eLife

Latest preprint reviews

1. Reconstitution of surface lipoprotein translocation through the Slam translocon

   This article has 6 authors:

   1. Minh Sang Huynh
   2. Yogesh Hooda
   3. Yuzi Raina Li
   4. Maciej Jagielnicki
   5. Christine Chieh-Lin Lai
   6. Trevor F Moraes

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work provides new insights into how surface-exposed lipoproteins of Gram-negative bacteria reach their destination in the outer membrane. Authors find that the outer membrane protein complex Slam serves as a translocon for the lipoproteins and the periplasmic chaperone Skp mediates their targeting to Slam. This work may contribute to the elucidation of host invasion mechanisms by pathogenic bacteria, in which surface lipoproteins play an important role.

     (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. Dendritic branch structure compartmentalizes voltage-dependent calcium influx in cortical layer 2/3 pyramidal cells

   This article has 6 authors:

   1. Andrew T Landau
   2. Pojeong Park
   3. J David Wong-Campos
   4. He Tian
   5. Adam E Cohen
   6. Bernardo L Sabatini

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Synaptic plasticity typically requires the conjunction of dendritic action potentials and synaptic activation. Together these signals cause nonlinear changes in calcium influx that then drive plasticity. The strength of these interactions can vary in complex ways. The authors use an elegant combination of imaging and electrophysiology to convincingly show how some of these complexities in murine cortical neurons arise from electrical properties of neuronal dendrites and synaptic NMDA receptors. This is a thorough and well done analysis of a set of issues that have implications for the ways in which dendritic morphology affect plasticity "rules." The underlying principles are largely previously understood, but their implications (e.g. the difference between voltage dependence of calcium channel and NMDA receptor calcium influx) are not widely appreciated and yet have important effects on the resulting integration.

     (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

3. DNA circles promote yeast ageing in part through stimulating the reorganization of nuclear pore complexes

   This article has 7 authors:

   1. Anne C Meinema
   2. Anna Marzelliusardottir
   3. Mihailo Mirkovic
   4. Théo Aspert
   5. Sung Sik Lee
   6. Gilles Charvin
   7. Yves Barral

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This interesting study examines a potential relationship between the tethering of extrachromosomal DNA (ecDNA) to the nuclear pore complex (NPC) and its role in aging; a model is proposed whereby the nuclear basket is displaced by ecDNA anchoring, which leads to a broader remodeling of the NPC that is distinct from NPC damage. This idea is conceptually novel and will represent an important advance, although some more support for the conclusions is still needed.

     (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. The human FLT1 regulatory element directs vascular expression and modulates angiogenesis pathways in vitro and in vivo

   This article has 15 authors:

   1. Julian Stolper
   2. Holly K. Voges
   3. Michael See
   4. Neda Rahmani Mehdiabadi
   5. Gulrez Chahal
   6. Mark Drvodelic
   7. Michael Eichenlaub
   8. Tanya Labonne
   9. Benjamin G. Schultz
   10. Alejandro Hidalgo
   11. Lazaro Centanin
   12. Jochen Wittbrodt
   13. Enzo R. Porrello
   14. David A. Elliott
   15. Mirana Ramialison

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper aims to identify enhancers controlling human cardiovascular development. The authors identified a set of highly conserved regulatory elements bioinformatically and tested one of these in vivo, in medaka, and in vitro, in hESC differentiated into endothelial cells. They find deletion of this enhancer had no significant effect on the expression of FLT1 mRNA in the human cell line or on the formation of tube formation. However, deletion of the orthologous enhancer in medaka showed phenotypic effects in blood clot formation. Together, the data provide insights into the function of an enhancer controlling FLT1. This manuscript will be of interest to scientists interested in gene regulation, vascular biology and developmental biology.

     (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. Analyzing the brainstem circuits for respiratory chemosensitivity in freely moving mice

   This article has 6 authors:

   1. Amol Bhandare
   2. Joseph van de Wiel
   3. Reno Roberts
   4. Ingke Braren
   5. Robert Huckstepp
   6. Nicholas Dale

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study utilizes a miniscope approach and GCaMP6 in freely behaving conscious mice to record CO2-associated multicellular calcium responses of neurons or glia in brainstem regions implicated in CO2-dependent control of breathing. The application of this approach in this context is extremely attractive, and new to the respiratory neurobiology field. Several technical improvements could strengthen the manuscript. Foremost, the study is broad in scope and consequently not always technically rigorous in important aspects such as identification of cell types imaged. In some cases that affects interpretation of the significance of the results. Since some of the conclusions about cellular responses to CO2 are mostly at odds with a substantial literature using more established techniques, there is even greater onus on the authors to ensure reliability of the results.

     (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. Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates

   This article has 6 authors:

   1. Ali A Kermani
   2. Olive E Burata
   3. B Ben Koff
   4. Akiko Koide
   5. Shohei Koide
   6. Randy B Stockbridge

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     E. coli EmrE and other members of the SMR family of transporters utilize the proton motive force to pump out a broad spectrum of antibiotics, thereby contributing to multi-drug resistance. Here, a new multipurpose crystallization chaperone is used to determine the structure of EmrE in apo form and in complex with various substrates. The strength of the manuscript is in the description of six new structures of EmrE at a resolution sufficient for building an atomic model and understanding how the antimicrobial agents bind, allowing robust conclusions to be drawn regarding the molecular details of binding of the antimicrobial agents. The report will be of interest to both those studying antibiotic resistance and those studying transporters.

     (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

7. Modeling the consequences of the dikaryotic life cycle of mushroom-forming fungi on genomic conflict

   This article has 3 authors:

   1. Benjamin Auxier
   2. Tamás L Czárán
   3. Duur K Aanen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Unions between equal partners can be destabilized by matings with third parties. In this paper the authors demonstrated that in fungi, 'stable unions' of two nuclei (dikaryons) are predicted to experience costs to vegetative fitness from investment in such mating opportunities. 'Open unions', in which third parties have access to the resources of established partnerships, are evolutionarily highly unstable. This paper will be of general interest to those who study evolutionary conflicts and to fungal geneticists.

     (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

8. Machine learning sequence prioritization for cell type-specific enhancer design

   This article has 18 authors:

   1. Alyssa J Lawler
   2. Easwaran Ramamurthy
   3. Ashley R Brown
   4. Naomi Shin
   5. Yeonju Kim
   6. Noelle Toong
   7. Irene M Kaplow
   8. Morgan Wirthlin
   9. Xiaoyu Zhang
   10. BaDoi N Phan
   11. Grant A Fox
   12. Kirsten Wade
   13. Jing He
   14. Bilge Esin Ozturk
   15. Leah C Byrne
   16. William R Stauffer
   17. Kenneth N Fish
   18. Andreas R Pfenning

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes an exciting new approach for tagging and isolation of unique neuronal subpopulations, which has traditionally been challenging without the incorporation of expensive and time consuming transgenic animal colonies. While the manuscript highlights a specific test case of this technology with neurons expressing Parvalbumin, in theory this method could be applied to any neuronal or even non-neuronal cell type. Further, this approach could be applied to other model organisms for which transgenic technologies are limited, thereby facilitating research in other species.

     (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

9. Speed variations of bacterial replisomes

   This article has 5 authors:

   1. Deepak Bhat
   2. Samuel Hauf
   3. Charles Plessy
   4. Yohei Yokobayashi
   5. Simone Pigolotti

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript uses experiments and theory to characterize the variations in replication speed of E.coli throughout cell cycle. The authors developed a theory to account for fluctuations in the replication velocity as well as a cell-cycle-dependent speed, and by using sequencing data they analyzed the variations in the speed for E. coli. They found that replication speed increases with increasing temperature, and also observed oscillatory patterns in the speed of the replisome, consistent with variations in mutation rate (accuracy) across the genome. These observations suggest a tradeoff between replication speed and accuracy in E.coli.

     (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

10. Measuring the tolerance of the genetic code to altered codon size

    This article has 3 authors:

    1. Erika Alden DeBenedictis
    2. Dieter Söll
    3. Kevin M Esvelt

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Using a phage-based library generation and selection, the authors generated a suite of 4-base decoding tRNAs with improved efficiency in quadruplet decoding. The data represent an important step toward enhancing protein synthesis with 4-base codons. Overall, the approach to generate many tRNA variants with quadruplet anticodons is intriguing and provides a wealth of valuable information to the field. The results, once some of the reviewer concerns have been addressed, should become foundational for the field of synthetic biology.

      (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