eLife

Latest preprint reviews

1. An image reconstruction framework for characterizing initial visual encoding

   This article has 3 authors:

   1. Ling-Qi Zhang
   2. Nicolas P Cottaris
   3. David H Brainard

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This rigorous computational study simulates the sampling of the visual image by cone photoreceptors in the human eye, and explains how the image content can be reconstructed from those cone signals. The authors show that a number of properties of the human retina and of human perception are predicted from these simulations. The manuscript could be further improved by analysis of how these conclusions compare to those reached by alternate theoretical approaches, and by a consideration of human eye movements.

     (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

2. Evolutionary footprints of a cold relic in a rapidly warming world

   This article has 5 authors:

   1. Eva Wolf
   2. Emmanuel Gaquerel
   3. Mathias Scharmann
   4. Levi Yant
   5. Marcus A Koch

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript has the potential to be of broad interest to scientists seeking to understand the evolutionary dynamics of plants during past periods of rapid climate change. Specifically, within the target genus of Cochlearia, the results indicate increased rates of speciation and diversification in response to pronounced glacial cycles. Future work to establish more direct mechanistic links between the results and conclusions will improve our understanding of adaptation and speciation.

     (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

3. Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection

   This article has 2 authors:

   1. Karthik Hullahalli
   2. Matthew K Waldor

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Monitoring changes in pathogenic bacterial populations after bloodstream infection are poorly understood and in this work the authors develop new genetic analytic tools to dissect bacterial population dynamics at sites of infection. By harvesting bacteria from different sites and times of infection and performing deep sequencing to define the distribution of specific tagged-strains the authors provide a highly detailed snapshot of populations, with discriminatory power superior to prior studies. The work paves the way to future such studies in other organisms that cause persistent infection in humans.

     (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

4. De novo synthesized polyunsaturated fatty acids operate as both host immunomodulators and nutrients for Mycobacterium tuberculosis

   This article has 12 authors:

   1. Thomas Laval
   2. Laura Pedró-Cos
   3. Wladimir Malaga
   4. Laure Guenin-Macé
   5. Alexandre Pawlik
   6. Véronique Mayau
   7. Hanane Yahia-Cherbal
   8. Océane Delos
   9. Wafa Frigui
   10. Justine Bertrand-Michel
   11. Christophe Guilhot
   12. Caroline Demangel

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, the authors highlight a role for de novo biosynthesis of Poly-unsaturated Fatty Acids and the consequence effect of these metabolites on the production of arachidonic acid. The increased bio-availability of arachidonic acid seemingly promotes mycobacterial growth whilst inhibition of arachidonic acid formation, and its resultant downstream eicosanoid products, affect macrophage function but somewhat surprisingly do not affect growth of M. tuberculosis in macrophages or in mice. The uptake of the different classes of fatty acids in axenic culture as well as in macrophages is explored and the authors demonstrate that the Mce1 transporter is largely responsible for their uptake during in vitro growth but only plays a partial role in their uptake during growth of the pathogen in host cells. This work will be of interest to bacteriologists and those studying infectious diseases.

     (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

5. Simplifying the development of portable, scalable, and reproducible workflows

   This article has 5 authors:

   1. Stephen R Piccolo
   2. Zachary E Ence
   3. Elizabeth C Anderson
   4. Jeffrey T Chang
   5. Andrea H Bild

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper by Piccolo and collaborators provides a general introduction to the common workflow language (CWL) with working examples taken from bioinformatics. The authors also introduce the ToolJig web application intended as a way of interactively creating CWL documents. This work should be of interest not only to beginner bioinformaticians but also to more experienced professionals that do not routinely make use of the latest developments in reproducible research.

     (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. An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei

   This article has 8 authors:

   1. Giulia Bandini
   2. Sebastian Damerow
   3. Maria Lucia Sempaio Guther
   4. Hongjie Guo
   5. Angela Mehlert
   6. Jose Carlos Paredes Franco
   7. Stephen Beverley
   8. Michael AJ Ferguson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study demonstrates for the first time that the single annotated fucosyltransferase (TbFUT1) in the parasitic protist, Trypanosoma brucei is specifically targeted to the mitochondrion, rather than in the secretory pathway or cytoplasm, as in other eukaryotes. TbFUT1 utilizes glycan substrates in vitro and conditional down-regulation of TbFUT1 expression causes a severe growth defect in the two major developmental stages of these pathogens, indicating that it is essential for pathogenesis and a potential drug target.

     (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

7. Protein kinase Cδ is essential for the IgG response against T-cell-independent type 2 antigens and commensal bacteria

   This article has 4 authors:

   1. Saori Fukao
   2. Kei Haniuda
   3. Hiromasa Tamaki
   4. Daisuke Kitamura

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The unexpected key finding is that T-cell-independent B cell activation engages the intracellular protein kinase PKC-delta to induce the necessary machinery of altered gene transcription culminating in IgG production. The methodology and the experimental setting are well-controlled, although how exactly B-cell stimulation by T-cell-independent antigens triggers PKC-delta remains to be elucidated.

     (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

8. Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

   This article has 7 authors:

   1. Jugal Mohapatra
   2. Kyuto Tashiro
   3. Ryan L Beckner
   4. Jorge Sierra
   5. Jessica A Kilgore
   6. Noelle S Williams
   7. Glen Liszczak

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Poly-ADP-ribosylation (poly-ADPr) is a major histone modification that plays critical roles in DNA damage. However careful mechanistic dissection of the role of poly-ADPr has been challenging as the modification is found on multiple proteins and there is heterogeneity in terms of poly-ADP-ribosylation chain length and amino acid location of attachment. The PARP1-dependent semi-synthetic strategy developed by the authors allows generation of nucleosomes with mono ADP ribose and defined lengths of poly-ADPr chains at specific histone serine residues. The utility of this method is clearly demonstrated by the authors' findings that ALC1, a chromatin remodeler that recognizes poly-ADPr is stimulated substantially by the presence of poly-ADPr on H2A and H3.

     (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

9. Single-cell growth inference of Corynebacterium glutamicum reveals asymptotically linear growth

   This article has 4 authors:

   1. Joris JB Messelink
   2. Fabian Meyer
   3. Marc Bramkamp
   4. Chase P Broedersz

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper presents a method for inferring the growth dynamics of bacteria from noisy single-cell data and applies this to C. glutamicum. Applying the method to experiments three phases of growth during the cell cycle are identified, including a dominant period of linear growth, which is interpreted in terms of a growth mode that is limited by polar cell wall synthesis.

     (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 universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation

    This article has 12 authors:

    1. Gajanan S Patil
    2. Priyadarshan Kinatukara
    3. Sudipta Mondal
    4. Sakshi Shambhavi
    5. Ketan D Patel
    6. Surabhi Pramanik
    7. Noopur Dubey
    8. Subhash Narasimhan
    9. Murali Krishna Madduri
    10. Biswajit Pal
    11. Rajesh S Gokhale
    12. Rajan Sankaranarayanan

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study addresses the structural basis of the ability of fatty acyl-AMP ligases (FAAL) to exclude condensation of activated fatty acids with coenzyme-A and facilitate the reaction with other 4-phosphopantetheine linked acceptors. This issue is of significant interest with regard to understanding how certain fatty acids are channeled to specific metabolic fates. The structural question at hand is the apparent discrimination of the CoA moiety (adenosine 3',5'-bisphosphate) versus a holo-ACP tethered to the 4-phosphopantethein head group. This work will contribute significantly to our current knowledge of how distinct classes of enzymes divert fatty acids to virulent lipids in mycobacteria, and it will be more broadly of interest for metabolic engineering.

      (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