more complex bacterial populations show that bile contributes only a minor fraction of the tags. Given the large founding population size in these animals' GI tracts, which is larger than in orogastrically infected animals, the authors suggest a highly permissive second reseeding route, largely independent of bile. They speculate that this route may involve a reversal of known mechanisms that the pathogen uses to escape from the intestine.

The manuscript presents a substantial body of work that offers a meticulously detailed understanding of the population dynamics of S. Typhimurium in mice. It quantifies the processes shaping the within-host dynamics of this pathogen and provides new insights into its spread, including previously unrecognized dissemination routes. The methodology is appropriate and carefully executed, and the manuscript is well-written, clearly presented, and concise. The authors' conclusions are well-supported by experimental results and thoroughly discussed. This work underscores the power of using highly diverse barcoded pathogens to uncover the within-host population dynamics of infections and will likely inspire further investigations into the molecular mechanisms underlying the bottlenecks and dissemination routes described here.

Major point:

Substantial conclusions in the manuscript rely on genetic distance measurements using the Cavalli-Sforza chord distance. However, it is unclear whether these genetic distance measurements are independent of the founding population size. I would anticipate that in populations with larger founding population sizes, where the relative tag frequencies are closer to those in the inoculum, the genetic distances would appear smaller compared to populations with smaller founding sizes independent of their actual relatedness. This potential dependency could have implications for the interpretation of findings, such as those in Figures 2B and 2D, where antibiotic-pretreated animals consistently exhibit higher founding population sizes and smaller genetic distances compared to untreated animals.

Reviewer #1 (Public review):

Summary:

The investigators in this study analyzed the dataset assembly from 540 Salmonella isolates, and those from 45 recent isolates from Zhejiang University of China. The analysis and comparison of the resistome and mobilome of these isolates identified a significantly higher rate of cross-region dissemination compared to localized propagation. This study highlights the key role of the resistome in driving the transition and evolutionary history of S. Gallinarum.

Strengths:

The isolates included in this study were from 16 countries in the past century (1920 to 2023). While the study uses S. Gallinarun as the prototype, the conclusion from this work will likely apply to other Salmonella serotypes and other pathogens.

Weaknesses:

While the isolates came from 16 countries, most strains in this study were originally from China.

Reviewer #1 (Public review):

Summary:

In the manuscript "Heat Shock Factor Regulation of Antimicrobial Peptides Expression Suggests a Conserved Defense Mechanism Induced by Febrile Temperature in Arthropods," Xiao and colleagues examine the role of the shrimp Litopenaeus vannamei HSF1 ortholog (LvHSF1) in the response to viral infection. The authors provide compelling support for their conclusions that the activation of LvHSF1 limits viral load at high temperatures. Specifically, the authors convincingly show that (i) LvHSF1 mRNA and protein are induced in response to viral infection at high temperatures, (ii) increased LvHSF1 levels can directly induce the expression of the nSWD (and directly or indirectly other antibacterial peptides, AMPs), (ii) nSWD's antimicrobial activities can limit viral load, and, (iv) LvHSF1 protects survival at high temperatures following virus infection. These data thus provide a model by which an increase in HSF1 levels limits viral load through the transcription of antimicrobial peptides and provides a rationale for the febrile response as a conserved response to viral infection.

Strengths:

The large body of careful time series experiments, tissue profiling, and validation of RNA-seq data is convincing. Several experimental methodologies are used to support the authors' conclusions that nSWD is an LvHSf1 target and increased LvHSF1 alone can explain increased levels of nSWD. Similar carefully conducted experiments also conclusively implicate nSWD protein in limiting WSSV viral loads.

Weaknesses:

Despite this compelling data regarding the protective role of HSF1 in the febrile response, what remains unexplained and complicates the authors' model is the observation that losing LvHSF1 at 'normal' temperatures of 25C is not detrimental to survival, even though viral loads increase and nSWD is likely still subject to LvHSF1 regulation. These observations suggest that WSSV infection may have other detrimental effects on the cell not reflected by viral load and that LvHSF1 may play additional roles in protecting the organism from these effects of WSSV infection, such as perhaps, perturbations to protein homeostasis. This is worth discussing, especially in light of the rather complicated roles of hormesis in protection from infection, the role of HSF1 in hormesis responses, and the findings from other groups that the authors discuss.

https://www.liberatingstructures.com/1-1-2-4-all/

https://app.thebrain.com/brain/3d80058c-14d8-5361-0b61-a061f89baf87/fee4a5d8-6d7d-417a-8be2-2b2cc0e97966

Reviewer #1 (Public review):

Summary:

Dr. Santamaria's group previously utilized antigen-specific nanomedicines to induce immune tolerance in treating autoimmune diseases. The success of this therapeutic strategy has been linked to expanded regulatory mechanisms, particularly the role of T-regulatory type-1 (TR1) cells. However, the differentiation program of TR1 cells remained largely unclear. Previous work from the authors suggested that TR1 cells originate from T follicular helper (TFH) cells. In the current study, the authors aimed to investigate the epigenetic mechanisms underlying the transdifferentiation of TFH cells into IL-10-producing TR1 cells. Specifically, they sought to determine whether this process involves extensive chromatin remodeling or is driven by pre-existing epigenetic modifications. Their goal was to understand the transcriptional and epigenetic changes facilitating this transition and to explore the potential therapeutic implications of manipulating this pathway.

The authors successfully demonstrated that the TFH-to-TR1 transdifferentiation process is driven by pre-existing epigenetic modifications rather than extensive new chromatin remodeling. The comprehensive transcriptional and epigenetic analyses provide robust evidence supporting their conclusions.

Strengths:

(1) The study employs a broad range of bulk and single-cell transcriptional and epigenetic tools, including RNA-seq, ATAC-seq, ChIP-seq, and DNA methylation analysis. This comprehensive approach provides a detailed examination of the epigenetic landscape during the TFH-to-TR1 transition.

(2) The use of high-throughput sequencing technologies and sophisticated bioinformatics analyses strengthens the foundation for the conclusions drawn.

(3) The data generated can serve as a valuable resource for the scientific community, offering insights into the epigenetic regulation of T cell plasticity.

(4) The findings have significant implications for developing new therapeutic strategies for autoimmune diseases, making the research highly relevant and impactful.

Weaknesses:

(1) While the study focuses on transcriptional and epigenetic analyses, the authors are currently undertaking efforts to validate these findings functionally. Ongoing research aims to further explore the roles of key transcription factors in the TFH-to-TR1 transition, reflecting the authors' commitment to building on the insights gained from this study.

(2) The identification of key transcription factors and epigenetic marks is a strong foundation for future work. The authors are actively investigating how these factors drive chromatin remodeling, which will enhance the mechanistic understanding of the TFH-to-TR1 process in future studies.

(3) Although the study provides a valuable snapshot of the epigenetic landscape, the authors are pursuing additional research to assess the dynamics of these changes over time. These ongoing efforts will contribute to a deeper understanding of the stability and progression of the observed epigenetic modifications.

Comments on revised version:

The authors have effectively discussed and addressed all previously raised questions. There are no further concerns.

Reviewer #1 (Public review):

Summary:

The authors have developed a valuable method based on a fully cell-free system to express a channel protein and integrated it into a membrane vesicle in order to characterize it biophysically. The study presents a useful alternative to study channels that are not amenable to be studied by more traditional methods.

Strengths:

The evidence supporting the claims of the authors is solid and convincing. The method will be of interest to researchers working on ionic channels, allowing to study a wide range of ion channel functions such as those involved in transport, interaction with lipids or pharmacology.

Weaknesses:

The inclusion of a mechanistic interpretation how the channel protein folds into a protomer or a tetramer to become functional into the membrane, would strengthen the study.

Comments on revised version:

In the revised version, the authors did not experimentally addressed how tetrameric or protomeric proteins are actually produced. However, they performed new experiments to assess the amount of tetramers that are being actually formed. They used a size-exclusion chromatography to conclude that the protomers and tetramers species of complexes are formed and assembled.

The authors have addressed most of my minor concerns and have modified or updated the manuscript following my recommendations, so I have no further comments.

Reviewer #1 (Public review):

In this paper, the authors show that disruption of calcineurin, which is encoded by tax-6 in C. elegans, results in increased susceptibility to P. aeruginosa but extends lifespan. In exploring the mechanisms involved, the authors show that disruption of tax-6 decreases the rate of defecation leading to intestinal accumulation of bacteria and distension of the intestinal lumen. The authors further show that the lifespan extension is dependent on hlh-30, which may be involved in breaking down lipids following deficits in defecation, and nhr-8, whose levels are increased by deficits in defecation. The authors propose a model in which disruption of the defecation motor program is responsible for the effect of calcineurin on pathogen susceptibility and lifespan, but do not exclude the possibility that calcineurin affects these phenotypes independently of defecation.

Reviewer #1 (Public review):

The authors present the cryo-EM structure of PSI-fucoxanthin chlorophyll a/c-binding proteins (FCPs) supercomplex from the diatom Thalassiosira pseudonana CCMP1335 at a global resolution of 2.3 Å. This exceptional resolution allows the authors to construct a near-atomic model of the entire supercomplex and elucidate the molecular details of FCPs arrangement. The high-resolution structure reveals subunits not previously identified in earlier reconstructions and models, as well as sequence analysis of PSI-FCPIs from other diatoms and red algae. Additionally, the authors use their model in conjunction with a phylogenetic analysis to compare and contrast the structural features of the T. pseudonana supercomplex with those of Chaetoceros gracilis, uncovering key structural features that contribute to the efficiency of light energy conversion in diatoms.

The study employs the advanced technique of single particle cryo-electron microscopy to visualize the complex architecture of the PSI supercomplex at near-atomic resolution and analyze the specific roles of FCPs in enhancing photosynthetic performance in diatoms.

Overall, the approach and data are both compelling and of high quality. The paper is well written and will be of wide interest for comprehending the molecular mechanisms of photosynthesis in diatoms. This work provides valuable insights for applications in bioenergy, environmental conservation, plant physiology, and membrane protein structural biology.

Reviewer #1 (Public review):

Summary:

The authors aim at dissecting the relationship between hair-cell directional mechanosensation and orientation-linked synaptic selectivity, using mice and the zebrafish. They find that Gpr156 mutant animals homogenize the orientation of hair cells without affecting the selectivity of afferent neurons, suggesting that hair-cell orientation is not the feature that determines synaptic selectivity. Therefore, the process of Emx2-dependent synaptic selectivity bifurcates downstream of Gpr156.

Strengths:

This is an interesting and solid paper. It solves an interesting problem and establishes a framework for the following studies. That is, to ask what are the putative targets of Emx2 that affect synaptic selectivity.<br /> The quality of the data is generally excellent.

Weaknesses:

The feeling is that the advance derived from the results is very limited.

Comments on revised version:

I am happy with the authors' reply and do not wish to modify my initial assessment.

Reviewer #1 (Public review):

Summary:

This work proposes a new method, DyNetCP, for inferring dynamic functional connectivity between neurons from spike data. DyNetCP is based on a neural network model with a two-stage model architecture of static and dynamic functional connectivity.<br /> This work evaluates the accuracy of the synaptic connectivity inference and shows that DyNetCP can infer the excitatory synaptic connectivity more accurately than a state-of-the-art model (GLMCC) by analyzing the simulated spike trains. Furthermore, it is shown that the inference results obtained by DyNetCP from large-scale in-vivo recordings are similar to the results obtained by the existing methods (jitter-corrected CCG and JPSTH). Finally, this work investigates the dynamic connectivity in the primary visual area VISp and in the visual areas using DyNetCP.

Strengths:

The strength of the paper is that it proposes a method to extract the dynamics of functional connectivity from spike trains of multiple neurons. The method is potentially useful for analyzing parallel spike trains in general, as there are only a few methods (e.g. Aertsen et al., J. Neurophysiol., 1989, Shimazaki et al., PLoS Comput Biol 2012) that infer the dynamic connectivity from spikes. Furthermore, the approach of DyNetCP is different from the existing methods: while the proposed method is based on the neural network, the previous methods are based on either the descriptive statistics (JSPH) or the Ising model.

Weaknesses:

Although the paper proposes a new method, DyNetCP, for inferring the dynamic functional connectivity, its strengths are neither clear nor directly demonstrated in this paper. That is, insufficient analyses are performed to support the usefulness of DyNetCP.<br /> First, this paper attempts to show the superiority of DyNetCP by comparing the performance of synaptic connectivity inference with GLMCC (Fig. 2). However, the improvement in the synaptic connectivity inference does not seem to be convincing. While this paper compares the performance of DyNetCP with a state-of-the-art method (GLMCC), there are several problems with the comparison. For example,

(1) It is unclear how accurately the proposed method can infer the dynamic connectivity.<br /> (2) This paper does not compare with existing approach (e.g., classical JPSTH: Aertsen et al., J. Neurophysiol., 1989, and other methods : Stevenson and Koerding, NIPS, 2011; Linderman et al., NIPS, 2014; Song et al., J. Neurosci. Methods, 2015), and<br /> (3) only a population of neurons generated from the Hodgkin-Huxley model was evaluated.

Thus, the results in this paper are not sufficient to conclude the superiority of DyNetCP in the estimation of synaptic connections. In addition, this paper compares the proposed method with the standard statistical methods Jitter-corrected CCG (Fig. 3) and JPSTH (Fig. 4). Unfortunately, these results do not show the superiority of the proposed method. It only shows that the results obtained by the proposed method are consistent with those obtained by the existing methods (CCG or JPSTH). This paper also compares the proposed method with the standard statistical methods, such as jitter-corrected CCG (Fig. 3) and JPSTH (Fig. 4). It only shows that the results obtained by the proposed method are consistent with those obtained by the existing methods (CCG or JPSTH), which does not show the superiority of the proposed method.

In summary, although DyNetCP has the potential to infer the dynamic (time-dependent) correlation more accurately than existing methods, the paper does not provide sufficient analysis to make this claim. It is also unclear whether the proposed method is superior to the existing methods for estimating functional connectivity, such as JPSTH and statistical approach (Stevenson and Koerding, NIPS, 2011; Linderman et al., NIPS, 2014). Thus, the strength of DyNetCP is unclear.

Reviewer #1 (Public review):

Summary:

In this work, 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:

Diverse set of relevant tasks<br /> Similarity measure well chosen<br /> Explored various hyperparameter settings

Weaknesses:

One of the major connections to 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 maybe 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.

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

Versatility of oblique regime could lead to differences between subjects in neural data.

Reviewer #1 (Public review):

Koesters and colleagues investigated the role of the small GTPase Rab3A in homeostatic scaling of miniature synaptic transmission in primary mouse cortical cultures using electrophysiology and immunohistochemistry. The major finding is that TTX incubation for 48 hours does not induce an increase in the amplitude of excitatory synaptic miniature events in neuronal cultures derived from Rab3A KO and Rab3A Earlybird mutant mice. NASPM application had comparable effects on mEPSC amplitude in control and after TTX, implying that Ca2+-permeable glutamate receptors are unlikely modulated during synaptic scaling. Immunohistochemical analysis revealed no significant changes in GluA2 puncta size, intensity, and integral in control and Rab3A KO cultures. Finally, they provide evidence that loss of Rab3A in neurons, but not astrocytes, blocks homeostatic scaling. Based on these data, the authors propose a model in which neuronal Rab3A is required for homeostatic scaling of synaptic transmission through GluA2-dependent and independent mechanisms.

While the title of the manuscript is mostly supported by data of solid quality, many conclusions, as well as the final model, cannot be derived from the results presented. Importantly, the data do not support that GluA2 levels change upon TTX treatment in control cultures, rendering conclusions regarding Rab3A's role in TTX-dependent GluA2 modulation spurious. Other aspects of the model, such as a Rab3A-dependent release of a tropic factor, cannot be derived from the data.

The following points should be addressed:

(1) There is no (significant) increase in GluA2 levels (intensity, area, or integral) upon TTX treatment in controls (Fig. 5). Conclusions regarding Rab3As role in TTX-dependent GluA2 modulation should be revised accordingly. Hence, the data shown in Fig. 4 - 7 do not allow drawing conclusions in the context of Rab3A-dependent GluA2 modulation and scaling.

(2) The effects of Rab3A on TTX-induced mini frequency modulation remains unclear, because TTX does not induce a change in mini frequency in the Rab3A+/Ebd control (Fig. 2). The respective conclusions should be revised accordingly (l. 427).

(3) The model is still not supported by the data. In particular, data supporting a negative regulation of Rab3A by APs, Rab3A-dependent release of a tropic factor, or a Rab3A-dependent increase in GluA2 abundance are not presented.

(4) Data points are not overlapping and appear "quantal" in most box plots. How were the data rounded?

Reviewer #1 (Public review):

Summary:

The authors conducted a study on one of the fundamental research topics in neuroscience: neural mechanisms of credit assignment. Building on the original studies of Walton and his colleagues and subsequent studies on the same topic, the authors extended the research into the delayed credit assignment problem with clever task design, which compared the non-delayed (direct) and delayed (indirect) credit assignment processes. Their primary goal was to elucidate the neural basis of these processes in humans, advancing our understanding beyond previous studies.

Strengths:

(1) Innovative task design distinguishing between direct and indirect credit assignment.

(2) Use of sophisticated multivariate pattern analysis to identify neural correlates of pending representations.

(3) Well-executed study with clear presentation of results.

(4) Extension of previous research to human subjects, providing valuable comparative insights.

Considerations for Future Research:

(1) The task design, while clear and effective, might be further developed to capture more real-world complexity in credit assignment.

(2) There's potential for deeper exploration of the role of task structure understanding in credit assignment processes.

(3) The interpretation of lateral orbitofrontal cortex (lOFC) involvement could be expanded to consider its role in both credit assignment and task structure representation.

Achievement of Aims and Support of Conclusions:

The authors successfully achieved their aim of investigating direct and indirect credit assignment processes in humans. Their results provide valuable insights into the neural representations involved in these processes. The study's conclusions are generally well-supported by the data, particularly in identifying neural correlates of pending representations crucial for delayed credit assignment.

Impact on the Field and Utility of Methods:

This study makes a significant contribution to the field of credit assignment research by bridging animal and human studies. The methods, particularly the multivariate pattern analysis approach, provide a robust template for future investigations in this area. The data generated offers valuable insights for researchers comparing human and animal models of credit assignment, as well as those studying the neural basis of decision-making and learning.

The study's focus on the lOFC and its role in credit assignment adds to our understanding of this brain region's function.

Additional Context and Future Directions:

(1) Temporal ambiguity in credit assignment: While the current design provides clear task conditions, future studies could explore more ambiguous scenarios to further reflect real-world complexity.

(2) Role of task structure understanding: The difference in task comprehension between human subjects in this study and animal subjects in previous studies offers an interesting point of comparison.

(3) The authors used a sophisticated method of multivariate pattern analysis to find the neural correlate of the pending representation of the previous choice, which will be used for the credit assignment process in the later trials. The authors tend to use expressions that these representations are maintained throughout this intervening period. However, the analysis period is specifically at the feedback period, which is irrelevant to the credit assignment of the immediately preceding choice. This task period can interfere with the ongoing credit assignment process. Thus, rather than the passive process of maintaining the information of the previous choice, the activity of this specific period can mean the active process of protecting the information from interfering and irrelevant information. It would be great if the authors could comment on this important interpretational issue.

(4) Broader neural involvement: While the focus on specific regions of interest (ROIs) provided clear results, future studies could benefit from a whole-brain analysis approach to provide a more comprehensive understanding of the neural networks involved in credit assignment.

Reviewer #1 (Public review):

In this study, Deshmukh et al. provide an elegant illustration of Haldane's sieve, the population genetics concept stating that novel advantageous alleles are more likely to fix if dominant because dominant alleles are more readily exposed to selection. To achieve this, the authors rely on a uniquely suited study system, the female-polymorphic butterfly Papilio polytes.

Deshmukh et al. first reconstruct the chronology of allele evolution in the P. polytes species group, clearly establishing the non-mimetic cyrus allele as ancestral, followed by the origin of the mimetic allele polytes/theseus, via a previously characterized inversion of the dsx locus, and most recently, the origin of the romulus allele in the P. polytes lineage, after its split from P. javanus. The authors then examine the two crucial predictions of Haldane's sieve, using the three alleles of P. polytes (cyrus, polytes, and romulus). First, they report with compelling evidence that these alleles are sequentially dominant, or put in other words, novel adaptive alleles either are or quickly become dominant upon their origin. Second, the authors find a robust signature of positive selection at the dsx locus, across all five species that share the polytes allele.

In addition to exquisitely exemplifying Haldane's sieve, this study characterizes the genetic differences (or lack thereof) between mimetic alleles at the dsx locus. Remarkably, the polytes and romulus alleles are profoundly differentiated, despite their short divergence time (< 0.5 my), whereas the polytes and theseus alleles are indistinguishable across both coding and intronic sequences of dsx. Finally, the study reports incidental evidence of exon swaps between the polytes and romulus alleles. These exon swaps caused intermediate colour patterns and suggest that (rare) recombination might be a mechanism by which novel morphs evolve.

This study advances our understanding of the evolution of the mimicry polymorphism in Papilio butterflies. This is an important contribution to a system already at the forefront of research on the genetic and developmental basis of sex-specific phenotypic morphs, which are common in insects. More generally, the findings of this study have important implications for how we think about the molecular dynamics of adaptation. In particular, I found that finding extensive genetic divergence between the polytes and romulus alleles is striking, and it challenges the way I used to think about the evolution of this and other otherwise conserved developmental genes. I think that this study is also a great resource for teaching evolution. By linking classic population genetic theory to modern genomic methods, while using visually appealing traits (colour patterns), this study provides a simple yet compelling example to bring to a classroom.

In general, I think that the conclusions of the study, in terms of the evolutionary history of the locus, the dominance relationships between P. polytes alleles, and the inference of a selective sweep in spite of contemporary balancing selection, are strongly supported; the data set is impressive and the analyses are all rigorous. I nonetheless think that there are a few ways in which the current presentation of these data could lead to confusion, and should be clarified and potentially also expanded.

(1) The study is presented as addressing a paradox related to the evolution of phenotypic novelty in "highly constrained genetic architectures". If I understand correctly, these constraints are assumed to arise because the dsx inversion acts as a barrier to recombination. I agree that recombination in the mimicry locus is reduced and that recombination can be a source of phenotypic novelty. However, I'm not convinced that the presence of a structural variant necessarily constrains the potential evolution of novel discrete phenotypes. Instead, I'm having a hard time coming up with examples of discrete phenotypic polymorphisms that do not involve structural variants. If there is a paradox here, I think it should be more clearly justified, including an explanation of what a constrained genetic architecture means. I also think that the Discussion would be the place to return to this supposed paradox, and tell us exactly how the observations of exon swaps and the genetic characterization of the different mimicry alleles help resolve it.

(2) While Haldane's sieve is clearly demonstrated in the P. polytes lineage (with cyrus, polytes, and romulus alleles), there is another allele trio (cyrus, polytes, and theseus) for which Haldane's sieve could also be expected. However, the chronological order in which polytes and theseus evolved remains unresolved, precluding a similar investigation of sequential dominance. Likewise, the locus that differentiates polytes from theseus is unknown, so it's not currently feasible to identify a signature of positive selection shared by P. javanus and P. alphenor at this locus. I, therefore, think that it is premature to conclude that the evolution of these mimicry polymorphisms generally follows Haldane's sieve; of two allele trios, only one currently shows the expected pattern.

Reviewer #1 (Public review):

Summary:

The authors compared four types of hiPSCs and four types of hESCs at the proteome level to determine their differences. Semiquantitative calculations of protein copy number revealed increased protein content in iPSCs. In particular, the results suggest that mitochondria- and cytoplasm-associated proteins in iPSCs reflect to some extent the state of the original differentiated cells. Basically, it contains responses to almost all comments and adds text mainly to the discussion. No additional experiments were performed in the revision, but I believe that future validation using methods other than proteomics would provide more support for the results.

Pros:

Mitochondrial function was verified by high-resolution respirometry, indicating increased ATP-producing capacity of the phosphorylation system in iPSCs.

Weaknesses:

The proteome data in this study may be the result of a simple examination of differences between the clones, and proteome data should be verified using various methods in the future.

Reviewer #1 (Public review):

The molecular interactions which determine infection (and disease) trajectory following human exposure to Mycobacterium tuberculosis (Mtb) are critical to understanding mycobacterial pathogenicity and tuberculosis (TB), a global public health threat which disproportionately impacts a number of high-burden countries and, owing to the emergence of multidrug-resistant Mtb strains, is a major contributor to antimicrobial resistance (AMR). In this submission, Qin and colleagues extend their own previous work which identified a potential role for host galectin-9 in recognizing the major Mtb cell wall component, arabinogalactan (AG). First, the authors present data indicating that galectin-9 inhibits mycobacterial growth during in vitro culture in liquid and on solid media, and that the inhibition depends on carbohydrate recognition by galectin-9. Next, the authors identify anti-AG antibodies in sera of TB patients and use this observation to inform isolation of monoclonal anti-AG antibodies (mAbs) via an in vitro screen. Finally, they apply the identified anti-AG mAbs to inhibit Mtb growth in vitro via a mechanism which proteomic and microscopic analyses suggest is dependent on disruption of cell wall structure. In summary, the dual observation of (i) the apparent role of naturally arising host anti-AG antibodies to control infection and (ii) the potential utility of anti-AG monoclonal antibodies as novel anti-Mtb therapeutics is compelling; however, as noted in the comments below, the evidence presented to support these insights is not adequate and the authors should address the following:

(1) The experiment which utilizes lactose or glucose supplementation to infer the importance of carbohydrate recognition by galectin-9 cannot be interpreted unequivocally owing to the growth-enhancing effect of lactose supplementation on Mtb during liquid culture in vitro.

(2) Similar to the comment above, the apparent dose-independent effect of galectin-9 on Mtb growth in vitro is difficult to reconcile with the interpretation that galectin is functioning as claimed.

(3) The claimed differences in galectin-9 concentration in sera from tuberculin skin test (TST)-negative or TST-positive non-TB cases versus active TB patients are not immediately apparent from the data presented.

(4) Neither fluorescence microscopy nor electron microscopy analyses are supported by high-quality, interpretable images which, in the absence of supporting quantitative data, renders any claims of anti-AG mAb specificity (fluorescence microscopy) or putative mAb-mediated cell wall swelling (electron microscopy) highly speculative.

(5) Finally, the absence of any discussion of how anti-AG antibodies (similarly, galectin-9) gain access to the AG layer in the outer membrane of intact Mtb bacilli (which may additionally possess an extracellular capsule/coat) is a critical omission - situating these results in the context of current knowledge about Mtb cellular structure (especially the mycobacterial outer membrane) is essential for plausibility of the inferred galectin-9 and anti-AG mAb activities.

Reviewer #1 (Public review):

Summary:

This paper investigates the relationship between ocular drift - eye movements long thought to be random - and visual acuity. This is a fundamental issue for how vision works. The work uses adaptive optics retinal imaging to monitor eye movements and where a target object is in the cone photoreceptor array. The surprising result is that ocular drift is systematic - causing the object to move to the center of the cone mosaic over the course of each perceptual trial. The tools used to reach this conclusion are state-of-the-art and the evidence presented is convincing.

Strengths

The central question of the paper is interesting, as far as I know, it has not been answered in past work, and the approaches employed in this work are appropriate and provide clear answers.

The central finding - that ocular drift is not a completely random process - is important and has a broad impact on how we think about the relationship between eye movements and visual perception.

The presentation is quite nice: the figures clearly illustrate key points and have a nice mix of primary and analyzed data, and the writing (with one important exception) is generally clear.

Weaknesses

The primary concern I had about the previous version of the manuscript was how the Nyquist limit was described. The changes the authors made have improved this substantially in the current version.

Reviewer #1 (Public review):

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

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

The match between fractal and classical cycles is not one-to-one. For example, the fractal method identifies a correlation between age and cycle duration in adults that is not apparent with the classical method.<br /> The difference between the fractal and classical methods appear to be linked to the uncertain definition of sleep cycles since they are tied to when exactly the cycle begins/ends and whether or not to count cycles during fractured sleep architecture at sleep onset. Moreover, the discrepancies between the two are on the order of that found between classical cycles defined manually or via an automatic algorithm.

Overall the fractal cycle is an attractive method to study sleep architecture since it dispenses with time-consuming and potentially subjective manual identification of sleep cycles. However, given its difference from the classical method, it is unlikely that fractal scoring will be able to replace classical scoring directly. By providing a complementary quantification, it will likely contribute to refining the definition of sleep cycles that is currently ambiguous in certain cases. Moreover, it has the potential to be applied to animal studies which rarely deal with sleep cycle structure.

Reviewer #1 (Public review):

Summary:

Liu and colleagues applied the hidden Markov model on fMRI to show three brain states underlying speech comprehension. Many interesting findings were presented: brain state dynamics were related to various speech and semantic properties, timely expression of brain states (rather than their occurrence probabilities) was correlated with better comprehension, and the estimated brain states were specific to speech comprehension but not at rest or when listening to non-comprehensible speech.

Strengths:

Recently, the HMM has been applied to many fMRI studies, including movie watching and rest. The authors cleverly used the HMM to test the external/linguistic/internal processing theory that was suggested in comprehension literature. I appreciated the way the authors theoretically grounded their hypotheses and reviewed relevant papers that used the HMM on other naturalistic datasets. The manuscript was well written, the analyses were sound, and the results had clear implications.

Weaknesses:

Further details are needed for the experimental procedure, adjustments needed for statistics/analyses, and the interpretation/rationale is needed for the results.

Joint Public Review:

Summary:

The study by Akita B. Jaykumar et al. explores an interesting and relevant hypothesis whether serine/threonine With-No-lysine (K) kinases (WNK)-1, -2, -3, and -4 engage in insulin-dependent glucose transporter-4 (GLUT4) signaling in the murine central nervous system. The authors especially focused on the hippocampus as this brain region exhibits high expression of insulin and GLUT4. Additionally, disrupted glucose metabolism in the hippocampus has been associated with anxiety disorders, while impaired WNK signaling has been linked to hypertension, learning disabilities, psychiatric disorders, or Alzheimer's disease. The study took advantage of selective pan-WNK inhibitor WNK 643 as the main tool to manipulate WNK 1-4 activity both in vivo by daily, per-oral drug administration to wild-type mice, and in vitro by treating either adult murine brain synaptosomes, hippocampal slices, primary cortical cultures, and human cell lines (HEK293, SH-SY5Y). Using a battery of standard behavior paradigms such as open field test, elevated plus maze test, and fear conditioning, the authors convincingly demonstrate that the inhibition of WNK1-4 results in behavior changes, especially in enhanced learning and memory of WNK643-treated mice. To shed light on the underlying molecular mechanism, the authors implemented multiple biochemical approaches including immunoprecipitation, glucose-uptake assay, surface biotylination assay, immunoblotting, and immunofluorescence. The data suggest that simultaneous insulin stimulation and WNK1-4 inhibition results in increased glucose uptake and the activity of insulin's downstream effectors, phosphorylated Akt and phosphorylated AS160. Moreover, the authors demonstrate that insulin treatment enhances the physical interaction of the WNK effector OSR1/SPAK with Akt substrate AS160. As a result, combined treatment with insulin and the WNK643 inhibitor synergistically increases the targeting of GLUT4 to the plasma membrane. Collectively, these data strongly support the initial hypothesis that neuronal insulin- and WNK-dependent pathways do interact and engage in cognitive functions.

Strengths:

The insulin-dependent signaling in the central nervous system is relatively understudied. This explorative study delves into several interesting and clinically relevant possibilities, examining how insulin-dependent signaling and its crosstalk with WNK kinases might affect brain circuits involved in memory formation and/or anxiety. Therefore, these findings might inspire follow-up studies performed in disease models for disorders that exhibit impaired glucose metabolism, deficient memory, or anxiety, such as Diabetes mellitus, Alzheimer's disease, or most psychiatric disorders.

The graphical presentation of the figures is of high quality, which helps the reader to obtain a good overview and easily understand the experimental design, results, and conclusions.

The behavioral studies are well conducted and provide valuable insights into the role of WNK kinases in glucose metabolism and their effect on learning and memory. Additionally, the authors evaluate the levels of basal and induced anxiety in Figures 1 and 2, enhancing our understanding of how WNK signaling might engage in cognitive function and anxiety-like behavior, particularly in the context of altered glucose metabolism.

Weaknesses:

The study used a WNK643 inhibitor as the only tool to manipulate WNK1-4 activity. This inhibitor seems selective; however, it has been reported that it exhibits different efficiency in inhibiting the individual WNK kinases among each other (e.g. PMID: 31017050, PMID: 36712947). Additionally, the authors do not analyze nor report the expression profiles or activity levels of WNK1, WNK2, WNK3, and WNK4 within the relevant brain regions (i.e. hippocampus, cortex, amygdala). Combined, these weaknesses raise concerns about the direct involvement of WNK kinases within the selected brain regions and behavior circuits. It would be beneficial if the authors provided gene profiling for WNK1, 2, 3, and -4 (e.g. using Allen brain atlas). To confirm the observations, the authors should either add results from using other WNK inhibitors or, preferentially, analyze knock-down or knock-out animals/tissue targeting the single kinases.

The authors do not report any data on whether the global inhibition of WNKs affects insulin levels. Since the authors wish to demonstrate the synergistic effect of simultaneous insulin treatment and WNK1-4 inhibition, such data are missing.

The study discovered that the Sortilin receptor binds to OSR1, leading the authors to speculate that Sortilin may be involved in the insulin-dependent GLUT4 surface trafficking. However, the authors do not provide any evidence supporting Sortilin's involvement in insulin- or WNK-dependent GLUT4 trafficking. Thus, this conclusion should be qualified, rephrased, or additional data included.

Reviewer #1 (Public review):

Summary:

This paper examines plasticity in early cortical (V1-V3) areas in an impressively large number of rod monochromats (individuals with achromatopia). The paper examines three things:

(1) Cortical thickness. It is now well established that early complete blindness leads to increases in cortical thickness. This paper shows increased thickness confined to the foveal projection zone within achromats. This paper replicates the work by Molz (2022) and Lowndes (2021), but the detailed mapping of cortical thickness as a function of eccentricity and the inclusion of higher visual areas is particularly elegant.

(2) Failure to show largescale reorganization of early visual areas using retinotopic mapping. This is a replication of a very recent study by Molz et al. but I believe, given anatomical variability (and the very large n in this study) and how susceptible pRF findings are to small changes in procedure, this replication is also of interest.

(3) Connective field modelling, examining the connections between V3-V1. The paper finds changes in the pattern of connections, and smaller connective fields in individuals with achromatopsia than normally sighted controls, and suggests that these reflect compensatory plasticity, with V3 compensating for the lower resolution V1 signal in individuals with achromatopsia.

Strengths:

This is a carefully done study (both in terms of data collection and analysis) that is an impressive amount of work. I have a number of methodological comments but I hope they will be considered as constructive engagement - this work is highly technical with a large number of factors to consider.

Weaknesses:

(1) Effects of eye-movements

I have some concerns with how the effects of eye-movements are being examined. There are two main reasons the authors give for excluding eye-movements as a factor in their results. Both explanations have limitations.

a) The first is that R2 values are similar across groups in the foveal confluence. This is fine as far as it goes, but R2 values are going to be low in that region. So this shows that eye-movements don't affect coverage (the number of voxels that generate a reliable pRF), but doesn't show that eye-movements aren't impacting their other measures.

b) The authors don't see a clear relationship between coverage and fixation stability. This seems to rest on a few ad hoc examples. (What happens if one plots mean fixation deviation vs. coverage (and sets the individuals who could not be calibrated as the highest value of calibrated fixation deviation. Does a relationship then emerge?).

In any case, I wouldn't expect coverage to be particularly susceptible to eye-movements. If a voxel in the cortex entirely projects to the scotoma then it should be robustly silent. The effects of eye-movements will be to distort the size and eccentricity estimates of voxels that are not entirely silent.

There are many places in the paper where eye-movements might be playing an important role.

Examples include the larger pRF sizes observed in achromats. Are those related to fixation instability? Given that fixation instability is expected to increase pRF size by a fixed amount, that would explain why ratios are close to 1 in V3 (Figure 4).

(2) Topography

The claim of no change in topography is a little confusing given that you do see a change in eccentricity mapping in achromats.

Either this result is real, in which case there *is* a change in topography, albeit subtle, or it's an artifact.

Perhaps these results need a little bit of additional scrutiny.

One reason for concern is that you see different functions relating eccentricity to V1 segments depending on the stimulus. That almost certainly reflects biases in the modelling, not reorganization - the curves of Figure 2D are exactly what Binda et al. predict.

Another reason for concern is that I'm very surprised that you see so little effect of including/not including the scotoma - the differences seem more like what I'd expect from simply repeating the same code twice. (The quickest sanity check is just to increase the size of the estimated scotoma to be even bigger?).

I'd also look at voxels that pass an R2>0.2 threshold for both the non-selective and selective stimulus. Are the pRF sizes the same for both stimuli? Are the eccentricity estimates? If not, that's another clear warning sign.

(3) Connective field modelling

Let's imagine a voxel on the edge of the scotoma. It will tend to have a connective field that borders the scotoma, and will be reduced in size (since it will likely exclude the cortical region of V1 that is solely driven by resting state activity). This predicts your rod monochromat data. The interesting question is why this doesn't happen for controls. One possibility is that there is top-down 'predictive' activity that smooths out the border of the scotoma (there's some hint of that in the data), e.g., Masuda and Wandell.

One thing that concerns me is that the smaller connective fields don't make sense intuitively. When there is a visual stimulus, connective fields are predominantly driven by the visual signal. In achromats, there is a large swath of cortex (between 1-2.5 degrees) which shows relatively flat tuning as regards eccentricity. The curves for controls are much steeper, See Figure 2b. This predicts that visually driven connective fields should be larger for achromats. So, what's going on? The beta parameter is not described (and I believe it can alter connective field sizes). Similarly, it's possible to get very small connective fields, but there wasn't a minimum size described in the thresholding. I might be missing something obvious, but I'm just deeply confused as to how the visual maps and the connectome maps can provide contradictory results given that the connectome maps are predominantly determined by the visual signal. Some intuition would be helpful.

Some analyses might also help provide the reader with insight. For example, doing analyses separately on V3 voxels that project entirely to scotoma regions, project entirely to stimulus-driven regions, and V3 voxels that project to 'mixed' regions.

The finding that pRF sizes are larger in achromats by a constant factor as a function of eccentricity is what differences in eye-movements would predict. It would be worth examining the relationship between pRF sizes and fixation stability.

Reviewer #1 (Public review):

The findings of Ziolkowska and colleagues show that a specific projection from the nucleus reuniens of the thalamus (RE) to dorsal hippocampal CA1 neurons plays an important role in fear extinction learning in male and female mice. In and of itself, this is not a particularly new finding, although the authors' identification of structural alterations from within dorsal CA1 stratum lacunosum moleculare (SLM) as a candidate mechanism for the learning-related plasticity is potentially novel and exciting. The authors use a range of anatomical and functional approaches to demonstrate structural synaptic changes in dorsal CA1 that parallel the necessary role of RE inputs in modulating extinction learning. Yet, the significance of these findings is substantially limited by several technical shortcomings in the experimental design, and the authors' central interpretation. Otherwise, there remain several strengths in the design and interpretation that offset some of these concerns.

Given that much is already known about the role of RE and hippocampus in modulating fear learning and extinction, it remains unclear whether addressing these concerns would substantially increase the impact of this study beyond the specific area of speciality. Below, several major weaknesses will be highlighted, followed by several miscellaneous comments.

Methodological:

One major methodological weakness in the experimental design involves the widespread misapplication of Ns used for the statistical analyses. Much of the anatomical analyses of structural synaptic changes in the RE-CA1 pathway use N = number of axons (Figs. 1, 2), N = number of dendrites (Figs. 3, 4), and N = number of sections (Fig. 7; note that there are 7 figures in total). In every instance, N = animal number should be used. It is unclear which of these results would remain significant if N = animal number were used in each or how many more animals would be required. This is problematic since these data comprise the main evidence for the authors' central conclusion that specific structural synaptic changes are associated with fear extinction learning.

There is a lack of specific information regarding what constitutes learning with respect to behavioral freezing. It is never clearly stated what specific intervals are used over which freezing is measured during acquisition, extinction, and in extinction retrieval tests. Additionally, assessment of freezing during retrieval at 5- and 30-min time points doesn't lay to rest the possibility that there were differences in the decay rate over the 30-min period (also see below).

A minor-to-moderate methodological weakness concerns the authors' decision to utilize saline injected groups as controls for the chemogenetics experiments (Figs. 5, 6). The correct design is to have a CNO-only group with the same viral procedure sans hM4Di. This concern is partly mitigated by the inclusion of a CNO vs. saline injection control experiment (Fig. 6).

In the electron microscopic analyses of dendritic spines (Fig. 5), comparison of only the fear acquisition versus extinction training, and the lack of inclusion of a naïve control group, makes it difficult to understand how these structural synaptic changes are occurring relative to baseline. It is noteworthy that the authors utilize the tripartite design in other anatomical analyses (Fig. 2-4).

Interpretation:

The main interpretive weakness in the study is the authors' claim that their data shows a role for the RE-CA1 pathway in memory consolidation (i.e., see Abstract). This claim is based on the premise that, although RE-CA1 pathway inactivation with CNO treatment 30 min prior to contextual fear extinction did not affect freezing at 5- and 30-min time points relative to saline controls, these rats showed greater freezing when tested on extinction retrieval 24 h thereafter. First, the data do not rule out possible differences in the decay rate of freezing during extinction training due to CNO administration. Next, the fact that CNO is given prior to training still leaves open the possibility that acquisition was affected, even if there were not any frank differences in freezing. Support for this latter possibility derives from the fact that mice tested for extinction retrieval as early as 5 min after extinction training (Fig. 6C) showed the same impairments as mice tested 24 h later (Figs. 6A). Further, all the structural synaptic changes argued to underlie consolidation were based on analysis at a time point immediately following extinction training, which is too early to allow for any long-term changes that would underlie memory consolidation, but instead would confer changes associated with the extinction training event.

Reviewer #1 (Public review):

Summary:

McDougal et al. aimed to characterize the antiviral activity of mammalian IFIT1 orthologs. They first performed three different evolutionary selection analyses within each major mammalian clade and identified some overlapping positive selection sites in IFIT1. They found that one site that is positively selected in primates is in the RNA-binding exit tunnel of IFIT1 and is tolerant of mutations to amino acids with similar biochemical properties. They then tested 9 diverse mammalian IFIT1 proteins against VEEV, VSV, PIV3, and SINV and found that each ortholog has distinct antiviral activities. Lastly, they compared human and chimpanzee IFIT1 and found that the determinant of their differential anti-VEEV activity may be partly attributed to their ability to bind Cap0 RNA.

Strengths:

The study is one of the first to test the antiviral activity of IFIT1 from diverse mammalian clades against VEEV, VSV, PIV3, and SINV. Cloning and expressing these 39 IFIT1 orthologs in addition to single and combinatorial mutants is not a trivial task. The positive connection between anti-VEEV activity and Cap0 RNA binding is interesting, suggesting that differences in RNA binding may explain differences in antiviral activity.

Weaknesses:

The evolutionary selection analyses yielded interesting results, but were not used to inform follow-up studies except for a positively selected site identified in primates. Since positive selection is one of the two major angles the authors proposed to investigate mammalian IFIT1 orthologs with, they should integrate the positive selection results with the rest of the paper more seamlessly, such as discussing the positive selection results and their implications, rather than just pointing out that positively selected sites were identified. The paper should elaborate on how the positive selection analyses PAML, FUBAR, and MEME complement one another to explain why the tests gave them different results. Interestingly, MEME which usually provides more sites did not identify site 193 in primates that was identified by both PAML and FUBAR. The authors should also provide the rationale for choosing to focus on the 3 sites identified in primates only. One of those sites, 193, was also found to be positively selected in bats, although the authors did not discuss or integrate that finding into the study. In Figure 1A, they also showed a dN/dS < 1 from PAML, which is confusing and would suggest negative selection instead of positive selection. Importantly, since the authors focused on the rapidly evolving site 193 in primates, they should test the IFIT1 orthologs against viruses that are known to infect primates to directly investigate the impact of the evolutionary arms race at this site on IFIT1 function.

Some of the data interpretation is not accurate. For example:

(1) Lines 232-234: "...western blot analysis revealed that the expression of IFIT1 orthologs was relatively uniform, except for the higher expression of orca IFIT1 and notably lower expression of pangolin IFIT1 (Figure 4B)." In fact, most of the orthologs are not expressed in a "relatively uniform" manner e.g. big brown bat vs. shrew are quite different.

(2) Line 245: "...mammalian IFIT1 species-specific differences in viral suppression are largely independent of expression differences." While it is true that there is no correlation between protein expression and antiviral activity in each species, the authors cannot definitively conclude that the species-specific differences are independent of expression differences. Since the orthologs are clearly not expressed in the same amounts, it is impossible to fully assess their true antiviral activity. At the very least, the authors should acknowledge that the protein expression can affect antiviral activity. They should also consider quantifying the IFIT1 protein bands and normalizing each to GAPDH for readers to better compare protein expression and antiviral activity. The same issue is in Line 267.

(3) Line 263: "SINV... was modestly suppressed by pangolin, sheep, and chinchilla IFIT1 (Figure 4E)..." The term "modestly suppressed" does not seem fitting if there is 60-70% infection in cells expressing pangolin and chinchilla IFIT1.

(4) The study can be significantly improved if the authors can find a thread to connect each piece of data together, so the readers can form a cohesive story about mammalian IFIT1.

Reviewer #1 (Public review):

Summary:

The authors analyze the roles of PD-1 in the early stages (pre-activation) of T cell differentiation and show that naïve CD4+ T cell differentiation is altered, especially Th2 differentiation is strongly impaired, upon early PD-1 stimulation. The results have important implications for the immunotherapy area, but I think the manuscript requires some revisions.

Strengths:

(1) Novel Insights into PD-1 in Early T Cell Differentiation:<br /> The study provides new insights into the role of PD-1 during the pre-activation phase of T cell differentiation, particularly its impact on naïve CD4+ T cells and Th2 differentiation. This is a significant contribution to immunotherapy research.

(2) Relevance to Immunotherapy:<br /> The findings have potential implications for the development of immunotherapies by demonstrating how PD-1 signaling affects specific T cell subsets early in differentiation.

Weaknesses:

(1) Inconsistent and Confusing Data:<br /> There are contradictions between the figures and the conclusions, particularly regarding IL-4 and IFNgamma production in PD-1-expressing cells. This raises concerns about data interpretation and experimental accuracy.

(2) Unclear Experimental Rationale:<br /> The reviewer questions the rationale behind key methodological choices, such as the high concentration of PDL-1 antibody and varying OVA peptide concentrations. These decisions need more justification.

Reviewer #1 (Public review):

Summary:

This paper reports fossil soft-tissue structures (tail vanes) of pterosaurs, and attempts to relate this to flight performance and other proposed functions for the tail

Strengths:

The paper presents new evidence for soft-tissue strengthening of vanes using exciting new methods.

Weaknesses:

There seems to be no discussion of bias in the sample selection method - even a simple consideration of whether discarded specimens were likely not to have had the cross-linking lattice, or if it was not visible.

There seems to be no supporting evidence or theory to show how the lattice could have functioned, other than a narrative description. Moreover, there is no comparison to extant organisms where a comparison of function might be drawn.

Joint Public Review

This work investigates numerically the propagation of subthreshold waves in a model neural network that is derived from the C. elegans connectome. Using a scattering formalism and tight-binding description of the network -- approximations which are commonplace in condensed matter physics -- this work attempts to show the relevance of interference phenomena, such as wavenumber-dependent propagation, for the dynamics of subthreshold waves propagating in a network of electrical synapses.

The primary strength of the work is in trying to use theoretical tools from a far-away corner of fundamental physics to shed light on the properties of a real neural system.<br /> While a system composed of neurons and synapses is classical in nature, there are occasions in which interference or localization effects are useful for understanding wave propagation in complex media [review, van Rossum & Nieuwenhuizen, 1999]. However, it is expected that localization effects only have an impact in some parameter regimes and with low phase dissipation. The authors should have addressed the existence of this validity regime in detail prior to assuming that interference effects are important.

An additional approximation that was made without adequate justification is the use of a tight-binding Hamiltonian. This can be a reasonable approximation, even for classical waves, in particular in the presence of high-quality-factor resonators, where most of the wave amplitude is concentrated on the nodes of the network, and nodes are coupled evanescently with each other. Neither of these conditions were verified for this study.

The motivation for this work is to understand the basic mechanisms underlying subthreshold intrinsic oscillations in the inferior olive, but detailed connectivity patterns in this brain area are not available. The connectome is known for C elegans, but sub-threshold oscillations have not been observed there, and the implications of this work for C elegans neuroscience remain unclear. The authors should also give more evidence for the claim that their study may give a mechanism for synchronized rhythmic activity in the mammalian inferior olive nucleus, or refrain from making this conclusion.

In the same vein, since the work emphasizes the dependence on the wavenumber for the propagation of subthreshold oscillations, they should make an attempt at estimating the wavenumber of subthreshold oscillations in C elegans if they were to exist and be observed. Next, the presence of two "mobility edges" in the transmission coefficient calculated in this work is unmistakably due to the discrete nature of the system, coming from the tight-binding approximation, and it is unclear if this approximation is justified in the current system.

Similarly, it is possible that the wavenumber-dependent transmission observed depends strongly on the addition of a large number of virtual nodes (VNs) in the network, which the authors give little to no motivation for. As these nodes are not present in the C elegans connectome, the authors should explain the motivation for their inclusion in the model and should discuss their consequences on the transmission properties of the network.

As it stands, the work would only have a very limited impact on the understanding of subthreshold oscillations in the rat or in C elegans. Indeed, the preprint falls short of relating its numerical results to any phenomena which could be observed in the lab.

Reviewer #1 (Public review):

Summary:

In this study, Avila et al. tested the hypothesis that chronic pain states are associated with changes in the excitability of the medial prefrontal cortex (mPFC). The authors used the slope of the aperiodic component of the EEG power spectrum (= the aperiodic exponent) as a novel, non-invasive proxy for the cortical excitation-inhibition ratio. They performed source localization to estimate the EEG signals generated specifically by the mPFC. By pooling resting-state EEG recordings from three existing datasets, the authors were able to compare the aperiodic exponent in the mPFC and across the whole brain (at all modeled cortical sources) between 149 chronic pain patients and 115 healthy controls. Additionally, they assessed the relationship between the aperiodic exponent and pain intensity reported by the patients. To account for heterogeneity in pain etiology, the analysis was also performed separately for two patient subgroups with different chronic pain conditions (chronic back pain and chronic widespread pain). The study found robust evidence against differences in the aperiodic exponent in the mPFC between people with chronic pain and healthy participants, and no correlation was observed between the aperiodic exponent and pain intensity. These findings were consistent across different patient subgroups and were corroborated by the whole-brain analysis.

Strengths:

The study is based on sound scientific reasoning and rigorously employs suitable methods to test the hypothesis. It follows a pre-registered protocol, which greatly increases the transparency and, consequently, the credibility of the reported results. In addition to the planned steps, the authors used a multiverse analysis to ensure the robustness of the results across different methodological choices. I find this particularly interesting, as the EEG aperiodic exponent has only recently been linked to network excitability, and the most appropriate methods for its extraction and analysis are still being determined. The methods are clearly and comprehensively described, making this paper very useful for researchers planning similar studies. The results are convincing, and supported by informative figures, and the lack of the expected difference in mPFC excitability between the tested groups is thoroughly and constructively discussed.

Weaknesses:

Firstly, although I appreciate the relatively large sample size, pooling data recorded by different researchers using different experimental protocols inevitably increases sample variability and may limit the availability of certain measures, as was the case here with the reports of pain intensity in the patient group. Secondly, the analysis heavily relies on the estimation of cortical sources, an approach that offers many advantages but may yield imprecise results, especially when default conduction models, source models, and electrode coordinates are used. In my opinion, this point should be discussed as well.

Reviewer #1 (Public review):

Summary:

This work represents a new development in the theory of odor coding and recognition, based on mapping odor mixtures in low-dimensional hyperbolic spaces. The authors describe the dynamics of odor mapping, across stages of ripening and fermentation (trajectories in odor space), which, surprisingly, generalize across fruit types.

Strengths:

The approach provides a remarkably concise and clear description of the odor dynamics. As a model, the approach is mathematically exhaustive and generalizable. The analyses are technically correct and statistically robust.

Weaknesses:

None.

DOI: 10.1038/s41596-024-01048-1

Resource: (IMSR Cat# JAX_008538,RRID:IMSR_JAX:008538)

Curator: @dhovakimyan1

SciCrunch record: RRID:IMSR_JAX:008538

What is this?

Reviewer #2 (Public review):

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

Reviewer #1 (Public review):

Summary:

In this technical paper, the authors introduce an important variation on the fully automated multi-electrode patch-clamp recording technique for probing synaptic connections that they term "patch-walking". The patch-walking approach involves coordinated pipette route-planning and automated pipette cleaning procedures for pipette reuse to improve recording throughput efficiency, which the authors argue can theoretically yield almost twice the number of connections to be probed by paired recordings on a multi-patch electrophysiology setup for a given number of cells compared to conventional manual patch-clamping approaches used in brain slices in vitro. The authors show convincing results from recordings in mouse in vitro cortical slices, demonstrating the efficient recording of dozens of paired neurons with a dual patch pipette configuration for paired recordings and detection of synaptic connections. This approach will be of interest and valuable to neuroscientists conducting automated multi-patch in vitro electrophysiology experiments and seeking to increase efficiency of neuron connectivity detection while avoiding the more complex recording configurations (e.g., 8 pipette multi-patch recording configurations) used by several laboratories that are not readily implementable by most of the neuroscience community.

Strengths:

(1) The authors introduce the theory and methods and show experimental results for a fully automated electrophysiology dual patch-clamp recording approach with a coordinated patch-clamp pipette route-planning and automated pipette cleaning procedures to "patch-walk" across an in vitro brain slice.

(2) The patch-walking approach offers throughput efficiency improvements over manual patch clamp recording approaches, especially for investigators looking to utilize paired patch electrode recordings in electrophysiology experiments in vitro.

(3) Experimental results are presented from in vitro mouse cortical slices demonstrating the efficiency of recording dozens of paired neurons with a two-patch pipette configuration for paired recordings and detection of synaptic connections, demonstrating the feasibility and efficiency of the patch-walking approach.

(4) The authors suggest extensions of their technique while keeping the number of recording pipettes employed and recording rig complexity low, which are important practical technical considerations for investigators wanting to avoid the more complex recording configurations (e.g., 8-10 pipette multi-patch recording configurations) used by several laboratories that are not readily implementable by most of the neuroscience community.

Reviewer #1 (Public review):

Summary:

As the scientific community identifies increasing numbers of genes and genetic variants that cause rare human diseases, a challenge in the field quickly identify pharmacological interventions to address known deficits. The authors point out that defining phenotypic outcomes required for drug screen assays is often a bottleneck, and emphasize how invertebrate models can be used for quick ID of compounds that may address genetic deficits. A major contribution of this work is to establish a framework for potential intervention drug screening based on quantitative imaging of morphology and mobility behavior, using methods that the authors show can define subtle phenotypes in a high proportion of disease gene knockout mutants. Overall, the work constitutes an elegant combination of previously developed high-volume imaging with highly detailed quantitative phenotyping (and some paring down to specific phenotypes) to establish proof of principle on how the combined applications can contribute to screens for compounds that may address specific genetic deficits, which can, in turn, suggest both mechanism and therapy.

In brief, the authors selected 25 genes for which loss of function is implicated in human neuro-muscular disease and engineered deletions in the corresponding C. elegans homologs. The authors then imaged morphological features and behaviors prior to, during, and after blue light stimuli, quantitating features, and clustering outcomes as they elegantly developed previously (PMID 35322206; 30171234; 30201839). In doing so, phenotypes in 23/25 tested mutants could be separated enough to distinguish WT from mutant and half of those with adequate robustness to permit high-throughput screens, an outcome that supports the utility of related general efforts to ID phenotypes in C. elegans disease orthologs. A detailed discussion of 4 ciliopathy gene defects, and NACLN-related channelopathy mutants reveals both expected and novel phenotypes, validating the basic approach to modeling vetted targets and underscoring that quantitative imaging approaches reiterate known biology.

The authors then screened a library of nearly 750 FDA-approved drugs for the capacity to shift the unc-80 NACLN channel-disrupted phenotype closer to the wild type. Top "mover" compounds shift outcome in the experimental outcome space; and also reveal how "side effects" can be evaluated to prioritize compounds that confer the fewest changes of other parameters away from the center.

Strengths:

Although the imaging and data analysis approaches have been reported and the screen is restricted in scope and intervention exposure, it is impressive, encouraging and important that the authors strongly combine tools to demonstrate how quantitative imaging phenotypes can be integrated with C. elegans genetics to accelerate the identification of potential modulators of disease (easily extendable to other goals). Generation of deletion alleles and documentation of their associated phenotypes (available in supplemental data) provide potentially useful reagents/data to the field. The capacity to identify "over-shooting" of compound applications with suggestions for scale back and to sort efficacious interventions to minimize other changes to behavioral and physical profiles is a strong contribution.

Weaknesses:

The work does not have major weaknesses, and in revision, the authors have expanded the discussion to potential utility and application in the field.

The authors have also taken into account minor modifications in writing.

Reviewer #1 (Public review):

Summary:

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

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

Strengths:

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

Weaknesses:

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

Update After Revisions:

The authors have addressed the above comments and concerns appropriately. The addition of the new Figure 9 is particularly compelling and strengthens the authors' conclusions. This reviewer has no further concerns.

Reviewer #1 (Public Review):

Summary:

Wang and colleagues identify biallelic variants of DNAH3 in four unrelated Han Chinese infertile men through whole-exome sequencing, which contributes to abnormal sperm flagellar morphology and ultrastructure. To investigate the importance of DNAH3 in male infertility, the authors generated crispant Dnah3 knockout (KO) male mice. They observed that KO mice are also infertile, showing a severe reduction in sperm movement with abnormal IDA (inner dynein arms) and mitochondrion structure. Moreover, nonfunctional DNAH3 expression decreased the expression of IDA-associated proteins in the spermatozoa of patients and KO mice, which are involved in the disruption of sperm motility. Interestingly, the infertility of patients and KO mice is rescued by intracytoplasmic sperm injection (ICSI). Taken together, the authors propose that DNAH3 is a novel pathogenic gene for asthenoterozoospermia and male infertility.

Strengths:

This work investigates the role of DNAH3 in sperm mobility and male infertility. By using gold-standard molecular biology techniques, the authors demonstrate with exquisite resolution the importance of DNAH3 in sperm morphology, showing strong evidence of its role in male infertility. Overall, this is a very interesting, well-written, and appealing article. All aspects of the study design and methods are well described and appropriate to address the main question of the manuscript. The conclusions drawn are consistent with the analyses conducted and supported by the data.

Weaknesses:

The paper is solid, and in its current form, I have not detected relevant weaknesses.

Reviewer #1 (Public Review):

The authors showed that autophagy-related genes are involved in plant immunity by regulating the protein level of the salicylic acid receptor, NPR1.

The experiments are carefully designed and the data is convincing. The authors did a good job of understanding the relationship between ATG6 and NRP1.

Comments on latest version:

The authors have already addressed all my comments. I have no further issues with the manuscript.

Reviewer #1 (Public review):

Freas et al. investigated if the exceedingly dim polarization pattern produced by the moon can be used by animal to guide a genuine navigational task. The sun and moon are celestial beacons for directional information, but they can be obscured by clouds, canopy, or the horizon. However, even when hidden from view, these celestial bodies provide directional information through the polarized light patterns in the sky. While the sun's polarization pattern is famously used by many animals for compass orientation, until now it has never been shown that the extremely dim polarization pattern of the moon can be used for navigation. To test this, Freas et al. studied nocturnal bull ants, by placing a linear polarizer in the homing path on a freely navigating ant 45 degrees shifted to the moon's natural polarization pattern. They recorded the homing direction of an ant before entering the polarizer, under the polarizer, and again after leaving the area covered by the polarizer. The results very clearly show, that ants walking under the linear polarizer change their homing direction by about 45 degrees in comparison to the homing direction under the natural polarization pattern and change it back after leaving the area covered by the polarizer again. These results can be repeated throughout the lunar month, showing that bull ants can use the moon's polarization pattern even under crescent moon conditions. Finally, the authors show, that the degree in which the ants change their homing direction is dependent on the length of their home vector, just as it is for the solar polarization pattern.

The behavioral experiments are very well designed, and the statistical analyses are appropriate for the data presented. The authors' conclusions are nicely supported by the data and clearly show nocturnal bull ants use the dim polarization pattern of the moon for homing, in the same way many animals use the sun's polarization pattern during the day. This is the first proof of the use of the lunar polarization pattern in any animal.

Reviewer #1 (Public review):

Summary:

The authors aim to investigate the role of ORMDL3 in regulating Type 1 interferon (IFN) responses and its effect on tumor growth inhibition. The study focuses on the mechanisms involving the RIG-I pathway and USP10-mediated degradation and attempts to establish a link between ORMDL3 expression and the effectiveness of cancer therapy. The authors also explore the broader implications of ORMDL3 in immune signaling, particularly within the context of Type 1 IFN signaling and its therapeutic potential.

Strengths:

• The manuscript explores a novel aspect of cancer immunology by examining the relationship between ORMDL3 and Type 1 IFN signaling, potentially offering new therapeutic avenues.<br /> • A variety of experimental approaches are employed, including knockdown models, overexpression assays, and protein interaction analyses, to elucidate the role of ORMDL3 in modulating immune responses.<br /> • The findings suggest a potential mechanism by which ORMDL3 affects the tumor microenvironment and immune responses, which could have significant implications for understanding cancer progression and therapy.

Weaknesses:

• The study does not clearly establish the relationship between Type 1 IFN and cancer therapy, and more robust data are needed to support the claim that tumor growth inhibition occurs via Type 1 IFN upregulation following ORMDL3 knockdown.<br /> • There is ambiguity regarding whether ORMDL3 has a positive or negative role in the Type 1 IFN pathway, especially given conflicting findings in the literature that link higher ORMDL3 levels to increased Type 1 IFN expression.<br /> • The use of certain experimental models, such as HEK293T cells (which are not typical Type 1 IFN producers), raises concerns about the validity and generalizability of the results. Further clarity is needed regarding the rationale for using the same tag in overexpression experiments.<br /> • The manuscript contains several inconsistencies and lacks detailed explanations of critical areas, such as the mechanism by which ORMDL3 facilitates USP10 transfer to RIG-I despite no direct interaction between ORMDL3 and RIG-I.

Reviewer #1 (Public review):

Aging is associated with a number of physiologic changes including perturbed circadian rhythms. However, mechanisms by which rhythms are altered remain unknown. Here authors tested the hypothesis that age-dependent factors in the sera affect the core clock or outputs of the core clock in cultured fibroblasts. They find that both sera from young and old donors are equally potent at driving robust ~24h oscillations in gene expression, and report the surprising finding that the cyclic transcriptome after stimulation by young or old sera differs markedly. In particular, genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions, while genes associated with oxidative phosphorylation and Alzheimer's Disease lose rhythmicity in the aged condition. Also, the expression of cycling genes associated with cholesterol biosynthesis increases in the cells entrained with old serum. Together, the findings suggest that age-dependent blood-borne factors, yet to be identified, affect circadian rhythms in the periphery. The most interesting aspect of the paper is that the data suggest that the same system (BJ-5TA), may significantly change its rhythmic transcriptome depending on how the cells are synchronized. While there is a succinct discussion point on this, it should be expanded and described whether there are parallels with previous works, as well as what would be possible mechanisms for such an effect.

Comments on revised version:

The authors have done a thorough revision of their manuscripts and provided convincing answers to all of my points. In particular, I applaud the authors for having added raw luminescence traces, and for providing Figure S5 on the amplitudes. Perhaps the authors could add a comment in the final text that the amplitudes are fairly low, 10^0.1 = 1.25 which means that the bulk of those genes has rhythms of at most 25%, which could reflect that the synchronization of the cells is partial.

Reviewer #2 (Public review):

Summary:

In this study, the authors study intraflagellar transport (IFT) in cilia of diverse organs in zebrafish. They elucidate that IFT88-GFP (an IFT-B core complex protein) can substitute for endogenous IFT88 in promoting ciliogenesis and use it as a reporter to visualize IFT dynamics in living zebrafish embryo. They observe striking differences in cilia lengths and velocity of IFT trains in different cilia types, with smaller cilia length correlating with lower IFT speed. They generate several mutants and show that disrupting function of different kinesin-2 motors and BBSome or altering post translational modifications of tubulin does not have a significant impact on IFT velocity. They however observe that when the amount of IFT88 is reduced it impacts the cilia length, IFT velocity as well as the number and size of IFT trains. They also show that IFT train size is slightly smaller in one of the organs with shorter cilia (spinal cord). Based on their observations they propose that IFT velocity determines cilia length and go one step further to propose that IFT velocity is regulated by the size of IFT trains.

Strengths:

The main highlight of this study is the direct visualization of IFT dynamics in multiple organs of a living complex multi-cellular organism, zebrafish. The quality of the imaging is really good. Further, the authors have developed phenomenal resources to study IFT in zebrafish which would allow us to explore several mechanisms involved in IFT regulation in future studies. They make some interesting findings in mutants with disrupted function of kinesin-2, BBSome and tubulin modifying enzymes which are interesting to compare with cilia studies in other model organisms. Also, there observation of a possible link between cilia length and IFT speed is potentially fascinating.

Weaknesses:

The central hypothesis of the manuscript, which is cilia length regulation occurs via controlling IFT speed through the modulation of the size of the IFT complex, is supported only with preliminary data and needs stronger evidence.<br /> The authors have robustly shown that the cilia length and IFT train speeds are highly variable between organs and have a strong correlation. With this they hypothesize that IFT train speeds could play a role in determining ciliary length, which is an interesting hypothesis that merits discussion. However, the claim that the cilia length (and IFT velocity) in different organs is different due to difference in the sizes of IFT trains is based on weak evidence. This is based on a marginal difference of IFT train sizes they observe between cilia of crista and spinal cord in immunofluorescence experiments (Fig. 5C). Inferring that this minor difference is key to the striking difference in cilia length and IFT velocity is too bold in my opinion.<br /> To back this hypothesis, they look at ift88 morphants where there is a reduced pool of IFT88 (part of the IFTB1 complex which forms the core of IFT trains, based on multiple cryo-EM studies of IFT trains). Disruption (or reduced number) of IFTB1 complex could indeed lead to IFT trains not being formed properly, which can have an impact on IFT (train size, speed, frequency, etc.) and ciliary structure, as shown by the authors. However, this does not directly imply that under wild-type conditions, cilia in spinal cord have poorly formed slightly shorter IFT trains (cilia length ˜0.9 µm in spinal cord vs ˜1.2 µm in cristae; Fig. 3G) which results in strikingly lower speeds (˜0.4 µm/s in spinal cord vs ˜1.6 µm/s in cristae; Fig. 3G) and shorter cilia (˜3µm in spinal cord vs ˜26µm in cristae; Fig. 3H). Such a claim would require much stronger evidence.

Finally, if IFT train speeds directly correlate with size of IFT train, the authors should be able to see this within the same cilia, i.e., the velocity of a brighter IFT train (larger train) would be higher than the velocity of a dimmer IFT train (smaller train) within the same cilia. This is not apparent from the movies and such a correlation should be verified to make their claim stronger.

Impact:

Overall, I think this work develops an exciting new multicellular model organism to study IFT mechanisms. Zebrafish is a vertebrate where we can perform genetic modifications with relative ease. This could be an ideal model to study not just the role of IFT in connection with ciliary function but also ciliopathies. Further, from an evolutionary perspective, it is fascinating to compare IFT mechanisms in zebrafish with unicellular protists like Chlamydomonas, simple multicellular organisms like C elegans and primary mammalian cell cultures. Having said that, the central hypothesis of the manuscript in not backed with strong evidence and I would recommend the authors to not give too much weight on the hypothesis that IFT train velocity is determined by the size of IFT trains. Given the technological advancements made in this study, I think it is fine if it is a descriptive manuscript and doesn't necessarily need a breakthrough hypothesis based on the marginal correlation they observe.

Reviewer #1 (Public review):

Summary:

In the manuscript titled "Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy," Tom Smith and colleagues conducted a comparative evaluation of various sequencing-based tRNA quantification methods. The inherent challenges in accurately quantifying tRNA transcriptional levels, stemming from their short sequences (70-100nt), extensive redundancy (~600 copies in human genomes with numerous isoacceptors and isodecoders), and potential for over 100 post-transcriptional chemical modifications, necessitate sophisticated approaches. Several wet-experimental methods (QuantM-tRNA, mim-tRNA, YAMAT, DM-tRNA, and ALL-tRNA) combined with bioinformatics tools (bowtie2-based, SHRiMP, and mimseq) have been proposed for this purpose. However, their practical strengths and weaknesses have not been comprehensively explored to date. In this study, the authors systematically assessed and compared these methods, considering factors such as incorrect alignments, multiple alignments, misincorporated bases (experimental errors), truncated reads, and correct assignments. Additionally, the authors introduced their own bioinformatic approaches (referred to as Decision and Salmon), which, while not without flaws (as perfection is unattainable), exhibit significant improvements over existing methods.

Strengths:

The manuscript meticulously compares tRNA quantification methods, offering a comprehensive exploration of each method's relative performance using standardized evaluation criteria. Recognizing the absence of "ground-truth" data, the authors generated in silico datasets mirroring common error profiles observed in real tRNA-seq data. Through the utilization of these datasets, the authors gained insights into prevalent sources of tRNA read misalignment and their implications for accurate quantification. Lastly, the authors proposed their own downstream analysis pipelines (Salmon and Decision), enhancing the manuscript's utility.

Reviewer #1 (Public review):

This paper describes proteome solubility analysis (PISA) of 96 compounds in living cells and 70 compounds in cell lysates. A wealth of information related to on- and off-target engagement is uncovered. This work fits well the eLife profile, will be of interest to a large community of proteomics researchers, and thus is likely to be reasonably highly cited.

Reviewer #1 (Public review):

Summary:

The manuscript of Odermatt et al. investigates the volatiles released by two species of Desmodium plants and the response of herbivores to maize plants alone or in combination with these species. The results show that Desmodium releases volatiles in both the laboratory and the field. Maize grown in the laboratory also released volatiles, in a similar range. While female moths preferred to oviposit on maize, the authors found no evidence that Desmodium volatiles played a role in lowering attraction to or oviposition on maize.

Strengths:

The manuscript is a response to recently published papers that presented conflicting results with respect to whether Desmodium releases volatiles constitutively or in response to biotic stress, the level at which such volatiles are released, and the behavioral effect it has on the fall armyworm. These questions are relevant as Desmodium is used in a textbook example of pest-suppressive sustainable intercropping technology called push-pull, which has supported tens of thousands of smallholder farmers in suppressing moth pests in maize. A large number of research papers over more than two decades have implied that Desmodium suppresses herbivores in push-pull intercropping through the release of large amounts of volatiles that repel herbivores. This premise has been questioned in recent papers. Odermatt et al. thus contribute to this discussion by testing the role of odors in oviposition choice. The paper confirms that ovipositing FAW preferred maize, and also confirmed that odors released from Desmodium appeared not important in their bioassays.

The paper is a welcome addition to the literature and adds quality headspace analyses of Desmodium from the laboratory and the field. Furthermore, the authors, some of whom have since long contributed to developing push-pull, also find that Desmodium odors are not significant in their choice between maize plants. This advances our knowledge of the mechanisms through which push-pull suppresses herbivores, which is critically important to evolving the technique to fit different farming systems and translating this mechanism to fit with other crops and in other geographical areas.

Weaknesses:

Below I outline the major concerns:

(1) Clear induction of the experimental plants, and lack of reflective discussion around this: from literature data and previous studies of maize and Desmodium, it is clear that the plants used in this study, particularly the Desmodium, were induced. Maize appeared to be primarily manually damaged, possibly due to sampling (release of GLV, but little to no terpenoids, which is indicative of mostly physical stress and damage, for example, one of the coauthor's own paper Tamiru et al. 2011), whereas Desmodium releases a blend of many compounds (many terpenoids indicative of herbivore induction). Erdei et al. also clearly show that under controlled conditions maize, silver leaf and green leaf Desmodium release volatiles in very low amounts. While the condition of the plants in Odermatt et al. may be reflective of situations in push-pull fields, the authors should elaborate on the above in the discussion (see comments) such that the readers understand that the plant's condition during the experiments. This is particularly important because it has been assumed that Desmodium releases typical herbivore-induced volatiles constitutively, which is not the case (see Erdei et al. 2024). This reflection is currently lacking in the manuscript.

(2) Lack of controls that would have provided context to the data: The experiments lack important controls that would have helped in the interpretation:

(2a) The authors did not control the conditions of the plants. To understand the release of volatiles and their importance in the field, the authors should have included controlled herbivory in both maize and Desmodium. This would have placed the current volatile profiles in a herbivory context. Now the volatile measurements hang in midair, leading to discussions that are not well anchored (and should be rephrased thoroughly, see eg lines 183-188). It is well known that maize releases only very low levels of volatiles without abiotic and biotic stressors. However, this changes upon stress (GLVs by direct, physical damage and eg terpenoids upon herbivory, see above). Erdei et al. confirm this pattern in Desmodium. Not having these controls, means that the authors need to put the data in the context of what has been published (see above).

(2b) It would also have been better if the authors had sampled maize from the field while sampling Desmodium. Together with the above point (inclusion of herbivore-induced maize and Desmodium), the levels of volatile release by Desmodium would have been placed into context.

(2c) To put the volatiles release in the context of push-pull, it would have been important to sample other plants which are frequently used as intercrop by smallholder farmers, but which are not considered effective as push crops, particularly edible legumes. Sampling the headspace of these plants, both 'clean' and herbivore-induced, would have provided a context to the volatiles that Desmodium (induced) releases in the field - one would expect unsuccessful push crops to not release any of these 'bioactive' volatiles (although 'bioactive' should be avoided) if these odors are responsible for the pest suppressive effect of Desmodium. Many edible intercrops have been tested to increase the adoption of push-pull technology but with little success.

Because of the lack of the above, the conclusions the authors can draw from their data are weakened. The data are still valuable in the current discussion around push-pull, provided that a proper context is given in the discussion along the points above.

(3) 'Tendency' of the authors to accept the odor hypothesis (i.e. that Desmodium odors are responsible for repelling FAW and thereby reduce infestation in maize under push-pull management) in spite of their own data: The authors tested the effects of odor in oviposition choice, both in a cage assay and in a 'wind tunnel'. From the cage experiments, it is clear that FAW preferred maize over Desmodium, confirming other reports (including Erdei et al. 2024). However, when choosing between two maize plants, one of which was placed next to Desmodium to which FAW has no tactile (taste, structure, etc), FAW chose equally. Similarly in their wind tunnel setup (this term should not be used to describe the assay, see below), no preference was found either between maize odor in the presence or absence of Desmodium. This too confirms results obtained by Erdei et al. (but add an important element to it by using Desmodium plants that had been induced and released volatiles, contrary to Erdei et al. 2024). Even though no support was found for repellency by Desmodium odors, the authors in many instances in the manuscript (lines 30-33, 164-169, 202, 279, 284, 304-307, 311-312, 320) appear to elevate non-significant tendencies as being important. This is misleading readers into thinking that these interactions were significant and in fact confirming this in the discussion. The authors should stay true to their own data obtained when testing the hypothesis of whether odors play a role in the pest-suppressive effect of push-pull.

(4) Oviposition bioassay: with so many assays in close proximity, it is hard to certify that the experiments are independent. Please discuss this in the appropriate place in the discussion.

(5) The wind tunnel has a number of issues (besides being poorly detailed):

(5a) The setup which the authors refer to as a 'wind tunnel' does not qualify as a wind tunnel. First, there is no directional flow: there are two flows entering the setup at opposite sides. Second, the flow is way too low for moths to orient in (in a wind tunnel wind should be presented as a directional cue. Only around 1.5 l/min enters the wind tunnel in a volume of 90 l approximately, which does not create any directional flow. Solution: change 'wind tunnel' throughout the text to a dual choice setup /assay.

(5b) There is no control over the flows in the flight section of the setup. It is very well possible that moths at the release point may only sense one of the 'options'. Please discuss this.

(5c) Too low a flow (1,5 l per minute) implies a largely stagnant air, which means cross-contamination between experiments. An experiment takes 5 minutes, but it takes minimally 1.5 hours at these flows to replace the flight chamber air (but in reality much longer as the fresh air does not replace the old air, but mixes with it). The setup does not seem to be equipped with e.g. fans to quickly vent the air out of the setup. See comments in the text. Please discuss the limitations of the experimental setup at the appropriate place in the discussion.

(5d) The stimulus air enters through a tube (what type of tube, diameter, length, etc) containing pressurized air (how was the air obtained into bags (type of bag, how is it sealed?), and the efflux directly into the flight chamber (how, nozzle?). However, it seems that there is no control of the efflux. How was leakage prevented, particularly how the bags were airtight sealed around the plants?

(5e) The plants were bagged in very narrowly fitting bags. The maize plants look bent and damaged, which probably explains the GLVs found in the samples. The Desmodium in the picture (Figure 5 supplement), which we should assume is at least a representative picture?) appears to be rather crammed into the bag with maize and looks in rather poor condition to start with (perhaps also indicating why they release these volatiles?). It would be good to describe the sampling of the plants in detail and explain that the way they were handled may have caused the release of GLVs.

(6) Figure 1 seems redundant as a main figure in the text. Much of the information is not pertinent to the paper. It can be used in a review on the topic. Or perhaps if the authors strongly wish to keep it, it could be placed in the supplemental material.

Reviewer #1 (Public review):

Summary & Assessment:

The catalytic core of the eukaryotic decapping complex consists of the decapping enzyme DCP2 and its key activator DCP1. In humans, there are two paralogs of DCP1, DCP1a and DCP1b, that are known to interact with DCP2 and recruit additional cofactors or coactivators to the decapping complex; however, the mechanisms by which DCP1 activates decapping and the specific roles of DCP1a versus DCP1b, remain poorly defined. In this manuscript, the authors used CRISPR/Cas9-generated DCP1a/b knockout cells to begin to unravel some of the differential roles for human DCP1a and DCP1b in mRNA decapping, gene regulation, and cellular metabolism. While this manuscript presents some new and interesting observations on human DCP1 (e.g. human DCP1a/b KO cells are viable and can be used to investigate DCP1 function; only the EVH1 domain, and not its disordered C-terminal region which recruits many decapping cofactors, is apparently required for efficient decapping in cells; DCP1a and b target different subsets of mRNAs for decay and may regulate different aspects of metabolism), there is one key claim about the role of DCP1 in regulating DCP2-mediated decapping that is still incompletely or inconsistently supported by the presented data in this revised version of the manuscript.

Strengths & well-supported claims:

• Through in vivo tethering assays in CRISPR/Cas9-generated DCP1a/b knockout cells, the authors show that DCP1 depletion leads to significant defects in decapping and the accumulation of capped, deadenylated mRNA decay intermediates.<br /> • DCP1 truncation experiments reveal that only the EVH1 domain of DCP1 is necessary to rescue decapping defects in DCP1a/b KO cells.<br /> • RNA and protein immunoprecipitation experiments suggest that DCP1 acts as a scaffold to help recruit multiple decapping cofactors to the decapping complex (e.g. EDC3, DDX6, PATL1 PNRC1, and PNRC2), but that none of these cofactors are essential for DCP2-mediated decapping in cells.<br /> • The authors investigated the differential roles of DCP1a and DCP1b in gene regulation through transcriptomic and metabolomic analysis and found that these DCP1 paralogs target different mRNA transcripts for decapping and have different roles in cellular metabolism and their apparent links to human cancers. (Although I will note that I can't comment on the experimental details and/or rigor of the transcriptomic and metabolomic analyses, as these are outside my expertise.)

Weaknesses & incompletely supported claims:

(1) One of the key mechanistic claims of the paper is that "DCP1a can regulate DCP2's cellular decapping activity by enhancing DCP2's affinity to RNA, in addition to bridging the interactions of DCP2 with other decapping factors. This represents a pivotal molecular mechanism by which DCP1a exerts its regulatory control over the mRNA decapping process." Similar versions of this claim are repeated in the abstract and discussion sections. However, this claim appears to be at odds with the observations that: (a) in vitro decapping assays with immunoprecipitated DCP2 show that DCP1 knockout does not significantly affect the enzymatic activity of DCP2 (Fig 2C&D; I note that there may be a very small change in DCP2 activity shown in panel D, but this may be due to slightly different amounts of immunoprecipitated DCP2 used in the assay); and (b) the authors show only weak changes in relative RNA levels immunoprecipitated by DCP2 with versus without DCP1 (~2-3 fold change in Fig 3H, where expression of the EVH1 domain, previously shown in this manuscript to fully rescue the DCP1 KO decapping defects in cells, looks to be almost within error of the control in terms of increasing RNA binding). If DCP1 pivotally regulates decapping activity by enhancing RNA binding to DCP2, why is no difference in in vitro decapping activity observed in the absence of DCP1, and very little change observed in the amounts of RNA immunoprecipitated by DCP2 with the addition of the DCP1 EVH1 domain?

In the revised manuscript and in their response to initial reviews, the authors rightly point out that in vivo effects may not always be fully reflected by or recapitulated in in vitro experiments due to the lack of cellular cofactors and simpler environment for the in vitro experiment, as compared to the complex environment in the cell. I fully agree with this of course! And further completely agree with the authors that this highlights the critical importance of in cell experiments to investigate biological functions and mechanisms! However, because the in vitro kinetic and IP/binding data both suggest that the DCP1 EVH1 domain has minimal to no effects on RNA decapping or binding affinity, while the in cell data suggest the EVH1 domain alone is sufficient to rescue large decapping defects in DCP1a/b KO cells (and that all the decapping cofactors tested were dispensable for this), I would argue there is insufficient evidence here to make a claim that (maybe weakly) enhanced RNA binding induced by DCP1 is what is regulating the cellular decapping activity. Maybe there are as-yet-untested cellular cofactors that bind to the EVH1 domain of DCP1 that change either RNA recruitment or the kinetics of RNA decapping in cells; we can't really tell from the presented data so far. Furthermore, even if it is the case that the EVH1 domain modestly enhances RNA binding to DCP2, the authors haven't shown that this effect is what actually regulates the large change in DCP2 activity upon DCP1 KO observed in the cell.

Overall, while I absolutely appreciate that there are many possible reasons for the differences observed in the in vitro versus in cell RNA decapping and binding assays, because this discrepancy between those data exists, it seems difficult to draw any clear conclusions about the actual mechanisms by which DCP1 helps regulate RNA decapping by DCP2. For example, in the cell it could be that DCP1 enhances RNA binding, or recruits unidentified cofactors that themselves enhance RNA binding, or that DCP1 allosterically enhances DCP2-mediated decapping kinetics, or a combination of these, etc; my point is that without in vitro data that clearly support one of those mechanisms and links this mechanism back to cellular DCP2 decapping activity (for example, in cell data that show EVH1 mutants that impair RNA binding fail to rescue DCP1 KO decapping defects), it's difficult to attribute the observed in cell effects of DCP1a/b KO and rescue by the EVH1 domain directly to enhancement of RNA binding (precisely because, as the authors describe, the decapping process and regulation may be very complex in the cell!).

This contradiction between the in vitro and in-cell decapping data undercuts one of the main mechanistic takeaways from the first half of the paper; I still think this conclusion is overstated in the revised manuscript.

Additional minor comment:

• Related to point (1) above, the kinetic analysis presented in Fig 2C shows that the large majority of transcript is mostly decapped at the first 5 minute timepoint; it may be that DCP2-mediated decapping activity is actually different in vitro with or without DCP1, but that this is being missed because the reaction is basically done in less than 5 minutes under the conditions being assayed (i.e. these are basically endpoint assays under these conditions). It may be that if kinetics were done under conditions to slow down the reaction somewhat (e.g. lower Dcp2 concentration, lower temperatures), so that more of the kinetic behavior is captured, the apparent discrepancy between in vitro and in-cell data would be much less. Indeed, previous studies have shown that in yeast, Dcp1 strongly activates the catalytic step (kcat) of decapping by ~10-fold, and reduces the KM by only ~2 fold (Floor et al, NSMB 2010). It might be beneficial to use purified proteins here, if possible, to better control reaction conditions.

In their response to initial reviews, the authors comment that they tried to purify human DCP2 from E coli, but were unable to obtain active enzyme in this way. Fair enough! I will only comment that just varying the relative concentration of immunoprecipitated DCP2 would likely be enough to slow down the reaction and see if activity differences are seen in different kinetic regimes, without the need to obtain fully purified / recombinant Dcp2.

Reviewer #1 (Public review):

Summary

Das and Menon describe an analysis of a large open-source iEEG dataset (UPENN-RAM). From encoding and recall phases of memory tasks, they analyzed power and phase-transfer entropy as a measure of directed information flow in regions across a hypothesized tripartite network system. The anterior insula (AI) was found to have heightened high gamma power during encoding and retrieval, which corresponded to suppression of high gamma power in medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC) during encoding but not recall. In contrast, directed information flow from (but not to) AI to mPFC and PCC is high during both time periods when PTE is analyzed with broadband but not narrowband activity. They claim that these findings significantly advance an understanding of how network communication facilitates cognitive operations during memory tasks, and that the AI of the salience network (SN) is responsible for influencing both the frontoparietal network (FPN) and default-mode network (DMN) during memory encoding and retrieval.

I find this question interesting and important and agree with the authors that iEEG presents a unique opportunity to investigate the temporal dynamics within network nodes. Their findings convey intriguing information about the structure and order of communication between network regions during on-task cognition in general (though, perhaps not specific to memory - see Weaknesses), with the AI of the SN ostensibly playing an important role in possibly influencing the DMN and FPN.

Strengths

- The authors present results from an impressively-sized iEEG sample. For reader context, this type of invasive human data is difficult and time-consuming to collect and many similar studies in high-level journals include 5-20 participants, typically not all of whom have electrodes in all regions of interest. It is excellent that they have been able to leverage open-source data in this way.<br /> - Preprocessing of iEEG data also seems sensible and appropriate based on field standards.<br /> - The authors tackle the replication issues inherent in much of the literature by replicating findings across task contexts, demonstrating that the principles of network communication evidenced by their results generalize in multiple task memory contexts. Again, the number of iEEG patients who have multiple tasks' worth of data is impressive.<br /> - Though the revised manuscript presents a broader and more novel investigation of the tripartite network's role in memory encoding and retrieval (as opposed to cognitive control of memory) the authors now thoroughly review the literature motivating this investigation of open-source data.

Weaknesses

- As the authors discuss, it is currently unclear if the directed information flow from AI to DMN and FPN nodes truly arises from memory-associated processes as opposed to more general attentional and cognitive demands, especially given that information flow does not relate meaningfully to task performance (whether memory retrieval is successful or not). I also note this is a concern because - though the authors have now demonstrated that information flow is increased compared to an off-task baseline - influences of AI on DMN or FPN were not increased relative to baseline epochs during the task in the original preprint version, again suggesting these effects may not be specific to the memory component of the analyzed tasks. The authors have thoughtfully noted in the Discussion several ways that experimental design can be improved in future studies to address this limitation.

Reviewer #1 (Public review):

The authors survey the ultrastructural organization of glutamatergic synapses by cryo-ET and image processing tools using two complementary experimental approaches. The first approach employs so-called "ultra-fresh" preparations of brain homogenates from a knock-in mouse expressing a GFP-tagged version of PSD-95, allowing Peukes and colleagues to specifically target excitatory glutamatergic synapses. In the second approach, direct in-tissue (using cortical and hippocampal regions) targeting of the glutamatergic synapses employing the same mouse model is presented. In order to ascertain whether the isolation procedure causes any significant changes in the ultrastructural organization (and possibly synaptic macromolecular organization) the authors compare their findings using both of these approaches. The quantitation of the synaptic cleft height reveals an unexpected variability, while the STA analysis of the ionotropic receptors provides insights into their distribution with respect to the synaptic cleft.

The main novelty of this study lies in the continuous claims by the authors that the sample preservation methods developed here are superior to any others previously used. This leads them as well to systematically downplay or directly ignore a substantial body of previous cryo-ET studies of synaptic structure. Without comparisons with the cryo-ET literature, it is very hard to judge the impact of this work in the field. Furthermore, the data does not show any better preservation in the so-called "ultra-fresh" preparation than in the literature, perhaps to the contrary as synapses with strangely elongated vesicles are often seen. Such synapses have been regularly discarded for further analysis in previous synaptosome studies (e.g. Martinez-Sanchez 2021). Whilst the targeting approach using a fluorescent PSD95 marker is novel and seems sufficiently precise, the authors use a somewhat outdated approach (cryo-sectioning) to generate in-tissue tomograms of poor quality. To what extent such tomograms can be interpreted in molecular terms is highly questionable. The authors also don't discuss the physiological influence of 20% dextran used for high-pressure freezing of these "very native" specimens.

Lastly, a large part of the paper is devoted to image analysis of the PSD which is not convincing (including a somewhat forced comparison with the fixed and heavy-metal staining room temperature approach). Despite being a technically challenging study, the results fall short of expectations.

Joint Public Review:

Summary

Based on i) the documented role of FMNL1 proteins in IS formation; ii) their ability to regulate F-actin dynamics; iii) the implication of PKCdelta in MVB polarization to the IS and FMNL1beta phosphorylation; and iv) the homology of the C-terminal DAD domain of FMNL1beta with FMNL2, where a phosphorylatable serine residue regulating its auto-inhibitory function had been previously identified, the authors have addressed the role of S1086 in the FMNL1beta DAD domain in F-actin dynamics, MVB polarization and exosome secretion, and investigated the potential implication of PKCdelta, which they had previously shown to regulate these processes, in FMNL1beta S1086 phosphorylation. They demonstrate that FMNL1beta is indeed phosphorylated on S1086 in a PKCdelta-dependent manner and that S1086-phosphorylated FMNL1beta acts downstream of PKCdelta to regulate centrosome and MVB polarization to the IS and exosome release. They provide evidence that FMNL1beta accumulates at the IS where it promotes F-actin clearance from the IS center, thus allowing for MVB secretion.

Strengths

The work is based on a solid rationale, which includes previous findings by the authors establishing a link between PKCdelta, FMNL1beta phosphorylation, synaptic F-actin clearance and MVB polarization to the IS. The authors have thoroughly addressed the working hypotheses using robust tools. Among these, of particular value is an expression vector that allows for simultaneous RNAi-based knockdown of the endogenous protein of interest (here all FMNL1 isoforms) and expression of wild-type or mutated versions of the protein as YFP-tagged proteins to facilitate imaging studies. The imaging analyses, which are the core of the manuscript, have been complemented by immunoblot and immunoprecipitation studies, as well as by the measurement of exosome release (using a transfected MVB/exosome reporter to discriminate exosomes secreted by T cells).

Weaknesses

As stated in the title of the article, the main findings have been obtained in clones of Jurkat cells and have not been confirmed in primary T cells.

Reviewer #1 (Public review):

Summary:

This is an important contribution to the field of molecular embryology of the lung. The authors introduce a novel mesenchymally expressed molecule Svep1. Knocking it out in mice produces a profoundly hypoplastic phenotype which can be rescued in vitro. Svep1 interacts with the FGF signaling complex to control differentiation and expression of smooth muscle in lung mesenchyme, thereby affecting proximal-distal patterning of the airway branches by acting as a putative branch suppressor.

Strengths:

The study shows strong evidence in mouse knockouts, in vitro embryonic lung culture as well as gene expression and in vitro rescue studies that confirm a key role for Svep1. It is a beautiful piece of work and an important contribution to our understanding of early lung branching morphogenesis.

Weaknesses:

Claiming a possible therapeutic role for this gene is a bit far-fetched at the present state of the art.

Reviewer #1 (Public review):

Summary:

The manuscript by Zhang et al. analyzed 17 specimens of Cindarella eucalla with 3D technology and discussed the anatomical findings, the relationship to other artiopods, and the ecology of the animal. The results are excellent and the findings are very interesting. However, the discussion needs to be extended, as the point the authors are trying to make is not always clear. I also recommend some restructuring of the discussion. Overall this is an important manuscript, and I'm looking forward to reading the edited version.

Strengths:

The analyses, the 3D data is excellent and provides new information.

Weaknesses:

The discussion - the authors provide information for the findings, but do not discuss them in detail. More information is needed.

Reviewer #1 (Public review):

Summary:

In this work, a screening platform is presented for rapid and cost-effective screening of candidate genes involved in Fragile Bone Disorders. The authors validate the approach of using crispants, generating FO mosaic mutants, to evaluate the function of specific target genes in this particular condition. The design of the guide RNAs is convincingly described, while the effectiveness of the method is evaluated to 60% to 92% of the respective target genes being presumably inactivated. Thus, injected F0 larvae can be directly used to investigate the consequences of this inactivation.

Skeletal formation is then evaluated at 7dpf and 14dpf, first using a transgenic reporter line revealing fluorescent osteoblasts, and second using alizarin-red staining of mineralized structures. In general, it appears that the osteoblast-positive areas are more often affected in the crispants compared to the mineralized areas, an observation that appears to correlate with the observed reduced expression of bglap, a marker for mature osteoblasts, and the increased expression of col1a1a in more immature osteoblasts.

Finally, the injected fish (except two lines that revealed high mortality) are also analyzed at 90dpf, using alizarin red staining and micro-CT analysis, revealing an increased incidence of skeletal deformities in the vertebral arches, fractures, as well as vertebral fusions and compressions for all crispants except those for daam2. Finally, the Tissue Mineral Density (TMD) as determined by micro-CT is proposed as an important marker for investigating genes involved in osteoporosis.

Taken together, this manuscript is well presented, the data are clear and well analyzed, and the methods are well described. It makes a compelling case for using the crispant technology to screen the function of candidate genes in a specific condition, as shown here for bone disorders.

Strengths:

Strengths are the clever combination of existing technologies from different fields to build a screening platform. All the required methods are comprehensively described.

Weaknesses:

One may have wished to bring one or two of the crispants to the stage of bona fide mutants, to confirm the results of the screening, however, this is done for some of the tested genes as laid out in the discussion.

Reviewer #1 (Public review):

Summary:

In the submitted manuscript, Solomon et al carefully detail shifts in tissue-specific myeloid populations associated with trained immunity using intraperitoneal BCG injection as a model for induction. They define the kinetics of shifts in myeloid populations within the spleen and the transcriptional response associated with IP BCG exposure. In lineage tracing experiments, they demonstrate that tissue-resident macrophages, red-pulp macrophages (RPM) that are rapidly depleted after BCG exposure, are replenished from recruited monocytes and expansion of tissue-resident cells; they use transcriptional profiling to characterize those cells. In contrast to previous descriptions of BCG-driven immune training, they do not find BCG in the bone marrow in their model, suggesting that there is not direct training of myeloid precursor populations in the bone marrow. They then link the observed trained immunity phenotype (restriction of heterologous infection with ST) with early activation of STAT1 through IFN-γ.

Strengths:

The work includes careful detaining of shifts and origins of myeloid populations within tissue associated with trained immunity and is a meaningful advance for the field. Given that the temporality of exposure relative to trained immunity phenotypes is a major focus of the work, there are some additional experiments that would make the work stronger.

Weaknesses:

(1) The contribution of persistent BCG in spleen to the observed trained immunity phenotypes is not clear: The trained immunity phenotypes are interpreted as being driven by the early (within days) response to BCG exposure. While the fedratinib data generally support this interpretation, the authors show that BCG remains present in spleen albeit at low levels all the way out to 60 days post exposure. Given that the focus in the paper is on tissue-specific immune training, it would be helpful to know whether the ongoing presence of BCG at low levels in the profiled tissue contributes to the trained immunity phenotypes observed.

(2) Unclear temporality of STAT1/IFN-γ requirement for the trained immunity phenotype: The data demonstrate that STAT1/IFN-γ are required at the earliest time points post-BCG exposure for trained immunity to be initiated. Related to the point about BCG above, it would be helpful to understand whether this is a specifically time-limited requirement when trained immunity is first induced, or whether ongoing signaling through this axis is required for maintenance of the observed trained immunity phenotypes.

Reviewer #1 (Public review):

Summary:

Here, the authors are proposing a role for miR-196, a microRNA that has been shown to bind and enhance the degradation of mRNA targets in the regulation of cell processes, and has a novel role in allowing the emergence of CD19+ cells in cells in which Ebf1, a critical B-cell transcription factor, has been genetically removed.

Strengths:

That over-expression of mR-195 can allow the emergence of CD19+ cells missing Ebf1 is somewhat novel.

Their data does perhaps support to a degree the emergence of a transcriptional network that may bypass the absence of Ebf1, including the FOXO1 transcription factor, but this data is not strong or definitive.

Weaknesses:

It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system.

The authors have provided insufficient data to allow a thorough appraisal of the step-wise molecular changes that could account for their observed phenotype.

Reviewer #1 (Public review):

Summary:

Perlee et al. sought to generate a zebrafish line where CRISPR-based gene editing is exclusively limited to the melanocyte lineage, allowing assessment of cell-type restricted gene knockouts. To achieve this, they knocked in Cas9 to the endogenous mitfa locus, as mitfa is a master regulator of melanocyte development. The authors use multiple candidate genes - albino, sox10, tuba1a, ptena/ptenb, tp53 - to demonstrate their system induces lineage-restricted gene editing. This method allows researchers to bypass embryonic lethal and non-cell autonomous phenotypes emerging from whole body knockout (sox10, tuba1a), drive directed phenotypes, such as depigmentation (albino), and induce lineage-specific tumors, such as melanomas (ptena/ptenb, tp53, when accompanied with expression of BRAFV600E). While the genetic approaches are solid, the argued increase in efficiency of this model compared to current tools was untested, and therefore unable to be assessed. Furthermore, the mechanistic explanations proposed to underlie their phenotypes are mostly unfounded, as discussed further in the Weaknesses section. Despite these concerns, there is still a clear use for this genetic methodology and its implementation will be of value to many in vivo researchers.

Strengths:

The strongest component of this manuscript is the genetic control offered by the mitfa:Cas9 system and the ability to make stable, lineage-specific knockouts in zebrafish. This is exemplified by the studies of tuba1a, where the authors nicely show non-cell autonomous mechanisms have obfuscated the role of this gene in melanocyte development. In addition, the mitfa:Cas9 system is elegantly straightforward and can be easily implemented in many labs. Mostly, the figures are clean, controls are appropriate, and phenotypes are reproducible. The invented method is a welcomed addition to the arsenal of genetic tools used in zebrafish.

Weaknesses:

The major weaknesses of the manuscript include the overly bold descriptions of the value of the model and the superficial mechanistic explanations for each biological vignette.

The authors argue that a major advantage of this system is its high efficiency. However, no direct comparison is made with other tools that achieve the same genetic control, such as MAZERATI. This is a missed opportunity to provide researchers the ability to evaluate these two similar genetic approaches. In addition, Fig.1 shows that not all melanocytes express Cas9. This is a major caveat that goes unaddressed. It is of paramount importance to understand the percentage of mitfa+ cells that express Cas9. The histology shown is unclear and too zoomed out of a scale to make any insightful conclusions, especially in Fig.S1. It would also be beneficial to see data regarding Cas9 expression in adult melanocytes, which are distinct from embryonic melanocytes in zebrafish. Moreover, this system still requires the injection of a plasmid encoding gRNAs of interest, which will yield mosaicism. A prime example of this discrepancy is in Fig.6, where sox10 is clearly still present in "sox10 KO" tumors.

The authors argue that their model allows rapid manipulation of melanocyte gene expression. Enthusiasm for the speed of this model is diminished by minimal phenotypes in the F0, as exemplified in Fig.2. Although the authors say >90% of fish have loss of pigmentation, this is misleading as the phenotype is a very weak, partial loss. Only in the F1 generation do robust phenotypes emerge, which takes >6 months to generate. How this is more efficient than other tools that currently exist is unclear and should be discussed in more detail.

In Figure 3, the authors find that melanocyte-specific knockout of sox10 leads to only a 25% reduction in melanocytes in the F1 generation. This is in contradiction to prior literature cited describing sox10 as indispensable for melanocyte development. In addition, the authors argue that sox10 is required for melanocyte regeneration. This claim is not accurate, as >50% of melanocytes killed upon neocuproine treatment can regenerate. This data would indicate that sox10 is required for only a subset of melanocytes to develop (Fig.3C) and for only a subset to regenerate (Fig.3G). This is an interesting finding that is not discussed or interrogated further.

Tumor induction by this model is weak, as indicated by the tumor curves in Figs.5,6. This might be because these fish are mitfa heterozygous. Whereas the avoidance of mitfa overexpression driven by other models including MAZERATI is a benefit of this system, the effect of mitfa heterozygosity on tumor incidence was untested. This is an essential question unaddressed in the manuscript.

In Fig.6, the authors recapitulate previous findings with their model, showing sox10 KO inhibits tumor onset. The tumors that do develop are argued to be highly invasive, have mesenchymal morphology, and undergo phenotypic switching from sox10 to sox9 expression. The data presented do not sufficiently support these claims. The histology is not readily suggestive of invasive, mesenchymal melanomas. Sox10 is still present in many cells and sox9 expression is only found in a small subset (<20%). Whether sox10-null cells are the ones expressing sox9 is untested. If sox9-mediated phenotypic switching is the major driver of these tumors, the authors would need to knockout sox9 and sox10 simultaneously and test whether these "rare" types of tumors still emerge. Additional histological and genetic evaluation is required to make the conclusions presented in Fig.6. It feels like a missed opportunity that the authors did not attempt to study genes of unknown contribution to melanoma with their system.

Overall, this manuscript introduces a solid method to the arsenal of zebrafish genetic tools but falls short of justifying itself as a more efficient and robust approach than what currently exists. The mechanisms provided to explain observed phenotypes are tenuous. Nonetheless, the mitfa:Cas9 approach will certainly be of value to many in vivo biologists and lays the foundation to generate similar methods using other tissue-specific regulators and other Cas proteins.

Reviewer #1 (Public review):

Summary:

This study takes a detailed approach to understanding the effect of menopausal hormone therapy (MHT) in the brain aging of females. Neuroimaging data from the UK Biobank is used to explore brain aging and shows an unexpected effect of current MHT use and poorer brain health outcomes relative to never users. There is considerable debate about the benefits of MHT and estrogens in particular for brain health, and this analysis illustrates that the effects are certainly not straightforward and require greater consideration.

Strengths:

(1) The detailed approach to obtaining important information about MHT use from primary care records. Prior studies have suggested that factors such as estrogen/progestin type, route of administration, duration, and timing of use relative to menopause onset can contribute to whether MHT benefits brain health.

(2) Consideration of type of menopause (spontaneous, or surgical) in the analysis, as well as sensitivity diagnoses to rule out the effect being driven by those with clinical conditions.

(3) The incorporation of the brain age estimate along with hippocampal volume to address brain health.

(4) The complex data are also well explained and interpretations are reasonable.

(5) Limitations of the UK Biobank data are acknowledged

Weaknesses:

(1) Lifestyle factors are listed and the authors acknowledge group differences (at least between current users and never users of MHT). I was not able to find these analyses showing these differences.

(2) The distribution of women who were not menopausal was unequal across groups, and while the authors acknowledge this, one wonders to what extent this explains the observed findings.

(3) While the interpretations are reasonable, and relevant theories (healthy cell & critical window) are mentioned, the discussion is missing a more zoomed-out perspective of the findings. While I appreciate wanting to limit speculation, the reader is left having to synthesize a lot of complex details on their own. A particularly difficult finding to reconcile is under what conditions these women benefit from MHT and when do they not (and why that may be).

Reviewer #1 (Public review):

Summary:

This paper seeks to understand the upstream regulation and downstream effectors of glycolysis in retinal progenitor cells, using mouse retinal explants as the main model system. The paper presents evidence that high glycolysis in retinal progenitor cells is required for their proliferation and timely differentiation into photoreceptors. Retinal glycolysis increases after the deletion of Pten. The authors suggest that high glycolysis controls cell proliferation and differentiation by promoting intracellular alkalinization, beta-catenin acetylation and stabilization, and consequent activation of the canonical Wnt pathway.

Strengths:

(1) The experiments showing that PFKFB3 overexpression is sufficient to increase the proliferation of retinal progenitors (which are already highly dividing cells) and photoreceptor differentiation are striking and the result is unanticipated. It suggests that glycolytic flux is normally limiting for proliferation in embryos.

(2) Likewise the result that an increase in pH from 7.4 to 8.0 is sufficient to increase proliferation implies that pH regulation may have instructive roles in setting the tempo of retinal development and embryonic cell proliferation. Similarly, the results show that acetate supplementation increases proliferation (I think this result should be moved to the main figures).

Weaknesses:

(1) Epistatic experiments to test if changes in pH mediate the effects of glycolysis on photoreceptor differentiation, or if Wnt activation is the main downstream effector of glycolysis in controlling differentiation are not presented.

(2) It is likely that metabolism changes ex vivo vs in vivo, and therefore stable isotope tracing experiments in the explants may not reflect in vivo metabolism.

(3) The retina at P0 is composed of both progenitors and differentiated cells. It is not clear if the results of the RNA-seq and metabolic analysis reflect changes in the metabolism of progenitors, or of mature cells, or changes in cell type composition rather than direct metabolic changes in a specific cell type.

(4) The biochemical links between elevated glycolysis and pH and beta-catenin stability are unclear. White et al found that higher pH decreased beta-catenin stability (JCB 217: 3965) in contrast to the results here. Oginuma et al found that inhibition of glycolysis or beta-catenin acetylation does not affect beta-catenin stability (Nature 584:98), again in contrast to these results. Another paper showed that acidification inhibits Wnt signaling by promoting the expression of a transcriptional repressor and not via beta-catenin stability (Cell Discovery 4:37). There are also additional papers showing increased pH can promote cell proliferation via other mechanisms (e.g. Nat Metab 2:1212). It is possible that there is organ-specificity in these signaling pathways however some clarification of these divergent results is warranted.

(5) The gene expression analysis is not completely convincing. E.g. the expression of additional glycolytic genes should be shown in Figure 1. It is not clear why Hk1 and Pgk1 are specifically shown, and conclusions about changes in glycolysis are difficult to draw from the expression of these two genes. The increase in glycolytic gene expression in the Pten-deficient retina is generally small.

(6) Is it possible that glycolytic inhibition with 2DG slows down the development and production of most newly differentiated cells rather than specifically affecting photoreceptor differentiation?

(7) Are the prematurely-born cells caused by PFKFB3 overexpression photoreceptors as assessed by morphology or markers (in addition to position)?

Reviewer #1 (Public review):

Summary:

Siddiqui et al., investigate the question of how bacterial metabolism contributes to the attraction of C. elegans to specific bacteria. They show that C. elegans prefers three bacterial species when cultured in a leucine-enriched environment. These bacterial species release more isoamyl alcohol, a known C. elegans attractant, when cultured with leucine supplement than without leucine supplement. The study shows correlative evidence that isoamyl alcohol is produced from leucine by the Ehrlich pathway. In addition, they show that SRD-12 is likely a receptor for isoamyl alcohol because a null mutant of this receptor exhibits lower chemotaxis to isoamyl alcohol and lower preference for leucine-enriched bacteria.

Strengths:

(1) This study takes a creative approach to examine the question of what specific volatile chemicals released by bacteria may signify to C. elegans by examining both bacterial metabolism and C. elegans preference behavior. Although C. elegans has long been known to be attracted to bacterial metabolites, this study may be one of the first to examine the role of a specific bacterial metabolic pathway in mediating attraction.

(2) A strength of the paper is the identification of SRD-12 as a likely receptor for isoamyl alcohol. The ligands for very few olfactory receptors have been identified in C. elegans and so this is a significant addition to the field. The srd-12 null mutant strain will likely be a useful reagent for many labs examining olfactory and foraging behaviors.

Weaknesses:

(1) The authors write that the leucine metabolism via the Ehrlich pathway is required for the production of isoamyl alcohol by three bacteria (CEent1, JUb66, BIGb0170), but their evidence for this is correlation and not causation. They write that the gene ilvE is a bacterial homolog of the first gene in the yeast Ehrlich pathway (it would be good to include a citation for this) and that the gene is present in these three bacterial strains. In addition, they show that this gene, ilvE, is upregulated in CEent1 bacteria upon exposure to leucine. To show causation, they need to knockout ilvE from one of these strains, show that the bacteria does not have increased isoamyl alcohol production when cultured on leucine, and that the bacteria is no longer attractive to C. elegans.

(2) The authors examine three bacterial strains that C. elegans showed increased preference when grown with leucine supplementation vs. without leucine supplementation. However, there also appears to be a strong preference for another strain, JUb0393, when grown on plus leucine (Figure 1B). It would be good to include statistics and criteria for selecting the three strains.

3. Although the behavioral evidence that srd-12 gene encodes a receptor for isoamyl alcohol is compelling, it does not meet the standard for showing that it is an olfactory receptor in C. elegans. To show it is indeed a likely receptor one or more of the following should be done:<br /> (a) Calcium imaging of AWC neurons in response to isoamyl alcohol in the receptor mutant with the expectation that the response would be reduced or abolished in the mutant compared to wildtype.<br /> (b)"A receptor swap" experiment where the SRD-12 receptor is expressed in AWB repulsive neuron in SRD-12 receptor mutant background with the expectation that with receptor swap C. elegans will now be repulsed from isoamyl alcohol in chemotaxis assays (experiment from Sengupta et al., 1996 odr-10 paper).

(4) The authors conclude that C. elegans cannot detect leucine in chemotaxis assays. It is important to add the method for how leucine chemotaxis assay was done in order to interpret these results. Because leucine is not volatile if leucine is put on the plates immediately before the worms are added (as in a traditional odor chemotaxis assay), there is no leucine gradient for the worm to detect. It would be good to put leucine on the plate several hours before worms are introduced so worms have the possibility to be able to detect the gradient of leucine (for example, see Wakabayashi et al., 2009).

(5) The bacterial preference assay entitled "odor-only assay" is a misleading name. In the assay, C. elegans is exposed to both volatile chemicals (odors) and non-volatile chemicals because the bacteria are grown on the assay plate for 12 hours before the worms are introduced to the assay plate. In that time, the bacteria is likely releasing non-volatile metabolites into the plate which may affect the worm's preference. A true odor-only assay would have the bacteria on the lid and the worms on the plate.

(6) The findings of the study should be discussed more in the context of prior literature. For example, AWC neurons have been previously shown to be involved in bacterial preference (Harris et al., 2014; Worthy et al., 2018). In addition, CeMbio bacterial strains (the strains examined in this study) have been previously shown to release isoamyl alcohol (Chai et al. 2024).

Reviewer #1 (Public review):

Summary:

This study has as its goal to determine how the structure and function of the circuit that stabilizes gaze in the larval zebrafish depends on the presence of the output cells, the motor neurons. A major model of neural circuit development posits that the wiring of neurons is instructed by their postsynaptic cells, transmitting signals retrogradely on which cells to contact and, by extension, where to project their axons. Goldblatt et al. remove the motor neurons from the circuit by generating null mutants for the phox2a gene. The study then shows that, in this mutant that lacks the isl1-labelled extraocular motor neurons, the central projection neurons have 1) largely normal responses to vestibular input; 2) normal gross morphology; 3) minimally changed transcriptional profiles. From this, the authors conclude that the wiring of the circuit is not instructed by the output neurons, refuting the major model.

Strengths:

I found the manuscript to be exceptionally well-written and presented, with clear and concise writing and effective figures that highlight key concepts. The topic of neural circuit wiring is central to neuroscience, and the paper's findings will interest researchers across the field, and especially those focused on motor systems.

The experiments conducted are clever and of a very high standard, and I liked the systematic progression of methods to assess the different potential effects of removing phox2a on circuit structure and function. Analyses (including statistics) are comprehensive and appropriate and show the authors are meticulous and balanced in most of the conclusions that they draw. Overall, the findings are interesting and should leave little doubt about the paper's main conclusions.

Weaknesses:

All conclusions are supported by the data, and the characterisation of the effects of the main manipulation in the study, removing phox2a to take out the extra-ocular motor neurons, is extensive. I cannot see weaknesses that affect the conclusions in this manuscript.

The study raises interesting questions that could be addressed in future work, which would further explain how the projection neurons develop. While the cells that would have been extraocular motor neurons are still there in phox2a mutants, they can no longer be called motor neurons as they lack expression of vachta and isl1. It would therefore be interesting to see what an alternative manipulation, e.g., the physical removal of the motor neurons using laser ablation, would have. Furthermore, the motor neurons are dispensable for the projection neurons' wiring, but the projection neurons innervate several other cell types that could affect their development. A future project could determine the precise contribution of each postsynaptic population on the projection neurons' development.

Reviewer #1 (Public review):

Summary:

In this study, the authors describe the participation of the Hes4-BEST4-Twist axis in controlling the process of epithelial-mesenchymal transition (EMT) and the advancement of colorectal cancers (CRC). They assert that this axis diminishes the EMT capabilities of CRC cells through a variety of molecular mechanisms. Additionally, they propose that reduced BEST4 expression within tumor cells might serve as an indicator of an adverse prognosis for individuals with CRC.

The revised manuscript and figures still need further improvement because some of the authors' claims are difficult to understand from a scientific perspective.

Strengths:

• Exploring the correlation between the Hes4-BEST4-Twist1 axis, EMT, and the advancement of CRC is a novel perspective and gives readers a fresh standpoint.<br /> • The potential role of BEST4 in EMT through the Hes4-BEST4-Twist1 axis, rather than through its channel function, is also a novel perspective.<br /> • The whole transcriptome sequence analysis (Figure 5) showing low expression of BEST4 in CRC samples will be of broad interest to cancer specialists as well as cell biologists although further corroborative data is essential to strengthen these findings (See Weaknesses).

Weaknesses:

• The authors employed three kinds of CRC cell lines, but not untransformed cells such as intestinal epithelial organoids which are commonly used in recent research. Since all the data from in vitro and in vivo experiments are generated from CRC cell lines with forced expression of proteins of interest, the authors' claim may not reflect a common biological process.<br /> • Most of experiments were performed to show changes in EMT markers, but not EMT itself.<br /> • The in vivo and in vitro data supporting the whole transcriptome sequence analysis (Figure 5) is mostly insufficient. Since BEST4 is a marker of a subset of terminally differentiated colonocytes, its lower expression in CRC compared to adjacent normal tissue could be within the range of common expectations.<br /> • Some experiments do not appear to have a direct relevance to their claims.

Major comments:

• The authors employed three kinds of CRC cell lines, but not untransformed cells such as intestinal epithelial organoids which are commonly used in recent research. Please include this limitation of the study in the discussion section with other possible limitations.<br /> • Some experiments do not appear to have direct relevance to their claims. Figure 1A-1F and 2E-2H relate to cell proliferation or viability of CRC cell lines, but not to EMT. The focus of this study should be on EMT, but the summary sentence for Figure 1 (Line 118-119) says "inhibitory effects of BEST4 on CRC development". This sentence, along with some others (such as Line 262-263), seems to be deviating. Cancer development and EMT are distinct biological processes, so please revise the manuscript with this in mind.<br /> • The context around Line 194-197, "Additionally, the knockdown of endogenous BEST4 in Hes4-expressing HCT116 cells substantially decreased Flag-Hes4 coprecipitation from the nuclear protein lysates, while Myc-Twist1 expression remained constant, as determined by co-IP with antibodies to Flag or My (Figure 4E; Figure 4-figure supplement 1C)." is difficult to follow.<br /> • The in vivo and in vitro data supporting the whole transcriptome sequence analysis (Figure 5) are mostly insufficient. Since BEST4 is a marker of a subset of terminally differentiated colonocytes, its lower expression in CRC compared to adjacent normal tissue could be within the range of common expectations.<br /> • As the reviewer #2 mentioned, the quality of some figures is quite suboptimal. It is not due to their pixel size, but rather due to other factors, such as the inconsistencies of aspect ratios. Improvement of the overall quality is needed. Figure legends also need improvements.<br /> • The formatting of genes and proteins is inconsistent. Please correct it according to the general formatting guidelines.

Reviewer #2 (Public Review):

Summary:

This article mainly explores the neural circuit mechanism of recovery of consciousness after midazolam administration and proves that the LC-VLPO NEergic neural circuit helps to promote the recovery of midazolam, and this effect is mainly caused by α1 adrenergic receptors. (α1-R) mediated.

Strengths:

This article uses innovative methods such as optogenetics and fiber optic photometry in the experimental methods section to make the stimulation of neuronal cells more precise and the stimulation intensity more accurate in experimental research. In addition, fiber optic photometry adds confidence to the results of calcium detection in mouse neuronal cells.

This article explains the results from the entire system down to cells, and then cells gradually unfold to explain the entire mechanism. The entire explanation process is logical and orderly. At the same time, this article conducted a large number of rescue experiments, which greatly increased the credibility of the experimental conclusions.

Throughout the full text and all conclusions, this article has elucidated the neural circuit mechanism of recovery of consciousness after midazolam administration and successfully verified that the LC-VLPO NEergic neural circuit helps promote the recovery of midazolam.

The conclusions of this article are crucial to ameliorate the complications of its abuse. It will pinpoint relevant regions involved in midazolam response and provide a perspective to help elucidate the dynamic changes in neural circuits in the brain during altered consciousness and suggest a promising approach towards the goal of timely recovery from midazolam. New research avenues.

At the same time, this article also has important clinical translation significance. The application of clinical drug midazolam and animal experiments have certain guiding significance for subsequent related clinical research.

Comments on revised version: I have no further questions for this manuscript.

Reviewer #1 (Public review):

Summary:

Tobón and Moser reveal a remarkable amount of presynaptic diversity in the fundamental Ca dependent exocytosis of synaptic vesicles at the afferent fiber bouton synapse onto the pilar or mediolar sides of single inner hair cells of mice. These are landmark findings with profound implications for understanding acoustic signal encoding and presynaptic mechanisms of synaptic diversity at inner hair cell ribbon synapses. The paper will have an immediate and long-lasting impact in the field of auditory neuroscience.

Main findings: 1) Synaptic delays and jitter of masker responses are significantly shorter (synaptic delay: 1.19 ms) at high SR fibers (pilar) than at low SR fibers (mediolar; 2.57 ms). 2) Masked evoked EPSC are significantly larger in high SR than in low SR. 3) Quantal content and RRP size are 14 vesicles in both high and low SR fibers. 4) Depression is faster in high SR synapses suggesting they have a higher release probability and tighter Ca nanodomain coupling to docked vesicles. 5) Recovery of master-EPSCs from depletion is similar for high and low SR synapses, although there is a slightly faster rate for low SR synapses that have bigger synaptic ribbons, which is very interesting. 6) High SR synapses had larger and more compact (monophasic) sEPSCs, well suited to trigger rapidly and faithfully spikes. 7) High SR synapses exhibit lower voltage (~sound pressure in vivo) dependent thresholds of exocytosis.

Great care was taken to use physiological external pH buffers and physiological external Ca concentrations. Paired recordings were also performed at higher temperatures with IHCs at physiological resting membrane potentials and in more mature animals than previously done for paired recordings. This is extremely challenging because it becomes increasingly difficult to visualize bouton terminals when myelination becomes more prominent in the cochlear afferents. In addition, perforated patch recordings were used in the IHC to preserve its intracellular milieu intact and thus extend the viability of the IHCs. The experiments are tour-de-force and reveal several novel aspects of IHC ribbon synapses. The data set is rich and extensive. The analysis is detailed and compelling.

Reviewer #1 (Public review):

Summary:

The circuit mechanism underlying the formation of grid cell activity and the organization of grid cells in the medial entorhinal cortex (MEC) is still unclear. To understand the mechanism, the current study investigated synaptic interactions between stellate cells (SC) and PV+ interneurons (IN) in layer 2 of the MEC by combing optogenetic activations and paired patch-clamp recordings. The results convincingly demonstrated highly structured interactions between these neurons: specific and direct excitatory-inhibitory interactions existed at the scale of grid cell phase clusters, and indirect interactions occurred at the scale of grid modules.

Strengths:

Overall, the manuscript is very well written, the approaches used are clever, and the data were thoroughly analyzed. The study conveyed important information towards understanding the circuit mechanism that shapes grid cell activity. It is important not only for the field of MEC and grid cells, but also for broader fields of continuous attractor network and neural circuit.

Weaknesses:

The study largely relies on the fact that ramp-like wide field optogenetic stimulation and focal optogenetic activation both drove asynchronous action potentials in SCs, and therefore, if a pair of PV+ INs exhibited correlated activity, they should receive common inputs. While the asynchronization of action potentials during ramp-like wide field optogenetics was shown in Figure 2 Figure Supplement 1, the asynchronization during focal optogenetic activation was not confirmed in the current experimental setting. More data and statistical analysis in this aspect would strengthen the foundation of this study.

Reviewer #1 (Public review):

Summary:

Guglielmo et al. characterized addiction-like behaviors in more than 500 outbred heterogeneous stock (HS) rats using extended access to cocaine self-administration (6 h/daily) and analyzed individual differences in escalation of intake, progressive-ratio (PR) responding, continued use despite adverse consequence (contingent foot shocks), and irritability-like behavior during withdrawal. By principal component analysis, they found that escalation of intake, progressive ratio responding, and continued use despite adverse consequences loaded onto the same factor, whereas irritability-like behaviors loaded onto a separate factor. Characterization of rats in four categories of resilient, mild, moderate, and severe addiction-like phenotypes showed that females had higher addiction-like behaviors, particularly due to a lower number of resilient individuals, than males. The authors suggest that escalation of intake, continued use despite adverse consequences, and progressive ratio responding are highly correlated measures of the same psychological construct and that a significant proportion of males, but not females may be resilient to addiction-like behaviors. The amount of work in this study is impressive, and the results are interesting.

Strengths: Large dataset. Males and females included.

Reviewer #1 (Public review):

Summary:

In this work, the authors apply TDCS to awake and anesthetized macaques to determine the effect of this modality on dynamic connectivity measured by fMRI. The question is to understand the extent to which TDCS can influence conscious or unconscious states. Their target was the PFC. During the conscious states, the animals were executing a fixation task. Unconsciousness was achieved by administering a constant infusion of propofol and a continuous infusion of the muscle relaxant cisatracurium. They observed the animals while awake receiving anodal or cathodal hd-TDCS applied to the PFC. During the cathodal stimulation, they found disruption of functional connectivity patterns, enhanced structure-function correlations, a decrease in Shannon entropy, and a transition towards patterns that were more commonly anatomically based. In contrast under propofol anesthesia anodal hd-TDCS stimulation appreciably altered the brain connectivity patterns and decreased the correlation between structure and function. The PFC stimulations altered patterns associated with consciousness as well as those associated with unconsciousness.

Strengths:

The authors carefully executed a set of very challenging experiments that involved applying tDCS in awake and anesthetized non-human primates while conducting functional imaging.

Weaknesses:

The authors show that tDCS can alter functional connectivity measured by fMRI but they do not make clear what their studies teach the reader about the effects of tDCS on the brain during different states of consciousness. No important finding is stated contrary to what is stated in the abstract. It is also not clear what the work teaches us about how tDCS works nor is it clear what are the "clinical implications for disorders of consciousness." The deep anesthesia is akin to being in a state of coma. This was not discussed.

While the authors have executed a set of technically challenging experiments, it is not clear what they teach us about how tDCS works, normal brain neurophysiology, or brain pathological states such as disorders of consciousness.

Reviewer #1 (Public review):

Wang et al. studied an old, still unresolved problem: Why are reaching movements often biased? Using data from a set of new experiments and from earlier studies, they identified how the bias in reach direction varies with movement direction, and how this depends on factors such as the hand used, the presence of visual feedback, the size and location of the workspace, the visibility of the start position and implicit sensorimotor adaptation. They then examined whether a visual bias, a proprioceptive bias, a bias in the transformation from visual to proprioceptive coordinates and/or biomechanical factors could explain the observed patterns of biases. The authors conclude that biases are best explained by a combination of transformation and visual biases.

A strength of this study is that it used a wide range of experimental conditions with also a high resolution of movement directions and large numbers of participants, which produced a much more complete picture of the factors determining movement biases than previous studies did. The study used an original, powerful, and elegant method to distinguish between the various possible origins of motor bias, based on the number of peaks in the motor bias plotted as a function of movement direction. The biomechanical explanation of motor biases could not be tested in this way, but this explanation was excluded in a different way using data on implicit sensorimotor adaptation. This was also an elegant method as it allowed the authors to test biomechanical explanations without the need to commit to a certain biomechanical cost function.

The main weakness of the study is that it rests on the assumption that the number of peaks in the bias function is indicative of the origin of the bias. Specifically, it is assumed that a proprioceptive bias leads to a single peak, a transformation bias to two peaks, and a visual bias to four peaks, but these assumptions are not well substantiated. Especially the assumption that a transformation bias leads to two peaks is questionable. It is motivated by the fact that biases found when participants matched the position of their unseen hand with a visual target are consistent with this pattern. However, it is unclear why that task would measure only the effect of transformation biases, and not also the effects of visual and proprioceptive biases in the sensed target and hand locations. Moreover, it is not explained why a transformation bias would lead to this specific bias pattern in the first place. Also, the assumption that a visual bias leads to four peaks is not well substantiated as one of the papers on which the assumption was based (Yousif et al., 2023) found a similar pattern in a purely proprioceptive task. Another weakness is that the study looked at biases in movement direction only, not at biases in movement extent. The models also predict biases in movement extent, so it is a missed opportunity to take these into account to distinguish between the models.

Overall, the authors have done a good job mapping out reaching biases in a wide range of conditions, revealing new patterns in one of the most basic tasks, but unambiguously determining the origin of these biases remains difficult, and the evidence for the proposed origins is incomplete. Nevertheless, the study will likely have a substantial impact on the field, as the approach taken is easily applicable to other experimental conditions. As such, the study can spark future research on the origin of reaching biases.

Reviewer #1 (Public review):

Summary:

The authors test the "OHC-fluid-pump" hypothesis by assaying the rates of kainic acid dispersal both in quiet and in cochleae stimulated by sounds of different levels and spectral content. The main result is that sound (and thus, presumably, OHC contractions and expansions) results in faster transport along the duct. OHC involvement is corroborated using salicylate, which yielded results similar to silence. Especially interesting is the fact that some stimuli (e.g. tones) seem to provide better/faster pumping than others (e.g. noise), ostensibly due to the phase profile of the resulting cochlear traveling-wave response.

Strengths:

The experiments appear well controlled and the results are novel and interesting. Some elegant cochlear modeling that includes coupling between the organ of Corti and the surrounding fluid as well as advective flow supports the proposed mechanism.

Weaknesses:

It's not clear whether the effect size (e.g., the speed of sound-induced pumping relative to silence) is large enough to have important practical applications (e.g., for drug delivery). The authors should comment on the practical requirements and limitations.

Although helpful so far as it goes, the modeling could be taken much further to help understand some of the more interesting aspects of the data and to obtain testable predictions. In particular, the authors should systematically explore the level effects they find experimentally and determine whether the model can replicate the finding that different sounds produce different results (e.g. noise vs tone).

The model should also be used to relate the model's flow rates more quantitatively to the properties of the traveling wave (e.g., its phase profile).

Finally, the model should be used to investigate differences between active and passive OHCs (e.g., simulating the salicylate experiment by disabling the model's OHCs).

The manuscript would be stronger if the authors discussed ways to test their hypothesis that OHC motility serves a protective effect by pumping fluid. For example, do animals held in quiet after noise exposure (TTS) take longer to recover?

Reviewer #1 (Public review):

Summary:

In the abstract and throughout the paper, the authors boldly claim that their evidence, from the largest set of data ever collected on inattentional blindness, supports the views that "inattentionally blind participants can successfully report the location, color, and shape of stimuli they deny noticing", "subjects retain awareness of stimuli they fail to report", and "these data...cast doubt on claims that awareness requires attention." If their results were to support these claims, this study would overturn 25+ years of research on inattentional blindness, resolve the rich vs. sparse debate in consciousness research, and critically challenge the current majority view in cognitive science that attention is necessary for awareness.

Unfortunately, these extraordinary claims are not supported by extraordinary (or even moderately convincing) evidence. At best, the results support the more modest conclusion: If sub-optimal methods are used to collect retrospective reports, inattentional blindness rates will be overestimated by up to ~8% (details provided below in comment #1). This evidence-based conclusion means that the phenomenon of inattentional blindness is alive and well as it is even robust to experiments that were specifically aimed at falsifying it. Thankfully, improved methods already exist for correcting the ~8% overestimation of IB rates that this study successfully identified.

Comments:

(1) In experiment 1, data from 374 subjects were included in the analysis. As shown in figure 2b, 267 subjects reported noticing the critical stimulus and 107 subjects reported not noticing it. This translates to a 29% IB rate, if we were to only consider the "did you notice anything unusual Y/N" question. As reported in the results text (and figure 2c), when asked to report the location of the critical stimulus (left/right), 63.6% of the "non-noticer" group answered correctly. In other words, 68 subjects were correct about the location while 39 subjects were incorrect. Importantly, because the location judgment was a 2-alternative-forced-choice, the assumption was that if 50% (or at least not statistically different than 50%) of the subjects answered the location question correctly, everyone was purely guessing. Therefore, we can estimate that ~39 of the subjects who answered correctly were simply guessing (because 39 guessed incorrectly), leaving 29 subjects from the non-noticer group who may have indeed actually seen the location of the stimulus. If these 29 subjects are moved to the noticer group, the corrected rate of IB for experiment 1 is 21% instead of 29%. In other words, relying only on the "Y/N did you notice anything" question leads to an overestimate of IB rates by 8%. This modest level of inaccuracy in estimating IB rates is insufficient for concluding that "subjects retain awareness of stimuli they fail to report", i.e. that inattentional blindness does not exist.

In addition, this 8% inaccuracy in IB rates only considers one side of the story. Given the data reported for experiment 1, one can also calculate the number of subjects who answered "yes, I did notice something unusual" but then reported the incorrect location of the critical stimulus. This turned out to be 8 subjects (or 3% of the "noticer" group). Some would argue that it's reasonable to consider these subjects as inattentionally blind, since they couldn't even report where the critical stimulus they apparently noticed was located. If we move these 8 subjects to the non-noticer group, the 8% overestimation of IB rates is reduced to 6%.

The same exercise can and should be carried out on the other 4 experiments, however, the authors do not report the subject numbers for any of the other experiments, i.e., how many subjects answered Y/N to the noticing question and how many in each group correctly answered the stimulus feature question. From the limited data reported (only total subject numbers and d' values), the effect sizes in experiments 2-5 were all smaller than in experiment 1 (d' for the non-noticer group was lower in all of these follow-up experiments), so it can be safely assumed that the ~6-8% overestimation of IB rates was smaller in these other four experiments. In a revision, the authors should consider reporting these subject numbers for all 5 experiments.

(2) Because classic IB paradigms involve only one critical trial per subject, the authors used a "super subject" approach to estimate sensitivity (d') and response criterion (c) according to signal detection theory (SDT). Some readers may have issues with this super subject approach, but my main concern is with the lack of precision used by the authors when interpreting the results from this super subject analysis.

Only the super subject had above-chance sensitivity (and it was quite modest, with d' values between 0.07 and 0.51), but the authors over-interpret these results as applying to every subject. The methods and analyses cannot determine if any individual subject could report the features above-chance. Therefore, the following list of quotes should be revised for accuracy or removed from the paper as they are misleading and are not supported by the super subject analysis:

"Altogether this approach reveals that subjects can report above-chance the features of stimuli (color, shape, and location) that they had claimed not to notice under traditional yes/no questioning" (p.6)

"In other words, nearly two-thirds of subjects who had just claimed not to have noticed any additional stimulus were then able to correctly report its location." (p.6)

"Even subjects who answer "no" under traditional questioning can still correctly report various features of the stimulus they just reported not having noticed, suggesting that they were at least partially aware of it after all." (p.8)

"Why, if subjects could succeed at our forced-response questions, did they claim not to have noticed anything?" (p.8)

"we found that observers could successfully report a variety of features of unattended stimuli, even when they claimed not to have noticed these stimuli." (p.14)

"our results point to an alternative (and perhaps more straightforward) explanation: that inattentionally blind subjects consciously perceive these stimuli after all... they show sensitivity to IB stimuli because they can see them." (p.16)

"In other words, the inattentionally blind can see after all." (p.17)

(3) In addition to the d' values for the super subject being slightly above zero, the authors attempted an analysis of response bias to further question the existence of IB. By including in some of their experiments critical trials in which no critical stimulus was presented, but asking subjects the standard Y/N IB question anyway, the authors obtained false alarm and correct rejection rates. When these FA/CR rates are taken into account along with hit/miss rates when critical stimuli were presented, the authors could calculate c (response criterion) for the super subject. Here, the authors report that response criteria are biased towards saying "no, I didn't notice anything". However, the validity of applying SDT to classic Y/N IB questioning is questionable.

For example, with the subject numbers provided in Box 1 (the 2x2 table of hits/misses/FA/CR), one can ask, 'how many subjects would have needed to answer "yes, I noticed something unusual" when nothing was presented on the screen in order to obtain a non-biased criterion estimate, i.e., c = 0?' The answer turns out to be 800 subjects (out of the 2761 total subjects in the stimulus-absent condition), or 29% of subjects in this condition.

In the context of these IB paradigms, it is difficult to imagine 29% of subjects claiming to have seen something unusual when nothing was presented. Here, it seems that we may have reached the limits of extending SDT to IB paradigms, which are very different than what SDT was designed for. For example, in classic psychophysical paradigms, the subject is asked to report Y/N as to whether they think a threshold-level stimulus was presented on the screen, i.e., to detect a faint signal in the noise. Subjects complete many trials and know in advance that there will often be stimuli presented and the stimuli will be very difficult to see. In those cases, it seems more reasonable to incorrectly answer "yes" 29% of the time, as you are trying to detect something very subtle that is out there in the world of noise. In IB paradigms, the stimuli are intentionally designed to be highly salient (and unusual), such that with a tiny bit of attention they can be easily seen. When no stimulus is presented and subjects are asked about their own noticing (especially of something unusual), it seems highly unlikely that 29% of them would answer "yes", which is the rate of FAs that would be needed to support the null hypothesis here, i.e., of a non-biased criterion. For these reasons, the analysis of response bias in the current context is questionable and the results claiming to demonstrate a biased criterion do not provide convincing evidence against IB.

(4) One of the strongest pieces of evidence presented in the entire paper is the single data point in Figure 3e showing that in Experiment 3, even the super subject group that rated their non-noticing as "highly confident" had a d' score significantly above zero. Asking for confidence ratings is certainly an improvement over simple Y/N questions about noticing, and if this result were to hold, it could provide a key challenge to IB. However, this result hinges on a single data point, it was not replicated in any of the other 4 experiments, and it can be explained by methodological limitations. I strongly encourage the authors (and other readers) to follow up on this result, in an in-person experiment, with improved questioning procedures.

In the current Experiment 3, the authors asked the standard Y/N IB question, and then asked how confident subjects were in their answer. Asking back-to-back questions, the second one with a scale that pertains to the first one (including a tricky inversion, e.g., "yes, I am confident in my answer of no"), may be asking too much of some subjects, especially subjects paying half-attention in online experiments. This procedure is likely to introduce a sizeable degree of measurement error.

An easy fix in a follow-up study would be to ask subjects to rate their confidence in having noticed something with a single question using an unambiguous scale:

On the last trial, did you notice anything besides the cross?

(1) I am highly confident I didn't notice anything else<br /> (2) I am confident I didn't notice anything else<br /> (3) I am somewhat confident I didn't notice anything else<br /> (4) I am unsure whether I noticed anything else<br /> (5) I am somewhat confident I noticed something else<br /> (6) I am confident I noticed something else<br /> (7) I am highly confident I noticed something else

If we were to re-run this same experiment, in the lab where we can better control the stimuli and the questioning procedure, we would most likely find a d' of zero for subjects who were confident or highly confident (1-2 on the improved scale above) that they didn't notice anything. From there on, the d' values would gradually increase, tracking along with the confidence scale (from 3-7 on the scale). In other words, we would likely find a data pattern similar to that plotted in Figure 3e, but with the first data point on the left moving down to zero d'. In the current online study with the successive (and potentially confusing) retrospective questioning, a handful of subjects could have easily misinterpreted the confidence scale (e.g., inverting the scale) which would lead to a mixture of genuine high-confidence ratings and mistaken ratings, which would result in a super subject d' that falls between zero and the other extreme of the scale (which is exactly what the data in Fig 3e shows).

One way to check on this potential measurement error using the existing dataset would be to conduct additional analyses that incorporate the confidence ratings from the 2AFC location judgment task. For example, were there any subjects who reported being confident or highly confident that they didn't see anything, but then reported being confident or highly confident in judging the location of the thing they didn't see? If so, how many? In other words, how internally (in)consistent were subjects' confidence ratings across the IB and location questions? Such an analysis could help screen-out subjects who made a mistake on the first question and corrected themselves on the second, as well as subjects who weren't reading the questions carefully enough. As far as I could tell, the confidence rating data from the 2AFC location task were not reported anywhere in the main paper or supplement.

(5) In most (if not all) IB experiments in the literature, a partial attention and/or full attention trial (or set of trials) is administered after the critical trial. These control trials are very important for validating IB on the critical trial, as they must show that, when attended, the critical stimuli are very easy to see. If a subject cannot detect the critical stimulus on the control trial, one cannot conclude that they were inattentionally blind on the critical trial, e.g., perhaps the stimulus was just too difficult to see (e.g., too weak, too brief, too far in the periphery, too crowded by distractor stimuli, etc.), or perhaps they weren't paying enough attention overall or failed to follow instructions. In the aggregate data, rates of noticing the stimuli should increase substantially from the critical trial to the control trials. If noticing rates are equivalent on the critical and control trials one cannot conclude that attention was manipulated.

It is puzzling why the authors decided not to include any control trials with partial or full attention in their five experiments, especially given their online data collection procedures where stimulus size, intensity, eccentricity, etc. were uncontrolled and variable across subjects. Including such trials could have actually helped them achieve their goal of challenging the IB hypothesis, e.g., excluding subjects who failed to see the stimulus on the control trials might have reduced the inattentional blindness rates further. This design decision should at least be acknowledged and justified (or noted as a limitation) in a revision of this paper.

(6) In the discussion section, the authors devote a short paragraph to considering an alternative explanation of their non-zero d' results in their super subject analyses: perhaps the critical stimuli were processed unconsciously and left a trace such that when later forced to guess a feature of the stimuli, subjects were able to draw upon this unconscious trace to guide their 2AFC decision. In the subsequent paragraph, the authors relate these results to above-chance forced-choice guessing in blindsight subjects, but reject the analogy based on claims of parsimony.

First, the authors dismiss the comparison of IB and blindsight too quickly. In particular, the results from experiment 3, in which some subjects adamantly (confidently) deny seeing the critical stimulus but guess a feature at above-chance levels (at least at the super subject level and assuming the online subjects interpreted and used the confidence scale correctly), seem highly analogous to blindsight. Importantly, the analogy is strengthened if the subjects who were confident in not seeing anything also reported not being confident in their forced-choice judgments, but as mentioned above this data was not reported.

Second, the authors fail to mention an even more straightforward explanation of these results, which is that ~8% of subjects misinterpreted the "unusual" part of the standard IB question used in experiments 1-3. After all, colored lines and shapes are pretty "usual" for psychology experiments and were present in the distractor stimuli everyone attended to. It seems quite reasonable that some subjects answered this first question, "no, I didn't see anything unusual", but then when told that there was a critical stimulus and asked to judge one of its features, adjusted their response by reconsidering, "oh, ok, if that's the unusual thing you were asking about, of course I saw that extra line flash on the left of the screen". This seems like a more parsimonious alternative compared to either of the two interpretations considered by the authors: (1) IB does not exist, (2) super-subject d' is driven by unconscious processing. Why not also consider: (3) a small percentage of subjects misinterpreted the Y/N question about noticing something unusual. In experiments 4-5, they dropped the term "unusual" but do not analyze whether this made a difference nor do they report enough of the data (subject numbers for the Y/N question and 2AFC) for readers to determine if this helped reduce the ~8% overestimate of IB rates.

(7) The authors use sub-optimal questioning procedures to challenge the existence of the phenomenon this questioning is intended to demonstrate. A more neutral interpretation of this study is that it is a critique on methods in IB research, not a critique on IB as a manipulation or phenomenon. The authors neglect to mention the dozens of modern IB experiments that have improved upon the simple Y/N IB questioning methods. For example, in Michael Cohen's IB experiments (e.g., Cohen et al., 2011; Cohen et al., 2020; Cohen et al., 2021), he uses a carefully crafted set of probing questions to conservatively ensure that subjects who happened to notice the critical stimuli have every possible opportunity to report seeing them. In other experiments (e.g., Hirschhorn et al., 2024; Pitts et al., 2012), researchers not only ask the Y/N question but then follow this up by presenting examples of the critical stimuli so subjects can see exactly what they are being asked about (recognition-style instead of free recall, which is more sensitive). These follow-up questions include foil stimuli that were never presented (similar to the stimulus-absent trials here), and ask for confidence ratings of all stimuli. Conservative, pre-defined exclusion criteria are employed to improve the accuracy of their IB-rate estimates. In these and other studies, researchers are very cautious about trusting what subjects report seeing, and in all cases, still find substantial IB rates, even to highly salient stimuli. The authors should consider at least mentioning these improved methods, and perhaps consider using some of them in their future experiments.

Reviewer #1 (Public review):

Summary:

Rossi et al. asked whether gait adaptation is solely a matter of slow perceptual realignment or if it also involves fast/flexible stimulus-response mapping mechanisms. To test this, they conducted a series of split-belt treadmill experiments with ramped perturbations, revealing behavior indicative of a flexible, automatic stimulus-response mapping mechanism.

Strengths:

(1) The study includes a perceptual test of leg speed, which correlates with the perceptual realignment component of motor aftereffects. This indicates that there are motor performances that are not accounted for by perceptual re-alignment.

(2) They study incorporates qualitatively distinct, hypothesis-driven models of adaptation and proposes a new framework that integrates these various mechanisms.

Weaknesses:

(1) The study could benefit from considering other alternative models. As the authors noted in their discussion, while the descriptive models explain some patterns of behaviour/aftereffects, they don't currently account for how these mechanisms influence the initial learning process itself.

a. For example, the pattern of gait asymmetric might differ for perceptual realignment (a smooth, gradual process), structural learning (more erratic, involving hypothesis testing/reasoning to understand the perturbation, see (Tsay et al. 2024) for a recent review on Reasoning), and stimulus-response mapping (possibly through a reinforcement based trial-and-error approach). If not formally doing a model comparison, the manuscript might benefit from clearly laying out the behavioural predictions for how these different processes shape initial learning.

b. Related to the above, the authors noted that the absence of difference during initial learning suggests that the differences in Experiment 2 in the ramp-up phase are driven by two distinct processes: structural learning and memory-based processes. If the assumptions about initial learning are not clear, this logic of this conclusion is hard to follow.

c. The authors could also test a variant of the dual-rate state-space model with two perceptual realignment processes where the constraints on retention and learning rate are relaxed. This model would be a stronger test for two perceptual re-alignment processes: one that is flexible and another that is rigid, without mandating that one be fast learning and fast forgetting, and the other be slow learning and slow forgetting.

(2) The authors claim that stimulus-response mapping operates outside of explicit/deliberate control. While this could be true, the survey questions may have limitations that could be more clearly acknowledged.

a. Specifically, asking participants at the end of the experiments to recall their strategies may suffer from memory biases (e.g., participants may be biased by recent events, and forget about the explicit strategies early in the experiment), be susceptible to the framing of the questions (e.g., participants not being sure what the experimenter is asking and how to verbalize their own strategy), and moreover, not clear what is the category of explicit strategies one might enact here which dictates what might be considered "relevant" and "accurate".

b. The concept of perceptual realignment also suggests that participants are somewhat aware of the treadmill's changing conditions; therefore, as a thought experiment, if the authors have asked participants throughout/during the experiment whether they are trying different strategies, would they predict that some behaviour is under deliberate control?

(3) The distinction between structural and memory-based differences in the two subgroups was based on the notion that memory-based strategies increase asymmetry. However, an alternative explanation could be that unfamiliar perturbations, due to the ramping up, trigger a surprise signal that leads to greater asymmetry due to reactive corrections to prevent one's fall - not because participants are generalizing from previously learned representations (e.g., (Iturralde & Torres-Oviedo, 2019)).

Further contextualization:

Recognizing the differences in dependent variables (reaching position vs. leg speed/symmetry in walking), could the Proprioceptive/Perceptual Re-alignment model also apply to gait adaptation (Tsay et al., 2022; Zhang et al., 2024)? Recent reaching studies show a similar link between perception and action during motor adaptation (Tsay et al., 2021) and have proposed a model aligning with the authors' correlations between perception and action. The core signal driving implicit adaptation is the discrepancy between perceived and desired limb position, integrating forward model predictions with proprioceptive/visual feedback.

References

Iturralde, P. A., & Torres-Oviedo, G. (2019). Corrective Muscle Activity Reveals Subject-Specific Sensorimotor Recalibration. eNeuro, 6(2). https://doi.org/10.1523/ENEURO.0358-18.2019

Tsay, Jonathan S., Hyosub E. Kim, Samuel D. McDougle, Jordan A. Taylor, Adrian Haith, Guy Avraham, John W. Krakauer, Anne G. E. Collins, and Richard B. Ivry. 2024. "Fundamental Processes in Sensorimotor Learning: Reasoning, Refinement, and Retrieval." ELife 13 (August). https://doi.org/10.7554/eLife.91839.

Tsay, Jonathan S., Hyosub E. Kim, Darius E. Parvin, Alissa R. Stover, and Richard B. Ivry. 2021. "Individual Differences in Proprioception Predict the Extent of Implicit Sensorimotor Adaptation." Journal of Neurophysiology, March. https://doi.org/10.1152/jn.00585.2020.

Tsay, Jonathan S., Hyosub Kim, Adrian M. Haith, and Richard B. Ivry. 2022. "Understanding Implicit Sensorimotor Adaptation as a Process of Proprioceptive Re-Alignment." ELife 11 (August). https://doi.org/10.7554/eLife.76639.

Zhang, Zhaoran, Huijun Wang, Tianyang Zhang, Zixuan Nie, and Kunlin Wei. 2024. "Perceptual Error Based on Bayesian Cue Combination Drives Implicit Motor Adaptation." ELife. https://doi.org/10.7554/elife.94608.1.

Reviewer #1 (Public Review):

In this work, the authors aimed to understand how titins derived from different nuclei within the syncytium are organized and integrated after cell fusion during skeletal muscle development and remodeling. The authors developed mCherry titin knock-in mice with the fluorophore mCherry inserted into titin's Z-disk region to track the titin during cell fusion. The results suggested that titin exhibited homogenous distribution after cell fusion. The authors also probed on how titin behaves during muscle injury by implantation of titin-eGFP myoblasts into adult mCherry-titin mice. Interestingly, titin is retained at the proximal nucleus and does not diffuse across the whole syncytium in this system. The findings of the study are novel and interesting. The experimental approaches are appropriate. The results are described well. However, the manuscript needs revisions to enhance its clarity.

(1) In this work, the authors have not described the statistical analysis appropriately. In most of the figures, significance levels are not described. The information on the biological and technical replicates is missing in almost all the figures. This information is critical for understanding the strength of the experimentation.<br /> (2) The in vivo experiments are underpowered. The authors have used only 3 animals in the cardiotoxin injury experiment and eliminated another 3 animals from the analysis. How did they determine insufficient myoblast integration?<br /> (3) Similarly, the in vitro imaging experiments, especially the in vitro titin mobility assays used only 3 cells (Fig 2b) or 6-9 cells (Fig 2c-2e). The number of cells imaged is insufficient to derive a valid conclusion. What is the variability in the results between cells? Whether all the cells behave similarly in titin mobility assays?<br /> (4) Figure 1c-e, Figure 2a, Figure 3, Figure 4, Figure 5, Figure 6- please describe the replicates and also if possible, quantify the data and present them as separate figures.<br /> (5) Figure 2- the authors excluded samples with an obvious decrease in cell quality during imaging from the analysis. How do the authors assess the cell quality? Simply by visual examination? Or were the samples that did not show fluorescence recovery eliminated? I am wondering what percentage of cells showed poor cell quality. How do they avoid the bias? I recommend that the authors include these cells also for the analysis of data presented in Figures 2b, 2c, and 2f.<br /> (6) It is unclear how the authors identified the different stages of cell fusion in the microscopy images i.e. early fusion, distribution, and complete distribution.

Reviewer #1 (Public Review):

Lactobacillus plantarum is a beneficial bacterium renowned for its positive physiological effects and probiotic functions. Fu et al. conducted an investigation into the involvement of this bacterium in host purine metabolism. Initially, they employed microbiomics to analyze changes in L. plantarum within a hyperuricemia model, followed by isolation of the bacterium from this model. The gene map associated with purine nucleoside metabolism was determined through whole-genome analysis. Metabolic shifts in L. plantarum under nucleoside-enriched conditions were assessed using HPLC and metabolomics, while underlying mechanisms were explored through gene knockout experiments. Finally, the efficacy of L. plantarum was validated in hyperuricemia models involving goslings and mice. The authors presented their findings coherently and logically, addressing key questions using appropriate methodologies and yielding significant and innovative results. The authors demonstrated that host-derived Lactobacillus plantarum alleviates host hyperuricemia by influencing purine metabolism. However, their study primarily focused on this bacterium without delving deeper into the mechanisms underlying hyperuricemia beyond verification through two models. Nevertheless, these findings are sufficient to support their conclusion effectively. Additionally, further research is warranted to investigate the metabolites of Lactobacillus plantarum.

Reviewer #1 (Public review):

Theoretical principles of viscous fluid mechanics are used here to assess likely mechanisms of transport in the ER. A set of candidate mechanisms are evaluated, making good use of imaging to represent ER network geometries. Evidence is provided that contraction of peripheral sheets provides a much more credible mechanism than contraction of individual tubules, junctions or perinuclear sheets.

The work has been conducted carefully and comprehensively, making good use of underlying physical principles. There is good discussion of the role of slip; sensible approximations (low volume fraction, small particle size, slender geometries, pragmatic treatment of boundary conditions) allow tractable and transparent calculations; clear physical arguments, including an analysis of energy budgets, provide useful bounds; stochastic and deterministic features of the problem are well integrated.

Reviewer #1 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

(1) The overall writing is very difficult to follow and the authors need to work on significant re-writing<br /> (2) The paper in its current form really lacks detail and it is not possible for readers to repeat or follow their methods. For example: a) It is not clear whether the authors checked the serum to see if the mice were producing antibodies before they sacrificed them to harvest spleen/blood i.e. using ELISA? b) How long after administration of the second dose were the mice sacrificed? c) What cell types are taken for single B cell sorting? Splenocytes or PBMC? These are just some of the questions which need to be addressed.<br /> (3) According to the authors, 77 clones were sorted from the PR8+ and H2+ double positive quadrant. It is surprising that after transfection and re-analysing of bulk antibody presenting EXPI cells on FACS from, only 13 clones (or 8 clones? - unclear) seemed to be truly cross reactive. If that is the case, the approach is not as efficient as the authors claimed.

The authors have adequately addressed the issues raised

Reviewer #1 (Public review):

Summary:

This work sought to demonstrate that gut microbiota dysbiosis may promote the colonization of mycobacteria, and they tried to prove that Nos2 down-regulation was a key mediator of such gut-lung pathogenesis transition.

Strengths:

They did large-scale analysis of RNAs in lungs to analyze the gene expression of mice upon gut dysbiosis in MS-infected mice. This might help provide overview of gene pathways and critical genes for lung pathology in gut dysbiosis. This data is somewhat useful and important for the TB field.

Weaknesses:

(1) They did not use wide-type Mtb strain (e.g. H37Rv) to develop mouse TB infection models, and this may lead to the failure for establishment of TB granuloma and other TB pathology icons.<br /> (2) The usage of in vitro assays based on A542 to examine the regulation function of Nos2 expression on NO and ROS may not be enough. A542 is not the primary Mtb infection target in the lungs.<br /> (3) They did not examine the lung pathology upon gut dysbiosis to examine the true significance of increased colonization of Mtb.<br /> (4) Most of the studies are based on MS-infected mouse models with lack of clinical significance.

Reviewer #2 (Public Review):

Olszyński et al. claim that they identified a "new-type" ultrasonic vocalization around 44 kHz that occurs in response to prolonged fear conditioning (using foot-shocks of relatively high intensity, i.e. 1 mA) in rats. Typically, negative 22-kHz calls and positive 50-kHz calls are distinguished in rats, commonly by using a frequency threshold of 30 or 32 kHz. Olszyński et al. now observed so-called "44-kHz" calls in a substantial number of subjects exposed to 10 tone-shock pairings, yet call emission rate was low (according to Fig. 1G around 15%, according to the result text around 7.5%). They also performed playback experiments and concluded that "the responses to 44-kHz aversive calls presented from the speaker were either similar to 22-kHz vocalizations or in-between responses to 22-kHz and 50-kHz playbacks".

Strengths: Detailed spectrographic analysis of a substantial data set of ultrasonic vocalizations recorded during prolonged fear conditioning, combined with playback experiments.

Reviewer #1 (Public review):

Devakinandan et al. present a revised version of their manuscript. Their scRNA-seq data is a valuable resource to the community, and they further validate their findings via in situ hybridizations and electron microscopy. Overall, they have addressed my major concerns. I only have two minor comments.

(1) The authors note in Figure 4I, and K that because the number of C2 V2Rs or H2-Mv receptors increased while the normalized expression of Gnao1 remained constant (and likewise for V1Rs and Gnai2 in Figure 4-S4C) that their results are unlikely to be capturing doublets. I'm not sure that this is the case. If the authors added together two V2R cells the total count of every gene might double, but the normalized expression of Gnao1 would remain the same. To address this concern, the authors should also show the raw counts for Gnao1 as well as the total number of UMIs for these cells.

(2) As requested, the authors have now added a colorbar to the pseudocolored images in Figures 7. However, this colorbar still doesn't have any units. Can the authors add some units, or clarify in the methods how the raw data relates to the colors (e.g. is it mapped linearly, at a logscale, with gamma or other adjustments, etc.)? Moreover, it's also unclear what the dots in the backgrounds of plots like Figure 7E mean. Are they pixels? Showing the individual lines, the average for each animal, or omitting them entirely, might make more sense.

Reviewer #1 (Public review):

Summary:

In this study, Liu, Jiang, Diao et.al. investigated the role of GSDMD in psoriasis-like skin inflammation in mice. The authors have used full-body GSDMD knock-out mice and Gsdm floxed mice crossed with the S100A8- Cre. In both mice, the deficiency of GSDMD ameliorated the skin phenotype induced by the imiquimod. The authors also analyzed RNA sequencing data from the psoriatic patients to show an elevated expression of GSDMD in the psoriatic skin.

Overall, this is a potentially interesting study, however, the manuscript in its current format is not completely a novel study.

Strengths:

It has the potential to unravel the new role of neutrophils.

Weaknesses:

The main claims are only partially supported and have scope to improve

Disease: Von-willebrand Disorder, type 1

Patient 1 Variant: VWF NM_000552.5: c.4135C>T p.(Arg1379Cys) Exon 28

Family: History not mentioned

Patient 1 phenotype: near normal VWF:Ag and WVF:RCo levels RIPA within normal range Platelet VWF levels were normal normal pattern for multimeric analysis of plasma Slightly reduced VWF levels

In silico predictions available:

I-Mutant 3.0 value = -1.36 PYMOL prediction = substitution of ARG 1379 with a cysteine results in the loss of hydrogen bonds with Lys1407 and Lys1408, predicted change in secondary structure of A1 domain

Joint Public Reviews:

De Waele et al. framed the mass-spectrum-based prediction of antimicrobial resistance (AMR) prediction as a drug recommendation task. Neural networks were trained on the recently available DRIAMS database of MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry data and their associated antibiotic susceptibility profiles (Weis et al. 2022). Weis et al. (2022) also introduced the benchmark models which take as the input a single species and are trained to predict resistance to a single drug. Instead here, a pair of drugs and spectrum are fed to two neural network models to predict a resistance probability. In this manner, knowledge from different drugs and species can be shared through the model parameters. Questions asked: What is the best way to encode the drugs? Does the dual neural network outperform the single spectrum-drug network?

The authors showed consistent performance of their strategy to predict antibiotic susceptibility for different spectrum and antibiotic representations (i.e., embedders). Remarkably, the authors showed how small datasets collected at one location can improve the performance of a model trained with limited data collected at a second location. The authors also showed that species-specific models (trained in multiple antibiotic resistance profiles) outperformed both the single recommender model and the individual species-antibiotic combination models.

Strengths:

• A single antimicrobial resistance recommender system could potentially facilitate the adoption of MALDI-TOF based antibiotic susceptibility profiling into clinical practices by reducing the number of models to be considered, and the efforts that may be required to periodically update them.<br /> • The authors tested multiple combinations of embedders for the mass spectra and antibiotics while using different metrics to evaluate the performance of the resulting models. Models trained using different spectrum embedder-antibiotic embedder combinations had remarkably good performance for all tested metrics. The average ROC AUC scores for global and species-specific evaluations were above 0.8.<br /> • Authors developed species-specific recommenders as an intermediate layer between the single recommender system and single species-antibiotic models. This intermediate approach achieved maximum performance (with one type of the species-specific recommender achieving a 0.9 ROC AUC), outlining the potential of this type of recommenders for frequent pathogens.<br /> • Authors showed that data collected in one location can be leveraged to improve the performance of models generated using a smaller number of samples collected at a different location. This result may encourage researchers to optimize data integration to reduce the burden of data generation for institutions interested in testing this method.

Weaknesses:

• Authors do not offer information about the model features associated with resistance. While reviewers understand that it is difficult to map mass spectra to specific pathways or metabolites, mechanistic insights are much more important in the context of AMR than in the context of bacterial identification. For example, this information may offer additional antimicrobial targets. Thus, authors should at least identify mass spectra peaks highly associated with resistance profiles. Are those peaks consistent across species? This would be a key step towards a proteomic survey of mechanisms of AMR. See previous work on this topic (Hrabak et al. 2013, Torres-Sangiao et al. 2022).

References:

Hrabak et al. (2013). Clin Microbiol Rev 26. doi: 10.1128/CMR.00058-12.<br /> Torres-Sangiao et al. (2022). Front Med 9. doi: 10.3389/fmed.2022.850374.<br /> Weis et al. (2022). Nat Med 28. doi: 10.1038/s41591-021-01619-9.

Reviewer #2 (Public review):

Most neurodegenerative diseases are characterized by the self-templated misfolding of a particular protein in a manner that enables progressive spread throughout the central nervous system. In diseases including Parkinson's disease (PD) and multiple system atrophy (MSA), the protein a-synuclein misfolds into unique strains, which use this self-replicating mechanism to encode disease-specific information. Previous research suggests that a major contributor to the lack of successful clinical trials across neurodegenerative diseases is the lack of disease-relevant strains used in preclinical testing. While MSA patient samples are known to replicate efficiently in cell and mouse models of disease, Lewy body disease (LBD) patient samples do not. To overcome this obstacle, the seeding amplification assay (SAA) uses recombinant a-synuclein to amplify the misfolded protein structure present in a human patient sample. The resulting fibrils are then widely used by many laboratories as a model of PD. In this manuscript, Lee et al., set out to compare the strain properties of a-synuclein fibrils isolated from LBD and MSA patient samples with the resulting amplified fibrils following SAA. Using orthogonal biochemical and structural approaches to strengthen their analyses, the authors report that the SAA-amplified fibrils do not recapitulate the disease-relevant strains present in the patient samples. Moreover, their data suggest that regardless of which strain is used to seed the SAA reaction, the same strain is generated. These results clearly demonstrate that the SAA-amplified material is likely not disease-relevant. SAA fibrils are broadly used throughout academic and pharmaceutical laboratories. They are used in ongoing drug discovery efforts and recombinant fibrils broadly inform much of what is known about a-synuclein strain biology in LBD patients. The implications of the reported work are, therefore, expansive. These findings add to the growing ledger of reasons that the use of SAA fibrils in research should be halted until improved methods for amplification with high fidelity are developed.

Reviewer #1 (Public review):

Summary:

Assessment of cardiac LEC transcriptomes post-MI may yield new targets to improve lymphatic function. scRNAseq is a valid approach as cardiac LECs are rare compared to blood vessel endothelial cells.

Strengths:

Extensive bioinformatics approaches employed by the group

Weaknesses:

Too few cells included in scRNAseq data set and the spatial transcriptomics data that was exploited has little relevance, or rather specificity, for cardiac lymphatics. This study seems more a collection of preliminary transcriptomic data than a true scientific report to help advance the field.

Reviewer #1 (Public Review):

Tsai and Seymen et al. investigate associations between RTE expression and methylation and age and inflammation, using multiple public datasets. The text of the manuscript has been polished and the phrasing of several findings has been made clearer and more precise. The authors also provided ample discussion to the prior reviewer comments in their rebuttal, including new analyses.

Reviewer #2 (Public Review):

Summary:

The authors aimed to identify which regions of DVL2 contribute to its endogenous/basal clustering, as well as the relevance of such domains to condensate/phase separation and WNT activation.

Strengths:

A strength of the study is the focus on endogenous DVL2 to set up the research questions, as well as the incorporation of various techniques to tackle it. I found also quite interesting that DVL2-CFR addition to DVL1 increased its MW in density gradients.

Weaknesses:

The authors have addressed important drawbacks regarding the overexpression experiments, most notably by including DVL tKO cells in collaboration with Vita. I think that this part has clearly improved.

Unfortunately, I still stand with my key concern: at this stage in the field, with many papers on DVL over expression, there is a clear need to address how endogenous DVL behaves. While the attempts to o/e low levels of DVL mutants in tKO cells are useful for validation experiments, the manuscript does not -in my opinion - address the requirements of DVL2 condensation for WNT signalling. Of note, several of the described effects are partial, including in tKO cells, often indicating that the targeted domains contribute, but are not required, for these processes. I understand that generating endogenous tagged lines or targeting specific endogenous domains is not trivial. But, as indicated in both initial reviews, I think that monitoring endogenous proteins is required to fully address the proposed research question.

In my opinion, the current manuscript A) shows that endogenous DVL2 forms large complexes in a higher proportion as DVL1/3, B) identifies and describes a couple of motifs that contribute to clustering and signalling in overexpressed DVL, including in tKO cells* C) shows that one of those motifs (CFR) rewires o/e DVL1 into behaving similarly as DVL2.

*On a minor note, I am not sure how DVL tKO cells partially react to Wnt3a in Figure 7G

Reviewer #1 (Public review):

Summary:

In the manuscript the authors describe a new pipeline to measure changes in vasculature diameter upon opt-genetic stimulation of neurons.<br /> The work is useful to better understand the hemodynamic response on a network /graph level.

Strengths:

The manuscript provides a pipeline that allows to detect changes in the vessel diameter as well as simultaneously allows to locate the neurons driven by stimulation.<br /> The resulting data could provide interesting insights into the graph level mechanisms of regulating activity dependent blood flow.

Weaknesses:

(1) The manuscript contains (new) wrong statements and (still) wrong mathematical formulas.<br /> (2) The manuscript does not compare results to existing pipelines for vasculature segmentation (opensource or commercial).<br /> Comparing performance of the pipeline to a random forest classifier (illastik) on images that are not preprocessed (i.e. corrected for background etc.) seems not a particularly useful comparison.<br /> (3) The manuscript does not clearly visualize performance of the segmentation pipeline (e.g. via 2d sections, highlighting also errors etc.). Thus, it is unclear how good the pipeline is, under what conditions it fails or what kind of errors to expect.<br /> (4) The pipline is not fully open-source due to use of matlab. Also, the pipeline code was not made available during review contrary to the authors claims (the provided link did not lead to a repository). Thus, the utility of the pipeline was difficult to judge.

Detailed remarks to the revision and new manuscript:

- Generalizability: The authors addressed the point of generalizability by applying the pipeline to other data sets. This demonstrates that their pipeline can be applied to other data sets and makes it more useful.<br /> However, from the visualizations it's unclear to see the performance of the pipeline, where the pipelines fails etc. The 3d visualizations are not particularly helpful in this respect .<br /> In addition, the dice measure seems quite low, indicating roughly 20-40% of voxels do not overlap between inferred and ground truth. I did not notice this high discrepancy earlier. A through discussion of the errors appearing in the segmentation pipeline would be necessary in my view to better asses the quality of the pipeline.

Reviewer #1 (Public review):

Summary:

This is a detailed description of the role of PKCδ in Drosophila learning and memory. The work is based on a previous study (Placais et al. 2017) that has already shown that for the establishment of long-term memory, the repetitive activity of MP1 dopaminergic neurons via the dopamine receptor DAMB is essential to increase mitochondrial energy flux in the mushroom body. In this paper, the role of PKCδ is now introduced. PKCδ is a molecular link between the dopaminergic system and the mitochondrial pyruvate metabolism of mushroom body Kenyon cells. For this purpose, the authors establish a genetically encoded FRET-based fluorescent reporter of PKCδ-specific activity, δCKAR.

Strengths:

This is a thorough study on the long-term memory of Drosophila. The work is based on the extensive, high-quality experience of the senior authors. This is particularly evident in the convincing use of behavioral assays and imaging techniques to differentiate and explore various memory phases in Drosophila. The study also establishes a new reporter to measure the activity of PKCδ - the focus of this study - in behaving animals. The authors also elucidate how recurrent spaced training sessions initiate a molecular gating mechanism, linking a dopaminergic punishment signal with the regulation of mitochondrial pyruvate metabolism. This advancement will enable a more precise molecular distinction of various memory phases and a deeper comprehension of their formation in the future.

Weaknesses:

The study offers novel insights into the molecular mechanisms underlying long-term memory formation and presents no apparent weaknesses in either content or methodology.

Reviewer #1 (Public review):

Summary:

The authors use the teleost medaka as an animal model to study the effect of seasonal changes in day-length on feeding behaviour and oocyte production. They report a careful analysis of how day-length affects female medakas and a thorough molecular genetic analysis of genes potentially involved in this process. They show a detailed analysis of two genes and include a mutant analysis of one gene to support their conclusions

Strengths:

The authors pick their animal model well and exploit the possibilities to examine in this laboratory model the effect of a key environmental influence, namely the seasonal changes of day-length. The phenotypic changes are carefully analysed and well-controlled. The mutational analysis of the agrp1 by a ko-mutant provides important evidence to support the conclusions. Thus this report exceeds previous findings on the function of agrp1 and npyb as regulators of food-intake and shows how in medaka these genes are involved in regulating the organismal response to an environmental change. It thus furthers our understanding of how animals react to key exogenous stimuli for adaptation.

Weaknesses:

The authors are too modest when it comes to underscoring the importance of their findings. Previous animal models used to study the effect of these neuropeptides on feeding behaviour have either lost or were most likely never sensitive to seasonal changes of day length. Considering the key importance of this parameter on many aspects of plant and animal life it could be better emphasised that a suitable animal model is at hand that permits this.<br /> The molecular characterization of the agrp1 ko-mutant that the authors have generated lacks some details that would help to appreciate the validity of the mutant phenotype. Additional data would help in this respect.

Reviewer #1 (Public review):

Summary:

In this manuscript, Shibata describes a method to assess rapidly fluctuating CpG sites (fCpGs) from single-cell methylation sequencing (sc-MeSeq) data. Assuming that fCpGs are largely consistent over time with changes induced by inheritable events during replication, the author infers lineage relationships in available brain-derived sc-MeSeq. Supplementing current lineage tracing through genomic and mitochondrial mosaic variants is an interesting concept that could supplement current work or allow additional lineage analysis in existing data.

However, the author failed to convincingly show the power of fCpG analysis to determine lineages in the human brain. While the correlation with cellular division and distinction of cell types appears plausible and strong, the application to detect specific lineages is less convincing. Aspects of this might be due to a lack of clarity in presentation and erroneous use of developmental concepts. However, without addressing these problems it is challenging for a reader to come to the same conclusions as the author.

On the flip side, this novel application of fCpGs will allow the re-use of existing sc-MeSeq to infer additional features that were previously unavailable, once the biological relevance has been further elucidated.

Strengths:

(1) Novel re-analysis application of methylation data to infer the status of fCpGs and the use as a lineage marker.

(2) Application of this method to an innovative existing data set to benchmark this framework against existing developmental knowledge.

Weaknesses:

(1) Insufficient clarity when presenting results (this includes an incredible shortness of the methods section making an informed assessment very difficult). This makes it hard to fully grasp and evaluate the presented results.

(2) Inconsistent or erroneous use of neurodevelopmental concepts which hinders appropriate interpretation of the results.

(3) Lack of consideration for alternative explanations for the observed data (i.e., considering fCpGs as a cellular division clock that diverges over 'time').

Reviewer #1 (Public review):

Summary:

This theoretical paper addresses how to optimize reward-rate-maximizing decisions in certain foraging-style environments. It presents a series of equations and graphical illustrations for quantities such as reward rates and time-related costs that a decision maker could estimate as a basis for such decisions. One of the main takeaways is that if the hypothetical agent underweights the time spent outside a focal reward pursuit relative to the time spent within it, this can predict a broadly realistic pattern of impatience in two alternative intertemporal choices paired with well-calibrated take-it-or-leave-it decisions. Another takeaway is that if the optimally estimated subjective value of a reward pursuit is plotted as a function of a range of temporal durations, the result resembles a hyperbolic discounting function and is affected in empirically realistic ways by the magnitude and sign of the reward. Thus, the rate-maximization framework might lead to a hypothesis about the basis for the magnitude and sign effects in discounting.

Strengths:

The paper makes a useful contribution by broadening the application of reward-rate maximization to time-related decision scenarios. The paper's breadth of scope includes applying the same framework to accept/reject decisions and multi-alternative discounting decisions. The figures take a creative approach to illustrating the internal quantities in the model. It's particularly useful that the paper gives consideration to internal distortions that could give rise to documented anomalies in decision behavior.

Weaknesses:

(1) Although there are many citations acknowledging relevant previous work, there often isn't a very granular attribution of individual previous findings to their sources. In the results section, it's sometimes ambiguous when the paper is recapping established background and when it is breaking new ground. For example, around equation 8 in the results (sv = r - rho*t), it would be good to refer to previous places where versions of this equation have been presented. Offhand, McNamara 1982 (Theoretical Population Biology) is one early instance and Fawcett et al. 2012 (Behavioural Processes) is a later one. Line 922 of the discussion seems to imply this formulation is novel here.

(2) The choice environments that are considered in detail in the paper are very simple. The simplicity facilitates concrete examples and visualizations, but it would be worth further consideration of whether and how the conclusions generalize to more complex environments. The paper considers "forgo" scenario in which the agent can choose between sequences of pursuits like A-B-A-B (engaging with option B at all opportunities, which are interleaved with a default pursuit A) and A-A-A-A (forgoing option B). It considers "choice" scenarios where the agent can choose between sequences like A-B-A-B and A-C-A-C (where B and C are larger-later and smaller-sooner rewards, either of which can be interleaved with the default pursuit). Several forms of additional complexity would be valuable to consider. One would be a greater number of unique pursuits, not repeated identically in a predictable sequence, akin to a prey-selection paradigm. It seems to me this would cause t_out and r_out (the time and reward outside of the focal prospect) to be policy-dependent, making the 'apportionment cost' more challenging to ascertain. Another relevant form of complexity would be if there were variance or uncertainty in reward magnitudes or temporal durations or if the agent had the ability to discontinue a pursuit such as in patch-departure scenarios.

(3) I had a hard time arriving at a solid conceptual understanding of the 'apportionment cost' around Figure 5. I understand the arithmetic, but it would help if it were possible to formulate a more succinct verbal description of what makes the apportionment cost a useful and meaningful quality to focus on. I think Figure 6C relates to this, but I had difficulty relating the axis labels to the points, lines, and patterned regions in the plot. I also was a bit confused by how the mathematical formulation was presented. As I understood it, the apportionment cost essentially involves scaling the rest of the SV expression by t_out/(t_in + t_out). The way this scaling factor is written in Figure 5C, as 1/(1 + (1/t_out)t_in), seems less clear than it could be. Also, the apportionment cost is described in the text as being subtracted from SV rather than as a multiplicative scaling factor. It could be written as a subtraction, by subtracting a second copy of the rest of the SV expression scaled by t_in/(t_in + t_out). But that shows the apportionment cost to depend on the opportunity cost, which is odd because the original motivation on line 404 was to resolve the lack of independence between terms in the SV expression.

(4) In the analysis of discounting functions (line 664 and beyond), the paper doesn't say much about the fact that many discounting studies take specific measures to distinguish true time preferences from opportunity costs and reward-rate maximization. In many of the human studies, delay time doesn't preclude other activities. In animal studies, rate maximization can serve as a baseline against which to measure additional effects of temporal discounting. This is an important caveat to claims about discounting anomalies being rational under rate maximization (e.g., line 1024).

(5) The paper doesn't feature any very concrete engagement with empirical data sets. This is ok for a theoretical paper, but some of the characterizations of empirical results that the model aims to match seem oversimplified. An example is the contention that real decision-makers are optimal in accept/reject decisions (line 816 and elsewhere). This isn't always true; sometimes there is evidence of overharvesting, for example.

(6) Related to the point above, it would be helpful to discuss more concretely how some of this paper's theoretical proposals could be empirically evaluated in the future. Regarding the magnitude and sign effects of discounting, there is not a very thorough overview of the several other explanations that have been proposed in the literature. It would be helpful to engage more deeply with previous proposals and consider how the present hypothesis might make unique predictions and could be evaluated against them. A similar point applies to the 'malapportionment hypothesis' although in this case there is a very helpful section on comparisons to prior models (line 1163). The idea being proposed here seems to have a lot in common conceptually with Blanchard et al. 2013, so it would be worth saying more about how data could be used to test or reconcile these proposals.

Reviewer #1 (Public review):

Summary:

This manuscript by Shan, Guo, Zhang, Chen et al., shows a raft of interesting data including the first cryo-EM structures of human PIEZO1. Clearly, the molecular basis of PIEZO channel inactivation is of great interest and as such this manuscript provides some valuable extra information that may help to ultimately build a molecular picture of PIEZO channel inactivation. However, the current manuscript though does not provide any compelling evidence for a detailed mechanism of PIEZO inactivation.

Strengths:

This manuscript documents the first cryo-EM structures of human PIEZO1 and the gain of function mutants associated with hereditary anaemia. It is also the first evidence showing that PIEZO1 gain of function mutants are also regulated by the auxiliary subunit MDFIC.

Weaknesses:

While the structures are interesting and clear differences can be seen in the presence of the auxiliary subunit MDFIC the major conclusions and central tenets of the paper, especially a role for pore lipids in inactivation, lack data to support them. The post-translational modification of PIEZOs auxiliary subunit MDFIC is not modelled as a covalent interaction.

Reviewer #1 (Public review):

Summary:

The concept that trained immunity, as defined, can be beneficial to subsequent immune challenges is important in the broad context of health and disease. The significance of this manuscript is the finding that trained immunity is actually a two-edged sword, herein, detrimental in the context of LPS-induced Acute Lung Injury that is mediated by AMs.

Strengths:

Several lines of evidence in different mouse models support this conclusion. The postulation that differences in immune responses in individuals are linked to differences in the mycobiome and consequent B-glucan makeup is provocative.

Weaknesses:

The findings that the authors state are relevant to sepsis, are actually confined to a specific lung injury model and not classically-defined sepsis. In addition, the ontogeny of the reprogrammed AMs is uncertain. Links in the proposed signaling pathways need to be strengthened.

Reviewer #1 (Public Review):

Summary:

This study investigates the hypoxia rescue mechanisms of neurons by non-neuronal cells in the brain from the perspective of exosomal communication between brain cells. Through multi-omics combined analysis, the authors revealed this phenomenon and logically validated this intercellular rescue mechanism under hypoxic conditions through experiments. The study proposed a novel finding that hemoglobin maintains mitochondrial function, expanding the conventional understanding of hemoglobin. This research is highly innovative, providing new insights for the treatment of hypoxic encephalopathy.

Overall, the manuscript is well organized and written, however, there are some minor/major points that need to be revised before this manuscript is accepted.

Major points:

(1) Hypoxia can induce endothelial cells to release exosomes carrying hemoglobin, however, how neurons are able to actively take up these exosomes? It is possible for other cells to take up these exosomes also? This point needs to be clarified in this study.

(2) The expression of hemoglobin in neurons is important for mitochondrial homeostasis, but its relationship with mitochondrial homeostasis needs to be further elucidated in the study.

Reviewer #1 (Public review):

The authors examine how probabilistic reversal learning is affected by dopamine by studying the effects of methamphetamine (MA) administration. Based on prior evidence that the effects of pharmacological manipulation depend on baseline neurotransmitter levels, they hypothesized that MA would improve learning in people with low baseline performance. They found this effect, and specifically found that MA administration improved learning in noisy blocks, by reducing learning from misleading performance, in participants with lower baseline performance. The authors then fit participants' behavior to a computational learning model and found that an eta parameter, responsible for scaling learning rate based on previously surprising outcomes, differed in participants with low baseline performance on and off MA.

Questions:

(1) It would be helpful to confirm that the observed effect of MA on the eta parameter is responsible for better performance in low baseline performers. If performance on the task is simulated for parameters estimated for high and low baseline performers on and off MA, does the simulated behavior capture the main behavioral differences shown in Figure 3?

(2) In Figure 4C, it appears that the main parameter difference between low and high baseline performance is inverse temperature, not eta. If MA is effective in people with lower baseline DA, why is the effect of MA on eta and not IT?

Also, this parameter is noted as temperature but appears to be inverse temperature as higher values are related to better performance. The exact model for the choice function is not described in the methods.

Reviewer #1 (Public review):

Summary:

The current work explored the link between the pulvinar intrinsic organisation and its functional and structural connectivity patterns of the cortex using different dimensional reduction techniques. Overall they find relationships between pulvinar-cortical organization and cortico-cortical organization, and little evidence for clustered organization. Moreover, they investigate PET maps to understand how neurotransmitter/receptor distributions vary within the pulvinar and along its structural and functional connectivity axes.

Strengths:

There is a replication dataset and different modalities are compared against each other to understand the structural and functional organisation of the pulvinar complex.

Weaknesses:

(1) What is the motivation of the study and how does this work extend previous assessments of the organization of the complete thalamus within the gradient framework?

(2) Why is the current atlas chosen for the delineation of the pulvinar and individualised maps not considered? Given the size of the pulvinar, more validation of the correctness of the atlas may be helpful.

(3) Overall the study feels a little incremental and a repetition of what others have done already in the thalamus. It would be good to know how focussing only on the pulvinar changes interpretation, for example by comparing thalamic and pulvinar gradients?

(4) Could it be that the gradient patterns stem from lacking anatomical and functional resolutions (or low SNR) therefore generating no sharp boundaries?

Reviewer #1 (Public review):

Summary:

The overall analysis and discovery of the common motif is important and exciting. Very few human/primate ribozymes have been published and this manuscript presents a detailed analysis of two of them. The minimized domains appear to be some of the smallest known self-cleaving ribozymes.

Strengths:

The manuscript is rooted in deep mutational analysis of the human OR4K15 and LINE1 ribozymes and subsequently in modeling of their active site based on the closely-related core of the TS ribozyme. The experiments support the HTS findings and provide convincing evidence that the ribozymes are structurally related to the core of the TS ribozyme, which has not been found in primates prior to this work.

Reviewer #1 (Public review):

Summary:

The aim of the present work is to evaluate the role of BMP9 and BMP10 in liver by depleting Bmp9 and Bmp10 from the main liver cell types (endothelial cells (EC), hepatic stellate cells (HSC), Kupffer cells (KC) and hepatocytes (H)) using cell-specific cre recombinases. They show that HSCs are the main source of BMP9 and BMP10 in the liver. Using transgenic ALK1 reporter mice, they show that ALK1, the high affinity type 1 receptor for BMP9 and BMP10, is expressed on KC and EC. They have also performed bulk RNAseq analyses on whole liver, and cell-sorted EC and KC, and showed that loss of Bmp9 and Bmp10 decreased KC signature and that KC are replaced by monocyte-derived macrophages. EC derived from these Bmp9fl/flBmp10fl/flLratCre mice also lost their identity and transdifferentiated into continuous ECs. Liver iron metabolism and metabolic zonation were also affected in these mice. In conclusion, this work supports that BMP9 and BMP10 produced by HSC play a central role in mediating liver cell-cell crosstalk and liver homeostasis.

Strengths:

This work further supports the role of BMP9 and BMP10 in liver homeostasis. Using a specific HSC-Cre recombinase, the authors show for the first time that it is the BMP9 and BMP10 produced by HSC that play a central role in mediating liver cell-cell crosstalk to maintain a healthy liver. Although the overall message of the key role of BMP9 in liver homeostasis has been described by several groups, the role of hepatic BMP10 has not been studied before. Thus, one of the novelties of this work is to have used liver cell specific Cre recombinase to delete hepatic Bmp9 and Bmp10. The second novelty is the demonstration of the role of BMP9 and BMP10 in KC Differentiation/homeostasis which has already been slightly addressed by this group by knocking out ALK1, the high affinity receptor of BMP9 and BMP10 (Zhao et al. JCI, 2022).

Weaknesses:

This work remains rather descriptive and the molecular mechanisms are barely touched upon and could have been more explored.

Reviewer #1 (Public review):

The study by Korona and colleagues presents a rigorous experimental strategy for generating and maintaining a nearly complete set of monosomic yeast lines, thereby establishing a new standard for studying monosomes. Their careful approach in generating and handling monosome yeast lines, coupled with their use of high-throughput DNA sequencing and RNA sequencing, addresses concerns related to genomic instability and is commendable. However, I would like to express my concerns regarding the second part of the study, particularly the calculation of epistasis and the conclusion that vast positive epistatic effects have been observed. I believe that the conclusion of positive epistasis for fitness might be premature due to potential errors in estimating the expected fitness.

The method used to calculate fitness expectation (1 + sum(di), where di = rDRi - 1) may be inappropriate. The logarithm transformation mentioned by the authors is designed to transform the exponential growth curve into a linear relation for estimating doubling rate, and thus the fitness expectation should be calculated as the product of rDRi values. As an illustration, if gene A exhibits a 20% reduction in fitness when halved (A/-) and gene B exhibits a 30% reduction (B/-), the expected fitness of A/- B/- should be 56%, rather than the 50% estimated in the study. In other words, the formula used by the authors could underestimate the fitness expectation.

This issue is evident in Figure 2b, where negative values were obtained due to the use of an incorrect formula for estimating fitness expectations. It is worth noting that Figure 2a shows rDR values around one, indicating that no further logarithmic transformation was applied.

While widespread positive epistasis in yeast has been reported by other studies (e.g., doi: 10.1038/ng.524, but not to the extent reported in this study), the conclusion of the current study might not be sufficiently supported. I recommend that the authors revisit their calculation methods to provide a more convincing conclusion on the presence of positive epistasis for fitness in their dataset. Overall, I appreciate the authors' efforts in this study but believe that addressing these concerns is essential for strengthening the validity of their findings.

Comments on revised version:

The authors have adequately addressed all my previous concerns during revision.

Reviewer #2 (Public review):

Summary:

The authors set out to study whether the cooling agent binding site in TRPM8, which is located between the S1-S4 and the TRP domain, is conserved within the TRPM family of ion channels. They specifically chose the TRPM4 channel as the model system, which is directly activated by intracellular Ca2+. Using electrophysiology, the authors characterized and compared the Ca2+ sensitivity and the voltage-dependence of TRPM4 channels in the absence and presence of synthetic cooling agonist icilin. They also analyzed the mutational effects of residues (A867G and R901H; equivalent mutations in TRPM8 were shown involved in icilin sensitivity) on Ca2+ sensitivity and voltage-dependence of TRPM4 in the absence and presence of Ca2+. Based on the results as well as structure/sequence alignment, the authors concluded that icilin likely binds to the same pocket in TRPM4 and suggested that this cooling agonist binding pocket is conserved in TRPM channels.

Strengths:

The authors gave a very thorough introduction of the TRPM channels. They have nicely characterized the Ca2+ sensitivity and the voltage-dependence of TRPM4 channels and demonstrated icilin potentiates the Ca2+ sensitivity and diminishes the outward rectification of TRPM4. These results indicate icilin modulates TRPM4 activation by Ca2+.

The authors have incorporated additional data analysis and control experiments in the revised manuscript to strengthen their findings. They have well addressed the concerns raised by reviewers in the responses.

Weaknesses:

The study is conducted based on an assumption that TRPM4 activation is controlled by Ca2+ binding to a single site in the S1-S4 pocket in each subunit, and the second Ca2+ site in the cytoplasmic MHRs is simplified.

Despite the technical reasons presented by the authors in the rebuttal, the conclusion of this study can be strengthened if more cooling compounds- the most well-studied natural cooling agonist menthol, and/or other cooling agonists such as WS-12 and/or C3-are tested for their effects on TRPM4 and several other TRPM channels.

Reviewer #1 (Public review):

In this manuscript, Yang et al report a novel regulatory role of SIRT4 in the progression of kidney fibrosis. The authors showed that in the fibrotic kidney, SIRT4 exhibited an increased nuclear localization. Deletion of Sirt4 in renal tubule epithelium attenuated the extent of kidney fibrosis following injury, while overexpression of SIRT4 aggravates kidney fibrosis. Employing a battery of in vitro and in vivo experiments, the authors demonstrated that SIRT4 interacts with U2AF2 in the nucleus upon TGF-β1 stimulation or kidney injury and deacetylates U2AF2 at K413, resulting in elevated CCN2 expression through alternative splicing of Ccn2 gene to promote kidney fibrosis. The authors further showed that the translocation of SIRT4 is through the BAX/BAK pore complex and is dependent on the ERK1/2-mediated phosphorylation of SIRT4 at S36, and consequently the binding of SIRT4 to importin α1. This fundamental work substantially advances our understanding of the progression of kidney fibrosis and uncovers a novel SIRT4-U2AF2-CCN2 axis as a potential therapeutic target for kidney fibrosis.

Comment on revised version:

In the new version of the manuscript, the authors have addressed most of my concerns . Overall, the authors have done an extensive, well-performed study. The results are convincing, and the conclusions are mostly well supported by the data. The message is interesting to a wider community working on kidney fibrosis, protein acetylation and SIRT4 biology. This work substantially advances our understanding of the mechanism of kidney fibrosis and uncovers a novel SIRT4-U2AF2-CCN2 axis as a potential therapeutic target for kidney fibrosis.

Reviewer #1 (Public review):

Summary:

The authors want to determine the role of the sperm hook of the house mouse sperm in movement through the uterus. They use transgenic lines with fluorescent labels to sperm proteins, and they cross these males to C57BL/6 females in pathogen-free conditions. They use 2-photon microscopy on ex vivo uteri within 3 hours of mating and the appearance of a copulation plug. There are a total of 10 post-mating uteri that were imaged with 3 different males. They provide 10 supplementary movies that form that basis for some of the quantitative analysis in the main body figures. Their data suggest that the role of the sperm hook is to facilitate movement along the uterine wall.

Strengths:

Ex vivo live imaging of fluorescently labeled sperm with 2-photon microscopy is a powerful tool for studying the behavior of sperm.

Weaknesses:

The paper is descriptive and the data are correlations.

The authors cannot directly test their proposed function of the sperm hook in sliding and preventing backward slipping.

Reviewer #1 (Public Review):

Summary:

This is a well-written and detailed manuscript showing important results on the molecular profile of 4 different cohorts of female patients with lung cancer.

Strengths:

The authors used several different methods to identify potential novel targets for therapeutic interventions.

Weaknesses:

Statistical test results need to be provided in comparisons between cohorts. This was addressed by the authors in the revisions.

Reviewer #1 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

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

Comments on revised submission:

The authors have effectively addressed my concerns. This revision is excellent.

Reviewer #1 (Public Review):

Summary:

This manuscript provides a solid advance to the scavenger receptor field by reporting the crystal structures of the domains of SCARF1 that bind modified LDL such as oxidized LDL and acylated LDL. The crystal packing reveals a new interface for homodimerization of SCARF1. The authors characterize SCARF1 binding to modified LDL using flow cytometry, ELISA, and fluorescent microscopy. They identify a positively-charged surface on the structure that they predict will bind the LDLs, and they support this hypothesis with several mutant constructs in binding experiments.

Strengths:

The authors have crystallized domains of an understudied scavenger receptor and used the structure to identify a putative binding site for modified LDL particles. An especially strong set of experiments are binding studies with chimeras of SCARF1 and SCARF2, where they show gain-of-function results (binding of modified LDLs) by SCARF2, a related protein that does not normally bind modified LDLs. The paper is a straightforward set of experiments that identify the likely binding site of modified LDL on SCARF1

Weaknesses:

In the current revision, the authors addressed my technical concerns.<br /> Two remaining considerations that may limit the broader impact of this paper are 1) that it does not explain the structural basis for specificity of the binding of SCARF1 to various lipoproteins (i.e. why SCARF1 binds oxLDL and AcLDL but not LDL or HDL) and 2) a lack of a biological assay to interpret the functional consequences of the SCARF1 mutants. These may be addressed in future work.

Reviewer #1 (Public review):

The authors have tried to identify the plausible Na+ entry pathway in an important SLC6 member GAT1, using computational approaches to assess residence times of the ions as they enter the vestibule of GAT1. The authors identify a patch of negative residues in TM6a and implicate them for being important to attract the Na+ ions during their movement towards the binding sites Na1 and Na2. Besides this they also suggest that sodium binding at site 1 is flexible and at times can occupy the primary binding site when the substrate is not available. Na2 site as other literature also suggests is demonstrated to be vital for the stability of the outward-open state.

Studies of ion permeation are challenging given that the states are challenging to trap through structural studies and computational methods are vital for understanding these steps. The authors suggest that two negatively charged residues are vital to attract Na+ ions to the vestibule. Using a combination of simulations and PCA analysis the authors identify the importance of Na+ binding at site 2 that stabilises the outward-open state and the flexibility observed in Na1 site for ion binding which happens alongside substrate in the GABA bound state. The study reconfirms earlier observations in the SLC6 family that Na2 site is critical for conformational transitions and Na1 site is substrate dependent in amino acid transporters.<br /> One of the challenges in such studies is to conclusively establish the presence of additional Na+ sites or regions of ion-binding with experimental structures as they are nearly impossible to trap. Such studies using simulations therefore become the only resort to understand such phenomena.

The work is likely to further provide insights into the transport mechanism of GAT1 and lends credence to some structural studies where the sodium at site1 is displaced but the ion remains proximal to the bound substrate.