eLife

Latest preprint reviews

1. Task-specific roles of local interneurons for inter- and intraglomerular signaling in the insect antennal lobe

   This article has 2 authors:

   1. Debora Fusca
   2. Peter Kloppenburg

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The question investigated - to understand the computational significance of different types of local interneurons in neural circuits - is an important and significant problem. Here authors elucidate the role of the two types of LNs, by combining whole-cell patch clamp recordings with calcium imaging via single cell dye injection. This method enables them to monitor calcium dynamics of the different axons and branches of single LNs in identified glomeruli of the antennal lobe, while the membrane potential can be recorded at the same time. They conclude that non-spiking LNs with graded responses show glomerular restricted responses to odorants and spiking LNs show similar responses across glomeruli.

     (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. The roles of history, chance, and natural selection in the evolution of antibiotic resistance

   This article has 6 authors:

   1. Alfonso Santos-Lopez
   2. Christopher W Marshall
   3. Allison L Haas
   4. Caroline Turner
   5. Javier Rasero
   6. Vaughn S Cooper

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work, which will be of value to evolutionary and clinical microbiologists, uses a well-designed experimental evolution strategy to tease apart contributions of history, chance, and selection on the evolution of antibiotic resistance in A. baumannii, an important microbial pathogen. While relevant, the work will benefit from further clarification regarding some of the concepts and procedures used and revision of some of the interpretations.

     (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. Lying in a 3T MRI scanner induces neglect-like spatial attention bias

   This article has 3 authors:

   1. Axel Lindner
   2. Daniel Wiesen
   3. Hans-Otto Karnath

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper examines the visual-ocular response in participants when exposed to the static magnetic field of a 3T MRI system. Historically, this problem has been approached from a safety perspective. In the present study, the authors ask about the behavioral consequences of this field given that it induces a response in the vestibular system, hypothesized to mimic that of a caloric vestibular stimulation event. As such, one should anticipate a biased vestibulo-ocular reflex in the static field as well as biases in spatial attention. These predictions were confirmed, with the attentional bias manifest in eye movements during a visual search task. This is an important finding because it reveals functional "artifacts" that may arise during fMRI studies, effects that may need to be considered by those conducting research in the MR environment (especially functional studies).

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

   Reviewed by eLife

4. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

   This article has 13 authors:

   1. Francisco Díaz-Pascual
   2. Martin Lempp
   3. Kazuki Nosho
   4. Hannah Jeckel
   5. Jeanyoung K Jo
   6. Konstantin Neuhaus
   7. Raimo Hartmann
   8. Eric Jelli
   9. Mads Frederik Hansen
   10. Alexa Price-Whelan
   11. Lars EP Dietrich
   12. Hannes Link
   13. Knut Drescher

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this manuscript the authors use a combination of transcriptomics, metabolomics, and quantitative measurements of growth to characterize the temporal and spatial distribution of cells with different metabolic states within colony of biofilms of the model bacterium Escherichia coli. They show that within the biofilm cells performing different metabolic functions are distributed in different regions of the colonies, and propose a model where nutrient cross-feeding through the amino acid alanine explains the phenotypic heterogeneity observed within the biofilm. The findings reported have potential broad implications for thinking about the spatial structure of communities of all bacterial 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 agreed to share their name with the authors.)

   Reviewed by eLife

5. The E3 ligase Thin controls homeostatic plasticity through neurotransmitter release repression

   This article has 3 authors:

   1. Martin Baccino-Calace
   2. Katharina Schmidt
   3. Martin Müller

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In the study presented here, the authors used the fruitfly Drosophila melanogaster to identify a new molecular regulator - the E3 ubiquitin ligase Thin - of presynaptic homeostatic plasticity (PHP), a process where synaptic signaling between motorneurons and muscle cells is dynamically adapted to compensate exogenously imposed changes in synapse strength. Based on a very substantial set of high quality data, the authors propose that Thin functions presynaptically during PHP, that presynaptic thin negatively regulates neurotransmitter release under baseline conditions by limiting the number of release-ready synaptic vesicles, and that Thin controls transmitter release by regulating Dysbindin, a schizophrenia-susceptibility gene required for PHP. The authors' conclusion is that Thin links protein-degradation-dependent proteostasis of Dysbindin to homeostatic regulation of neurotransmitter release. The major claims of the paper are well supported by the data, but alternative hypotheses cannot yet be unequivocally excluded.

     (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

6. Framework for rapid comparison of extracellular vesicle isolation methods

   This article has 7 authors:

   1. Dmitry Ter-Ovanesyan
   2. Maia Norman
   3. Roey Lazarovits
   4. Wendy Trieu
   5. Ju-Hyun Lee
   6. George M Church
   7. David R Walt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes a framework for rapidly quantifying relative extracellular vesicle (EV) yield and purity across isolation methods, with a focus on using size exclusion chromatography (SEC) for EV isolation from small volumes of pooled plasma and cerebrospinal fluid (CSF) samples. The authors used single molecule array (Simoa) assays for the quantification of EVs using three tetraspanins (CD9, CD63, and CD81), and report the outcomes of assessing EV yields and purity with respect to albumin by various SEC parameters (Sepharose size, column length, fractions collected). This is the first demonstration of the use of Simoa with three commonly used tetraspanins to measure EVs from small volumes of CSF, of great relevance to human CSF biomarker studies, but these methods could also be applied to compare EV isolation methods from other fluids such as cell culture media.

     (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

7. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae

   This article has 7 authors:

   1. Tingting Zhao
   2. Irina O Vvedenskaya
   3. William KM Lai
   4. Shrabani Basu
   5. B Franklin Pugh
   6. Bryce E Nickels
   7. Craig D Kaplan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Kaplan and colleagues build upon their earlier work using genetic phenotypes to find and analyze mutations that determine how mRNA start sites are chosen. Here they provide convincing genetic evidence supporting a model in which the Transcription Factor II H (TFIIH) protein complex pushes downstream DNA back into the RNA polymerase active site, creating a window within which the polymerase can choose particular start sites. This will primarily interest those in the transcription field who are thinking about initiation mechanisms.

     (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

8. Single-nucleus transcriptomic analysis of human dorsal root ganglion neurons

   This article has 5 authors:

   1. Minh Q Nguyen
   2. Lars J von Buchholtz
   3. Ashlie N Reker
   4. Nicholas JP Ryba
   5. Steve Davidson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this work, Minh Nguyen and colleagues performed single nuclear RNAseq of human dorsal root ganglion (DRG) neurons and classified them into 15 clusters. A bioinformatic comparison to mouse lumbar DRG single nucleus sequencing results is also described. The importance of reporting the single nucleus or single cell molecular profiles of human DRG cannot be overstated. Proper molecular targeting of therapeutics requires knowing this information. Given that the field is just starting to understand the human specific molecular signature of primary somatosensory neurons using single cell/nuclear RNAseq, this study is important and timely, providing one of the first gene expression databases of individual human DRG neurons.

     (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. Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP protein ENAH

   This article has 8 authors:

   1. Theresa Hwang
   2. Sara S Parker
   3. Samantha M Hill
   4. Robert A Grant
   5. Meucci W Ilunga
   6. Venkatesh Sivaraman
   7. Ghassan Mouneimne
   8. Amy E Keating

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript introduces a new molecular screen, MassTitr, to screen for long (36-mer) peptides derived from the human proteome that can bind a specific target. The method is demonstrated using the EVH1 domain of the actin-associated ENAH protein as target. About 100 peptides were isolated, and further analysis identified sequence features that contribute to the binding of the EVH1 domain by these peptides. The human proteome contains many short linear motifs of 4-6 residues that are critical for protein-protein interactions. The work here helps to better understand how the sequence surrounding such motifs contributes to protein-protein interactions.

     (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

10. Clathrin-independent endocytic retrieval of SV proteins mediated by the clathrin adaptor AP-2 at mammalian central synapses

    This article has 7 authors:

    1. Tania López-Hernández
    2. Koh-ichiro Takenaka
    3. Yasunori Mori
    4. Pornparn Kongpracha
    5. Shushi Nagamori
    6. Volker Haucke
    7. Shigeo Takamori

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Local recycling of synaptic vesicles is required to maintain neurotransmission via clathrin-mediated endocytosis and clathrin-independent ultrafast endocytosis. Clathrin also plays a role in ultrafast endocytosis to regenerate vesicles from a recycling endosome. Here the authors have further tested the role of clathrin and clathrin adaptors in synaptic vesicle endocytosis. This paper raises the interesting possibility that adaptor protein AP-2 but not clathrin contributes to the endocytosis of synaptic vesicle proteins. There are some concerns about differential knockdown of clathrin and AP-2 but if the authors can resolve these, this would be an important result.

      (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