eLife

Latest preprint reviews

1. Criticality-driven enhancer-promoter dynamics in Drosophila chromosomes

   This article has 4 authors:

   1. Gautham Ganesh
   2. Jean-Bernard Fiche
   3. Marcelo Nöllmann
   4. Julien Mozziconacci

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript uses modeling approaches to provide mechanistic insight into the structural and dynamic properties of enhancer-promoter interactions in Drosophila. Given the interest in this field, this is a timely approach, and the results give useful insights by providing predictions about the processivity of cohesin loop extrusion in Drosophila and concluding that the compartmental interaction strength is poised near criticality in the coil-globule phase space. The evidence provided to support some of the conclusions is, however, incomplete and would be strengthened by better considering some of the caveats in the data used to constrain the models, such as the use of "homie" genetic elements in the dynamic data. There is insufficient evidence provided for the dynamics being criticality-driven, and in addition, consideration of alternative models would further strengthen the conclusions of the manuscript.

   Reviewed by eLife

2. RubyACRs Enable Red-Shifted Optogenetic Inhibition in Freely Behaving Drosophila

   This article has 9 authors:

   1. Daniel Bushey
   2. Hiroshi Shiozaki
   3. Yichun Shuai
   4. Jihong Zheng
   5. Vivek Jayaraman
   6. Jeremy P Hasseman
   7. Ilya Kolb
   8. GENIE Project Team
   9. Glenn C Turner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work describes the adaptation and evaluation of two red-shifted anion channelrhodopsins (RubyACRs) for optogenetic inhibition in Drosophila. The study provides convincing evidence for the effectiveness of RubyACRs in fly neurons, including electrophysiology, calcium imaging, and behavioral analysis. With minor revisions to address potential toxicity and compatibility with 2-photon imaging, this paper and the publicly available fly lines it describes will be resources that are of value to the neuroscience community.

   Reviewed by eLife

3. Mycobacterial Metallophosphatase MmpE Acts as a Nucleomodulin to Regulate Host Gene Expression and Promote Intracellular Survival

   This article has 7 authors:

   1. Liu Chen
   2. Baojie Duan
   3. Qiang Jiang
   4. Yifan Wang
   5. Yingyu Chen
   6. Lei Zhang
   7. Aizhen Guo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript is useful as it demonstrates that Rv2577, a Fe³⁺/Zn²⁺-dependent metallophosphatase, is secreted by Mycobacterium bovis BCG and localizes to the nucleus of mammalian cells, altering transcriptional and inflammatory responses. However, the study is incomplete as it lacks activity validation in macrophage cells and with virulent Mycobacterium tuberculosis strains. It is necessary to confirm Rv2577 secretion from a virulent strain and to clarify the direct or indirect role of MmpE in modulating host pathways, together with mechanistic insight into how MmpE influences lysosomal biogenesis and trafficking.

   Reviewed by eLife

4. Decision-making components and times revealed by the single-trial electroencephalogram

   This article has 3 authors:

   1. Gabriel Weindel
   2. Jelmer P Borst
   3. Leendert van Maanen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Weindel et al examine behavioural and EEG data in an innovative contrast comparison paradigm where they vary mean contrast widely while keeping contrast difference constant. As intended, this allowed an elegant decomposition of processing stages: while sensory encoding shortened with increasing contrast in keeping with Pieron's law, the period of decision formation lengthened, in keeping with Fechner's law, which was applied to drift rates in a diffusion model of that period. This is an important demonstration of how these two laws apply in concert, to two distinct processing levels, and the multivariate topography parsing, mixed effect models and diffusion models are convincing.

   Reviewed by eLife

5. iGABASnFR2: Improved genetically encoded protein sensors of GABA

   This article has 19 authors:

   1. Ilya Kolb
   2. Jeremy P Hasseman
   3. Akihiro Matsumoto
   4. Thomas P Jensen
   5. Olga Kopach
   6. Benjamin J Arthur
   7. Yan Zhang
   8. Arthur Tsang
   9. Daniel Reep
   10. Getahun Tsegaye
   11. Jihong Zheng
   12. Ronak H Patel
   13. Loren L Looger
   14. Jonathan S Marvin
   15. Wyatt L Korff
   16. Dmitri A Rusakov
   17. Keisuke Yonehara
   18. GENIE Project Team
   19. Glenn C Turner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript reports the development and characterization of iGABASnFR2, a genetically encoded GABA sensor that demonstrates substantially improved performance compared to its predecessor, iGABASnFR1. The work is comprehensive and methodologically rigorous, combining high-throughput mutagenesis, functional screening, structural analysis, biophysical characterization, and in vivo validation. The significance of the findings is fundamental, and the supporting evidence is compelling. iGABASnFR2 represents a notable advance in GABA sensor engineering, enabling enhanced imaging of GABA transmission both in brain slices and in vivo, and constitutes a timely, technically robust addition to the molecular toolkit for neuroscience research.

   Reviewed by eLife, PREreview

6. Modality-Agnostic Decoding of Vision and Language from fMRI

   This article has 6 authors:

   1. Mitja Nikolaus
   2. Milad Mozafari
   3. Isabelle Berry
   4. Nicholas Asher
   5. Leila Reddy
   6. Rufin VanRullen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study introduces a valuable dataset for investigating the relationship between vision and language in the brain. The authors provide convincing evidence that decoders trained on brain responses to both images and captions outperform those trained on responses to a single modality. The dataset and decoder results will be of interest to communities studying brain and machine decoding.

   Reviewed by eLife

7. A forebrain hub for cautious actions via the midbrain

   This article has 4 authors:

   1. Ji Zhou
   2. Muhammad Sarmad Sajid
   3. Sebastian Hormigo
   4. Manuel A Castro-Alamancos

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study uses fiber photometry, implantable lenses, and optogenetics, to show that a subset of subthalamic nucleus neurons are active during movement, and that active but not passive avoidance depends in part on STN projections to substantia nigra. The strength of the evidence for these claims is solid and this paper may be of interest to basic and applied behavioural neuroscientists working on movement or avoidance.

   Reviewed by eLife

8. Pathogenic O-GlcNAc dyshomeostasis associated with cortical malformations and hyperactivity

   This article has 15 authors:

   1. Florence Authier
   2. Asad Jan
   3. Islam Faress
   4. Christian Stald Skoven
   5. Iria Esperon-Abril
   6. Shagana Tharmakulasingam Balasubramaniam
   7. Kévin-Sébastien Coquelin
   8. Jens R Nyengaard
   9. Carsten Scavenius
   10. Benedetta Attianese
   11. Oscar G Sevillano-Quispe
   12. Simon Fristed Eskildsen
   13. Jesper Skovhus Thomsen
   14. Brian Hansen
   15. Daan MF van Aalten

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that takes a key step towards understanding developmental disorders linked to mutations in the O-GlcNAc transferase enzyme by generating a mouse model harboring the C921Y mutation. The study thoroughly examines behavioral and anatomical differences in these mice and finds behavioral hyperactivity and learning/memory deficits, as well as phenotypic differences in skull and brain formation. However, the experimental evidence is incomplete owing to discrepancy in OGT protein/RNA levels in the C921Y mutant mice in this paper and the previous paper ("Neurodevelopmental defects in a mouse model of O-GlcNAc transferase intellectual disability "). This line of research will benefit from investigation of the differences in associated glycoproteins and mechanistic insights. This study will be of interest to those studying neurodevelopment, learning and behavior, or associated brain mechanisms.

   Reviewed by eLife

9. Inferring variant-specific effective reproduction numbers from combined case and sequencing data

   This article has 2 authors:

   1. Marlin D Figgins
   2. Trevor Bedford

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides new important insights concerning pathogen variant-specific reproduction parameters from molecular sequencing and case finding. The methods for inferring which variants will likely emerge in subsequent epidemic cycles are solid. This article is of broad interest to infectious disease epidemiology researchers and mathematical modellers of the COVID-19 pandemic.

   Reviewed by eLife, ScreenIT

10. Mood computational mechanisms underlying increased risk behavior in adolescent suicidal patients

    This article has 9 authors:

    1. Zhihao Wang
    2. Tian Nan
    3. Fengmei Lu
    4. Yue Yu
    5. Xiao Cai
    6. Zongling He
    7. Yuejia Luo
    8. Ting Wang
    9. Bastien Blain

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This valuable study combined careful computational modeling, a large patient sample, and replication in an independent general population sample to provide a computational account of a difference in risk-taking between people who have attempted suicide and those who have not. It is proposed that this difference reflects a general change in the approach to risky (high-reward) options and a lower emotional response to certain rewards. Evidence for the specificity of the effect to suicide, however, is incomplete, which would require additional analyses.

    Reviewed by eLife