eLife

Latest preprint reviews

1. REPOP: bacterial population quantification from plate counts

   This article has 6 authors:

   1. Pedro Pessoa
   2. Carol Lu
   3. Stanimir Asenov Tashev
   4. Rory Kruithoff
   5. Douglas P Shepherd
   6. Steve Pressé

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces a Bayesian method to determine bacterial counts that accounts for the experimental noise inherent to dilution and plating methods, and distinguishes it from biological uncertainty. The evidence supporting the conclusions is convincing, combining simulated data and experimental data. The method will be of interest to microbial ecologists, and potentially to the broader community interested in inference from biological data, even more so if the domain of application and the limitations are further clarified.

   Reviewed by eLife

2. Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

   This article has 11 authors:

   1. Wei Dong
   2. Guihu Wang
   3. Senyang Li
   4. Yichao Chai
   5. Qian Wang
   6. Yucheng Li
   7. Qiaoman Fei
   8. Yujin Zong
   9. Jing Geng
   10. Pengfei Liu
   11. Zongfang Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents an innovative noninvasive immunotherapeutic strategy for hepatocellular carcinoma by combining ultrasound stimulation with calcium-loaded nanodroplets to activate splenic immune responses. The authors provide solid preclinical data, including single-cell transcriptomic analyses and evidence of tumor growth suppression, supported by a creative and well-executed methodology. Further validation of the calcium signaling mechanisms and assessment of long-term safety will strengthen the translational potential of this approach. The work will be of broad interest to researchers in oncology, immunotherapy, and biomedical engineering.

   Reviewed by eLife

3. The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

   This article has 10 authors:

   1. Terence Li
   2. Marcus Alvarez
   3. Cuining Liu
   4. Kevin Abuhanna
   5. Yu Sun
   6. Jason Ernst
   7. Kathrin Plath
   8. Brunilda Balliu
   9. Chongyuan Luo
   10. Noah Zaitlen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study introduces ambisim, a rigorously validated and well-documented simulation framework that enables the generation of synthetic, genotype-aware single-cell RNA and ATAC sequencing datasets under realistic conditions. The authors provide solid evidence of its utility by benchmarking multiple demultiplexing methods and proposing a new variant consistency metric. While the tool is valuable for guiding method selection, the interpretation of the new metric requires further clarification.

   Reviewed by eLife

4. Neural Representation of Time across Complementary Reference Frames

   This article has 4 authors:

   1. Yangwen Xu
   2. Nicola Sartorato
   3. Léo Dutriaux
   4. Roberto Bottini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on the neural representation of time from two distinct egocentric and allocentric reference frames. The presentation of evidence in the version of the original submission is incomplete, as further conceptual clarifications, methodological details, and addressing potential confounds would strengthen the study. The work will be of interest to cognitive neuroscientists working on the perception and memory of time.

   Reviewed by eLife

5. Reorganization of spinal neural connectivity following recovery after thoracic spinal cord injury: insights from computational modelling

   This article has 5 authors:

   1. Natalia A Shevtsova
   2. Andrew B Lockhart
   3. Ilya A Rybak
   4. David SK Magnuson
   5. Simon M Danner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study describes a computational model of the rat spinal locomotor circuits and how they could be plastically reconfigured after lateral hemisection or contusion injuries to replicate gaits observed experimentally in vivo. Overall, the simulation results convincingly mirror the gait parameters observed experimentally. The model suggests the emergence of detour circuits after lateral hemisection, whereas after a midline contusion, the model suggests plasticity of left-right and sensory inputs below the injury.

   Reviewed by eLife

6. G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa

   This article has 2 authors:

   1. Alain Garcia De Las Bayonas
   2. Nicole King

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study fills an gap in our knowledge of the evolution of GPCRs in holozoans, as well as the phylogeny of associated signaling pathway components such as G proteins, GRKs, and RIC8 proteins. The evidence supporting the conclusions is compelling, with the analysis of extensive new genomic data from choanoflagellates and other non-animal holozoans. Overall, the study is thorough and well-executed. It will be a resource for researchers interested in both the comparative genomics of multicellularity and GPCR biology more broadly, especially given the importance of GPCRs as highly druggable targets.

   Reviewed by eLife

7. Genetic compensation in podocalyxin-like mutants during zebrafish liver development

   This article has 8 authors:

   1. Alexis N Ross
   2. Natalie M Miscik
   3. Sharanya Maanasi Kalasekar
   4. James D Harris
   5. Mimi Tran
   6. Aavrati Saxena
   7. Steven Andrew Baker
   8. Kimberley Jane Evason

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The manuscript by Ross, Miscik, and others describes an intriguing series of observations made when investigating the requirement for podxl during hepatic development in zebrafish. Understanding how genetic compensation pathways are involved in gene function is an important question. However, there is incomplete evidence provided in the manuscript at this point to conclude that discrepancies between observed phenotypes are due to genetic compensation.

   Reviewed by eLife

8. Insights from aquaporin structures into drug-resistant sleeping sickness

   This article has 23 authors:

   1. Modestas Matusevicius
   2. Robin A Corey
   3. Marcos Gragera
   4. Keitaro Yamashita
   5. Teresa Sprenger
   6. Marzuq A Ungogo
   7. James N Blaza
   8. Pablo Castro-Hartmann
   9. Dimitri Y Chirgadze
   10. Sundeep Chaitanya Vedithi
   11. Pavel Afanasyev
   12. Roberto Melero
   13. Rangana Warshamanage
   14. Anastasiia Gusach
   15. Jose Maria Carazo
   16. Mark Carrington
   17. Tom L Blundell
   18. Garib Murshudov
   19. Phillip Stansfeld
   20. Mark Sansom
   21. Harry P de Koning
   22. Christopher G Tate
   23. Simone N Weyand

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this important study, the authors set out to determine the molecular interactions between the AQP2 from Trypanosoma brucei (TbAQP2) and the trypanocidal drugs pentamidine and melarsoprol in order to clarify the origins of clinically observed drug resistance and facilitate future drug design. Using cryo-EM, molecular dynamics simulations, and lysis assays, the authors present a solid theory for how drug resistance mutations in TbAQP2 prevent drug uptake. Overall, even though a few methodological issues still need minor clarification, this study will be of interest to those working on aquaporins and the development of drugs targeting aquaporins.

   Reviewed by eLife

9. Glial betaPix is essential for blood vessel integrity in the zebrafish brain

   This article has 7 authors:

   1. ShihChing Chiu
   2. Qinchao Zhou
   3. Chenglu Xiao
   4. Linlu Bai
   5. Xiaojun Zhu
   6. Wanqiu Ding
   7. Jing-Wei Xiong

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable manuscript presents findings supported by solid data to identify a surprising glia-exclusive function for betapix in vascular integrity and angiogenesis. The manuscript also describes the optimisation of a modified CRISPR-based Zwitch approach to generate conditional knockouts in zebrafish.

   Reviewed by eLife

10. Molecular Landscape of the Mouse Adrenal Gland and Adjacent Adipose by Spatial Transcriptomics

    This article has 9 authors:

    1. Małgorzata Blatkiewicz
    2. Szymon Hryhorowicz
    3. Marta Szyszka
    4. Joanna Suszyńska-Zajczyk
    5. Andrzej Pławski
    6. Adam Plewiński
    7. Andrea Porzionato
    8. Ludwik K. Malendowicz
    9. Marcin Rucinski

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This useful study provides a spatial transcriptomic analysis of the mouse adrenal gland that could have implications for future research and applications. The authors present solid results that allow the dissection of the cell signalling pathways and cellular composition of different zones of the adrenal glands in the mouse model; they propose new zone-specific gene markers and specific intra- and inter-zonal signaling pathways based on receptor-ligand expression patterns. Their web tool is user-friendly and will be helpful for adrenal scientists; however, the validation of crucial results of the large dataset is necessary. There are also several contradictory results/interpretations, and the opportunity to dissect the sexually dimorphic gene expression pattern and mouse-human interspecies differences is a missed opportunity.

    Reviewed by eLife