eLife

Latest preprint reviews

1. Pu.1/Spi1 dosage controls the turnover and maintenance of microglia in zebrafish and mammals

   This article has 9 authors:

   1. Yi Wu
   2. Weilin Guo
   3. Haoyue Kuang
   4. Xiaohai Wu
   5. Thi Huong Trinh
   6. Yuexin Wang
   7. Shizheng Zhao
   8. Zilong Wen
   9. Tao Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings on the regulation of survival and maintenance of brain-resident immune cells called microglia. Using compelling and sophisticated genetic tools, the authors demonstrate a gene dosage-dependent mechanism using which microglia are eliminated. This research on cell competition and survival will be of broad interest to the cell biology community.

   Reviewed by eLife

2. Distributed subthreshold representation of sharp wave-ripples by hilar mossy cells

   This article has 4 authors:

   1. Ayako Ouchi
   2. Taro Toyoizumi
   3. Nobuyoshi Matsumoto
   4. Yuji Ikegaya

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Using intracellular in vitro and in vivo recordings and a deep learning approach, this study shows that mouse dentate gyrus mossy cells (MCs) and CA3 pyramidal cells process information from an important electrophysiological hall mark of hippocampus, sharp wave-ripples (SWRs). The innovative use of deep learning to predict SWR waveforms from MC membrane potentials represents an interesting methodological advance. While the key findings are potentially fundamental, some of the evidence is currently incomplete and should be revised to better support the findings.

   Reviewed by eLife

3. Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

   This article has 10 authors:

   1. Jessica Jocher
   2. Philipp Janssen
   3. Beate Vieth
   4. Fiona C Edenhofer
   5. Tamina Dietl
   6. Anita Térmeg
   7. Paulina Spurk
   8. Johanna Geuder
   9. Wolfgang Enard
   10. Ines Hellmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors make an important contribution to comparative functional genomics by developing a semi-automated computational pipeline that integrates classification and marker-based cluster annotation to identify orthologous cell types. Using a single-cell RNA-seq dataset of induced pluripotent stem cells and derived embryonic bodies from four primate species: humans, orangutans, cynomolgus macaques, and rhesus macaques, the authors provide convincing evidence that cell type-specific marker genes are substantially less transferable across species than broadly expressed genes, with transferability declining as phylogenetic distance increases. This study establishes a key framework and reference dataset for comparative single-cell analyses and encourages more rigorous evaluation of marker gene transferability across species.

   Reviewed by eLife

4. MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

   This article has 41 authors:

   1. Naomi Martin
   2. Paul Olsen
   3. Jacob Quon
   4. Jazmin Campos
   5. Nasmil Valera Cuevas
   6. Josh Nagra
   7. Marshall VanNess
   8. Zoe Maltzer
   9. Emily C Gelfand
   10. Alana Oyama
   11. Amanda Gary
   12. Yimin Wang
   13. Angela Alaya
   14. Augustin Ruiz
   15. Cade Reynoldson
   16. Cameron Bielstein
   17. Christina Alice Pom
   18. Cindy Huang
   19. Cliff Slaughterbeck
   20. Elizabeth Liang
   21. Jason Alexander
   22. Jeanelle Ariza
   23. Jocelin Malone
   24. Jose Melchor
   25. Kaity Colbert
   26. Krissy Brouner
   27. Lyudmila Shulga
   28. Melissa Reding
   29. Patrick Latimer
   30. Raymond Sanchez
   31. Stuard Barta
   32. Tom Egdorf
   33. Zachary Madigan
   34. Chelsea M Pagan
   35. Jennie L Close
   36. Brian Long
   37. Michael Kunst
   38. Ed S Lein
   39. Hongkui Zeng
   40. Delissa McMillen
   41. Jack Waters

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides a valuable contribution to spatial transcriptomics by introducing MerQuaCo, a computational tool for standardizing quality control in image-based spatial transcriptomics datasets. The tool addresses the lack of consensus in the field and provides robust metrics to identify and quantify common imperfections in datasets. The work is supported by an impressive dataset and compelling analyses, and will be of significant interest to researchers focused on data reproducibility and downstream analysis reliability in spatial transcriptomics.

   Reviewed by eLife

5. Thrifty wide-context models of B cell receptor somatic hypermutation

   This article has 7 authors:

   1. Kevin Sung
   2. Mackenzie M Johnson
   3. Will Dumm
   4. Noah Simon
   5. Hugh Haddox
   6. Julia Fukuyama
   7. Frederick A Matsen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides an important method to model the statistical biases of hypermutations during the affinity maturation of antibodies. The authors show convincingly that their model outperforms previous methods with fewer parameters; this is made possible by the use of machine learning to expand the context dependence of the mutation bias. They also show that models learned from nonsynonymous mutations and from out-of-frame sequences are different, prompting new questions about germinal center function. Strengths of the study include an open-access tool for using the model, a careful curation of existing datasets, and a rigorous benchmark; it is also shown that current machine-learning methods are currently limited by the availability of data, which explains the only modest gain in model performance afforded by modern machine learning.

   Reviewed by eLife

6. Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma

   This article has 13 authors:

   1. James Purzner
   2. Alexander S Brown
   3. Teresa Purzner
   4. Lauren Ellis
   5. Sara Broski
   6. Ulrike Litzenburger
   7. Kaytlin Andrews
   8. Aryaman Sharma
   9. Xin Wang
   10. Michael D Taylor
   11. Yoon-Jae Cho
   12. Margaret T Fuller
   13. Matthew P Scott

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Using an unbiased approach, this important study discovered a role of Ezh2 in the differentiation of granule neuron precursors, the cell of origin for Shh group of medulloblastoma. Furthermore, the authors also provided solid evidence that combined inhibition of Ezh2 and CDK4/6 likely represents a promising strategy for the treatment of this subgroup of MB. Validation of these findings using the FDA-approved Ezh2 inhibitor is needed to further strengthen this preclinical study.

   Reviewed by eLife

7. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2409.19469v1

8. Late maturation of semantic control promotes conceptual development

   This article has 3 authors:

   1. Rebecca L Jackson
   2. Matthew A Lambon Ralph
   3. Timothy T Rogers

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings suggesting that the late maturation of prefrontal cortex-based control processes enhances conceptual learning by allowing a period of less-constrained knowledge acquisition. The authors provide convincing computational evidence that delayed semantic control promotes learning without compromising representation integrity, with the strongest benefits emerging when control connections target intermediate layers of the model. However, the model's narrow scope raises concerns about scalability to more complex, real-world learning environments, and the meta-analysis, while supporting the developmental trajectory, does not directly test the model's specific predictions regarding task outcomes or error patterns.

   Reviewed by eLife

9. A titin missense variant drives atrial electrical remodeling and is associated with atrial fibrillation

   This article has 15 authors:

   1. Mahmud Arif Pavel
   2. Hanna Chen
   3. Michael Hill
   4. Arvind Sridhar
   5. Miles Barney
   6. Jaime DeSantiago
   7. Abhinaya Baskaran
   8. Asia Owais
   9. Shashank Sandu
   10. Faisal A Darbar
   11. Aylin Ornelas Loredo
   12. Bahaa Al-Azzam
   13. Brandon Chalazan
   14. Jalees Rehman
   15. Dawood Darbar

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study presents important findings regarding the incidence and clinical impact of a mutation in a cardiac muscle protein and its association with the development of atrial fibrillation. The authors provide convincing evidence of electrophysiological disturbances in cells with this mutation and of its association with atrial fibrillation, which would be of interest to cardiologists. Evidence supporting the conclusion that this mutation causes atrial fibrillation would benefit from more rigorous electrophysiologic approaches.

   Reviewed by eLife

10. Heat stress induces phage tolerance in Enterobacteriaceae

    This article has 7 authors:

    1. Fan Zhang
    2. Hao-Ze Chen
    3. Bo Zheng
    4. Liang Huang
    5. Ye Xiang
    6. Jing-Ren Zhang
    7. Jia-Feng Liu

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study analyzes the effect of heat treatment on phage-bacterial interactions and convincingly shows that prior heat exposure alters the bacterial cell envelope, enhancing persistence and bacterial survival when exposed to lytic phages. The study will interest researchers working on antibiotic resistance, tolerance, and phage therapy.

    Reviewed by eLife