Evaluated articles

eLife Assessment

This valuable study identifies a novel regulator of stress-induced gene quiescence in C. elegans: the multi-Zinc-finger protein ZNF-236. The work provides evidence for an active mechanism that maintains the repressed state of inducible genes under basal conditions in the absence of stress. The claims for discovery made in the title and abstract are supported by solid experimental data. However, a deeper investigation into the mechanisms of ZNF-236 action could substantially enhance the manuscript's impact and value.

eLife Assessment

This study addresses an important problem in gene regulation, namely, which features of chromatin regulate potential RNA Polymerase 2 activity at a locus. The authors provided evidence that specific post-translational modifications of histones within the gene body are correlated with Pol II transcription, that these modifications are dynamic, and that they can be regulated by Pol II activity. The manuscript contributes to the concept of "fragile nucleosomes" as a unifying framework for key epigenetic drivers of transcription; however, the quality of the evidence provided is inadequate in support of the claims made, and further evidence teasing out the mechanistic aspects of the work would strengthen its impact. This work will be of interest to the fields of transcriptional regulation, chromatin structure, and epigenetics.

eLife Assessment

This important work advances our understanding of the development of the visual system. The data presented is compelling and provides a detailed single-cell atlas of post-natal anterior chamber development in mice, highlighting the trabecular meshwork and Schlemm's canal.

eLife Assessment

This study presents important findings on how cardiac regenerative capacity diverges across species by examining heart repair in two species of livebearers, platyfish and swordtails. In contrast to zebrafish, the livebearer species show persistent scarring after cryo-injury, and the work highlights how lineage-specific anatomical and immunological traits may constrain regenerative competence. The study is compelling, the data are convincing, and the results contribute to our understanding of the mechanisms underlying heart regeneration across vertebrates.

eLife Assessment

This is an important study on the sensory roles of Cerebrospinal fluid-contacting neurons (CBF-cn) in mammals. The authors identify PKD2L1 as the predominant pH-sensing channel CBF-cn and show how the apical extension is used as an amplifier of chemical changes in the content of the Cerebrospinal fluid. The evidence is solid in experimental design but limited in mechanistic interpretation, as the electrophysiological analyses require re-evaluation.

eLife Assessment

This important study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides solid evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

eLife Assessment

This fundamental work substantially advances our understanding of a major research question: whether collagen can be directly imaged with MRI. The evidence supporting the conclusion is compelling, with methods, data, and analyses that are more rigorous than those currently considered state-of-the-art. The work will be of high interest to MR physicists and clinicians, as collagen is the most abundant protein in the human body and plays an essential role in health.

eLife Assessment

Rickert and colleagues demonstrate that the host peptidoglycan-binding protein PGLYRP1 has both beneficial and detrimental effects on Bordetella pertussis infection in mice. Using a solid array of techniques, the study provides useful insights into how peptidoglycan species may alter host immune responses. The data on the bactericidal effects on B. pertussis are incomplete, and further experiments are needed to draw conclusions on this question.

eLife Assessment

This study presents a valuable analysis of a large dataset of [NiFe]-CODHs, integrating genomic context, operon organization, and clade-specific gene neighborhoods to discern patterns of functional diversification and adaptation. Carefully looking at the CODH genomic context, e.g., CODH-HCP co-occurrence, the authors gain insight into enzymatic activity, biotechnological potential, and differential functional roles. The approach aligns with current standards in genomic enzymology to characterize newly identified enzymes. With solid support, this work provides a broadly informative contribution to the field.

eLife Assessment

This potentially valuable manuscript focuses on the phosphorylation of residue T495 as a mechanism to inactivate HSP70 and disrupt cell cycle progression in response to DNA damage. The evidence supporting this model is incomplete and would be strengthened by additional studies defining the extent of T495 phosphorylation induced by DNA damage, identifying the kinase responsible for phosphorylating T495 of HSP70, and further elucidation of the functional implications of T495 phosphorylation in human cells. This work will be of interest to scientists focused on topics including chaperone biology, proteostasis, cell cycle progression, and DNA damage.

eLife Assessment

This study makes an important contribution by revealing how saccades selectively disrupt spatial working memory while sparing other object features, and by demonstrating how this mechanism is altered in aging and neurodegeneration. The findings are supported by convincing evidence derived from well-controlled eye-tracking experiments and systematic generative model comparisons. Together, the work provides a computationally grounded framework that is of importance for understanding trans-saccadic memory and its clinical relevance.

eLife Assessment

This study addresses a key question in developmental cognitive neuroscience by identifying early neural correlates of variability in language learning and showing how syllable tracking and word segmentation develop from birth to two years in infants with differing likelihoods of autism. The evidence is generally strong, with rigorous longitudinal EEG acquisition, careful preprocessing, and validated statistical approaches, though several methodological clarifications would further strengthen confidence in the inferences. Overall, the findings offer important insights with clear theoretical implications for understanding early mechanisms of speech perception and statistical learning, supported by convincing evidence.

eLife Assessment

This important study combines optogenetic manipulations and wide-field imaging to show that the retrosplenial cortex controls behavioral responses to whisker deflection in a context-dependent manner. The evidence is convincing, but the study would benefit from additional analyses to disentangle the contributions of movement initiation to the recorded neural signals. The paper should be of strong interest to neuroscientists studying cortical mechanisms of sensorimotor processing.

eLife Assessment

This is an important study showing that movement vigor is not solely an individual property but emerges through interaction when two people are physically linked. The evidence is convincing, supported by a well-controlled experimental design and modeling that closely match the observed behavior. While the authors provided a helpful comparison of several candidate models of human-human interaction dynamics, the statistical power and the statistical analyses could be further improved.

eLife Assessment

This important study reports three experiments examining how the subjective experience of task regularities influences perceptual decision-making. Although the evidence linking subjective ratings to behavioral measures is solid, the study would be strengthened if potential reverse influences of response times on subjective ratings were ruled out and if more comprehensive model comparisons supporting the main claims were performed. The findings will appeal to a wide range of researchers in decision-making and perception.

eLife Assessment

This study offers important insight into the pathogenic basis of intragenic frameshift deletions in the carboxy-terminal domain of MECP2, which account for some Rett syndrome cases, yet similar variants also appear in unaffected individuals. Using base editing and mouse models, the authors present convincing evidence supporting the pathogenicity of select deletion variants, with potential implications for therapeutic development. However, comments regarding the analysis of publicly available genetic databases should be addressed to strengthen the conclusions and provide greater clarity to the field.

eLife Assessment

The goal of this useful study is to examine learning-related changes in neural representations of global and local spatial reference frames in a spatial navigation task. Although the study addresses an interesting question, the evidence for neural representations in the hippocampus and retrosplenial cortex remains incomplete because of confounds in the experimental design and partial data analysis. There are further concerns about the framing of the study in the context of the relevant literature as well as the discussion.

eLife Assessment

This important work advances our understanding of the role of kisspeptin neurons in regulating the luteinizing hormone (LH) surge in females. The evidence demonstrating increased neuronal activity in anterior hypothalamic kisspeptin neurons just before the LH surge is compelling, though additional neuroanatomical evidence showing the specificity of the methods would strengthen the study. It also confirms that high circulating levels of estradiol, but also other unidentified factors, are required for the full daily activation. This research will be of interest to reproductive biologists and neuroscientists studying the female ovarian cycle.

eLife Assessment

This study provides an important assessment of how body size influences the occurrence of macro-organisms in urban areas across the globe. Size in most plants, but only some animal families, was positively associated with urban tolerance. The data set is impressive, but the evidence for broad-scale conclusions is incomplete due to methodological issues that need to be resolved.

eLife Assessment

This study reports important advances in our understanding of how enteropathogenic E. coli (EPEC) interacts at the intestinal interface. Solid data describe a novel model of spatially coordinated calcium signaling to modulate NF-kB activation; additional data and clarification of methods would improve the strength of these conclusions. These findings, which integrate imaging, genetics, and computational modeling, provide a new way to consider host-pathogen interactions in EPEC infections that may lead to improved therapies.