Evaluated articles

Progressive overfilling of readily releasable pool underlies short-term facilitation at recurrent excitatory synapses in layer 2/3 of the rat prefrontal cortex

1. Jiwoo Shin
2. Seung Yeon Lee
3. Yujin Kim
4. Suk-Ho Lee

• Curated by eLife

  eLife Assessment

  This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the work is of very high quality and that the methodological approach is praiseworthy. The experimental data support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release. Overall, this is a convincing study.

Reviewed by eLife

A stimulus-computable rational model of visual habituation in infants and adults

1. Gal Raz
2. Anjie Cao
3. Rebecca Saxe
4. Michael C Frank

• Curated by eLife

  eLife Assessment

  In this important study, the authors provide compelling evidence that the likelihood of looking behaviour is predicted by the expected information gain, hence constituting an invaluable formal model and explanation of habituation. Such modelling represents a crucial advance in explanation, over-and-above less specified models that can be fitted post hoc to any empirical pattern. The findings would be of interest to researchers studying cognitive development, and perception and learning more broadly.

Reviewed by eLife

The Mac1 ADP-ribosylhydrolase is a therapeutic target for SARS-CoV-2

1. Rahul K Suryawanshi
2. Priyadarshini Jaishankar
3. Galen J Correy
4. Moira M Rachman
5. Patrick C O'Leary
6. Taha Y Taha
7. Yusuke Matsui
8. Francisco J Zapatero-Belinchón
9. Maria McCavitt-Malvido
10. Yagmur U Doruk
11. Maisie GV Stevens
12. Morgan E Diolaiti
13. Manasi P Jogalekar
14. Huadong Chen
15. Alicia L Richards
16. Pornparn Kongpracha
17. Sofia Bali
18. Mauricio Montano
19. Julia Rosecrans
20. Michael Matthay
21. Takaya Togo
22. Ryan L Gonciarz
23. Saumya Gopalkrishnan
24. R Jeffrey Neitz
25. Nevan J Krogan
26. Danielle L Swaney
27. Brian K Shoichet
28. Melanie Ott
29. Adam R Renslo
30. Alan Ashworth
31. James S Fraser

• Curated by eLife

  eLife Assessment

  This important study presents the development of a novel inhibitor for SARS-CoV-2 Mac1 that has potential utility both as an antiviral therapeutic and as a tool for probing the molecular mechanisms by which infection-induced ADP-ribosylation triggers robust host antiviral responses. Though minor gaps in understanding the compound's precise molecular mechanism of action and its ability to target Mac1 from other coronaviruses remain, the evidence for its effects on SARS-CoV-2 in relevant biological models is compelling.

Reviewed by eLife

Toward stable replication of genomic information in pools of RNA molecules

1. Ludwig Burger
2. Ulrich Gerland

• Curated by eLife

  eLife Assessment

  This important theoretical study examines the possibility of encoding genomic information in a collective of short overlapping strands (e.g., the Virtual Circular Genome (VCG) model). The study presents convincing theoretical arguments, simulations and comparisons to experimental data to point at potential features and limitations of such distributed collective encoding of information. The work should be of relevance to colleagues interested in molecular information processing and to those interested in pre-Central Dogma or prebiotic models of self-replication.

Reviewed by eLife

PPARγ mediated enhanced lipid biogenesis fuels Mycobacterium tuberculosis growth in a drug-tolerant hepatocyte environment

1. Binayak Sarkar
2. Jyotsna Singh
3. Mohit Yadav
4. Priya Sharma
5. Raman Deep Sharma
6. Shweta Singh
7. Aakash Chandramouli
8. Kritee Mehdiratta
9. Ashwani Kumar
10. Siddhesh S Kamat
11. Devram S Ghorpade
12. Debasisa Mohanty
13. Dhiraj Kumar
14. Rajesh S Gokhale

• Curated by eLife

  eLife Assessment

  This fundamental study examines infection of the liver and hepatocytes during tuberculosis infection. The authors convincingly demonstrate that aerosol infection of mice and guinea pigs leads to appreciable infection of the liver as well as the lung. A further strength of the study lies in clinical evaluation of the presence of tuberculosis bacteria in human autopsied liver samples from individuals with miliary tuberculosis and the presence of a clear granuloma-like structure, which will prompt further study.

Reviewed by eLife, preLights

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robusta

1. Ojas Natarajan
2. Susanne L Gibboney
3. Morgan N Young
4. Shen Jean Lim
5. Felicia Nguyen
6. Natalia Pluta
7. Celine GF Atkinson
8. Assunta Liberti
9. Eric D Kees
10. Brittany A Leigh
11. Mya Breitbart
12. Jeffrey A Gralnick
13. Larry J Dishaw

• Curated by eLife

  eLife Assessment

  This valuable study presents findings linking prophage carriage to lifestyle regulation in the marine bacterium Shewanella fidelis, with potential implications for niche occupation within a host (Ciona robusta) and mediation of host immune responses. The study leverages a unique animal model system that offers distinct advantages in identifying select phenotypes to present overall solid evidence that supports findings relating to the impact of a prophage on host-microbe interaction. Understanding the role of integrated lysogenic phages in bacterial fitness, both within a host and in the environment, is a significant concept in bacterial eco-physiology, potentially contributing to the success of certain strains.

Reviewed by eLife

SICKO: Systematic Imaging of Caenorhabditis Killing Organisms

1. Luis S Espejo
2. Samuel Freitas
3. Vanessa Hofschneider
4. Leah Chang
5. Angelo Antenor
6. Jonah Balsa
7. Anne Haskins
8. Destiny DeNicola
9. Hope Dang
10. Sage Hamming
11. Delaney Kelser
12. George L Sutphin

• Curated by eLife

  eLife Assessment

  This work describes a valuable method, SICKO, for real-time longitudinal quantification of bacterial colonization in the gut of individual C. elegans. The authors present convincing evidence to support the validity of the approach. SICKO provides an experimental framework that will enable progress in our understanding of host-microbe interactions.

Reviewed by eLife

DDX3 Regulates the Cap‐Independent Translation of the Japanese Encephalitis Virus via Its Interactions with PABP1 and the Untranslated Regions of the Viral Genome

1. Chenxi Li
2. Linjie Zhang
3. Chenyang Tang
4. Xuan Chen
5. Jing Shi
6. Qingyu Li
7. Xue Jiao
8. Jinyao Guo
9. Bin Wang
10. Kefan Bu
11. Abdul Wahaab
12. Yuguo Yuan
13. Ming‐an Sun
14. Yanhua Li

• Curated by eLife

  eLife Assessment

  This work is a valuable study that presents a detailed analysis of translation, driven by the untranslated regions of the Japanese encephalitis virus. It reports a role for the RNA helicase DDX3 in promoting a cap-independent translation mechanism. The conclusions are based on generally solid evidence, although there are some weaknesses in the overall model based on suboptimal experimental approaches and over-interpretation of some of the data. Addressing deficiencies noted in peer review could elevate the impact of the study.

Reviewed by eLife

Companion cells with high florigen production express other small proteins and reveal a nitrogen-sensitive FT repressor

1. Hiroshi Takagi
2. Shogo Ito
3. Jae Sung Shim
4. Akane Kubota
5. Andrew K Hempton
6. Nayoung Lee
7. Takamasa Suzuki
8. Jared S Wong
9. Chansie Yang
10. Christine T Nolan
11. Kerry L Bubb
12. Cristina M Alexandre
13. Daisuke Kurihara
14. Yoshikatsu Sato
15. Yasuomi Tada
16. Takatoshi Kiba
17. Jose L Pruneda-Paz
18. Christine Quietsch
19. Josh T Cuperus
20. Takato Imaizumi

• Curated by eLife

  eLife Assessment

  This fundamental study uncovers the unique molecular features of Arabidopsis phloem companion cells that highly express FLOWERING LOCUS T (FT). These FT-expressing cells constitute a distinct subpopulation marked by elevated ATP biosynthesis and co-expression of small mobile proteins such as FLP1 and BFT, highlighting a fine balance between florigen and anti-florigen signals. Motif analyses and transgenic studies further identify NIGT1 transcription factors as direct, nitrogen-inducible repressors of FT, providing a mechanism for delayed flowering under nitrogen-rich conditions. Together, the compelling findings show that florigen-producing companion cells integrate energy metabolism, systemic protein signals, and nutrient-responsive repression to fine-tune the seasonal and nutritional regulation of flowering.

Reviewed by eLife

Screening Envelope Genes Across Primate Genomes Reveals Evolution and Diversity Patterns of Endogenous Retroviruses

1. Saili Chabukswar
2. Nicole Grandi
3. Elena Soddu
4. Liang-Tzung Lin
5. Enzo Tramontano

• Curated by eLife

  eLife Assessment

  The manuscript provides an important assessment of the number and distribution of different retrovirus env genes present in primate genomes in the form of ancient endogenous retroviruses (ERV loci) and the potential role that viral recombination played in the diversification of retrovirus env genes and their propagation in the primate germline over millions of years. The paper convincingly describes how intermixing/recombination occurs with this viruses, representing a conceptual advance with potentially broad implications.

Reviewed by eLife

An increase in reactive oxygen species underlies neonatal cerebellum repair

1. Anna Pakula
2. Salsabiel El Nagar
3. N Sumru Bayin
4. Jens Bager Christensen
5. Daniel Stephen
6. Adam James Reid
7. Richard P Koche
8. Alexandra L Joyner

• Curated by eLife

  eLife Assessment

  This important work substantially advances our understanding of reactive oxygen species (ROS) as a regenerative signal during postnatal cerebellum repair by activating adaptive progenitor reprogramming. The evidence supporting the conclusions is compelling, with rigorous genomic assays and in vivo analyses. This work will be of broad interest to biologists working on stem cells, neurodevelopment and regenerative medicine.

Reviewed by eLife

Branched actin polymerization drives invasive protrusion formation to promote myoblast fusion during mouse skeletal muscle regeneration

1. Yue Lu
2. Tezin Walji
3. Pratima Pandey
4. Chuanli Zhou
5. Christa W Habela
6. Scott B Snapper
7. Rong Li
8. Elizabeth H Chen

• Curated by eLife

  eLife Assessment

  This study presents a valuable finding regarding the role of Arp2/3 and the actin nucleators N-WASP and WAVE complexes in myoblast fusion. The data presented is convincing, and the work will be of interest to biologists studying skeletal muscle stem cell biology in the context of skeletal muscle regeneration.

Reviewed by eLife

The first complete 3D reconstruction and morphofunctional mapping of an insect eye

1. Anastasia A Makarova
2. Nicholas J Chua
3. Anna V Diakova
4. Inna A Desyatirkina
5. Pat Gunn
6. Song Pang
7. C Shan Xu
8. Harald F Hess
9. Dmitri B Chklovskii
10. Alexey A Polilov

• Curated by eLife

  eLife Assessment

  This valuable study sets new standards in analyzing the ultrastructure of insect eyes, which have long served as models for understanding how vision works. The way it describes an entire eye with the resolution of electron microscopy is convincing. On top of this, a miniaturized visual system provides additional, remarkable insights towards understanding optimized solutions.

Reviewed by eLife

Efficacy and safety of neoadjuvant stereotactic body radiation therapy plus dalpiciclib and exemestane for hormone receptor-positive, HER2-negative breast cancer: A prospective pilot study

1. Yu Zhang
2. Shuo Cao
3. Nan Niu
4. Huilian Shan
5. Jinqi Xue
6. Guanglei Chen
7. Yongqing Xu
8. Jianqiao Yin
9. Chao Liu
10. Lisha Sun
11. Xiaofan Jiang
12. Meiyue Tang
13. Qianshi Xu
14. Mingxuan Jia
15. Xu Zhang
16. Zhenyong Zhang
17. Qingfu Zhang
18. Jianfei Wang
19. Ailin Li
20. Yongliang Yang
21. Caigang Liu

• Curated by eLife

  eLife Assessment

  The study evaluates the feasibility, safety, and tolerability of neoadjuvant radiotherapy followed by a CDK4/6 inhibitor (dalpiciclib) and hormonal therapy in treatment-naive patients with unilateral early-stage HR+/HER2- breast cancer. The findings are convincing, with a strong scientific rationale supported by integrated correlative studies. The trial is considered to be important as the outcomes could inform the design of larger, future studies. The limitations of the study have been acknowledged and outlined in this manuscript, which include only a small cohort of patients (n=12), which was not adequately powered to definitively assess the efficacy or safety of this combinatorial treatment approach.

Reviewed by eLife

Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes

1. Upasana L Mallimadugula
2. Matthew A Cruz
3. Neha Vithani
4. Maxwell I Zimmerman
5. Gregory R Bowman

• Curated by eLife

  eLife Assessment

  This study provides important insights into how cryptic pockets play a role in shaping binding preferences of protein-nucleic acid interactions. By combining biochemical assays and state-of-the-art molecular dynamics simulations, mechanism underlying viral protein 35 (VP35) homologs to bind the backbone of double stranded RNA is presented. The evidence is compelling for molecular determinants that suggest two different dsRNA binding modes for VP35 and also underscores the evolutionary importance of these pockets.

Reviewed by eLife

Identifying genetic variations in emm89 Streptococcus pyogenes associated with severe invasive infections

1. Masayuki Ono
2. Masaya Yamaguchi
3. Daisuke Motooka
4. Yujiro Hirose
5. Kotaro Higashi
6. Tomoko Sumitomo
7. Tohru Miyoshi-Akiyama
8. Rumi Okuno
9. Takahiro Yamaguchi
10. Ryuji Kawahara
11. Hitoshi Otsuka
12. Noriko Nakanishi
13. Yu Kazawa
14. Chikara Nakagawa
15. Ryo Yamaguchi
16. Hiroo Sakai
17. Yuko Matsumoto
18. Tadayoshi Ikebe
19. Shigetada Kawabata

• Curated by eLife

  eLife Assessment

  This study provides an important and timely analysis of invasive and non-invasive Streptococcus pyogenes emm89 isolates, which have become a dominant serotype in the past decade. Using genome sequencing of 311 strains from Japan and comparing them with 666 global strains, the authors present compelling evidence in support of the identification of genetic factors linked to the invasive phenotype of emm89. The findings are both theoretically and practically significant in medical microbiology.

Reviewed by eLife

A whole-organism landscape of X-inactivation in humans

1. Bjorn Gylemo
2. Maike Bensberg
3. Colm E Nestor

• Curated by eLife

  eLife Assessment

  The study provides a valuable analysis of escape from X-inactivation based on three rare female GTEX-donors with non-mosaic X-inactivation. The methods and analyses are solid and broadly support the authors' claims. Their data are more comprehensive than those presented previously and add significant weight to evidence for which genes are inactivated or escape from X inactivation in humans.

Reviewed by eLife

NR2F2 is required in the embryonic testis for fetal Leydig cell development

1. Aitana Perea-Gomez
2. Natividad Bellido Carreras
3. Magali Dhellemmes
4. Furong Tang
5. Coralie Le Gallo
6. Marie-Christine Chaboissier

Reviewed by eLife

Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics

1. Leonid Peshkin
2. Enrico maria Daldello
3. Elizabeth S Van Itallie
4. Matthew Sonnett
5. Johannes Kreuzer
6. Wilhelm Haas
7. Marc W Kirschner
8. Catherine Jessus

• Curated by eLife

  eLife Assessment

  This important paper describes a comprehensive quantitative phospho-proteomic analysis of the meiotic progression of Xenopus oocytes. Using time-resolved proteomic analyses, the authors provide insights into changes in protein levels and phosphorylation states to an unprecedented depth, quality, and quantitative detail. The key findings are compelling and offer a helpful resource for the scientific community.

Reviewed by eLife

Upstream open reading frames buffer translational variability during Drosophila evolution and development

1. Yuanqiang Sun
2. Yuange Duan
3. Peixiang Gao
4. Chenlu Liu
5. Kaichun Jin
6. Shengqian Dou
7. Wenxiong Tang
8. Hong Zhang
9. Jian Lu

• Curated by eLife

  eLife Assessment

  This study reveals the important role of upstream open reading frames (uORFs) in limiting the translational variability of downstream coding sequences. Through a combination of computational simulations, comparative analyses of translation efficiency across different developmental stages in two closely related Drosophila species, and manipulative, experimental validation of translation buffering by an uORF for a gene, the authors provide convincing evidence supporting their conclusions. This work will be of broad interest to molecular biologists and geneticists.

Reviewed by eLife