eLife

Latest preprint reviews

1. Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

   This article has 1 author:

   1. Fabrizio Menardo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an interesting simulation-based study focusing on the genomic epidemiology of Mycobacterium tuberculosis. The work nicely relates key biological and epidemiological parameters to how M. tuberculosis isolates cluster together, and to the terminal branch lengths in M. tuberculosis phylogenies. These concepts have both been applied to comparative studies of M. tuberculosis success and have often been interpreted as reflecting differences in transmission. The author finds that clustering and terminal branch lengths can also be modified by differences in the latent period, the mutation rate or the sampling fraction. This work will be of broad interest to readers studying tuberculosis epidemiology and transmission modelling.

     (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 name with the authors.)

   Reviewed by eLife

2. Botulinum neurotoxin accurately separates tonic vs. phasic transmission and reveals heterosynaptic plasticity rules in Drosophila

   This article has 7 authors:

   1. Yifu Han
   2. Chun Chien
   3. Pragya Goel
   4. Kaikai He
   5. Cristian Pinales
   6. Christopher Buser
   7. Dion Dickman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors describe a new tool to completely block both evoked and spontaneous release in a selective manner using the GAL4 system in Drosophila. Surprisingly, they see no effects on either pre or postsynaptic development when both evoked and spontaneous release are blocked, in contrast to prior studies in the field. Overall, the results are provocative and will be of interest to the field. The study contradicts a number of published works, so it is important for the field to see the data and be able to evaluate it themselves.

     (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 name with the authors.)

   Reviewed by eLife

3. Higher-order olfactory neurons in the lateral horn support odor valence and odor identity coding in Drosophila

   This article has 4 authors:

   1. Sudeshna Das Chakraborty
   2. Hetan Chang
   3. Bill S Hansson
   4. Silke Sachse

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Information about the environment obtained through sensory organs is processed and utilized at multiple levels in the brain. In this study, the authors use a variety of modern genetic and optophysiological tools to uncover the function and connectivity of glutamatergic neurons in a higher brain center of Drosophila - the lateral horn. They find that these neurons do not only encode chemical odor identity, but also the hedonic value (attractive or repulsive) of odors. This advances our understanding of how odors are represented in the brain will be of value to those who are interested in odour coding and behavioural valence of various odours.

     (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 name with the authors.)

   Reviewed by eLife

4. Characterization of sequence determinants of enhancer function using natural genetic variation

   This article has 5 authors:

   1. Marty G Yang
   2. Emi Ling
   3. Christopher J Cowley
   4. Michael E Greenberg
   5. Thomas Vierbuchen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes a useful dataset for those interested in regulatory variation. The large scale of variants surveyed offers the potential to look for dependencies between nearby TF binding events at the same accessible site, and will likely be useful to those interested in dissecting sequence determinants of transcription-factor binding genome-wide.

     (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. The transcription factor Bach2 negatively regulates murine natural killer cell maturation and function

   This article has 11 authors:

   1. Shasha Li
   2. Michael D Bern
   3. Benpeng Miao
   4. Changxu Fan
   5. Xiaoyun Xing
   6. Takeshi Inoue
   7. Sytse J Piersma
   8. Ting Wang
   9. Marco Colonna
   10. Tomohiro Kurosaki
   11. Wayne M Yokoyama

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The strength of this paper is identifying a novel factor Bach2 that might be involved in the generation and/or maintenance of NK cells. To date, the full molecular network guiding the development, maturation and maintenance of NK cells has not been fully defined and Bach2 has not yet been investigated.

     (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 PREreview, eLife

6. Complex fitness landscape shapes variation in a hyperpolymorphic species

   This article has 6 authors:

   1. Anastasia V Stolyarova
   2. Tatiana V Neretina
   3. Elena A Zvyagina
   4. Anna V Fedotova
   5. Alexey S Kondrashov
   6. Georgii A Bazykin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Stolyarova et al. investigate a highly polymorphic species, the fungus Schizophyllum commune, finding that compared to synonymous mutations, levels of linkage disequilibrium between nonsynonymous mutations are higher within genes than between genes. The authors propose this observation may be explained by compensatory interactions between nonsynonymous alleles, pointing to the presence of positive epistasis. This paper should be of interest to population geneticists and evolutionary biologists studying the role of natural selection.

     (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. Early detection of cerebrovascular pathology and protective antiviral immunity by MRI

   This article has 11 authors:

   1. Li Liu
   2. Steve Dodd
   3. Ryan D Hunt
   4. Nikorn Pothayee
   5. Tatjana Atanasijevic
   6. Nadia Bouraoud
   7. Dragan Maric
   8. E Ashley Moseman
   9. Selamawit Gossa
   10. Dorian B McGavern
   11. Alan P Koretsky

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript by Liu et al., aims to develop a novel MRI-based approach to monitor virus specific CD8+ T cells and their relationship to cerebrovascular pathology in living brains. Using a mouse model of VSV brain infection, they show that MRI approaches can be used to identify microbleeds in the brain, and these microbleeds occur independent of immune cell influx. Furthermore, the transfer of low numbers of virus specific CD8+ T cells can reduce cerebrovascular bleeding. The capacity to track virus specific T cells and cerebrovascular pathology in real time in living brains would be a major technological advance.

     (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

8. The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

   This article has 4 authors:

   1. Stéphane Peyrégne
   2. Janet Kelso
   3. Benjamin M Peter
   4. Svante Pääbo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Peyregne et al. studied the genes encoding proteins of the spindle apparatus. These genes have an elevated number of nonsynonymous substitutions in modern humans, and by comparison of modern and archaic alleles the authors identify that some Neanderthals had already the modern human haplotype at the KNL1 gene, raising the possibility that Neanderthals acquired it from modern humans. This study will be of interest to evolutionary biologists and anthropologists, because it supports the hypothesis that modern humans and Neanderthals interacted more than once in the past.

     (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

9. Endothelial SIRPα signaling controls VE-cadherin endocytosis for thymic homing of progenitor cells

   This article has 7 authors:

   1. Boyang Ren
   2. Huan Xia
   3. Yijun Liao
   4. Hang Zhou
   5. Zhongnan Wang
   6. Yaoyao Shi
   7. Mingzhao Zhu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The primary audience that will be keenly interested in these findings will be those with an interest in T cell development and thymic function, however given the broad applicability of transendothelial migration, there will also likely be broader interest in these findings. The manuscript provides key new insight into the importation of hematopoietic progenitors into the thymus to initiate T cell development. Overall, the main claims of the paper are well supported by the studies presented, although some clarification is needed regarding some experimental details, in particular the thymus reconstitution model used to test the effects of CD47-SIRPa inhibition in immunotherapy.

     (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 names with the authors.)

   Reviewed by eLife

10. Modified viral-genetic mapping reveals local and global connectivity relationships of ventral tegmental area dopamine cells

    This article has 1 author:

    1. Kevin Beier

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      By addressing shortcomings in rabies viral-mediated labeling of monosynaptic inputs to ventral tegmental area dopamine neurons, this study provides a previously unattained precision local inputs to VTA dopamine neurons. Main findings include the preservation of a medial to lateral topography in the projection patterns within VTA microcircuitry, prominence of inhibition of DA neurons from the substantial nigra pars reticulata (SNr), DA-DA transmission, and inputs from raphe serotonin neurons. The precise local VTA connectivity described here is important for identifying how dopamine neurons compute reward, prediction, and movement-related signals during behavior, and thus is likely to be of interest to neuroscientists interest in those processes and the midbrain dopamine system.

      (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