Evaluated articles

Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina

1. Sören J Zapp
2. Mohammad H Khani
3. Helene M Schreyer
4. Shashwat Sridhar
5. Varsha Ramakrishna
6. Steffen Krüppel
7. Matthias Mietsch
8. Dario A Protti
9. Dimokratis Karamanlis
10. Tim Gollisch

• Curated by eLife

  eLife assessment

  This paper introduces an efficient approach to identify subunits in the receptive fields of retinal ganglion cells. The general approach has been used in this application previously and this limits the conceptual advance of the paper. The improved speed is valuable, as it allows a more thorough exploration of the control parameters in this analysis and facilitates application to larger populations of cells. Validation of the approach is convincing. The paper would benefit from a more thorough exploration of the method and its limitations, or an extension of the new results about subunit populations.

Reviewed by eLife

Near infrared radiation-driven oxygenic photosynthesis contributes substantially to primary production in biofilms harboring chlorophyll f-containing cyanobacteria

1. Maria Mosshammer
2. Erik CL Trampe
3. Niels-Ulrik Frigaard
4. Michael Kühl

• Curated by eLife

  eLife assessment

  This valuable study investigates the contribution of far-red light photo-acclimated cyanobacteria to primary production in intertidal beachrock habitats. Though the study presents solid evidence, the text would benefit from an improved discussion section and some additional methodological details.

Reviewed by eLife

Adipocyte microRNA-802 promotes adipose tissue inflammation and insulin resistance by modulating macrophages in obesity

1. Yue Yang
2. Bin Huang
3. Yimeng Qin
4. Danwei Wang
5. Yinuo Jin
6. Linmin Su
7. Qingxin Wang
8. Yi Pan
9. Yanfeng Zhang
10. Yumeng Shen
11. Wenjun Hu
12. Zhengyu Cao
13. Liang Jin
14. Fangfang Zhang

• Curated by eLife

  eLife assessment

  This important study utilizes a comprehensive array of animal and cellular models, alongside various techniques, to elucidate the mechanism by which adipose tissue miR-802 contributes to inflammation and metabolic dysfunction in obesity. The data is solid, with clear, reproducible changes showing low variability among biological replicates and consistency across different models. However, some conclusions should be further substantiated with additional data to enhance the scope and strength of the manuscript.

Reviewed by eLife

Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells

1. Eleanor Martin
2. Rossana Girardello
3. Gunnar Dittmar
4. Alexander Ludwig

• Curated by eLife

  eLife assessment

  This important study uses convincing time-resolved proximity proteomics, validated with proximity ligation assays, to provide new insight into mechanical regulation of caveolin-1 complexes that form in migrating cells. Solid follow up experiments reveal a reciprocal relationship between mechanosensitive caveolae and RhoGTPase signalling in migrating cells, but evidence supporting a direct link between the newly identified factors with a specific caveolae subpopulation remains incomplete at this stage.

Reviewed by eLife

Integration of overlapping sequences emerges with consolidation through medial prefrontal cortex neural ensembles and hippocampal–cortical connectivity

1. Alexa Tompary
2. Lila Davachi

• Curated by eLife

  eLife assessment

  This important study investigates how memory representations are transformed over time (24h period). The work advances our understanding of the neural processes supporting the behavioral integration of memories for distinct events that are never experienced together in time but are linked by shared predictive cues. Evidence supporting the claims is solid, and reporting of additional comparisons would have strengthened the study.

Reviewed by eLife

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

1. Mehul Vora
2. Jonathan Dietz
3. Zachary Wing
4. Karen George
5. Jun Kelly Liu
6. Christopher Rongo
7. Cathy Savage-Dunn

• Curated by eLife

  eLife Assessment

  Modulation of BMP signalling affects body size in the nematode Caenorhabditis elegans, and this paper examines the effects on C. elegans body size brought about by the modulation of BMP signalling. Thw study provides valuable analyses of ChIP-seq and RNA-Seq data to understand the function of SMA-3 (Smad) and SMA-9 (Schnurri) in this model. The authors provide compelling evidence that the BMP-dependent body size effect could be due to defects in cuticle collagen secretion, a finding of interest to those studying organismal growth and epidermal function.

Reviewed by eLife

Artificial intelligence driven tumor risk stratification from single-cell transcriptomics using phenotype algebra

1. Namrata Bhattacharya
2. Anja Rockstroh
3. Sanket Suhas Deshpande
4. Sam Koshy Thomas
5. Anunay Yadav
6. Chitrita Goswami
7. Smriti Chawla
8. Pierre Solomon
9. Cynthia Fourgeux
10. Gaurav Ahuja
11. Brett Hollier
12. Himanshu Kumar
13. Antoine Roquilly
14. Jeremie Poschmann
15. Melanie Lehman
16. Colleen C Nelson
17. Debarka Sengupta

• Curated by eLife

  eLife Assessment

  This manuscript presents an important contribution to the field of single-cell transcriptomic analysis in cancer by introducing a novel computational framework-SCellBOW-which applies embedding techniques from natural language processing to model phenotypic heterogeneity in tumors. The revised version includes new validation experiments and significant clarifications that provide convincing evidence for the method's utility. The authors have benchmarked SCellBOW across diverse datasets, including glioblastoma, breast, and metastatic prostate cancer, and have demonstrated its superior performance compared to existing state-of-the-art methods.

Reviewed by eLife

Neural basis of cognitive control signals in anterior cingulate cortex during delay discounting

1. Jeremy K Seamans
2. Shelby White
3. Mitchell Morningstar
4. Eldon Emberly
5. David Linsenbardt
6. Baofeng Ma
7. Cristine L Czachowski
8. Christopher C Lapish

Reviewed by eLife

Systems genomics of salinity stress response in rice

1. Sonal Gupta
2. Simon Niels Groen
3. Maricris L Zaidem
4. Andres Godwin C Sajise
5. Irina Calic
6. Mignon Natividad
7. Kenneth McNally
8. Georgina V Vergara
9. Rahul Satija
10. Steven J Franks
11. Rakesh K Singh
12. Zoé Joly-Lopez
13. Michael D Purugganan

• Curated by eLife

  eLife Assessment

  Working with a diverse panel of rice accessions grown in field conditions, this valuable study measures changes in transcript abundance, tests for patterns of selection on gene expression, and maps the genetic basic of variation in gene expression in normal and elevated salinity treatments. The manuscript provides solid evidence that mean gene expression levels are further from the optimum abundance for more genes under the elevated salinity treatment compared to normal treatment, and that a relatively small number of genes are hotspots that harbor genetic variants which affect broader genome-wide patterns of natural variation in gene expression under high salinity conditions. However, the design, clarity, and interpretation of several statistical analyses can be improved, some opportunities for integration among datasets and analyses could yet be realized, and genetic manipulation is required to confirm functional involvement of any specific genes in regulatory networks or organismal traits that confer adaptation to higher salinity conditions. The manuscript will be of interest to evolutionary biologists studying the genetics of complex traits and a resource for plant biologists studying mechanisms of abiotic stress tolerance.

Reviewed by eLife

Stochastic tug-of-war among sarcomeres mediates cardiomyocyte response to environmental stiffness

1. Daniel Haertter
2. Lara Hauke
3. Til Driehorst
4. Kengo Nishi
5. Wolfram-Hubertus Zimmermann
6. Christoph F Schmidt

• Curated by eLife

  eLife assessment

  This study provides a valuable characterization of individual sarcomere's contractility and synchrony in spontaneously beating cardiomyocytes as a function of substrate stiffness. The authors, however, provide an incomplete explanation for the observed heterogeneous and stochastic dynamics, so that the work remains mainly descriptive. The work will be of interest to scientists working on muscle biophysics, nonlinear dynamics, and synchronization phenomena in biological systems.

Reviewed by eLife

Nuclear translocation of SIRT4 mediates deacetylation of U2AF2 to modulate renal fibrosis through alternative splicing-mediated upregulation of CCN2

1. Guangyan Yang
2. Jiaqing Xiang
3. Xiaoxiao Yang
4. Xiaomai Liu
5. Yanchun Li
6. Lixing Li
7. Lin Kang
8. Zhen Liang
9. Shu Yang

• Curated by eLife

  eLife Assessment

  This study demonstrates a novel role for SIRT4; a mitochondrial deacetylase, shown to translocate into nuclei where it regulates RNA alternative splicing by modulating U2AF2 and the gene expression of CCN2 in tubular cells in response to TGF-β. This fundamental work substantially advances our understanding of kidney fibrosis development and offers a potential therapeutic approach. The evidence supporting the conclusions of a SIRT4-U2AF2-CCN2 axis activated by TGF-β is compelling and adds a new layer of complexity to the pathogenesis of chronic kidney disease.

Reviewed by eLife

A human forebrain organoid model reveals the essential function of GTF2IRD1-TTR-ERK axis for the neurodevelopmental deficits of Williams syndrome

1. Xingsen Zhao
2. Qihang Sun
3. Yikai Shou
4. Weijun Chen
5. Mengxuan Wang
6. Wenzheng Qu
7. Xiaoli Huang
8. Ying Li
9. Chao Wang
10. Yan Gu
11. Chai Ji
12. Qiang Shu
13. Xuekun Li

• Curated by eLife

  eLife assessment

  Zhao et al. report valuable adverse effects on cell proliferation, differentiation and gene expression, possibly linked to reduced binding activity of the transcription factor GTF2IRD1 to the transthyretin (TTR) promoter, in a human forebrain organoid model of Williams Syndrome (WS). The authors provide incomplete evidence of the effects of GTF2IRD1, a mutated gene in WS, on altering MAPK/ERK pathway activity, a well-recognized target in cell proliferation.

Reviewed by eLife

RAG suppresses group 2 innate lymphoid cells

1. Aaron M Ver Heul
2. Madison Mack
3. Lydia Zamidar
4. Masato Tamari
5. Ting-Lin Yang
6. Anna M Trier
7. Do-Hyun Kim
8. Hannah Janzen-Meza
9. Steven J Van Dyken
10. Chyi-Song Hsieh
11. Jenny M Karo
12. Joseph C Sun
13. Brian S Kim

• Curated by eLife

  eLife Assessment

  This study provides new insights into the expression profile of ILCs that demonstrate a history of RAG expression. It examines in part the potential intrinsic regulation of RAG expression and seeks to understand how the epigenetic state of ILCs is established, although a full understanding of intrinsic factors is only partially supported. The work provides a convincing and important molecular dataset, and strengthens our understanding of intrinsic regulation, and would be of interest more broadly to cell biologists seeking to understand immune cell development.

Reviewed by eLife

Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary sex classification of somatic tissues

1. Chen Xie
2. Sven Künzel
3. Diethard Tautz

• Curated by eLife

  eLife Assessment

  This study presents data on sex differences in gene expression across organs of four mice taxa. The authors have generated a unique and convincing dataset that fills a gap left by previous studies. They claim that sex-biased expression in the soma can overlap between genetic males and females, and that the relevant patterns both turn over quickly over short evolutionary times and do so faster in somatic than gonadal tissues. These conclusions could largely have been predicted by extrapolating from previous findings in the field, but nevertheless demonstrating them directly is a fundamental advance.

  [Editorial note: The work was originally assessed by colleagues who are active in the field of evolution of sex differences or in areas adjacent to this field (see initial assessment at https://doi.org/10.7554/eLife.99602.2). The appeals process involved consultation with experts working in other areas of evolutionary biology. The above assessment synthesises the opinions of both sets of reviewers.]

Reviewed by eLife, Arcadia Science

IL-2 enhances effector function but suppresses follicular localization of CD8+ T cells in chronic infection

1. Yaping Chen
2. Pengcheng Zhou
3. Patrick Marc Gubser
4. Yew Ann Leong
5. Jing He
6. Yunbo Wei
7. Fadzai Victor Makota
8. Mehrdad Pazhouhandeh
9. Ting Zheng
10. Joseph Yunis
11. Zhanguo Li
12. Axel Kallies
13. Di Yu

• Curated by eLife

  eLife assessment

  This paper provides valuable findings related to the impact and timing of exogenous interleukin 2 on the balance of exhausted (Tex) versus effector (Teff) that differentiate from precursors T cells (Tpex) during chronic viral infection. While the data appear solid, the overall claims that IL-2 suppresses Tpex are only partially supported, with the rationale for the timing of IL-2 treatment and its underlying mechanisms remaining unclear.

Reviewed by eLife

SARS-CoV-2 NSP13 interacts with TEAD to suppress Hippo-YAP signaling

1. Fansen Meng
2. Jong Hwan Kim
3. Chang-Ru Tsai
4. Jeffrey D Steimle
5. Jun Wang
6. Yufeng Shi
7. Rich G Li
8. Bing Xie
9. Vaibhav Deshmukh
10. Shijie Liu
11. Xiao Li
12. James F Martin

• Curated by eLife

  eLife Assessment

  This important study elucidates the molecular function of the SARS-CoV-2 helicase NSP13, which inhibits the transcriptional activity of the YAP/TEAD complex in vitro and in vivo. The evidence supporting the authors' claims is compelling, based on cell biological assays and multi-omic studies. This work contributes to the understanding of the new regulatory mechanism of YAP/TEAD after SARS-CoV-2 infection and will be of interest to researchers investigating COVID-19 infection and the Hippo-YAP signaling pathway.

Reviewed by eLife

Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans

1. Dipti Ranjan Lenka
2. Shakti Virendra Dahe
3. Odetta Antico
4. Pritiranjan Sahoo
5. Alan R Prescott
6. Miratul MK Muqit
7. Atul Kumar

• Curated by eLife

  eLife assessment

  This is a useful manuscript describing the competitive binding between Parkin domains to define the importance of dimerization in the mechanism of Parkin regulation and catalytic activity. The evidence supporting the importance of Parkin dimerization for an 'in trans' model of Parkin activity described in this manuscript is solid, but lacks more stringent and biochemical characterization of competitive binding that could provide more direct evidence to support the author's conclusions. This work will be of interest to those focused on defining the molecular mechanisms involved in ubiquitin ligase interactions, PINK-Parkin-mediated mitophagy, and mitochondrial organellar quality control.

Reviewed by eLife

A comparative study of the cryo-EM structures of Saccharomyces cerevisiae and human anaphase-promoting complex/cyclosome (APC/C)

1. Ester Vazquez-Fernandez
2. Jing Yang
3. Ziguo Zhang
4. Antonina E Andreeva
5. Paul Emsley
6. David Barford

• Curated by eLife

  eLife assessment

  This study provides compelling data that defines the structure of the S. cerevisiae APC/C. The structure reveals overall conservation of its mechanism of action compared to the human APC/C but some important differences that indicate that activation by co-activator binding and phosphorylation are not identical to the human APC/C. Thus this study will be of considerable value to the field.

Reviewed by eLife

AARS2 ameliorates myocardial ischemia via fine-tuning PKM2-mediated metabolism

1. Zongwang Zhang
2. Lixia Zheng
3. Yang Chen
4. Yuanyuan Chen
5. Junjie Hou
6. Chenglu Xiao
7. Xiaojun Zhu
8. Shi-Min Zhao
9. Jing-Wei Xiong

• Curated by eLife

  eLife Assessment

  This important study highlights the essential role of AARS2 in safeguarding cardiomyocytes against ischemic stress by modulating energy metabolism towards glycolysis via PKM2. This mechanism unveils a promising new therapeutic target for treating myocardial infarction. Convincing findings are underpinned by a comprehensive dataset, including cardiomyocyte-specific genetic modifications, functional assays, and ribosome profiling, all collectively providing strong evidence for the critical involvement of the AARS2-PKM2 signalling pathway in cardiac protection.

Reviewed by eLife

Semantic plasticity across timescales in the human brain

1. Sarah H Solomon
2. Kendrick Kay
3. Anna C Schapiro

• Curated by eLife

  eLife assessment

  This valuable study investigates how the human brain flexibly adjusts its representations of the world as the environment continually changes. It utilizes a unique dataset in which participants view thousands of natural scenes across many fMRI sessions over multiple months. The evidence supporting the claims of the authors is incomplete, with statistical inference not always warranted. The study would interest a broad readership in cognitive neuroscience.

Reviewed by eLife