eLife assessment

This manuscript presents a valuable approach to exploring CD4+ T-cell response in mice across stimuli and tissues through the analysis of their T-cell receptor repertoires. The authors use a transgenic mouse model, in which the possible diversity of the T-cell receptor repertoire is reduced, such that each of a diverse set of immune exposures elicits more detectably consistent T-cell responses across different individuals. However, whereas the proposed experimental system could be utilized to study convergent T-cell responses, the analyses done in this manuscript are incomplete and do not support the claims due to limitations in the statistical analyses and lack of data/code access.

eLife assessment

This valuable study describes a new role of epithelial intercellular adhesion molecule 1 (ICAM-1) protein in controlling bile duct size. The effect is mediated via EBP-50 and subapical actomyosin to regulate size of bile canaliculi. These solid findings have theoretical and practical implications in hepatology and human disorders of bile ducts.

eLife assessment

This is a solid methods paper developing a machine learning based protocol differentiating normal and diseased myofibers. It emerges with and validates a potentially valuable approach to diifferentiate healthy and Duchenne muscle dystrophy myofibers.

eLife assessment

The studies are important to the field of hepatic steatosis and inflammation. The data provided are convincing that treatment with I3A mitigated Western diet (WD)-induced hepatic steatosis, inflammation and reversed WD-induced alterations in liver bile acids and free fatty acids in mice.

eLife assessment

This study provides a useful description of two evolutionary conserved motifs in CD4 that contribute to the CD4-mediated enhancement of T cell receptor (TCR) signaling, which are notably acting independently of the CD4-LCK interaction. The supporting evidence is solid and supported using a T cell hybridoma in vitro system, but remains incomplete without experiments with primary T cells or the use of in vivo models to assess the importance of the CD4 motifs in T-cell biology.

eLife assessment

This important work identifies a previously uncharacterized capacity for songbirds to recover vocal targets even without sensory experience. While the evidence supporting this claim is solid, with innovative experiments exploring vocal plasticity in deafened birds, additional behavioral controls and analyses are necessary to shore up the main claims. If improved, this work has the potential for broad relevance to the fields of vocal and motor learning.

eLife assessment

In this important study, the rabbit was used as a non-rodent mammalian model to show that DMRT1 has a testicular promoting function as it does in humans. The experiments are meticulous and compelling, and the arguments are clear and convincing. These results may explain the gonadal dysgenesis associated with mutations in human DMRT1 and highlight the need for mammalian models other than mice to better understand the process of gonadal sex determination in humans.

eLife assessment

This study presents Bactabolize, a valuable tool for the rapid genome-scale reconstruction of bacteria and the prediction of growth phenotypes. Using validated methodology, the tool relies on a reference pan-genome model to create strain-specific draft metabolic models, as demonstrated in this study using Klebsiella pneumoniae. While the evidence in this specific case is solid, validation across diverse bacterial species is yet to be confirmed.

eLife assessment

This is an important study showing how dendritic plateau potentials can enable neurons to perform reliable 'binary' computations in the face of realistic spike time jitter in cortical networks. The authors make a surprising and novel claim that dendritic plateau potentials perform equally well in short integration windows of only 10 ms and detail a biophysical mechanism for how this effect may occur. While the authors make many good arguments, and the general concept underlying the paper is sound, the evidence as of now is incomplete, with some unsupported statements that should be more thoroughly defended in the manuscript.

eLife assessment:

Chen and colleagues utilize an in situ explant model of the neural retina and retinal pigment epithelium (RPE), along with small molecule inhibition of key metabolic enzymes and targeted metabolomic analysis, to decipher key differences in metabolic pathways used by rods, cones, Muller glia, and the RPE. They conclude that rods are heavily reliant on oxidative metabolism, cones are heavily reliant on glycolysis, and multiple mechanisms exist to decouple glycolysis from oxidative metabolism in the retina. This study provides valuable metabolomic data and insights into the metabolic flexibility of different retinal cells. However, the evidence supporting the authors' claims is incomplete and would benefit from validating their evidence with animal models, comparing their data to previously published literature, performing C13 tracing experiments, and assessing mitochondrial function.

eLife assessment

This valuable study shows that distinct midbrain dopaminergic axons in the medial prefrontal cortex respond to aversive and rewarding stimuli and suggest that they are biased toward aversive processing. The use of innovative microprism based two-photon calcium imaging to study single axon heterogeneity is solid, although the experimental design could be optimized to distinguish aversive valence from stimulus salience and identity in this dopamine projection. This work will be of interest to neuroscientists working on neuromodulatory systems, cortical function and decision making.

eLife assessment

This work identifies cnidarian neuropeptides and pairs them to their GPCR, then shows that neuropeptide signaling systems have evolved and diversified independently in cnidarians and bilaterians. Neuropeptide-receptor partners were experimentally identified using established and widely used methodologies including single cell mapping, providing compelling evidence for the conclusions of the paper. This impressive accomplishment provides fundamental new insights into the evolution of neuropeptide signaling systems and will be of broad interest to neurobiologists and evolution of development researchers.

eLife assessment

The study by Chardon et al. is fundamental to advancing our understanding of presynaptic control of motor neuron output. Large-scale computer simulations were performed using well-established single motor neuron models to provide compelling evidence regarding the time-varying patterns of inputs that control motor neuron ensembles. The work will interest the community of motor control, motor unit physiology, neural engineering, and computational neuroscience.

eLife assessment

In this valuable study, Parrotta et al. showed that it is possible to modulate pain perception and heart rate by providing false heart rate (HR) acoustic feedback before administering electrical cutaneous shocks. The evidence supporting the claims of the authors is rather solid, although what they consider an interoceptive signal is not necessarily supported as such by the results. In this regard, including a larger number of trials per participant, increasing the sample size, and adding a measure of actual pain perception after its induction would have strengthened the study. Although mechanisms and some alternative explanations for this effect remain to be addressed, the work will nonetheless be of interest to neuroscientists working on predictions and perception, health psychologists, pain researchers, and placebo researchers.

eLife assessment

The study presents valuable insights into the regulation of astrocytes in the long-term potentiation of excitatory synapses onto inhibitory interneurons. However, reviewers identified concerns regarding originality and proper acknowledgment of replicated work, representation of interneuron diversity, and the robustness of certain conclusions. The strength of evidence provided is deemed incomplete, necessitating significant revisions for clarity, and accuracy, and to address highlighted concerns.

eLife assessment

This valuable study uses a combination of behavioral studies and computational modeling to argue that humans implicitly represent gravity as a Gaussian distribution (rather than as a deterministic vector). The experimental evidence is generally solid, with all experiments and model simulations being consistent with the proposed account. However, in the current version of the manuscript, the evidence for the main claim of the paper is incomplete: a number of alternative interpretations such as uncertainty about the presence of external lateral forces, or uncertainty about other object properties have not been considered sufficiently.

eLife assessment

The authors have updated a helpful resource for the neuroscience community regarding hippocampal cell types and their interactions, called the "hippocampome." The updates expand content, tools, and potential applications, and therefore the significance is important. The strong presentation makes the paper compelling.

eLife assessment

This valuable study analyzed a large cohort of Adolescent Idiopathic Scoliosis (AIS) patients and identified an association with a variant in COL11A1 (Pro1335Leu). Experimental testing of this potentially pathogenic variant suggests a link between Pax1, Col11a1, Mmp3, and estrogen signaling. While the connection between transcriptional regulation, the extracellular matrix, and estrogen signaling is compelling, the experimental evidence supporting this link is still incomplete and would benefit from a more direct and comprehensive approach. Strengthening the functional testing would help establish the pathogenicity of a collagen variant and the role of the proposed Pax1-Col11a1-Mmp3 signaling axis in AIS.

eLife assessment

This paper presents important new data related to the non-canonical SMC complex MukBEF in E. coli, which remains less well understood compared to more canonical SMC complexes in many other bacteria. The authors use a combination of Hi-C and ChIP-seq to demonstrate that MukBEF loads at multiple locations along the chromosome, preferentially in newly replicated DNA, with the MatP/matS system antagonizing MukBEF activity and localizing in terminus proximal regions. Most of the data to support these findings are compelling, with modest concerns raised about the effect sizes of the ChIP-seq data, which could be bolstered with some additional controls.

eLife assessment

This fundamental study provides compelling evidence to explain how chemical variations within a set of kinase inhibitors drive the selection of specific Erk2 conformations. Conformational selection plays a critical role in targeting medically relevant kinases such as Erk2 and the findings reported here open new avenues for designing small molecule inhibitors that block the active site while also steering the population of the enzyme into active or inactive conformations. Since protein dynamics and conformational ensembles are essential for enzyme function, this work will be of broad interest to those working in drug development, signal transduction, and enzymology.

eLife assessment

This is a valuable contribution to the electric fish community, and to studies of active sensing more generally, in that it provides evidence that a well-studied behavior (chirping) may serve in active sensing rather than communication. For the most part, the evidence is solid. In particular, the evidence showing increased chirping in more cluttered environments and the relationship between chirping and movement are convincing. Nevertheless, evidence to support the argument that chirps are mostly used for navigation rather than communication is incomplete.

eLife assessment

The authors investigate the mechanism of amyloid nucleation in a cellular system using novel ratiometric measurements, providing fundamental insight into the role of polyglutamine length and the sequence features of glutamine-rich regions in amyloid formation. The problem addressed by this study is very significant and the ability to assess nucleation in cells is of considerable value. The data, as presented and analyzed, are mostly convincing.

**Editors Assessment: **

While Bacterial Artificial Chromosomes libraries were once a key resource for building the human genome project over time they have been rendered relatively obsolete by long-read technologies. In the era of CRISPR-Cas systems pairing this data with one of the many guide-RNA libraries to find targets for manipulation with CRISPR tools is bringing back BACs advantages for genomics. With this in mind the authors have developed a BAC restriction map database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of available restriction enzymes. Alongside a set of Python functions to reconstruct the database and more easily access it (which were debugged and had improved documentation added during review). The presented data should be valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

*This evaluation refers to version 1 of the preprint *

**Editors Assessment: **

This work presents a new standardized graphical approach for visualizing genetic associations across a wide range of allele frequencies. These proposed TrumpetPlots have a distinctive trumpet shape, hence the proposed name. With the majority of variants having low frequency and small effects, while a small number of variants have higher frequency and larger effects, this view can help to provide new and valuable insights into the genetic basis of traits and diseases, and also help prioritize efforts to discover new risk variants. The tool is provided as a novel R package and R Shiny application and to demonstrate its use the article illustrates the distribution of variant effect sizes across the allele frequency range for over 100 continuous traits available in the UK Biobank. After some problems in testing the package is now available and easy to deploy via CRAN.

*This assessment refers to version 1 of this preprint. *

eLife assessment

This is an important biophysical study combining native mass spectrometry with mutant cycles to estimate the thermodynamic components of lipid A binding to the ABC transporter MsbA. Binding energies for lipid-protein interactions are proposed, but the evidence is currently incomplete as they rely on a number of technical and theoretical assumptions, mostly related to multiple lipid binding sites in the protein.

eLife assessment

The manuscript represents an important contribution to an ongoing discussion about the substrate binding site and mechanism of the Bile Acid Sodium Symporter (BASS) family of transporters. Structural and biochemical analysis of a bacterial homolog, ASTBnm, in complex with its native substrate (not bile acids, but a vitamin A precursor, pantoate) show a new binding site that is consistent with classical proposals for elevator-type transport mechanisms. Molecular dynamics (MD) simulations highlight the improved stability for the substrate in the active site when ions are present, suggesting a binding order during the transport cycle. The structural studies, binding assays, and MD simulations are convincing.

eLife assessment

This important study combines a range of advanced ultrastructural imaging approaches to define the unusual endosomal system of African trypanosomes. Compelling images show that instead of a distinct set of compartments, the endosome of these protists comprises a continuous system of membranes with functionally distinct subdomains as defined by canonical markers of early, late and recycling endosomes. The findings suggest that the endocytic system of bloodstream stages has evolved to facilitate the extraordinarily high rates of membrane turnover needed to remove immune complexes and survive in the blood, which is of interest to anyone studying infectious diseases.

eLife assessment

This important study addresses mechanisms of feedback inhibition between planar cell polarity (PCP) protein complexes during convergent extension movements in Xenopus embryos. The authors propose an interesting model, in which non-canonical Wnt ligand stimulates transition of Dishevelled from its complex with Vangl to Frizzled, with essential roles of Vangl, Prickle and Ror in this process. The main functional observations supporting this model are convincing, but the immunoprecipitation data are incomplete and would benefit from additional clarification. With more rigorous approaches, this work will likely be of broad interest to cell and developmental biologists.

eLife assessment

In this manuscript by Xiong L et al., through TLR2, the authors have uncovered an important link between innate immune signaling and hair regeneration. The authors provide convincing evidence supporting the critical roles of TLR2 in sensing CEP levels in hair follicles, counteracting the action of BMP signaling, and facilitating the activation of HFSCs during the hair cycle and wound repair. Importantly, the authors also propose that decreased CEP production and TLR2 expression might be factors contributing to the decreased hair regeneration associated with age-related and obesity-related hair thinning and hair loss phenotypes.

eLife assessment

This work presents a fundamental meta-analysis on the causes of glucocorticoid variations in birds and mammals. It provides convincing evidence that an increase in metabolic rates increases glucocorticoid concentrations. The work will be of broad interest to animal physiologists.

eLife assessment

The biogenesis of outer membrane proteins in Gram-negative bacteria is still not fully understood, particularly substrate recognition and insertion by beta-assembly machinery. This work reports important results identifying a new amino acid sequence motif (i.e., "internal beta-signal") on outer membrane proteins recognized by this machinery. The authors carried out rigorous biochemical approaches, providing convincing evidence to support their conclusions.

eLife assessment

This important study advances our understanding of early Cambrian cnidarian paleoecology and suggests that the reconstructed ancestral feeding and respiration mechanisms predate jet-propelled swimming utilized by modern jellyfish. The work combines solid evidence of fluid and structural mechanics modeling, simulating for the first time the feeding and respiratory capacities in a microfossil (Quadrapyrgites), which in turn opens new possibilities using this approach for paleontological research. Assuming that the prior interpretations and assumptions concerning the modeled organism's soft part and skeletal anatomy are correct, the hypotheses that (1) the organism could alternately contract and expand the oral region and (2) such movement increased feeding efficiency seem plausible.

eLife assessment

This important study uses near full-length HIV-1 sequencing to examine proviral persistence in various tissues derived from three individuals who received antiretroviral therapy until time of death. Intact as well as defective HIV-1 proviruses are found at various anatomical sites including the central nervous system; the results are convincing and relevant for our understanding of latent viral reservoirs, especially in the brain.

eLife assessment

The study presented in this manuscript makes important contributions to our understanding of cell fate decisions, as well as to the role and effects of noise at various scales in gene regulatory networks involved in such fate decisions. The modelling approach and analyses provide solid support for the conclusion that distinct driving forces behind fate decisions can be distinguished by their noise profiles and reprogramming trajectories.

eLife assessment

This study examines the role of interaction between the PAS domain and the Cyclic Nucleotide-Binding Homology Domain (CNBHD) in voltage-dependent gating of EAG channels. The authors make the extraordinary claim that they have identified a hidden open state, thus providing a window for observing early conformational transitions associated with channel gating. Although the data are intriguing, the evidence supporting the conclusions is incomplete, and the experimental conditions used to propose the channel gating mechanism need to be revisited. With sufficiently strong experimental support, this work could become important for understanding the gating mechanisms of the KCNH family and would appeal to biophysicists interested in ion channels and physiologists interested in cancer biology.

eLife assessment

In this manuscript, the authors tested the hypothesis that Aβ42 toxicity arises from its proven affinity for γ-secretases. The authors provide useful findings, however, the results are incomplete and do not fit physiological conditions in the brain. The data will be of interest to all scientists working on neurodegenerative diseases.

eLife assessment

This useful manuscript presents a new therapeutic formulation and these solid findings have potential clinical significance as the efficacy of CK21 is relevant in various pancreatic cancer models.Further validation studies would help to strengthen the findings.

eLife assessment

The authors use a clever experimental design and approach to tackle an important set of questions in the field of decision-making. From this work, the authors have a number of intriguing results. However, questions remain regarding the extent to which a number of alternative models and interpretations, not considered in the paper, could account for the observed effects.

eLife assessment

This fundamental study provides compelling evidence for a new mechanism of host-microbe interaction, with indole, produced by proliferating bacteria in the C. elegans digestive system, signalling through the host via the transcription factor DAF-16 to induce the expression of genes controlling bacterial growth in the gut. The work is relevant to a wide audience as it invites deeper research into this mechanism, while also serving as a template for similar microbiome/host interactions in other systems.

eLife assessment

This important study reports biochemical and structural experiments that were carried out to determine the molecular basis of calcium-sensitive regulation of the guanine exchange factor Ric8A by the neuronal calcium sensor 1 (NCS-1). Structural and biochemical evidence for the NCS-1/Ric8A interface is convincing, but evidence for the full-length interactions is incomplete due to the low resolution of cryo-EM maps. This work will have important implications for scientists interested in G-protein signaling and molecular interactions that contribute to synapse function.

eLife assessment

This paper reports fundamental findings that substantially advance our understanding of a major research question - how hybridization events influence gene regulatory programs and how evolutionary pressures have shaped these programs in response to such events. The methods, data, and analyses are solid and broadly support the claims with only minor weaknesses. This convincing work uses appropriate and validated methodology in line with the current state-of-the-art.

eLife assessment

This is an important study that investigates the role of astrocytic Gi signaling in the anterior cingulate cortex in the modulation of extracellular L-lactate level and consequently impairment in flavor-place associates (PA) learning. However, whereas some of the behavioral observations and signaling mechanism data are compelling, the conclusions about effects on memory and the role of L-lactate are based on inadequate methods. With the addition of a few key experiments, this work will be of interest to neuroscientists studying learning and memory and the contribution of astrocytes to these processes.

eLife assessment

This important study delineates the molecular changes driving the progression from actinic keratosis (AK) to cutaneous squamous cell carcinoma (cSCC). Using state-of-the-art single-cell RNA profiling of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC, and their matched normal tissues, thus covering comprehensive clinical courses of cSCC, the authors provide an invaluable data resource. This study identified several previously unreported and interesting candidate genes involved in different stages of the malignant progression of skin neoplasias, which have been validated in situ, and partially in vitro. Although data analysis needs improvement and comparison to other published data sets to fully support the claims and conclusions, these findings substantially advance our understanding of the molecular changes leading to skin cancer.

eLife assessment

Purines are native molecules that affect processes in the immune system, among others. The manuscript describes a valuable investigation of the mode of binding of purines, especially their carbohydrate moiety, to human receptors in cell culture and by computer-based modelling. Solid evidence is presented about the way purines interact with and activate two receptors.

eLife assessment

This study presents a valuable finding on an alternative method that combines multiple inhibitors to maximize on-target inhibition and minimize off-target inhibition. The evidence supporting the claims of the authors is solid, although a proper validation of the methodology could strengthen the paper. The work will be of interest to scientists working in the field of drug discovery, particularly in the field of kinase inhibitors.

eLife assessment

The authors developed a valuable mathematical model that describes the spatiotemporal dynamics of cells in the intestinal crypt. The proposed model makes an important contribution to the field, allowing a better understanding of the formation and response dynamics of the intestinal crypt through the effective evaluation of health, disease, and treatment conditions. The authors provided solid evidence of the validity of their model and their conclusions, but some minor claims are not properly justified in the current manuscript. This paper is meant for computational biologists and cancer researchers working on oncotherapies for the intestinal epithelium.

eLife assessment

This manuscript provides a useful qualitative analysis of hair extracts from mammals, with the goal of understanding how mosquitoes encode the chemicals in the odor. The data were collected using standard spectrometric approaches in the field of chemical ecology, but they suffer from artifacts associated with the sampling approach and analyses, and are limited in their replicates and sampling which may prevent inter-species comparisons at this point. Without additional analysis, the evidence supporting the claims currently remains unfortunately incomplete.

eLife assessment

This study presents a valuable comparison of the transcriptome and translatome between Drosophila neurons and glia. The data were collected and analyzed using validated methodology and the paper reports extensive variation in the translation efficiency of specific transcripts between neurons and glia. The authors argue that glia actively suppress the translation of neuronal transcripts by retaining ribosomes in their 5' leader regions. However, whereas the transcriptome and translatome analyses are convincing, the functional analyses are incomplete and would benefit from more rigorous validation to support the proposed model without over-interpretation.

eLife assessment

This study presents a useful resource for the gene expression profiles of different cell types in the parietal lobe of the cerebral cortex of prenatal macaques. The evidence supporting the claims of the authors is solid, although poor cell classification may be skewing interpretation of the results. This dataset will be of interest to developmental neurobiologists and could potentially be used for future comparative studies on early brain development.

eLife assessment

The reviewers found this manuscript to present convincing evidence for associative and non-associative behaviors elicited in male and female mice during a serial compound stimulus Pavlovian fear conditioning task. The work adds to ongoing efforts to identify multifaceted behaviors that reflect learning in classic paradigms and will be valuable to others in the field. The reviewers do note areas that would benefit from additional discussion and some minor gaps in data reporting that could be filled by additional analyses or experiments.

eLife assessment

Yogesh and Keller provide a set of important results describing the response properties of cholinergic input and its functional impacts in the mouse visual cortex. They found that cholinergic inputs are elevated by locomotion in a binary manner regardless of locomotor speeds, and activation of cholinergic input modulated the activity of visual cortex neurons in a layer dependent manner. The experiments are well executed and the results are relatively convincing although further analyses are required to fully support some conclusions.

eLife assessment:

This valuable manuscript investigates the roles of DKK3 in AD synapse integrity. Although previous work has identified the involvement of Wnt and DKK1 in synaptic physiology, this study provides compelling evidence that suppression of DKK3 rescues the changes in excitatory synapse numbers, as well as memory deficits in an established AD model mice. The authors provide both gain and loss of function data that support the main conclusion and advance our understanding of the mechanisms by which Wnt pathway mediates early synaptic dysfunction in AD models.

eLife assessment

This is a valuable paper demonstrating the validity of a novel task that could advance the field of reinforcement learning to better incorporate threat processing in approach-avoidance-conflict. A compelling methodology includes the use of online samples and computational modelling, psychometrics, discovery/replication and pre-registration. This work provides a foundation for future work, which is required to establish this task as relevant to psychopathology and treatment.

eLife assessment

This is an important paper that links distinctive stinging behavior of two related anemones occupying different ecological niches to varying inactivation properties of voltage-gated calcium channels conferred by auxiliary Cavβ subunits. Further convincing evidence is provided that these differences are mediated by alternative splicing of Cavβ subunit of the calcium channel. The study will be of interest to scientists studying Ca2+ signaling, ion channel biophysicists, and marine biologists.

eLife assessment

This is an important study that addresses the interesting question of whether stimulation of DA input to prefrontal cortex during adolescence can be used to rescue genetic defects on DA regulation of PFC function. The conclusions are convincingly supported by the data together with discussion of some limitations of the approach. This story will of interest to a broad group of neuroscientists interested in regulation of prefrontal cortical function in behavior.

eLife assessment

This study presents a comprehensive benchmarking approach, reviewing existing cell-type deconvolution methods in spatial transcriptomics. The authors not only assess these methods across various datasets but also successfully establish a reliable framework for their evaluation, notably highlighting RCTD and Cell2location for their performance. By implementing a full Nextflow pipeline, Docker containers, and a rigorous assessment of the simulator, this work offers robust insights that elevate the standards for future evaluations and provides a useful resource for those seeking to improve or develop new deconvolution methods. The thorough comparison and analysis of methods, coupled with a strong emphasis on reproducibility, provide solid support for the findings.

eLife assessment

This study demonstrates that plasticity of ocular dominance of binocular neurons in the visual thalamus persists in adulthood. The evidence supporting the authors' conclusion is convincing, and the findings are an important contribution to a growing body of work identifying plasticity in the adult visual system. This work will interest those in the field of ocular dominance plasticity in the visual system as well as scientists investigating the function of synaptic plasticity in the brain.

eLife assessment

This important study points out discrepancies between the clinical diagnosis of Clostridioides difficile infection and the lack of detectable C. difficile in gut microbiome samples, as well as different relationships between asymptomatic C. difficile carriage and adult or infant gut microbiota compositions. While the solid analysis of a comprehensive and diverse metagenomic dataset suggests an over-diagnosis of C. difficile infection and an under-diagnosis of other putative enteric pathogens, the work requires addressing the detection limitations of the approach to be more convincing. This work will interest microbiologists and clinicians concerned with understanding the role of C. difficile in gut microbiota health and dysbiosis.

eLife assessment

Necarsulmer et al describe an interesting new mouse model of TDP-43 proteinopathy in which gene editing was used to introduce a K145Q acetylation-mimic mutation previously shown to impair RNA-binding capacity and induce downstream misregulation of target genes. Mice homozygous for this mutation are convincingly shown to display cognitive/behavioral impairment, TDP-43 phosphorylation and insolubility, and changes in gene expression and splicing. This novel mouse model replicates some key hallmarks of human frontotemporal lobar degeneration and will be an important contribution to the field.

eLife assessment

This important and elegant study uses experimental structural data, ion affinity measurements, and computational methods to provide insight into the thermodynamic landscape of cation transporters of the Cation Diffusion Facilitator (CDF) superfamily, together with a detailed structural investigation of the role of the three zinc(II) binding sites of the YiiP family member. Overall, the support for the proposed transport cycle of YiiP is compelling. This work will be of interest to biologists and biophysics who work with membrane transporters.

eLife assessment

This is a useful investigation of the changes in gene expression and some of the physiological consequences of sublethal exposures to the neonicotinoid insecticide imidacloprid in honeybee larvae. While the study adds to our understanding of how this insecticide impacts development and growth of honeybees, the evidence supporting the major claims is incomplete. The study would benefit from a more thorough mechanistic characterization of the phenotypes to substantiate the conclusions.

eLife assessment

This fundamental study examines the human voltage-gated chloride channel CLC-2. A compelling approach that combines cryo-EM, electrophysiology, and computational analysis provides convincing support for a "ball and chain" mechanism of inactivation. This and other findings regarding the gating and inhibition mechanisms of the channel are fundamentally interesting to ion channel physiologists.

eLife assessment

This manuscript describes a fundamental strategy for developing isozyme-selective inhibitors of inositol hexakisphosphate kinases. The compelling evidence that subtle changes to the gatekeeper position can sensitize the inositol hexakisphosphate kinase mutant to allosteric inhibitors will undoubtedly inspire other analog-sensitive inhibitor studies. This manuscript will be of interest to researchers focusing on kinase regulation and inhibitor design.

eLife assessment

With a carefully collected dataset and compelling analyses, this fundamental manuscript demonstrates detailed links between societal and academic interest and natural species across the globe. In doing so, the authors reveal biases that may be diminishing our abilities to care for the species on our planet that may need our care the most. While some parts of this manuscript reflect previously published work, the authors are commended for putting all the puzzle pieces together for the first time. Their work highlights our uneven knowledge of biodiversity and its potential causes.

eLife assessment

This study reports the fundamental discovery of a novel structure in the developing gut that acts as a midline barrier between left and right asymmetries. The evidence supporting the dynamics, composition, and function of this novel basement membrane in the chick is in parts solid and in others convincing, but the investigation of its origin and impact on asymmetric organogenesis is not yet conclusive. This careful work is of broad relevance to anyone interested in patterning mechanisms, the importance of the extracellular matrix, and laterality disorders.

eLife assessment

This Research Advance provides compelling evidence connecting the ancient Egyptian trade of baboons with the ancient port city of Adulis. Combining ancient DNA methods from a single mummified baboon with historical accounts, this work fundamentally advances our understanding of the ancient baboon trade in the Red Sea. Some additional reporting of DNA contamination will make the evidence provided even stronger.

eLife assessment

The authors previously developed a tool with the goal of non-toxic trans-synaptic tracing using a modified rabies virus, an important goal for the neuroscience field. The tool has the propensity to accumulate mutations over time that promote toxicity, and the manuscript here describes techniques to avoid these mutations. It remains important to show that the non-mutated virus can serve as an effective trans-synaptic tracing tool.

eLife assessment

This important study shows that tree shrews can detect optogenetic stimulation of the lateral geniculate nucleus (LGN) after training detection of visual stimuli. The solid evidence links optogenetic stimulation of the LGN to behavioural detection and neurophysiological responses. This paper is potentially of interest to neuroscientists and clinicians working on the visual system and visual prostheses.

eLife assessment

Secondary cell walls support vascular plants and conduct water throughout the plant body, and are crucial resources for lignocellulosic feedstocks. Here the authors present convincing genetic and biochemical evidence that secondary cell wall synthesis, known already to be under complex transcriptional control, is also controlled post-transcriptionally by MUSASHI-like RNA-binding proteins. These important results point to a new mechanism for control of secondary cell wall synthesis, which will be interesting to cell biologists and biochemists studying and attempting to manipulate plant biomass.

eLife assessment

Dolgova et al present a well-written and important manuscript focused on the mechanism of MEMO1 function in tumor cells. The authors explore whether the mechanism of MEMO1 overexpression in breast cancer, especially TNBC, is related to regulating iron given evidence that MEMO1 binds multiple proteins in the iron regulation pathway. While the data is in part compelling, the claims are based on indirect evidence for a central role of MEMO1 in tumorogenesis and perhaps metastasis via its effect on iron homeostasis.

eLife assessment

FKBP35 is the only FK506-binding protein present in the malaria-causing parasite Plasmodium falciparum, and has been considered a promising drug target due to its high affinity to the macrolide compound FK506, an immunosuppressant with antiplasmodial activity. This study demonstrates the essentiality of FKBP35 in parasite growth, based on compelling genetic evidence. The data also suggest that FK506 may exert its antimalarial activity through FKBP35-independent mechanisms that have not yet been characterised. This important study will be of interest to scientists working on the parasite biology and antimalarial drug development.

eLife assessment

This valuable study reports on a positive feedback loop between ZEB2 and ACSL4, which regulates lipid metabolism to promote breast cancer metastasis. The evidence supporting the claims of the authors is solid, but inclusion of appropriate thresholds or False Discovery Rate (FDR) adjustments for the RNA-seq analysis would have strengthened the study. The work will be of interest to medical biologists working on breast cancer.

eLife assessment

This important study reports how heat stress affects centromere integrity by compromising the loading of the centromere protein CENH3 and by prolonging the spindle assembly checkpoint during male meiosis in Arabidopsis thaliana. The evidence supporting the claims by live cell imaging is convincing, although deeper mechanistic insight is lacking, making the study overall somewhat preliminary in nature. This work will be of interest to a broad audience of biologists working on how chromatin states are affected by stress conditions.

eLife assessment

This study identifies several modes of regulation or pathways that are valuable for understanding the entry or progression into meiosis, which implies both the repression of some mitotic cell cycle regulators and the expression of meiotic functions. Convincing approaches identify several of the involved genes, although some were known before. How these modes of regulation and genes cooperate remains to be understood.

eLife assessment

This fundamental study significantly advances our understanding of the role of water influx and swelling in neutrophil migration. The evidence supporting the conclusions, based on a genome-wide CRISPR screen and high-quality cellular observations, is compelling. This paper will be of interest to cell biologists and biophysicists working on cell migration.

eLife assessment

In this fundamental work, the authors demonstrated that maternal choline supplementation improved spatial memory, reduced hyperexcitability, and restored NeuN expression in a familial Alzheimer's disease mouse model. Interestingly, choline deficiency increased mortality, while paradoxically reduced hyperexcitability. Using behavior, electrophysiological, and histological measures, the authors present solid and convincing evidence supporting the significant role of maternal choline supplementation in protecting hippocampal functions vulnerable to Alzheimer's disease.

eLife assessment

This study reports the discovery of a new circuit mechanism for light-avoidance behavior in the marine annelid, Platynereis dumerilii. Using calcium imaging, molecular perturbations, behavioral measurements, and modeling, the authors provide compelling evidence that nitric oxide is released by postsynaptic neurons onto ciliary photoreceptors to prolong and enhance their response to ultraviolet light. The fundamental new role of nitric oxide described in this study may be conserved across animal phyla and thus will be of broad interests to neuroscientists and neuroendocrinologists.

eLife assessment

This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. The solid evolutionary analyses form a strong basis for experimental follow-up studies. The work should be of interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology.

eLife assessment

This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. The solid evolutionary analyses form an interesting basis for experimental follow-up studies. The work should be of interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology.

eLife assessment

This article studies how a human mutation in a specific potassium channel causes altered islet cell function and monogenic diabetes. The work uses CRISPR-engineered mice to show that the gain-of-function mutation causes increased potassium flux, reduced insulin secretion, and impaired glucose tolerance. The convincing data substantially support the conclusions, and the work is important for understanding islet cell function and glucose homeostasis.

eLife assessment

The authors describe a method to decouple the mechanisms supporting pancreatic progenitor self-renewal and expansion from feed-forward mechanisms promoting their differentiation. The findings are important because they have implications beyond a single subfield. The strength of evidence is solid in that the methods, data and analyses broadly support the claims with only minor weaknesses.

eLife assessment

This study highlights new insights into the mechanism of pheochromocytoma pathogenesis that remains poorly understood. In the context of hereditary syndromes, such as multiple endocrine neoplasia 2 (MEN-2), where RET mutation is the major driver of thyroid, parathyroid, and adrenal pathologies, including pheochromocytoma, this mechanistic dissection of RET and TMEM127 is fundamentally sound. While the significance was deemed important, the strength of the evidence was found to be solid, although additional validation work would strengthen the findings.

eLife assessment

This study provides insights into the early detection of malignancies with noninvasive methods by developing a framework, which assesses methylation, CNA, and other genomic features. They established a solid model in discriminating malignancies from healthy controls, as well as the ability to distinguish tumor of origin. This important study will demonstrate its practical impacts in the clinic and other researchers of the field.

eLife assessment

This manuscript reports a useful computational study of information encoding across the monkey prefrontal and pre-motor cortices during decision making. While many of the conclusions are supported with solid analyses, the evidence for the main claim, the role of an information bottleneck across areas, is incomplete. Refocusing the paper as an RNN modeling study would increase its appeal to a systems and computational neuroscience audience.

eLife assessment

This study develops valuable tools for optogenetic control of neuronal activity. The basic characterization of the activation of a red-shifted channelrhodopsin paired with a blue-light sensitive anion channel engineered to obtain desired inhibitory current kinetics is solid. However, guidelines and feasibility for their practical use under simultaneous multi-color stimulation are incomplete, as are comparisons with current state-of-the-art tools.

eLife assessment

The study used slice physiology and modeling to investigate neurotransmitter release at the cerebellar parallel fiber-to-molecular layer interneuron synapse, revealing that each docking site can accommodate up to two synaptic vesicles simultaneously. The authors have provided convincing evidence addressing how many vesicles can be released by a single release site in a short time. These findings are important for the validation of a two-step docking model and shed light on the mechanisms underlying short-term synaptic plasticity and strategies for achieving synaptic reliability, which plays a critical role in information processing in the brain.

eLife assessment

Pak et al. examined the relationship between the most common spatial patterns of neurodegeneration and the density of different cell types in the cerebral cortex. The study uses innovative methods but the main claims are incompletely supported due to some limitations. While the results might be considered preliminary, this work provides valuable findings and takes a step in the right direction by highlighting the contribution of non-neuronal cell type to the pathobiology of neurodegeneration.

eLife assessment

This fundamental study substantially advances our understanding of the role of zinc in metabolism, specifically a newly established clinical link between mutations in the zinc transporter SLC39A5, elevated serum zinc levels, and a reduction in the risk of Type 2 Diabetes. The provided evidence is solid with state-of-the-art genetic analysis of large human cohorts followed by a comprehensive analysis of a mouse SLC39A5 knockout mutant, establishing that SLC39A5 plays a role in hepatic lipid handling through AMPK signaling, although the limited analysis of a pancreatic phenotype that has previously been described constitutes a weakness. This study will be of relevance to researchers interested in metabolism, fatty liver disease, and the biology of trace elements.

eLife assessment

This valuable study provides a new perspective on preparatory activity occurring before the onset of movement. The authors report that, for a wide variety of recurrent networks, the optimal inputs should start before the desired network output. The authors present convincing evidence by combining mathematically tractable analyses in linear networks and numerical simulation in nonlinear networks. One limitation is that the only cost function considered for the input is that of magnitude. While this constraint is reasonable, it is suspected that other cost functions could lead to greater realism of model responses.

eLife assessment

This valuable study advances our knowledge of the effects of anxiety/depression treatment on metacognition, demonstrating that treatment increases metacognitive confidence alongside improving symptoms. The authors provide convincing evidence for the state-dependency of metacognitive confidence, based on a large longitudinal treatment dataset. However, it is unclear to what extent this effect is truly specific to treatment, as changes in metacognitive confidence in the group receiving online CBT were not statistically different from those in the control group.

eLife assessment

In this fundamental study, the authors propose analytical methods for inferring evolutionary parameters of interest from sequencing data in healthy tissue relevant to hematopoiesis. By combining analyses of single cell and bulk sequencing data, the authors can use a stochastic process to inform different aspects of genetic heterogeneity. The strength of evidence in support of the authors' claim is thus compelling. The work will be of broad interest to cell biologists and theoretical biologists.

eLife assessment

This important study identifies a spatial pattern of neural activity that corresponds to trust in an investment game. It provides a compelling assessment of the validity of this pattern by assessing its expression, or lack thereof, in a variety of datasets. This work, and the "neurometrics" approach it proposes, will be of broad interest to psychology researchers more generally.

eLife assessment

This important study advances our understanding of how listeners understand speech when there are multiple talkers by showing that the content of the speech affects acoustic processing. The evidence is generally solid, although additional details on the methods to allow replication would strengthen the study. The work will be of use to researchers interested in the neuroscience of speech and language processing.

eLife assessment

This is an important contribution that extends earlier single-unit work on orientation-specific center-surround interactions to the domain of population responses measured with Voltage Sensitive Dye (VSD) imaging and the first to relate these interactions to orientation-specific perceptual effects of masking. The authors provide convincing evidence of a pattern of results in which the initial effect of the mask seems to run counter to the behavioral effects of the mask, a pattern that reversed in the latter phase of the response. It seems likely that the physiological effects of masking reported here can be attributed to previously described signals from the receptive field surround.

eLife assessment

The primary goal of this paper is to examine microtubule detyrosination as a potential therapeutic target for axon regeneration. The valuable findings of this study provide convincing evidence for mechanistic links between microtubule detyrosination and neurite outgrowth in vitro and some evidence for axon regeneration in vivo.

eLife assessment

This important work presents an interesting perspective for the generation and interpretation of phase precession in the hippocampal formation. Through numerical simulations and comparison to experiments, the study provides a convincing theoretical framework explaining the segregation of sequences reflecting navigation and sequences reflecting internal dynamics in the DG-CA3 loop. This study will be of interest for researchers in the spatial navigation and computational neuroscience fields.

eLife assessment

This important study uses calcium imaging in mice to advance our understanding of the effect of antipsychotic drugs on neural functioning. The evidence supporting the conclusions is convincing, though some improvements could be made to the statistical testing of the data. This work will be of interest to neuroscientists working on visual processing and psychosis researchers.

eLife assessment

This is an important study that improves gene models for the ferret genome and identifies neural progenitors that are comparable to those found in developing human brains. The data are convincing and clearly presented. Of particular interest to the field, the work identifies enriched expression of FOXJ1 in late truncated radial glia, strongly indicating that towards the end of neurogenesis, these cells likely give rise to ependymal cells. The work is of interest to anyone studying the development of the nervous system, especially colleagues studying the evolution of development.

eLife assessment

This manuscript will provide a valuable method to evaluate the safety of MR in patients with orthopaedic implants, which is required in clinics. A strength of the work is that the in-silicon testbed is solid, based on the widely available human project, and validated. In addition, the toolbox will be open for clinical practice.

eLife assessment

This is important work that examines hepatic acetate production via ACOT12/18 in starvation and diabetes. The investigators use solid loss of function strategies in cells, including mouse primary hepatocytes, and in vivo mouse experiments to show that ACOTs are necessary for normal acetate production in the context of fasting and type 1 diabetes. Given that acetate is commonly thought to primarily represent a fermentation product, this study is of interest as it describes hepatic pathways converting fatty acids to acetate.

eLife assessment

The authors develop a cell culture system for studies of muscle tissue development and homeostasis. They convincingly validate a novel 3D cell model. Their thorough molecular and functional characterization will make this useful for future workers in the field.

eLife assessment

This fundamental study advances our understanding of the cell specific treatment of cone photoreceptor degeneration by Txnip. The evidence supporting the conclusions is convincing with rigorous genetic manipulation of Txnip mutations, however, there are a few areas in which the article may be improved through further analysis and application of the data. The work will be of broad interest to vision researchers, cell biologists and biochemists.

eLife assessment

This useful study presents convincing evidence that blood meal source and season affect Culex quinquefasciatus mosquito reproduction. Its unique focus on the interactive effects of both factors on mosquito fitness is of considerable relevance for the field, but the work suffers from inadequate experimental design - no replication, a population mismatch with the hypothesis region, and small sample sizes, limitations that were not sufficiently acknowledged in the discussion. The work will be of interest to those studying malaria and vector-borne diseases.

eLife assessment

This important study introduces a new therapeutic cell targeting system, where an active molecule is divided into inactive or less active parts that are subsequently linked via a bridging receptor on a target cell. Solid experimental proof of concept involving the activation of Wnt signaling in hepatocytes is presented, which could be further strengthened by demonstrating the specificity of the effect when applied to a mix of different cell types. This study may be of substantial interest to medical biologists focused on targeted therapeutics or seeking to utilize cell type-specific pathway modulation in their research.

eLife assessment

This study provides an important demonstration of how the false-positive rate of high-resolution 2D template matching to find particles of a given target structure in 2D cryo-EM images (2DTM) relates to overfitting the data towards the template. The authors present new methods to measure the amount of model bias that gets introduced in high-resolution features of such maps, with compelling evidence that high-resolution features that are not present in the template can still be reconstructed in 3D from images obtained by 2DTM. The paper could be strengthened by the inclusion of a more elaborate discussion (and possibly additional experiments) to describe the limitations of 2DTM for smaller target structures.

eLife assessment

This study presents valuable findings on the role of the small GTPase Rab3A in homeostatic plasticity. While the study demonstrates that Rab3A is required for homeostatic scaling, the evidence supporting the model put forward by the authors is incomplete. The work will be of interest to researchers in the field of synaptic transmission and plasticity.

eLife assessment

This is an important study that addresses a significant question in microbiome research. The authors provide convincing evidence that certain bacterial groups within the fly microbiome have critical functions for host development. Additionally, dietary aspects such as microbial community progression in a natural food source are integrated into their host-microbe interaction analyses.

eLife assessment

This manuscript analyzes large-scale Neuropixels recordings from visual areas and hippocampus of mice passively viewing repeated clips of a movie and reports that neurons respond with elevated firing activities to specific, continuous sequences of movie frames. The important results support a role of rodent hippocampal neurons in general episode encoding and advance understanding of visual information processing across different brain regions. The strength of evidence for the primary conclusion was found to be convincing.

eLife assessment

This is an important study that tests the effects of using neurofeedback, in the form of reward delivery when large sharp wave-ripples (SWRs) are detected, on neurophysiological and behavioral measures. The authors provide convincing evidence that the rate of SWRs increased prior to reward delivery and decreased in the period after reward delivery, with no significant effect on memory performance. The ability to manipulate SWR rate in a naturalistic way is a potentially exciting new tool for studies that seek to understand the function of SWRs.

eLife assessment

This manuscript represents a cleanly designed experiment for assessing biological motion processing in children (mean age = 9) with and without ADHD. The group differences concerning accuracy in global and local motion processing abilities are solid, but the analyses suggesting dissociable relationships between global and local processing and social skills, age, and IQ need further interrogation. The results are useful in terms of understanding ADHD and the ontogenesis of different components of the processing of biological motion.

eLife assessment

In this important study, the authors develop a promising experimental approach to a central question in ecology: What are the contributions of resource use and interactions in the shaping of an ecosystem? For this, they develop a synthetic ecosystem set-up, a variant of SELEX that allows very detailed control over ecological variables. The evidence is convincing, and the work should be of broad interest to the ecology community, leading to further quantitative studies.

eLife assessment

This important paper reports on the redistribution of Pol V and DNA methylation from euchromatic to heterochromatic regions in H1 mutants. While some of the evidence is solid, other parts of the genome-level model proposed to explain the molecular phenotype of H1 mutants (which includes a reduction of DNA methylation at some euchromatic sites) would benefit from additional experimental support. The work will be of broad interest to individuals interested in the mechanisms that have evolved to partition eukaryotic genomes into euchromatic and heterochromatic regions.

eLife assessment

This important study combines experiments and theory to develop a sex-based in silico model of arterial myocytes. The ionic currents of the model and its sex difference based on experimental data and comparisons of model properties with experimental data at the single cell and tissue scale are convincing. If the rigor used to assess the model (specifically the simplicity of the 1D vessel model) was improved, and there was an addition of quantitative analysis of the data examining similarity between male/female experimental/simulation, the paper would be improved.

eLife assessment

The study by Deichsel et al. reports valuable findings that suggest a new, possibly conserved, mechanism by which post-translational modification of a Notch regulator mediates the cellular immune response. However, the claims are only partially supported as the data and analysis are incomplete. The work will be of interest to biologists working on immune cell development or regulation of Notch.

eLife assessment

In this valuable study, patients homozygous for both minor frequency alleles of the APOL1 gene are shown to be at significant risk for progression into sepsis after infection. The study has enrolled a significant number of subjects and provides solid results. The study addresses to infectious diseases and critical care experts and one major weakness is the lack of inclusion of non-Black patients.

eLife assessment

This study presents a rather valuable finding that IQGAP1 interacts with TNFAIP2, which activates Rac1 to promote drug resistance in TNBC. The evidence supporting the claims of the authors is quite solid. The work will be of interest to scientists working on breast cancer.

eLife assessment