eLife

Latest preprint reviews

1. Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications

   This article has 5 authors:

   1. Rasa Giniūnaitė
   2. Rahul Sharma
   3. John H Maddocks
   4. Skirmantas Kriaucionis
   5. Daiva Petkevičiūtė-Gerlach

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable simulation study proposes a new coarse-grained model to explain the effects of CpG methylation on nucleosome wrapping energy. The model accurately reproduces the all-atom molecular dynamics simulation data, and the evidence to support the claims in the paper is solid. This work will be of interest to researchers working on gene regulation, mechanisms of DNA methylation and effects of DNA methylation on nucleosome positioning.

   Reviewed by eLife

2. Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age

   This article has 4 authors:

   1. Dylan C Sarver
   2. Muzna Saqib
   3. Fangluo Chen
   4. G William Wong

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides a comprehensive assessment of mitochondrial function across age and sex in mice. The strength of evidence supporting this resource is compelling, given the exhaustive number of tissues profiled and in-depth analyses performed.

   Reviewed by eLife

3. Ultra-low coverage fragmentomic model of cell-free DNA for cancer detection based on whole-exome regions

   This article has 4 authors:

   1. Apiwat Sangphukieo
   2. Pitiporn Noisagul
   3. Patcharawadee Thongkumkoon
   4. Parunya Chaiyawat

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides useful insights for anyone focusing on exonic regions when looking into the investigation of DNA fragmentation patterns (fragmentomics) for circulating tumor DNA (ctDNA) data for cancer detection. The method expands the DELFI method of Cristiano and colleagues (2019), but the datasets chosen are not ideal and the analysis remains incomplete.

   Reviewed by eLife

4. NE contribution to rebooting unconsciousness caused by midazolam

   This article has 15 authors:

   1. LeYuan Gu
   2. WeiHui Shao
   3. Lu Liu
   4. Qing Xu
   5. YuLing Wang
   6. JiaXuan Gu
   7. Yue Yang
   8. ZhuoYue Zhang
   9. YaXuan Wu
   10. Yue Shen
   11. Qian Yu
   12. XiTing Lian
   13. HaiXiang Ma
   14. YuanLi Zhang
   15. HongHai Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides a useful set of experiments showing the relative contribution of the Noradrenergic system in reversing the sedation induced by midazolam. The evidence supporting the claims of the authors is solid, although specificity issues in the pharmacology and neural-circuit investigations narrow down the strengths of the conclusions. Dealing with these limitations will make the paper attractive to medical biologists working on the neurobiology of anesthesia.

   Reviewed by eLife

5. Proteogenomic analysis of air-pollution-associated lung cancer reveals prevention and therapeutic opportunities

   This article has 16 authors:

   1. Honglei Zhang
   2. Chao Liu
   3. Shuting Wang
   4. Qing Wang
   5. Xu Feng
   6. Huawei Jiang
   7. Li Xiao
   8. Chao Luo
   9. Lu Zhang
   10. Fei Hou
   11. Minjun Zhou
   12. Zhiyong Deng
   13. Heng Li
   14. Yong Zhang
   15. Xiaosan Su
   16. Gaofeng Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful manuscript presents an interesting multi-modal omics analysis of lung adenocarcinoma patients with distinct clinical clusters, mutation hotspots, and potential risk factors identified in cases linked to air pollution. The findings show potential for clinical and therapeutic impact. Some of the conclusions remain incomplete as they are based on correlative or suggestive findings, and would benefit from further functional investigation and validating approaches.

   Reviewed by eLife

6. The protective roles of eugenol on type 1 diabetes mellitus through NRF2-mediated oxidative stress pathway

   This article has 9 authors:

   1. Yalan Jiang
   2. Pingping He
   3. Ke Sheng
   4. Yongmiao Peng
   5. Huilan Wu
   6. Songwei Qian
   7. Weiping Ji
   8. Xiaoling Guo
   9. Xiaoou Shan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study partially succeeds in providing solid evidence in support of the therapeutic potential of the plant-derived compound eugenol for ameliorating symptoms associated with STZ-induced oxidative stress, identifying Nuclear factor E2-related factor (Nrf2) as a mediator of the effects induced by eugenol. Although the study provides interesting data, there remain concerns associated with the STZ model and the rather superficial mechanistic assessment.

   Reviewed by eLife

7. Circular RNA HMGCS1 sponges MIR4521 to aggravate type 2 diabetes-induced vascular endothelial dysfunction

   This article has 5 authors:

   1. Ming Zhang
   2. Guangyi Du
   3. Lianghua Xie
   4. Yang Xu
   5. Wei Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents important findings linking circHMGCS1 and miR-4521 in diabetes-induced vascular endothelial dysfunction. Overall, the evidence supporting the claims of the authors is convincing. The work will be of interest to biomedical scientists working with cardiovascular and/or RNA biology, particularly those studying diabetes.

   Reviewed by eLife

8. Root-specific theanine metabolism and regulation at the single-cell level in tea plants (Camellia sinensis)

   This article has 13 authors:

   1. Shijia Lin
   2. Yiwen Zhang
   3. Shupei Zhang
   4. Yijie Wei
   5. Mengxue Han
   6. Yamei Deng
   7. Jiayi Guo
   8. Biying Zhu
   9. Tianyuan Yang
   10. Enhua Xia
   11. Xiaochun Wan
   12. William J Lucas
   13. Zhaoliang Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study combines experimental and theoretical approaches to examine metabolites at the single-cell level in tea plants. The authors skilfully integrated various tools available for this type of research, and meticulously presented and illustrated every step of the survey. The overall quality of the work is convincing, and it represents an important contribution to our understanding of the compartmentalization of biosynthesis pathways.

   Reviewed by eLife

9. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer’s disease risk genes

   This article has 5 authors:

   1. François Kroll
   2. Joshua Donnelly
   3. Güliz Gürel Özcan
   4. Eirinn Mackay
   5. Jason Rihel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important manuscript sets out to identify sleep/arousal phenotypes in larval zebrafish carrying mutations in Alzheimer's disease (AD)-associated genes. The authors provide detailed phenotypic data for F0 knockouts of each of 7 AD-associated genes and then compare the resulting behavioral fingerprints to those obtained from a large-scale chemical screen to generate new hypotheses about underlying molecular mechanisms. The data presented are solid, although extensive interpretation of pharmacological screen data does not necessarily reflect the limited mechanistic data. Nonetheless, the authors address most reviewer concerns in their revised version, providing invaluable new analyses. Phenotypic characterization presented is comprehensive, and the authors develop a well-designed behavioral analysis pipeline that will provide considerable value for zebrafish neuroscientists.

   Reviewed by eLife

10. Intracellular mechanical fingerprint reveals cell type specific mechanical tuning

    This article has 3 authors:

    1. Till M. Muenker
    2. Bart E. Vos
    3. Timo Betz

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      Münker and colleagues use an optical tweezer setup to apply oscillatory forces to endocytosed/phagocytosed glass beads over a wide frequency range (from ~1 to 1000 Hz) and probe cytoplasmic material properties at multiple time scales in six different cell types. Using statistical methods and principal component analysis, they find that the active and passive mechanical properties of cells can be described by 6 parameters (from power law fits) that allow characterizing the viscous and elastic nature of the cytoplasmic material as well as an effective active energy driven by cellular metabolism. Overall, this is very well done and important work, using convincing and state-of-the-art methods, albeit with some limitations related to the way the beads are internalized.

    Reviewed by eLife