eLife

Latest preprint reviews

1. Beta-Glucan Modulates Monocyte Plasticity and Differentiation Capacity to Mitigate DSS-Induced Colitis

   This article has 16 authors:

   1. Yinyin Lv
   2. Yanyun Fan
   3. Qingxiang Gao
   4. Qiongyun Chen
   5. Yiqun Hu
   6. Lin Wang
   7. Huaxiu Shi
   8. Ermei Chen
   9. Qinyu Xu
   10. Ying Cai
   11. Qingqi Fan
   12. Linying Li
   13. Dan Du
   14. Jianlin Ren
   15. Shih-Chin Cheng
   16. Hongzhi Xu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable and compelling evidence that β-glucan-induced trained immunity can protect against intestinal inflammation by reprogramming innate immune cells toward a reparative phenotype. The authors employ a convincing combination of functional assays, adoptive transfers, and single-cell transcriptomics to uncover mechanistic insights and demonstrate the therapeutic potential of innate immune memory in IBD. While the work is robust, addressing the underlying epigenetic mechanisms and including additional controls would further reinforce the trained immunity-specific interpretation.

   Reviewed by eLife

2. Synthetic auxotrophy reveals metabolic regulation of plasma cell generation, affinity maturation, and cytokine receptor signaling

   This article has 16 authors:

   1. Sung Hoon Cho
   2. Shawna K Brookens
   3. Ariel L Raybuck
   4. Kaylor Meyer
   5. Yeeun C Paik
   6. Jennie Hamilton
   7. Jingxin Li
   8. Karel Kalecky
   9. Chloe Park
   10. Sakeenah L Hicks
   11. John Karijolich
   12. Teodoro H Bottiglieri
   13. Jeffrey C Rathmell
   14. Denis Mogilenko
   15. Chris D Scharer
   16. Mark R Boothby

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors addressed an important biological question, namely the role of glutamine metabolism in humoral responses, and they obtained solid conclusions. The strength of this study is that the authors used state-of-the-art transgenic mouse models together with in vitro analysis, thereby providing significant insights into the question posed. The following would strengthen the manuscript: i) adding more in-depth functionality/physiological relevance in the discussion part, and ii) regarding the experiments, the inclusion of more appropriate controls and a clearer and more accurate description of the methods.

   Reviewed by eLife

3. PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

   This article has 12 authors:

   1. Jimena Druker
   2. Hao Jiang
   3. Dilem Shakir
   4. Fraser Child
   5. Vanesa Alvarez
   6. Melpomeni Platani
   7. Andrea Corno
   8. Constance Alabert
   9. Adrian T Saurin
   10. Jason R Swedlow
   11. Sonia Rocha
   12. Angus I Lamond

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This compelling work describes how the cell cycle-regulating phosphatase subunit, RepoMan, is regulated by the oxygen-dependent, metabolite-sensing hydroxylase PHD1. The characterisation of how proline hydroxylation alters signalling at the molecular and cellular level provides important evidence to enhance our understanding of how 2-oxoglutarate-dependent dioxygenases influence the cell cycle and mitosis.

   Reviewed by eLife

4. SLC4A1 MUTATIONS THAT CAUSE DISTAL RENAL TUBULAR ACIDOSIS ALTER CYTOPLASMIC PH AND CELLULAR AUTOPHAGY

   This article has 12 authors:

   1. Grace Essuman
   2. Midhat Rizvi
   3. Ensaf Almomani
   4. Shahid A. K M. Ullah
   5. Sarder M. A. Hasib
   6. Forough Chelangarimiyandoab
   7. Priyanka Mungara
   8. Manfred J. Schmitt
   9. Marguerite Hureaux
   10. Rosa Vargas-Poussou
   11. Nicolas Touret
   12. Emmanuelle Cordat

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work characterizes the function and localization of SLC4A1 variants associated with distal renal tubular acidosis in human patients. Cell culture and limited animal studies provide partial but incomplete support to the authors' claim that the variants disrupt normal protein degradative flux by alkalinizing the intracellular pH. The study is valuable in providing preliminary evidence for future exploration of the link between intracellular pH regulation by SLC4A1 and kidney cell function in vivo.

   Reviewed by eLife

5. Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish

   This article has 11 authors:

   1. Yosuke Ono
   2. Martin Peterka
   3. Michael Love
   4. Ashish Bhandari
   5. Euan Gordon
   6. Jonathan S Ball
   7. Charles R Tyler
   8. Steve Rees
   9. Mohammad Bohlooly-Y
   10. Marcello Maresca
   11. Steffen Scholpp

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable comparison of the efficiency and precision of two prime editing methods to introduce single-nucleotide variants and longer exogenous DNA sequences into the zebrafish genome. Solid data support the conclusion that the PE2 prime editor Nickase is more effective at introducing single-nucleotide variants, while the PEn prime editor nuclease is more effective at integrating short sequences from 3 up to 30 base pairs, for both somatic and germline editing. The results will be of interest to the zebrafish community, in particular to model human disease variants in this model organism.

   Reviewed by eLife

6. Decoding movie content from neuronal population activity in the human medial temporal lobe

   This article has 12 authors:

   1. Franziska Gerken
   2. Alana Darcher
   3. Pedro J Gonçalves
   4. Rachel Rapp
   5. Ismail Elezi
   6. Johannes Niediek
   7. Marcel S Kehl
   8. Thomas P Reber
   9. Stefanie Liebe
   10. Jakob H Macke
   11. Florian Mormann
   12. Laura Leal-Taixé

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study demonstrates that it is possible to decode information about characters and locations from single-unit responses in the human brain to a narrative movie, using a convincing technical approach to capture information in population-level dynamics. The study introduces an exciting dataset of single-unit responses in humans during a naturalistic and dynamic movie stimulus, with recordings from multiple regions within the medial temporal lobe. Using both a traditional firing-rate analysis as well as a population decoding analysis to connect these neural responses to the visual content of the movie, they show that in this dataset, the decoding of semantic scene features (e.g., the person currently on screen), but not scene transitions, is surprisingly driven by classically non-responsive neurons. Based on these findings, the authors argue that dynamic naturalistic semantic information may be processed within the medial temporal lobe at the population level.

   Reviewed by eLife

7. Specific GPCRs Elicit Unique Extracellular Vesicle MiRNA Array Signatures: An Exploratory Study

   This article has 6 authors:

   1. Xiao Shi
   2. Michelle C Palumbo
   3. Sheila Benware
   4. Jack Wiedrick
   5. Sheila Markwardt
   6. Aaron Janowsky

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings by demonstrating that specific GPCR subtypes induce distinct extracellular vesicle miRNA signatures, highlighting a potential novel mechanism for intercellular communication with implications for receptor pharmacology within the field. The data is compelling, however, more evidence is needed to determine whether the distinct extracellular vesicle miRNA signatures result from GPCR-dependent miRNA expression or GPCR-dependent incorporation of miRNAs into extracellular vesicles.

   Reviewed by eLife

8. New idtracker.ai: rethinking multi-animal tracking as a representation learning problem to increase accuracy and reduce tracking times

   This article has 3 authors:

   1. Jordi Torrents
   2. Tiago Costa
   3. Gonzalo G de Polavieja

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces an advance in multi-animal tracking by reframing identity assignment as a self-supervised contrastive representation learning problem. It eliminates the need for segments of video where all animals are simultaneously visible and individually identifiable, and significantly improves tracking speed, accuracy, and robustness with respect to occlusion. This innovation has implications beyond animal tracking, potentially connecting with advances in behavioral analysis and computer vision. While the strength of support for these advances is solid overall, the presentation could be greatly improved for clarity and broader accessibility; in addition, incorporating more standard metrics in the multi-animal tracking literature would better benchmark the approach against other methods.

   Reviewed by eLife

9. A rapid transfer of virions coated with heparan sulfate from the ECM to cell surface CD151 defines a step in the human papillomavirus infection cascade

   This article has 7 authors:

   1. Annika Massenberg
   2. Yahya Homsi
   3. Carl Niklas Schneider
   4. Snježana Mikuličić
   5. Tatjana Döring
   6. Luise Florin
   7. Thorsten Lang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study presents interesting observations on the potential importance of extracellular transport of human papillomaviruses along actin protrusions by retrograde flow. The focus on the events of HPV infection between ECM binding and keratinocyte-specific receptor binding is unique and interesting. However, the evidence supporting the conclusions is incomplete, and additional experimental support is needed. Because conclusions drawn regarding HS interactions are largely based on experiments using a single HS mAb, the specificity of this mAb needs to be described in more detail, either based on the literature or further experimentation.

   Reviewed by eLife

10. The evolution of gene expression in seasonal environments

    This article has 6 authors:

    1. Shuichi N Kudo
    2. Yuka Ikezaki
    3. Junko Kusumi
    4. Hideki Hirakawa
    5. Sachiko Isobe
    6. Akiko Satake

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      The authors collected valuable time-course RNA-seq data from four tree species in natural environments and analyzed seasonal patterns of gene expression. The genome assemblies and gene expression data across multiple species and tissues are convincing, but the overarching conclusions are inadequately supported due to weaknesses in the study design, which encompasses three different environments and two distinct time periods. This makes it impossible to disentangle genetic effects - which are critical for evolutionary inferences - from environmental influences on gene expression.

    Reviewed by eLife