eLife

Latest preprint reviews

1. 3D optogenetic control of arteriole diameter in vivo

   This article has 5 authors:

   1. Philip J O'Herron
   2. David A Hartmann
   3. Kun Xie
   4. Prakash Kara
   5. Andy Y Shih

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript by O'Herron et al. describes an all-optical method combining optogenetic stimulation and 2-photon microscopy imaging to simultaneously manipulate and monitor brain microvasculature contractility in three dimensions. The method employs a spatial light modulator to create three-dimensional activation patterns in the brains of cranial window-model transgenic mice expressing the excitatory opsin, ReaChR, in mural cells (smooth muscle cells and pericytes). This provides a powerful new in vivo technique to control blood flow into the brain and to understand its actions on brain function.

     (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 name with the authors.)

   Reviewed by eLife

2. In situ X-ray-assisted electron microscopy staining for large biological samples

   This article has 5 authors:

   1. Sebastian Ströh
   2. Eric W Hammerschmith
   3. David W Tank
   4. H Sebastian Seung
   5. Adrian Andreas Wanner

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study explores the kinetics of heavy metal staining of tissue using time-lapse imaging with X-ray micro computed tomography (CT). It will be of interest to the wide community of scientists preparing biological samples for electron microscopy (EM), in particular large-volume EM. While at present the relation between CT imaging and EM contrast remains to be quantified, this study has the potential to become a reference for the field in establishing a quantitative tool for assessing and developing staining protocols.

     (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

3. Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature

   This article has 6 authors:

   1. Ariel Ogran
   2. Tal Havkin-Solomon
   3. Shirly Becker-Herman
   4. Keren David
   5. Idit Shachar
   6. Rivka Dikstein

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, Ogran and colleagues provide evidence suggesting that T-Cell Leukemia/Lymphoma 1 (TCL1) protein may promote alternative transcription site selection and promoter usage in chronic lymphoid leukemia. It is further proposed that these TCL1-dependent alterations lead to the production of N-terminally truncated versions of proteins including chromatin regulators while bolstering expression of transcription factors including MYC. Collectively, it was found that these results are of broad interest inasmuch as they suggest previously unappreciated rewiring of epigenetic, transcriptional, and translational programs in leukemic cells. To this end, this article should be of significant interest across a variety of fields of biomedical research ranging from regulation of gene expression to cancer research. The paper would be strengthened by mechanistic data linking TCL1 to alterations in transcription site selection and/or alternative promoter usage and by stronger validation of the expression of N-truncated proteins and their functional consequences.

     (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

4. Green fluorescent protein-like pigments optimise the internal light environment in symbiotic reef-building corals

   This article has 6 authors:

   1. Elena Bollati
   2. Niclas H Lyndby
   3. Cecilia D'Angelo
   4. Michael Kühl
   5. Jörg Wiedenmann
   6. Daniel Wangpraseurt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to marine biologists, and has particular relevance to those studying symbiotic corals. The use of compelling experimental optical measurements performed in situ allows testing of previous predictions on protein-based pigments that are found in many coral species. Specifically, the study analyzes the role of two classes of pigments, the Red Fluorescent Proteins (RFPs) and the Chromo proteins. It provides direct measurement data that suggest that RFPs can indeed provide additional light to the symbionts by converting the prevalent blue-green light at depth in orange-red light that penetrates more in the tissues of the polyps, thus increasing the number of photons available for photosynthesis. The authors also provide evidence based on light measurement for a possible photoprotective role of Chromoproteins, although the study does not yet provide any direct evidence for an ecological benefit of such light conversion/light protective functions.

     (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

5. Histone H3 clipping is a novel signature of human neutrophil extracellular traps

   This article has 9 authors:

   1. Dorothea Ogmore Tilley
   2. Ulrike Abuabed
   3. Ursula Zimny Arndt
   4. Monika Schmid
   5. Stefan Florian
   6. Peter R Jungblut
   7. Volker Brinkmann
   8. Alf Herzig
   9. Arturo Zychlinsky

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study describes a new antibody to identify human neutrophil extracellular traps (NETs) also in tissue samples. The paper might not only introduce an important novel tool for many areas of biomedical research, but it also touches cell biological questions of importance. The usefulness of the NET-specific antibody is impressively developed in the paper, while the mechanistic concepts are not yet fully established.

     (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

6. Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxation mechanism

   This article has 2 authors:

   1. Amy Osterman
   2. Alfonso Mondragón

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Osterman and Modragon report the first crystal structure of topoisomerase V in complex with DNA. Topoisomerase V is an unusual protein in that homologs have only been found in the archaeal Methanopyrus genus. The paper is likely of interest to those studying topoisomerase biology and biochemistry, and the wider audience interested in DNA replication and repair transactions.

     (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. Rate-distortion theory of neural coding and its implications for working memory

   This article has 2 authors:

   1. Anthony MV Jakob
   2. Samuel J Gershman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of potential interest to readers in the fields of working memory and neural coding. It presents a model of a neural circuit that learns to optimally represent its inputs subject to an information capacity limit and claims that this model can account for a range of empirical phenomena in the visual working memory literature. However, the fit to empirical data is qualitative and in some cases unconvincing, certain aspects of the neural model seem difficult to square with established neurophysiology, and there is insufficient conceptual or quantitative comparison with other models in the WM literature that seek to explain the same data.

     (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. Mesoscopic in vivo human T 2 * dataset acquired using quantitative MRI at 7 Tesla

   This article has 8 authors:

   1. Omer Faruk Gulban
   2. Saskia Bollmann
   3. Laurentius (Renzo) Huber
   4. Konrad Wagstyl
   5. Rainer Goebel
   6. Benedikt A. Poser
   7. Kendrick Kay
   8. Dimo Ivanov

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The methods presented in this work are of potential broad interest across different domains of human neuroscience. Reliable methods for pushing the limits of spatial resolution for mesoscopic scale imaging of the living human cortex are of wide interest and utility. The image quality and high-spatial resolution of the data are exceptionally high. The paper in its current form demonstrates the application of the developed methods to a few exemplary cortical regions and sequences.

     (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

9. Altered regulation of Ia afferent input during voluntary contraction in humans with spinal cord injury

   This article has 2 authors:

   1. Bing Chen
   2. Monica A Perez

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to basic and clinical neurophysiologists who are focused on understanding neural mechanisms that influence recovery following spinal cord injury (SCI). The work compares the afferent regulation of motor output to soleus muscle in controls and individuals with SCI. The results indicate differences between groups such that there is less facilitation in the SCI group during muscle contraction.

     (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 name with the authors.)

   Reviewed by eLife

10. Genome-wide base editor screen identifies regulators of protein abundance in yeast

    This article has 4 authors:

    1. Olga T Schubert
    2. Joshua S Bloom
    3. Meru J Sadhu
    4. Leonid Kruglyak

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Schubert and coworkers report the development of a novel CRISPR-based screening method that allows probing interactions between (a large set of) specific mutations and the abundance of specific proteins, and, more generally, investigate the spectrum of effects that (point) mutations can have on protein abundance. This complements existing strategies for measuring effects of genetic perturbations on transcript levels, which is important as for some proteins mRNA and protein levels do not correlate well. The ability to measure proteins directly therefore promises to close an important gap in our understanding of the links between genotype and phenotype, and the strategy is broadly applicable beyond the current study.

      (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