eLife

Latest preprint reviews

1. Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription

   This article has 9 authors:

   1. Gonçalo Fernandes
   2. Huy Tran
   3. Maxime Andrieu
   4. Youssoupha Diaw
   5. Carmina Perez Romero
   6. Cécile Fradin
   7. Mathieu Coppey
   8. Aleksandra M Walczak
   9. Nathalie Dostatni

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors combine the study of synthetic transcriptional enhancers with theoretical models to understand the role of Bicoid, Hunchback and Zelda during syncytial cycles. They conclude that Bcd exists in active and inactive forms; that Hb regulates transcription during some stage after initiation; and that an equilibrium model captures the relevant behaviors, implying energy expenditure during DNA binding/transcription interaction with RNAP is theoretically unnecessary.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

2. Identification of bipotent progenitors that give rise to myogenic and connective tissues in mouse

   This article has 4 authors:

   1. Alexandre Grimaldi
   2. Glenda Comai
   3. Sebastien Mella
   4. Shahragim Tajbakhsh

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper will be of interest to a broad audience of developmental biologists, as it provides evidence for a population of novel bipotent cells, which possess a signature of both muscle and connective tissue. This work implies an adjustment to our current understanding of cell fate decision in myogenesis and fibrogenesis. Combining the sophisticated lineage tracing and single-cell RNAseq analysis, the key claims of the paper are well supported.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

3. Bayesian machine learning analysis of single-molecule fluorescence colocalization images

   This article has 4 authors:

   1. Yerdos A Ordabayev
   2. Larry J Friedman
   3. Jeff Gelles
   4. Douglas L Theobald

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to researchers who perform single-molecule fluorescence imaging experiments as well as those who want to include machine learning in their data analyses. The authors have developed a machine learning algorithm that addresses some of the data analysis challenges in the field of single-molecule fluorescence imaging. The methods are rigorously benchmarked using simulated data and tested using real data. There are some concerns whether Tapqir is general enough for use by the broader community of single-molecule fluorescence researchers.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

4. Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction

   This article has 6 authors:

   1. Alex Cornean
   2. Jakob Gierten
   3. Bettina Welz
   4. Juan Luis Mateo
   5. Thomas Thumberger
   6. Joachim Wittbrodt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an important study that comprehensively compares the activities of different base editors in both medaka and zebrafish. The authors also provide a web tool for experimental design allowing approximately 30% of known human disease associated nucleotide variants to be modeled in fish with validated editors within days following injection. While other studies have shown similar activities in zebrafish, the authors nicely demonstrate the ability to generate phenotypes using different base editors in both zebrafish and medaka that correlate with specific base changes. This gene editing system coupled with the ability to design gRNAs efficiently with a web interface will likely have a lasting impact on the field.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

5. Adiponectin receptor agonist AdipoRon improves skeletal muscle function in aged mice

   This article has 11 authors:

   1. Priya Balasubramanian
   2. Anne E Schaar
   3. Grace E Gustafson
   4. Alex B Smith
   5. Porsha R Howell
   6. Angela Greenman
   7. Scott Baum
   8. Ricki J Colman
   9. Dudley W Lamming
   10. Gary M Diffee
   11. Rozalyn M Anderson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this manuscript, the authors provide promising results for the treatment of age-related sarcopenia with AdipoRon, a drug that targets the receptors for adiponectin. This is a well done study using an agonist (AdipoRon) involved in lipid and mitochondrial metabolism regulation to mitigate age related muscle loss in mice.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

6. Probing the segregation of evoked and spontaneous neurotransmission via photobleaching and recovery of a fluorescent glutamate sensor

   This article has 4 authors:

   1. Camille S Wang
   2. Natali L Chanaday
   3. Lisa M Monteggia
   4. Ege T Kavalali

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper studies spontaneous and evoked excitatory synaptic transmission in cultured hippocampal neurons using a genetically encoded fluorescent glutamate sensor. The central finding of this study is that after photobleaching, the spontaneous release of glutamate recovers rapidly, while the evoked release of glutamate recovers much more slowly. This study is potentially of very high interest to neurobiologists as there has been a long-running interest in understanding spontaneous versus evoked neurotransmitter release. Clarification of a few key technical issues central to the study is required to fully interpret the study.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

7. Environmental enrichment enhances patterning and remodeling of synaptic nanoarchitecture as revealed by STED nanoscopy

   This article has 5 authors:

   1. Waja Wegner
   2. Heinz Steffens
   3. Carola Gregor
   4. Fred Wolf
   5. Katrin I Willig

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Synapses convey information in the brain, including signals from the environment. The changes in the incoming signals can alter the efficacy of synaptic transmission, which in turn can be represented by the changes in synaptic structure that is particularly evident in the postsynaptic compartment called spines. This study uses a custom-built superresolution microscope to follow individual spine shape and the dynamics of the resident scaffolding protein PSD95 simultaneously, to study the effects of rearing mice in an enriched environment relative to a simple standard cage. The imaging data are of superb quality. The authors find that regardless of the rearing condition, dynamic changes in the sizes of spine head and PSD95 are detected that do not necessarily correlate with each other. Furthermore, mice reared in an enriched environment show less variable spine head size. While these findings may be of potential interest to neuroscientists studying synaptic network architecture, a clarification of the biological question being addressed, and validation of the method used to monitor PSD95, would considerably strengthen the study and enhance its overall impact.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

8. Aggregation pheromone 4-vinylanisole promotes the synchrony of sexual maturation in female locusts

   This article has 8 authors:

   1. Dafeng Chen
   2. Li Hou
   3. Jianing Wei
   4. Siyuan Guo
   5. Weichan Cui
   6. Pengcheng Yang
   7. Le Kang
   8. Xianhui Wang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The current study follows up on previous studies from this group, uncovering the role of olfactory signaling in the migratory locust. Specifically, it follows up on a recent report demonstrating that 4-vinylanisole serves as a locust aggregation pheromone. Here, this pheromone is also assigned an instrumental role in control and synchronization of female sexual maturation. This study will be useful for the understanding of swarming behaviour in locusts, and it will also interest those who work on behaviour and its modulation.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

   Reviewed by eLife

9. Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock

   This article has 13 authors:

   1. Alex A Koch
   2. James S Bagnall
   3. Nicola J Smyllie
   4. Nicola Begley
   5. Antony D Adamson
   6. Jennifer L Fribourgh
   7. David G Spiller
   8. Qing-Jun Meng
   9. Carrie L Partch
   10. Korbinian Strimmer
   11. Thomas A House
   12. Michael H Hastings
   13. Andrew SI Loudon

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Koch et al. quantified the abundance of the core clock molecules and their binding affinities, thereby providing critical information for our quantitative understanding of the core transcriptional negative feedback loop of the mammalian circadian clock. Furthermore, they used mathematical modeling to incorporate the quantified information and identified the hidden role of PER:CRY complex, enhancing the mobility of BMAL1:CLOCK to new target sites. The work makes the important contribution that the displacement type repression frees CLOCK-BMAL1 to bind to other targets and activate several sets of genes. This is an important insight, but some of the data need further explanation and some statements ought to change to improve the manuscript.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study

    This article has 18 authors:

    1. Fernanda Morales Berstein
    2. Daniel L McCartney
    3. Ake T Lu
    4. Konstantinos K Tsilidis
    5. Emmanouil Bouras
    6. Philip Haycock
    7. Kimberley Burrows
    8. Amanda I Phipps
    9. Daniel D Buchanan
    10. Iona Cheng
    11. the PRACTICAL consortium
    12. Richard M Martin
    13. George Davey Smith
    14. Caroline L Relton
    15. Steve Horvath
    16. Riccardo E Marioni
    17. Tom G Richardson
    18. Rebecca C Richmond

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This paper describes a two-sample randomization study of the impact of several measures of epigenetic aging acceleration (four different DNA methylation clocks) on risk for various common cancers (prostate, colon, lung, ovary, and breast). Data from large case-control cancer GWAS results are leveraged, as well as large cohort GWAS (UK Biobank and FinnGen) and GWAS of epigenetic aging. The most convincing finding is an an estimated effect of GrimAge on colon cancer risk (while results for other cancers are null or suggestive). This analysis is an important contribution as it addresses a question of substantial interest in cancer epidemiology.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife