Evaluated articles

eLife Assessment

This is a valuable study, tackling the long-standing issue of the difficulty in imaging the inferior olive and addressing the most relevant questions with a rigorous approach. The technological advance allowed the authors to generate solid experimental evidence with high-quality data. The results are presented clearly and the analyses are rigorous.

eLife Assessment

This useful study presents findings on the developmental roles of Nup107, a key nucleoporin, in regulating the larval-to-pupal transition in Drosophila melanogaster through its involvement in ecdysone signaling. The evidence supporting the authors' claims is solid, with robust experimental approaches including RNAi knockdown and rescue experiments. The findings highlight Nup107's function in regulating ecdysone biosynthesis, specifically through the regulation of EcR levels and Halloween genes expression in the prothoracic gland; additionally, rescue experiments suggest that the RTK PTTH/Torso signaling pathway is disrupted upon Nup107 depletion, further emphasizing its role in ecdysone regulation. However, finding a mechanism, addressing potential off-target effects of RNAi, and exploring alternative mutant models would strengthen the findings as the currently proposed mechanism is not fully supported by the data.

eLife Assessment

This is a valuable study that explores the function of CCP5 in mouse ependymal cells. The methods, data, and analyses broadly support the claims. However, the study is incomplete as it stands. Minor weaknesses remain and the authors may wish to address them.

eLife Assessment

This is an important study with solid evidence that multi-voxel fMRI activity patterns for threat-conditioned stimuli are altered by learning CS-US contingencies. The analyses are dense but mostly rigorous. The protocol is quite nuanced and complex, but the authors have done a fair job of explaining and presenting the results, and the results could be further improved by adjustment for multiple comparisons. The readability could be improved for an audience without highly-specialised knowledge of the field and the fMRI analytical approach.

eLife Assessment

This study presents useful findings on the differences between male and hermaphrodite C. elegans connectomes and how they may result in changes in locomotory behavioural outputs. However, the study appears incomplete with respect to the relationship between sex-specific AVA wiring and male mate-finding. Another area of concern is that the analysis does not consider animal-to-animal variability in the wiring when attempting to identify significant differences between the male and hermaphrodite.

eLife Assessment

This study investigates trial-by-trial inter-areal interactions in the visual cortex of the mouse and the monkey by analyzing two previously published datasets. The authors find that activity in one layer (in mice) or one area (in monkeys) can partially predict neural activity in another layer or area on the single-trial level in different experimental contexts. This valuable finding expands previously known contributions of stimulus-independent downstream activity to neural responses in the visual cortex by demonstrating how these change under varying visual stimuli as well as in the absence of visual stimulation. While the methodology is solid, the analysis for the monkey data is incomplete and would benefit from including a second animal.

eLife Assessment

The paper addresses the question of gene epistasis and asks what is the correct null model for which we should declare no epistasis. By reanalyzing synthetic gene array datasets regarding single and double-knockout yeast mutants, and considering two theoretical models of cell growth, the authors reach the valuable conclusion that the product function is a good null model. The analysis is still incomplete, as some assumptions and hypotheses are not fully justified. However, once verified, the results have the potential to be of value to the field of gene epistasis.

eLife Assessment

This fundamental study provides a comprehensive analysis of the EmrE efflux pump and the role of the C-terminal domain in preventing uncoupled proton leak in the absence of substrate. The evidence supporting the conclusions is solid, although incomplete analyses limit some of the conclusions.

eLife Assessment

This important study offers a molecular characterization of neurons and glia in the adult nervous system of the fruit fly Drosophila melanogaster. The study focuses on the progeny of a specific set of neural stem cells that contribute to the central complex, a conserved brain region that plays key roles in sensorimotor integration. The data are convincing and collected using validated methodology, generating an invaluable resource for future studies. The study will be of interest to developmental neurobiologists.

eLife assessment

The study presents a useful computational analysis of how the ratio between excitatory and inhibitory neural numbers affects coding capacity. The authors show that increasing the proportion of inhibitory neurons (as observed in upper cortical layers compared to the input recipient layer 4) increases the dimensionality of neural activity and improves the encoding of time-varying stimuli. However, the evidence about the role of the inhibitory population in coding is incomplete because numerical results are neither supported by analytical mathematical results nor include controls for changes in firing thresholds or subtypes of inhibitory neurons.

eLife Assessment

This study presents a valuable finding of novel markers that may potentially identify resident tendon stem/progenitor cells (TSPCs). The study also presents a comprehensive single-cell transcriptional dataset that will be of value to the field. The evidence supporting the identification of novel markers of a TSPC is incomplete, requiring clarification of current analyses, additional analyses between ages, and additional validation experiments to demonstrate that these markers are indeed specific and these cells are indeed TSPCs. This work will be of interest to biologists and engineers focused on tendons and ligaments.

eLife Assessment

This important study uses advanced computational methods to elucidate how environmental dielectric properties influence the interaction strengths of tyrosine and phenylalanine in biomolecular condensates. The evidence supporting the claims of the authors is solid, as the simulations are performed rigorously providing mechanistic insights into the origin of the differences between the two aromatic amino acids considered. This study will be of broad interest to researchers studying biomolecular phase separation.

eLife Assessment

This important study by Liu et al. presents a comprehensive structure-function analysis of the presynaptic protein UNC-13, leading to new insights into how its distinct domains control neurotransmitter release. The methods, data, and analyses are convincing, and the genetic and electrophysiological approaches support many of their conclusions. The work will be of interest to neuroscientists studying synaptic transmission, as it provides a foundation for future mechanistic studies of Munc13/UNC-13 family proteins.

eLife Assessment

This manuscript presents an interesting new framework (VARX) for simultaneously quantifying effective connectivity in brain activity during sensory stimulation and how that brain activity is being driven by that sensory stimulation. The reviewers thought the model was original and its conclusion that intrinsic connectivity is largely unaltered during sensory stimulation is very interesting, but that future use of the model could potentially be affected by false positive conclusions. Overall, this work is important with solid evidence for its conclusions - it will be of interest to neuroscientists working on brain connectivity and dynamics.

eLife Assessment

This study combines mathematical models and experimental data to analyse the emergence of heterogeneity within clonal NK cell responses during antigen-specific cell expansion. Although it comprises different experimental data and tests different theoretical hypotheses, the main claims remain incomplete and would benefit from the consideration of several previous findings about clonal immune responses and corresponding mathematical approaches. The study presents valuable findings with the potential to provide key insights about NK cell development if proposed claims could be confirmed by additional analyses.

eLife Assessment

This study reports important advances in understanding how pyrazinamide, a first-line antibiotic for tuberculosis treatment, is effective in vivo. The experimental design and data provide solid evidence that the production of reactive oxygen species by host cells contributes to how pyrazinamide is more potent in the host than in culture conditions; however, additional experiments and controls would strengthen these conclusions. This work is of interest to the antibiotic drug development field.

eLife Assessment

You et al. present an important study that applied a high-resolution transposon-based barcoding system to show the clonal contribution of hematopoietic stem and progenitor cells during aging, after 5-FU treatment, and upon transplantation. The results are convincing and show that there are different categories of multipotent progenitors that are either active or indolent, and that long-term fates are dominated by clones that either favor differentiation or self-renewal. This study will be of broad interest to stem-cell biologists and could reach an even wider audience with a clearer and more concise presentation and discussion of the results.

eLife Assessment

This valuable study offers insights into the role of Leiomodin-1 (LMOD1) in muscle stem cell biology, advancing our understanding of myogenic differentiation and indicating LMOD1 as a regulator of muscle regeneration, aging, and exercise adaptation. The integration of in vitro and in vivo approaches, complemented by proteomic and imaging methodologies, is solid. However, certain aspects require further attention to improve the clarity, impact, and overall significance of the work, particularly in substantiating the in vivo relevance. This work will provide a starting point that will be of value to medical biologists and biochemists working on LMOD and its variants in muscle biology.

eLife Assessment

This manuscript presents important findings on how structural color can be manipulated through a specific single-gene mutation in the motile bacterium Flavobacterium IR1. It provides a promising model to identify genes and molecular mechanisms supporting this widespread optical phenomenon. The story relies on convincing data with proteomic analysis and well-designed experiments, although it remains rather descriptive. This work will be of interest to biophysicists and microbiologists working on structural colors and Flavobacterium.

eLife Assessment

This study provides a comprehensive exploration of the role of IL-1β signaling during development of lung injury induced by a combination of underlying inflammation and mechanical ventilation. The data are convincing, and while the translatability of the findings related to therapeutic hypothermia may be somewhat complicated, they have the potential to be very valuable to the field.