eLife

Latest preprint reviews

1. Genome reorganization and its functional impact during breast cancer progression

   This article has 8 authors:

   1. Kathleen S Metz Reed
   2. Andrew Fritz
   3. Haley Greenyer
   4. Kerstin Heselmeyer-Haddad
   5. Seth Frietze
   6. Janet Stein
   7. Gary Stein
   8. Tom Misteli

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study by Reed et al. provides fundamental findings and convincing evidence defining the topological changes that occur during tumorigenesis. The findings enhance the understanding of stable long-range connections among genes that reprogram cancer-related functions. Nevertheless, performing additional experiments is recommended.

   Reviewed by eLife

2. Dissecting organoid-bacteria interaction highlights decreased contractile force as a key factor for heart infection

   This article has 10 authors:

   1. Anheng Wang
   2. Jiaxian Wang
   3. Zhe Zhang
   4. Chuan Yang
   5. Chunhao Deng
   6. Guokai Chen
   7. Chengwu Li
   8. Qian Wang
   9. Lei Dong
   10. Chunming Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript reports important findings that have theoretical or practical implications beyond a single subfield. However, despite the combination of numerous analytical tools established and applied in the study, the work has substantial experimental limitations leading to incomplete evidence, indicating that the conclusions may be an over-interpretation of the findings.

   Reviewed by eLife

3. In silico design and validation of high-affinity RNA aptamers for SARS-CoV-2 comparable to neutralizing antibodies

   This article has 8 authors:

   1. Yanqing Yang
   2. Lulu Qiao
   3. Yangwei Jiang
   4. Zhiye Wang
   5. Dong Zhang
   6. Damiano Buratto
   7. Liquan Huang
   8. Ruhong Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study introduces CAAMO, a computational framework that combines structure prediction, in silico mutagenesis, molecular simulations, and energy calculations to design RNA aptamers with improved binding affinity. The computational methodology is solid, demonstrating strong theoretical foundations and systematic integration of multiple prediction techniques. However, the experimental validation is incomplete, with methodological weaknesses that limit the strength of support for the computational predictions.

   Reviewed by eLife

4. Associations Between Meteorological Factors and Influenza A/B Incidence in Subtropical China: A Six-Year Surveillance Study with Deep Learning Modelling for Influenza Early Warning

   This article has 14 authors:

   1. Long Xie
   2. Meng-Jie Zhang
   3. Jin-Lin Tan
   4. Yi-Xin Ling
   5. Zhe-Qiang Xue
   6. Jun-Ju Huang
   7. Jian-Ling Chen
   8. Ze-Fan Ruan
   9. Jing Qian
   10. Hai-Yong Pan
   11. Xiao Han
   12. Sheng Xiong
   13. Long-Mei Ling
   14. Xi-Wen Jiang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study is a valuable contribution to the evidence base. However, the evidence provided is incomplete as the study results only partially support the study conclusions. Addressing the methodological and reporting issues raised by the peer reviewers and properly aligning the claim made for providing a tool for early warning with the study analysis/results would improve the study quality and usefulness of its findings.

   Reviewed by eLife

5. A tool to pulse-label yeast Nuclear Pore Complexes in imaging and biochemical experiments

   This article has 5 authors:

   1. Annemiek C Veldsink
   2. Jonas S Fischer
   3. Sophie Hell
   4. Karsten Weis
   5. Liesbeth M Veenhoff

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study introduces a non-perturbative pulse-labeling strategy for yeast nuclear pore complexes (NPCs), employing a nanobody-based approach in order to selectively capture Nup84-containing complexes for imaging and biochemical analysis. The data convincingly demonstrate that a short induction period (20 minutes to 1 hour) yields a strong and sustained signal, enabling affinity purification that faithfully recapitulates the endogenous Nup84 interactome. This tool offers a powerful framework for investigating NPC dynamics and associated interactomes through both imaging and biochemical assays.

   Reviewed by eLife

6. Type I and type III interferon receptor knockout chickens: Novel models for unraveling interferon dynamics in influenza infection

   This article has 18 authors:

   1. Mohanned Naif Alhussien
   2. Hanna-Kaisa Vikkula
   3. Romina Klinger
   4. Christian Zenner
   5. Simon P Früh
   6. Rashi Negi
   7. Theresa von Heyl
   8. Sabrina Schleibinger
   9. Milena Brunner
   10. Tom VL Berghof
   11. Leora Avolio
   12. Arne Reich
   13. Benjamin Schade
   14. Bassel A Abukhadra
   15. Silke Rautenschlein
   16. Rudolf Preisinger
   17. Hicham Sid
   18. Benjamin Schusser

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports on the development and characterization of chickens with genetic deficiencies in type I or type III interferon receptors, which is an important contribution to the field of avian immunology. The data reflecting the development of the new interferon-receptor-deficient chickens is compelling. However, the characterization of IFN biology and infection responses in these knockout chickens is somewhat incomplete and could be improved by addressing the noted weaknesses.

   Reviewed by eLife

7. Host and antibiotic jointly select for greater virulence in Staphylococcus aureus

   This article has 7 authors:

   1. Michelle Su
   2. Kim L Hoang
   3. McKenna Penley
   4. Michelle H Davis
   5. Jennifer D Gresham
   6. Levi T Morran
   7. Timothy D Read

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study examines the evolution of virulence and antibiotic resistance in Staphylococcus aureus under multiple selection pressures. The evidence presented is convincing, with rigorous data that characterizes the outcomes of the evolution experiments. However, the manuscript's primary weakness is in its presentation, as claims about the causal relationship between genotypes and phenotypes are based on correlational evidence. The manuscript needs to be revised to address these limitations, clarify the implications of the experimental design, and adjust the overall narrative to better reflect the nature of the findings.

   Reviewed by eLife

8. Depletion of extracellular asparagine impairs self-reactive T cells and ameliorates autoimmunity in a murine model of multiple sclerosis

   This article has 15 authors:

   1. Peter Georgiev
   2. Sheila Johnson
   3. Kiran Kurmi
   4. Song-Hua Hu
   5. SeongJun Han
   6. Dillon Patterson
   7. Thao H Nguyen
   8. Linglin Huang
   9. Dan Liang
   10. Naomi Goldman
   11. Thomas Conway
   12. Hannah Creasey
   13. Jared Rowe
   14. Marcia C Haigis
   15. Arlene H Sharpe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Non-essential amino acids such as glutamine have been known to be required for T cell general activation through sustaining basic biosynthetic processes, including nucleotide biosynthesis, ATP generation, and protein synthesis. In this important study, the authors found that extracellular asparagine (Asn) is required not only for T cells to generally refuel metabolic reprogramming, but to produce helper T cell lineage-specific cytokine, for instance, IL17. In particular, the importance of Asn in IL17 production was convincingly demonstrated in the mouse experimental autoimmune encephalomyelitei (EAE) model, mimicking human multiple sclerosis disease.

   Reviewed by eLife

9. Tolerance to Lung Infection in TWIK2 K+ Efflux Mediated Macrophage Trained Immunity

   This article has 8 authors:

   1. Josh Thompson
   2. Yufan Li
   3. Yuanling Song
   4. Anas Anas
   5. Jaewon Cho
   6. Ki-Wook Kim
   7. Asrar B Malik
   8. Jingsong Xu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable data suggesting that ATP-induced modulation of alveolar macrophage (AM) functions is associated with NLRP3 inflammasome activation and enhanced phagocytic capacity. While the in vivo and in vitro data reveal an interesting phenotype, the evidence provided is incomplete and does not fully support the paper's conclusions. Additional investigations would be of value in complementing the data and strengthening the interpretation of the results. This study should be of interest to immunologists and the mucosal immunity community.

   Reviewed by eLife

10. Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species

    This article has 10 authors:

    1. Letong Xu
    2. Shenghai Shen
    3. Yizhou Zhang
    4. Zhihao Guo
    5. Beifang Lu
    6. Jiadai Huang
    7. Runsheng Li
    8. Yitong Shen
    9. Li-Sheng Zhang
    10. Xin Deng

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study illustrates a valuable application of BID-seq to bacterial RNA, allowing transcriptome-wide mapping of pseudouridine modifications across various bacterial species. The evidence presented includes solid data and analyses that would benefit from additional experimental validation. The work will interest a specialized audience involved in RNA biology.

    Reviewed by eLife