eLife

Latest preprint reviews

1. Molecular dynamics simulations illuminate the role of sequence context in the ELF3-PrD-based temperature sensing mechanism in plants

   This article has 6 authors:

   1. Richard J Lindsay
   2. Abhilash Sahoo
   3. Rafael Giordano Viegas
   4. Vitor BP Leite
   5. Philip A Wigge
   6. Sonya M Hanson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this potentially valuable computational study, the authors conducted extensive atomistic and coarse-grained simulations to probe the temperature-dependent phase behaviors of ELF3, a disordered component of the evening complex in plant. The results aim to highlight the role of polyQ tracts in modulating temperature-responsive structural and condensation behavior. Despite considerable improvements in the revised manuscript, the level of evidence is considered incomplete, since several of the supplementary observables introduced to support the revised claim indicate that the variants studied are not statistically distinguishable within the reported replicate uncertainty.

   Reviewed by eLife

2. Ferroptosis-related genes mediate tumor microenvironment and prognosis in triple-negative breast cancer via integrated RNA-seq analysis

   This article has 7 authors:

   1. Xuantong Gong
   2. Lishuang Gu
   3. Di Yang
   4. Yu He
   5. Qian Li
   6. Hao Qin
   7. Yong Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a useful finding for the ferroptosis-mediated tumor microenvironment (TME) in triple-negative breast cancer (TNBC) using public single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data. The data were collected and analyzed using solid and validated methodology and can be used as a starting point for functional studies of TME in TNBC. The work will be of interest to medical biologists working in the field of TNBC.

   Reviewed by eLife

3. In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins

   This article has 8 authors:

   1. Shinichi Kawaguchi
   2. Xin Xu
   3. Takashi Soga
   4. Kenta Yamaguchi
   5. Ryuuya Kawasaki
   6. Ryota Shimouchi
   7. Susumu Date
   8. Toshie Kai

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study employs AlphaFold2 to predict interactions among 20 nuage proteins, identifying five novel interaction candidates, three of which are validated experimentally through co-immunoprecipitation. Expanding the analysis to 430 oogenesis-related proteins and screening ~12,000 Drosophila proteins for interactions with Piwi, the study identifies 164 potential binding partners, demonstrating how computational predictions can streamline experimental validation. This study provides a solid basis for further investigations into eukaryotic protein interaction networks.

   Reviewed by eLife

4. Auditory cortex learns to discriminate audiovisual cues through selective multisensory enhancement

   This article has 5 authors:

   1. Song Chang
   2. Beilin Zheng
   3. Les Keniston
   4. Jinghong Xu
   5. Liping Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that aims to investigate the behavioral relevance of multisensory responses recorded in the auditory cortex. The experiments are elegant and well-designed and are supported by appropriate analyses of the data. Although solid evidence is presented that is consistent with learning-dependent encoding of visual information in auditory cortex, further work is needed to establish the origin and nature of these non-auditory signals and to definitively rule out any effects of movement-related activity.

   Reviewed by eLife

5. An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome

   This article has 13 authors:

   1. Pratibha Thakur
   2. Martin Lackinger
   3. Anastasia Diamantopoulou
   4. Sneha Rao
   5. Yijing Chen
   6. Khakima Khalizova
   7. Annie Ferng
   8. Curt Mazur
   9. Holly Kordasiewicz
   10. Robert J Shprintzen
   11. Sander Markx
   12. Bin Xu
   13. Joseph A Gogos

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that establishes how anti-sense oligonucleotides degrading a specific target protein called EMC10 can rescue neuronal function in models of chromosome 22.11.2 deletions. The authors use human iPSC-derived neurons and a mouse model to provide compelling data for the rescue of cellular and cognitive features of 22.11.2 phenotypes upon ASO regulation of EMC10. These pre-clinical data are of interest because they support reduction of ECM10 as a promising therapeutic strategy.

   Reviewed by eLife

6. RAS–p110α signalling in macrophages is required for effective inflammatory response and resolution of inflammation

   This article has 19 authors:

   1. Alejandro Rosell
   2. Agata Adelajda Krygowska
   3. Marta Alcón Pérez
   4. Cristina Cuesta
   5. Mathieu-Benoit Voisin
   6. Juan de Paz
   7. Héctor Sanz-Fraile
   8. Vinothini Rajeeve
   9. Ana Carreras-González
   10. Alberto Berral-González
   11. Ottilie Swinyard
   12. Enrique Gabandé-Rodríguez
   13. Julian Downward
   14. Jordi Alcaraz
   15. Juan Anguita
   16. Carmen García-Macías
   17. Javier De Las Rivas
   18. Pedro R Cutillas
   19. Esther Castellano Sanchez

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study investigates the impact of disrupting the interaction of RAS with the PI3K subunit p110α in macrophage function in vitro and inflammatory responses in vivo. Solid data overall supports a role for RAS-p110α signalling in regulating macrophage activity and so inflammation, however for many of the readouts presented the magnitude of the phenotype is not particularly pronounced. Further analysis would be required to substantiate the claims that RAS-p110α signalling plays a key role in macrophage function. Of note, the molecular mechanisms of how exactly p110α regulates the functions in macrophages have not yet been established.

   Reviewed by eLife

7. Introduction of cytosine-5 DNA methylation sensitizes cells to oxidative damage

   This article has 7 authors:

   1. Joanna Krwawicz
   2. Caroline J Sheeba
   3. Katie Hains
   4. Thomas McMahon
   5. Yimo Zhang
   6. Skirmantas Kriaucionis
   7. Peter Sarkies

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work advances our understanding of DNA methylation and its consequences for susceptibility to DNA damage. This work presents evidence that DNA methylation can accentuate the genomic damage propagated by DNA damaging agents as well as potentially being an independent source of such damage. The experimental results reported are sound. The evidence presented to support the conclusions drawn is convincing and alternative interpretations are considered. The work will be of broad interest to biochemists, cell and genome biologists.

   Reviewed by eLife

8. HNF4α-TET2-FBP1 axis contributes to gluconeogenesis and type 2 diabetes

   This article has 12 authors:

   1. Hongchen Li
   2. Xinchao Zhang
   3. Xiaoben Liang
   4. Shuyan Li
   5. Ziyi Cui
   6. Xinyu Zhao
   7. Kai Wang
   8. Bingbing Zha
   9. Haijie Ma
   10. Ming Xu
   11. Lei Lv
   12. Yanping Xu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Zhang et al. present important findings that reveal a new role for TET2 in controlling glucose production in the liver, showing that both fasting and a high-fat diet increase TET2 levels, while its absence reduces glucose production. TET2 works with HNF4α to activate the FBP1 gene upon glucagon stimulation, while metformin disrupts TET2-HNF4α interaction, lowering FBP1 levels and improving glucose homeostasis. The results are convincing and expand our understanding of gluconeogenesis regulation.

   Reviewed by eLife

9. Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors

   This article has 9 authors:

   1. Ximena Corso Diaz
   2. Xulong Liang
   3. Kiam Preston
   4. Bilguun Tegshee
   5. Milton A English
   6. Jacob Nellissery
   7. Sharda Prasad Yadav
   8. Claire Marchal
   9. Anand Swaroop

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study employed multiple orthogonal techniques and tissue samples to investigate the interaction between the NRL transcription factor and RNA-binding proteins in the retina. The findings are convincing to support an interaction between NRL and the DHX9 helicase. The significance of the study could be enhanced with functional experiments of NRL-R-loop interactions in the developing retina and their potential role in photoreceptor health and gene regulation.

   Reviewed by eLife

10. Protonation/deprotonation-driven switch for the redox stability of low-potential [4Fe-4S] ferredoxin

    This article has 18 authors:

    1. Kei Wada
    2. Kenji Kobayashi
    3. Iori Era
    4. Yusuke Isobe
    5. Taigo Kamimura
    6. Masaki Marukawa
    7. Takayuki Nagae
    8. Kazuki Honjo
    9. Noriko Kaseda
    10. Yumiko Motoyama
    11. Kengo Inoue
    12. Masakazu Sugishima
    13. Katsuhiro Kusaka
    14. Naomine Yano
    15. Keiichi Fukuyama
    16. Masaki Mishima
    17. Yasutaka Kitagawa
    18. Masaki Unno

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      Ferredoxins are ubiquitous electron transfer proteins that drive essential metabolic processes across all domains of life. This fundamental contribution to the field provides the first description of how specific amino acids, though a series of hydrogen bonds, control the ability of iron-sulfur clusters in ferrodoxins to accept and donate electrons. The evidence supporting the conclusions is compelling as is the combined use of neutron crystallography with X-ray crystallography and classical spectral/redox studies.

    Reviewed by eLife