eLife

Latest preprint reviews

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. An open-source, high-performance tool for automated sleep staging

   This article has 2 authors:

   1. Raphael Vallat
   2. Matthew P Walker

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study describes a novel algorithm to perform fully automated sleep staging in humans. It is well validated and performs at the level of other state of the art algorithms although it does not yet include comparisons against the existing tools available in the field. Given the efforts made by the authors to ensure ease of use and accessibility it may help extend the use of automated methods in the study of sleep.

     (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. Rat sensitivity to multipoint statistics is predicted by efficient coding of natural scenes

   This article has 6 authors:

   1. Riccardo Caramellino
   2. Eugenio Piasini
   3. Andrea Buccellato
   4. Anna Carboncino
   5. Vijay Balasubramanian
   6. Davide Zoccolan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This research will be of interest to neuroscientists who want to understand how visual systems are tuned to and encode natural scenes. It reports that rats share phenomenology with humans in sensitivity to spatial correlations in scenes. This work shows that an earlier paper's hypothesis about efficient coding may be broadly applicable, but it is perhaps most interesting in opening up the possibility of studying this sort of visual tuning in an animal where invasive techniques can be used to study this sensitivity and its development.

     (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. Experience-dependent weakening of callosal synaptic connections in the absence of postsynaptic FMRP

   This article has 3 authors:

   1. Zhe Zhang
   2. Jay R Gibson
   3. Kimberly M Huber

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors find that long-range interhemispheric synapses are selectively weakened following loss of function of the gene mediating fragile X syndrome, the most common inherited form of intellectual disability. Using clever genetic and physiological approaches in mice, the authors show that the effect is cell autonomous and occurs postnatally by impeding the normal developmental strengthening of these synapses. The results convincingly enhance our understanding of the complex pathophysiology of neurological dysfunction in this developmental disorder.

     (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

10. Physiological function of Flo11p domains and the particular role of amyloid core sequences of this adhesin in Saccharomyces cerevisiae

    This article has 7 authors:

    1. Clara Bouyx
    2. Marion Schiavone
    3. Marie-Ange Teste
    4. Etienne Dague
    5. Nathalie Sieczkowski
    6. Anne Julien
    7. Jean Marie Francois

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This work serves as an independent confirmation and expansion of previous work, suggesting that certain domains in fungal adhesins can form amyloid-like structures that are essential for cell-cell aggregation, but less so for cell-surface adhesion or invasive growth. Specifically, the expression of different adhesin constructs offers insight into the functional role of the different adhesin domains. Together, the results provide further insight into the molecular mechanisms underlying fungal adhesion, which does only further our understanding of basic fungal physiology, but also offers insight into fungal pathogenesis.

      (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