eLife

Latest preprint reviews

1. Diverse Genotype-by-Weather Interactions in Switchgrass

   This article has 13 authors:

   1. Alice H MacQueen
   2. Li Zhang
   3. Samuel Pattillo Smith
   4. Jason E Bonnette
   5. Arvid R Boe
   6. Philip A Fay
   7. Felix B Fritschi
   8. David B Lowry
   9. Robert B Mitchell
   10. Francis M Rouquette
   11. Yanqi Wu
   12. Arbel Harpak
   13. Thomas E Juenger

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study reports valuable findings on the nature of genotype-by-climate interaction, parameterised in a framework that allows integrating genetics and ecophysiological variation in switchgrass. The evidence provided is solid overall but the analysis could be improved to better support some of the claims.

   Reviewed by eLife

2. Loss of olfaction reduces caterpillar performance and increases susceptibility to a natural enemy

   This article has 8 authors:

   1. Qi Wang
   2. Yufei Jia
   3. Hans M Smid
   4. Berhane T Weldegergis
   5. Liana O Greenberg
   6. Maarten Jongsma
   7. Marcel Dicke
   8. Alexander Haverkamp

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important manuscript investigates the role of olfactory cues in Pieris brassicae larvae, focusing on their interactions with the host plant Brassica oleracea and the parasitoid wasp Cotesia glomerata. The authors' demonstration that impaired olfactory perception reduces caterpillar performance and increases susceptibility to parasitism is convincing. These findings highlight the ecological significance of olfaction in mediating feeding behavior and predator avoidance in herbivorous insects.

   Reviewed by eLife

3. DANCE provides an open-source and low-cost approach to quantify aggression and courtship in Drosophila

   This article has 11 authors:

   1. R Sai Prathap Yadav
   2. Paulami Dey
   3. Faizah Ansari
   4. Tanvi Kottat
   5. Manohar Vasam
   6. P Pallavi Prabhu
   7. Shrinivas Ayyangar
   8. Swathi Bhaskar S
   9. Krishnananda Prabhu
   10. Monalisa Ghosh
   11. Pavan Agrawal

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable open-source and cost-effective method for automating the quantification of male aggression and courtship in Drosophila melanogaster. The work as presented provides solid evidence that the use of the behavioral setup that the authors designed - using readily available laboratory equipment and standardised high-performing classifiers they developed using existing software packages - accurately and reliably characterises social behavior in Drosophila. The work will be of interest to Drosophila neurobiologists and particularly to those working on male social behaviors.

   Reviewed by eLife

4. Mac-/Lactosylceramide regulates intestinal homeostasis and secretory cell fate commitment by facilitating Notch signaling

   This article has 9 authors:

   1. Kebei Tang
   2. Xuewen Li
   3. Jiulong Hu
   4. Jingyuan Shi
   5. Yumei Li
   6. Yansu Chen
   7. Chang Yin
   8. Fengchao Wang
   9. Rongwen Xi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides convincing evidence that glucosylceramide synthase (GlcT), a rate-limiting enzyme for glycosphingolipid (GSL) production, plays a role in the differentiation of intestinal cells. Mutations in GlcT compromise Notch signaling in the Drosophila intestinal stem cell lineage, resulting in the formation of enteroendocrine tumors. Further data suggest that a homolog of glucosylceramide synthase also influences Notch signaling in the mammalian intestine. While the outstanding strengths of the initial genetic and downstream pathway analyses are noted, there are minor weaknesses in the data regarding the potential role of this pathway in Delta trafficking. Nevertheless, this study opens the way for future mechanistic studies addressing how specific lipids modulate Notch signalling activity.

   Reviewed by eLife

5. Generative modeling for RNA splicing prediction and design

   This article has 10 authors:

   1. Di Wu
   2. Natalie Maus
   3. Anupama Jha
   4. Kevin Yang
   5. Benjamin D Wales-McGrath
   6. San Jewell
   7. Anna Tangiyan
   8. Peter Choi
   9. Jacob R Gardner
   10. Yoseph Barash

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     TrASPr is an important contribution that leverages transformer models focused on regulatory regions to enhance predictions of tissue-specific splicing events. The revisions strengthen the manuscript by clarifying methodology and expanding analyses across exon and intron sizes, and the evidence supporting TrASPr's predictive performance is compelling. This work will be of interest to researchers in computational genomics and RNA biology, offering an improved model for splicing prediction and a promising approach to RNA sequence design.

   Reviewed by eLife

6. The ALS-associated co-chaperone DNAJC7 mediates neuroprotection against proteotoxic stress by modulating HSF1 activity

   This article has 5 authors:

   1. Andrew C Fleming
   2. Nalini R Rao
   3. Matthew Wright
   4. Jeffrey N Savas
   5. Evangelos Kiskinis

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Fleming et al sought to better understand DNAJC7's function in motor neurons as mutations in this gene have been associated with amyotrophic lateral sclerosis (ALS). Using iPSC-derived motor neurons, interactome, and transcriptomic data, they provide solid evidence that loss-of-function mutations in DNAJC7 disrupt RNA binding proteins and resistance to proteasomal stress. These important findings advance our understanding of DNAJC7 in motor neurons while providing clues to how its loss may be causal for ALS; nonetheless, the experiments were performed with a single iPSC line, while at least 3 are deemed to be required to validate the results. Furthermore, the mechanistic evidence is still incomplete with respect to how DNAJC7 mutations lead to HSF1 impaired activity, and whether it is direct or not.

   Reviewed by eLife

7. 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

8. 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

9. 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

10. 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