eLife

Latest preprint reviews

1. An Itch Receptor Drives Melanoma

   This article has 13 authors:

   1. Naina Gour
   2. Aishwarya Atakkatan
   3. Moloud Akbarzadeh
   4. Hwan Mee Yong
   5. Aishwarya Magesh
   6. Zhiping Wu
   7. Hyunkeun Joo
   8. Yash Chhabra
   9. Junmin Peng
   10. Ashani Weeraratna
   11. Mathieu Laplante
   12. Stephane Lajoie
   13. Xinzhong Dong

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work has much novelty, supportive data, and the potential for changing thinking about melanoma biology with the discovery of MRGPRX4 as a relatively melanoma-specific G protein-coupled receptor. MRGPRX4 is normally restricted to peripheral sensory neurons, but it is aberrantly expressed in human melanomas; melanomas with neural-crest-like/invasive features were most likely affected. When ectopically expressed in murine melanocytes, MRGPRX4 drives melanoma development with metastasis; the mechanism appears to involve ligand-independent receptor signaling. Overall, the text presents this as a novel model of oncogenesis driven by re-expression of a sensory GPCR - this is an important study with compelling data.

   Reviewed by eLife

2. Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

   This article has 6 authors:

   1. Kuan-Hao Chao
   2. Majed Mohamed Magzoub
   3. Emily H. Stoops
   4. Sean Hackett
   5. Johannes Linder
   6. David R. Kelley

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study shows that self-supervised pretraining on related fungal genomes can substantially improve sequence-to-expression prediction in budding yeast. The evidence for the main conclusion is convincing, with careful comparisons to models trained from random initialization and clear gains on held-out expression data. The broader claims about the optimal evolutionary scope and transfer of regulatory grammar are less fully supported.

   Reviewed by eLife

3. Novel but stable endosymbionts have contrasting effects on aphid dispersal and plant feeding damage in the cereal pest Diuraphis noxia

   This article has 12 authors:

   1. Xinyue Gu
   2. Alex Gill
   3. Qiong Yang
   4. Perran Ross
   5. Lucy Hayward
   6. Monica Stelmach
   7. Paul A Umina
   8. Sheik Nadeem Elahee Doomun
   9. Mel Berran
   10. Lauren Coakley
   11. Sonia Sharma
   12. Ary Hoffmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study investigates how experimentally introducing two facultative bacterial endosymbionts into the Russian wheat aphid, Diuraphis noxia, affects aphid performance, dispersal, and damage to cereal host plants and the authors provide solid evidence for contrasting symbiont-associated phenotypes under controlled conditions: Rickettsiella increases plant damage while reducing wing production and dispersal, whereas Regiella reduces feeding damage and, at some time points, aphid population growth. The stable establishment of these novel symbiont-host associations and complementary experiments spanning individual aphids, whole plants, populations, and mesocosms are notable strengths and the revised manuscript better clarifies the experimental approaches and the context dependence of symbiont effects; however, the underlying mechanisms remain unresolved, horizontal transmission is inferred rather than directly demonstrated, and limited replication and temporal variability constrain some population-level conclusions. Potential applications to pest management therefore require further validation under field conditions. The study will interest researchers working on insect symbiosis, plant-insect interactions, and biologically based pest management.

   Reviewed by eLife

4. IFNγ and IFNγ mimetics prevent IFN-I-mediated TB susceptibility by regulating iron metabolism and lipid peroxidation

   This article has 11 authors:

   1. Prasanna Babu Araveti
   2. Shivraj M Yabaji
   3. Muhammad Zainul Arifin
   4. Suruchi Lata
   5. Yuriy O Alekseyev
   6. Alexander A Gimelbrant
   7. William R Bishai
   8. Vadim Zhernovkov
   9. Oleksii S Rukhlenko
   10. Boris N Kholodenko
   11. Igor Kramnik

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Using a range of complementary approaches, this study examines how type I and type II interferon (IFN) programs exert opposing effects on macrophage responses relevant to tuberculosis. The work addresses a key biological question and provides valuable mechanistic insights. However, the data to support several key conclusions is incomplete and requires further strengthening; in particular, the role of ferritin needs to be established more definitively, the TNF stimulation findings should be validated in the context of M. tuberculosis infection, and in vivo evidence is needed to support the proposed therapeutic strategy. Additionally, aspects of iron metabolism, lipid peroxidation, and the translatability of the findings between mouse and human macrophages would benefit from greater clarity and deeper mechanistic investigation.

   Reviewed by eLife

5. Break-induced replication drives large-scale genomic amplifications in cancer cells

   This article has 4 authors:

   1. Mouadh Benamar
   2. Rebeka Eki
   3. Kang-Ping Du
   4. Tarek Abbas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents important findings that genome-wide DNA double-strand breaks trigger large-scale genomic amplification (DIGA), which does not require origin re-licensing, but is dependent on some proteins that are involved in break-induced replication (BIR). While the findings and model are compelling, the evidence supporting the claims is largely incomplete, as it depends primarily on a single assay to examine amplification. This work will be of interest to scientists in the DNA repair, replication, and cell cycle fields, as well as cancer biologists.

   Reviewed by eLife

6. Galectin and Myc enable cochlear progenitor expansion in vitro and in vivo

   This article has 8 authors:

   1. Marie Kubota
   2. Julia M. Abitbol
   3. Paul K. Lee
   4. Maggie S. Matern
   5. Sonia Bustos Barocio
   6. Taha A. Jan
   7. Alan G. Cheng
   8. Stefan Heller

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on a potential new regulatory mechanism for cellular proliferation in the mammalian cochlea, taking advantage of the organoid-forming potential of cells from the greater epithelial ridge (GER), or Kolliker's organ, a transient structure in the developing cochlea. The authors highlight three potential regulators - galectin 1, galectin 3, and Myc - providing solid evidence for potential roles in modulating the proliferation of cochlear GER cells using gene expression studies, single-cell profiling, pharmacological inhibition, and genetic overexpression both in vitro and in vivo. However, some of the analyses and interpretations are incomplete, and a better understanding of how the compounds and the gene overexpression studies affect the cells and modulate cell survival/death would aid a fuller interpretation of the data.

   Reviewed by eLife

7. A new diagnostic modality for bovine tuberculosis: accurate and robust classification of infected cattle using transcriptomics and machine learning

   This article has 18 authors:

   1. John F O’Grady
   2. Adriana Ivich
   3. Gillian P McHugo
   4. Adnan Khan
   5. Thomas J Hall
   6. Sarah L Faherty O’Donnell
   7. Carolina N Correia
   8. John A Browne
   9. Valentina Riggio
   10. James GD Prendergast
   11. Emily L Clark
   12. Hubert Pausch
   13. Kieran G Meade
   14. Isobel C Gormley
   15. Eamonn Gormley
   16. Stephen V Gordon
   17. Casey S Greene
   18. David E MacHugh

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study provides a proof of concept for the utility of transcriptomic methods to develop novel diagnostic tests for bovine tuberculosis. A comprehensive analysis using a suite of machine learning models provides convincing evidence for the use of mRNA biomarkers to distinguish between infected and disease-free animals. The analysis also provides major insights into both the levels of individual variation in expression between animals as well as systematic changes with respect to the time from infection.

   Reviewed by eLife

8. A quantitative portrait of habituation in Stentor coeruleus

   This article has 4 authors:

   1. Tejas Ramdas
   2. Nhi Doan
   3. Austen Theroux
   4. Samuel J. Gershman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study advances our understanding of habituation and related potentiation behavior in a single-celled organism, Stentor. The authors provide convincing evidence for their claims in the form of extensive data on habituation behavior. The work will be of interest to cell biologists, neuroscientists, and also scientists broadly interested in behavior in non-neural organisms.

   Reviewed by eLife

9. Alpha and theta dynamics successively resolve competition between rival visual stimuli

   This article has 4 authors:

   1. Wen Wen
   2. Yichen Wu
   3. Robert M.G. Reinhart
   4. Sheng Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this study, electroencephalography was recorded during a binocular-rivalry paradigm in which participants viewed a target and a distractor stimulus. The stimuli were independently frequency-tagged, allowing the researchers to track target and distractor processing over time. The findings suggest that parietal alpha oscillations initially segregate competing inputs, followed by frontal theta activity associated with suppression of distractor representations. The significance of these findings is valuable, although the strength of the evidence remains incomplete, because of specific experiment design choices and methodological limitations.

   Reviewed by eLife

10. Selective loss of Nkx2.1-lineage neurons in the lateral septum alters the balance between novelty seeking and threat avoidance

    This article has 12 authors:

    1. Miguel Turrero García
    2. Diana N Tran
    3. Ralph E Peterson
    4. Leena A Ibrahim
    5. Christopher M Reid
    6. Sarah M Hanson
    7. Yuqi Ren
    8. Fiona Dale-Huang
    9. Yajun Xie
    10. Sarah K Stegmann
    11. Steve Vu
    12. Corey C Harwell

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study integrates mouse genetics with sequencing, electrophysiological and behavioral tools to uncover the behavioral role and molecular profile of a developmentally defined subpopulation in the lateral septum. The data collected and analyzed are convincing, highlighting the role of this subpopulation in threat avoidance and stress, providing a framework by which developmental origin is linked to mature neuronal function. The work will be of interest to biologists and neuroscientists working on development and behavior.

    Reviewed by eLife