eLife

Latest preprint reviews

1. Mutation saturation for fitness effects at human CpG sites

   This article has 2 authors:

   1. Ipsita Agarwal
   2. Molly Przeworski

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Diminishing returns on sampling new variable sites with increasing samples sizes is a classic limitation of population genomics and one that limits the power of population genomic approaches to make site-specific inferences of natural selection. This timely study demonstrates that methylated CpG sites, which have a mutation rate an order of magnitude higher than other sites in the genome, are saturated with polymorphisms in modern human genomic datasets. They can thus serve as a starting point for understanding the effects of natural selection at the resolution of single nucleotide sites. The manuscript is a clearly written presentation of the state of the field and the claims are supported by a variety of thoughtful analyses. Additional work will be needed to take full advantage of the insights from this 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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

2. Local field potentials reflect cortical population dynamics in a region-specific and frequency-dependent manner

   This article has 5 authors:

   1. Cecilia Gallego-Carracedo
   2. Matthew G Perich
   3. Raeed H Chowdhury
   4. Lee E Miller
   5. Juan Álvaro Gallego

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to electrophysiologists, systems neuroscientists and neural engineers. The authors describe a framework for evaluating the comparison between LFP dynamics and spikes and perform this comparison for several datasets recorded from motor, premotor, and sensory areas of cortex in rhesus macaque monkeys. These results serve as an important benchmark for the information content of LFP recordings, which is relevant to data collection in neuroscientific investigations and to designing brain computer interfaces.

     (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

3. Alzheimer's Aβ assembly binds sodium pump and blocks endothelial NOS activity via ROS-PKC pathway in brain vascular endothelial cells

   This article has 5 authors:

   1. Tomoya Sasahara
   2. Kaori Satomura
   3. Mari Tada
   4. Akiyoshi Kakita
   5. Minako Hoshi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper examines the effects of amylospheroids, highly neurotoxic assemblies of β-amyloid, on aortic function and on cultured cells. The authors propose that the interaction of amylospheroids with the sodium pump in endothelial cells induces production of reactive oxygen species to ultimately comprise nitric oxide generation. The study provides some new insight into mechanisms underlying brain blood vessel dysfunction and will be interesting neuroscientists who study neurovascular contribution to neurodegenerative diseases. The conclusions of the manuscript are supported by the data, but alternative approaches would make the study stronger.

     (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. Remodeling of dermal adipose tissue alleviates cutaneous toxicity induced by anti-EGFR therapy

   This article has 11 authors:

   1. Leying Chen
   2. Qing You
   3. Min Liu
   4. Shuaihu Li
   5. Zhaoyu Wu
   6. Jiajun Hu
   7. Yurui Ma
   8. Liangyong Xia
   9. Ying Zhou
   10. Nan Xu
   11. Shiyi Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to oncologists and dermatologists and has high clinical relevance. It reveals a novel mechanism of EGFR inhibitor-induced rash which be may closely related to atrophy of dermal white adipose tissue (dWAT). A series of experimental manipulations dissect the mechanism with a murine model, supporting the major claims of the paper.

     (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

5. Therapeutic downregulation of neuronal PAS domain 2 (Npas2) promotes surgical skin wound healing

   This article has 12 authors:

   1. Yoichiro Shibuya
   2. Akishige Hokugo
   3. Hiroko Okawa
   4. Takeru Kondo
   5. Daniel Khalil
   6. Lixin Wang
   7. Yvonne Roca
   8. Adam Clements
   9. Hodaka Sasaki
   10. Ella Berry
   11. Ichiro Nishimura
   12. Reza Jarrahy

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors identify a novel compound called Dwn1 that suppresses the expression of Npas2, a key gene that delays wound healing. In doing so, they identify a novel treatment strategy for incisional surgical wounds that may have broader application to the treatment of scars in general.

     (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

6. Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes

   This article has 9 authors:

   1. Mark A Zaydman
   2. Alexander S Little
   3. Fidel Haro
   4. Valeryia Aksianiuk
   5. William J Buchser
   6. Aaron DiAntonio
   7. Jeffrey I Gordon
   8. Jeffrey Milbrandt
   9. Arjun S Raman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Since the inception of comparative genomics, mining phyletic patterns has been a powerful approach for the discovery of previously unknown biological interactions. The authors use a combination of singular value decomposition of the phyletic pattern matrix and random forests classification method to uncover potential protein-protein interactions. The work illustrates the utility of such methods, which are finding increasing application in addressing various computational biological problems, such as predicting protein-protein interactions from genomic information.

     (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

7. Overexpression screen of interferon-stimulated genes identifies RARRES3 as a restrictor of Toxoplasma gondii infection

   This article has 6 authors:

   1. Nicholas Rinkenberger
   2. Michael E Abrams
   3. Sumit K Matta
   4. John W Schoggins
   5. Neal M Alto
   6. L David Sibley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Toxoplasma gondii is a widespread parasite of warm blooded animals, with estimates suggesting 2 billion people are currently and chronically infected with this pathogen. Many questions remain as to how humans control and eliminate T. gondii following infection. In this manuscript, Rinkenberger et al. reveal a previously unidentified and understudied host factor, RARRES3 that promotes cell autonomous control of T. gondii in human cells. The precise mechanism of control and its in vivo relevance remain areas for additional work.

     (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

8. PBN-PVT projections modulate negative affective states in mice

   This article has 10 authors:

   1. Ya-Bing Zhu
   2. Yan Wang
   3. Xiao-Xiao Hua
   4. Ling Xu
   5. Ming-Zhe Liu
   6. Rui Zhang
   7. Peng-Fei Liu
   8. Jin-Bao Li
   9. Ling Zhang
   10. Di Mu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study will interest neuroscientists, in particular those interested in the neurocircuitry of emotional behaviors. Using modern neuroscience techniques, the authors demonstrate that anatomical projections from a brain stem structure called the parabrachial nucleus to the paraventricular nucleus thalamus contribute to aversive states like fear and anxiety. Overall, the study offers important details of a previously uncharacterized brain circuit, although some additional experiments are required to fully substantiate the authors' claims.

     (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. Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and fluconazole resistance

   This article has 9 authors:

   1. Maruti Nandan Rai
   2. Qing Lan
   3. Chirag Parsania
   4. Rikky Rai
   5. Niranjan Shirgaonkar
   6. Ruiwen Chen
   7. Li Shen
   8. Kaeling Tan
   9. Koon Ho Wong

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper by Rai and colleagues examines the transcriptional response of Candida glabrata, a common human fungal pathogen, during interaction with macrophages. They use RNA PolII profiling to identify not just the total transcripts but instead focus on the actively transcribing genes. By examining the profile over time, they identify particular transcripts that are enriched at each time point, building a hierarchical model for how a transcription factor, CgXbp1, may regulate part of this response. While the authors have generated a large and potentially impactful dataset, along with several interesting observations, it is important to be cautious as the direct targets of CgXbp1 were characterized under one particular condition and the transcriptional analyses were obtained in another condition, one shown to be highly dynamic as during macrophage infection.

     (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. A helicase-tethered ORC flip enables bidirectional helicase loading

    This article has 4 authors:

    1. Shalini Gupta
    2. Larry J Friedman
    3. Jeff Gelles
    4. Stephen P Bell

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The paper describes single-molecule experiments that address the assembly of a double hexamer of the Mcm2-7 complex that is required to license all origins of DNA replication in eukaryotic cells by formation of a pre-Replicative Complex (pre-RC). The observations show that one Origin Recognition Complex, an ATP-dependent DNA binding protein, can load both Mcm2-7 hexamers in opposite orientation. The results nicely complement prior data on the mechanism of pre-RC assembly.

      (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