eLife

Latest preprint reviews

1. Transforming a Fragile Protein Helix into an Ultrastable Scaffold via a Hierarchical AI and Chemistry Framework

   This article has 6 authors:

   1. Jun Qiu
   2. Guojin Tang
   3. Tianfu Feng
   4. Bin Zheng
   5. Yuanhao Liu
   6. Peng Zheng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable work describes a computational and experimental workflow that turns a moderately stable α-helical bundle into a very stable fold. The authors advance our understanding of α-helix stabilization and provide a convenient framework with implications for the protein design field. The main claims are supported by convincing evidence through sound and well-validated methods, yet further characterization would strengthen specific conclusions for the design of mechanically, thermally, and chemically stable α-helical bundles.

   Reviewed by eLife

2. AutoMorphoTrack: A modular framework for quantitative analysis of organelle morphology, motility, and interactions at single-cell resolution

   This article has 3 authors:

   1. Armin Bayati
   2. Jackson G Schumacher
   3. Xiqun Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work describes a useful computational tool for automated morphometry of dynamic organelles from microscope images. However, the supporting evidence and novelty of the manuscript as presented are incomplete and could be improved. The work will be of interest to microscopists and bioimage analysts who are non-experts but wish to improve quantitative analysis of cellular structures.

   Reviewed by eLife

3. Complex environmental cycles reveal evolution of circadian activity waveform and thermosensitive timeless splicing

   This article has 2 authors:

   1. Pragya Niraj Sharma
   2. Vasu Sheeba

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study examines how mismatched light and temperature cycles shape Drosophila locomotor timing and temperature-dependent timeless splicing, and leverages long-term early/late selection lines to probe evolutionary plasticity. The strength of evidence is incomplete at present, mainly because startle/masking under step cues could confound the behavioural readouts, and tim's involvement remains correlative. The authors should address masking in the behaviour analyses and provide causal support for tim's role.

   Reviewed by eLife

4. Simple Methods to Acutely Measure Multiple Timing Metrics among Sexual Repertoire of Male Drosophila

   This article has 6 authors:

   1. Yutong Song
   2. Dongyu Sun
   3. Xiao Liu
   4. Fan Jiang
   5. Xuejiao Yang
   6. Woo Jae Kim

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful paper describes a software tool, "DrosoMating", which allows automated, high-throughput quantification of 6 common metrics of courtship and mating behaviors in Drosophila melanogaster. The validity of the tool is quite convincingly demonstrated by comparing expert human assessments with those made by DrosoMating. The work, however, does not address how DrosoMating compares with or advances on other existing tools for exactly the same purpose, whether it can be used for studies of other Drosophila species, and/or whether finer aspects of courtship response timing - which depend on proximal female signals to the male - could be extracted with more detailed analyses. Some additional statistical analyses would also help further strengthen the authors' current conclusions.

   Reviewed by eLife

5. Rank- and Threat-Dependent Social Modulation of Innate Defensive Behaviors

   This article has 3 authors:

   1. Ling-yun Li
   2. Xinjian Gao
   3. Ya-tang Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors investigate how dominance hierarchy shapes defensive strategies in mice under two naturalistic threats: a transient visual looming stimulus and a sustained live rat. This study provides important insights into how social context and dominance hierarchy modulate innate defensive behaviors across distinct naturalistic threats. The strength of evidence is convincing, with detailed classification and analysis of behaviors.

   Reviewed by eLife

6. Decoding state specific connectivity during speech production and perception

   This article has 7 authors:

   1. Yasamin Esmaeili
   2. Amirhossein Khalilian-Gourtani
   3. Orrin Devinsky
   4. Werner K Doyle
   5. Patricia Dugan
   6. Daniel Friedman
   7. Adeen Flinker

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work represents a valuable finding of how single-trial functional connectivity may be used to infer different cognitive states involved in speech perception and production. Although the data and analyses are overall convincing, the theoretical advance and novelty of the finding are less clear. With a clearer idea of the functional significance of the connectivity data, the paper would be of interest to those interested in brain networks and communication.

   Reviewed by eLife

7. High-Throughput Quantification of Population Dynamics using Luminescence

   This article has 4 authors:

   1. Malte Muetter
   2. Daniel Angst
   3. Roland Regoes
   4. Sebastian Bonhoeffer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Muetter et al. provide an important argument that luminescence is a reliable, high-throughput alternative to colony-forming units (CFU) for super-MIC investigations, particularly when the quantity of interest is biomass. By examining 20 antimicrobials spanning 11 classes, the work shows that discrepancies between CFU and luminescence are often biological (filamentation, Viable But Not Culturable). The work provides a compelling view of how these three common measurements (luminescence, optical density, and CFU) relate to one another across a range of drug treatments, although testing on clinical isolates could be of further benefit.

   Reviewed by eLife

8. E3 Ubiquitin Ligase Highwire/Phr1 Phase Separation Mediates Endocytic Control of JNK Signaling in Drosophila Neurons

   This article has 7 authors:

   1. Srikanth Pippadpally
   2. Anjali Bisht
   3. Saumitra Dey Choudhury
   4. Manish Kumar Dwivedi
   5. Zeeshan Mushtaq
   6. Suneel Reddy-Alla
   7. Vimlesh Kumar

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable findings on how the activity of the E3 ubiquitin ligase Highwire (Hiw/Phr1) is regulated and its impact on synaptic growth. The authors propose that impaired endocytosis leads to condensation of Hiw, resulting in increased synaptic growth. They also integrate such a mechanism within the known JNK (c-JUN N-terminal Kinase) and BMP (Bone Morphogenetic Protein) signalling pathways involved in synapse regulation. While the work raises an interesting mechanistic framework, several aspects of the experimental design and methodology are incomplete, and key conclusions, particularly those regarding the liquid-liquid phase separation of the E3 ubiquitin ligase, are not fully supported by the presented data.

   Reviewed by eLife

9. Disentangling Cephalopod Chromatophores Motor Units with Computer Vision

   This article has 7 authors:

   1. Mathieu DM Renard
   2. Johann Ukrow
   3. Margot Elmaleh
   4. Dominic A Evans
   5. Yifan Wu
   6. Xitong Liang
   7. Gilles Laurent

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study uses a computer vision pipeline to infer the motor control of cephalopod skin, revealing that individual chromatophores exhibit anisotropic deformations and can be associated with multiple putative motor units. The evidence supporting these claims is solid, although the study's conclusions are limited to stationary or sedated animals, and the analyses of motor unit characteristics and electrophysiological validation remain incomplete. This work will be of significant interest to biologists studying cephalopod behavior and motor control.

   Reviewed by eLife

10. Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data

    This article has 5 authors:

    1. Alessio P Buccino
    2. Arjun Sridhar
    3. David Feng
    4. Karel Svoboda
    5. Joshua H Siegle

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study presents a valuable and well-documented computational pipeline for the scalable analysis and spike sorting of large extracellular electrophysiology datasets, with particular relevance for high-density recordings such as Neuropixels. The authors demonstrate the pipeline's utility for benchmarking spike sorter performance and evaluating the effects of data compression, supported by thorough testing, clear figures, and openly available code. The workflow is reproducible, portable, and practical, providing concrete guidance on computational cost and runtime. Overall, the evidence supporting the pipeline's performance and output quality is compelling, and this work will be of broad interest to the systems neuroscience community.

    Reviewed by eLife