eLife

Latest preprint reviews

1. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

   This article has 10 authors:

   1. Michael Jahn
   2. Nick Crang
   3. Markus Janasch
   4. Andreas Hober
   5. Björn Forsström
   6. Kyle Kimler
   7. Alexander Mattausch
   8. Qi Chen
   9. Johannes Asplund-Samuelsson
   10. Elton Paul Hudson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work combines elegant experimental approaches with modelling predictions to study of metabolic adaptations in the bacterium Cupriavidus necator, a microorganism of interest given its metabolic versatility and potential industrial applications. This manuscript will be interesting for microbiologists and systems biologists who want to understand how protein production and economy and enzyme utilization differs in a versatile microorganism in different conditions.

     (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

2. A model of preferential pairing between epithelial and dendritic cells in thymic antigen transfer

   This article has 9 authors:

   1. Matouš Vobořil
   2. Jiří Březina
   3. Tomáš Brabec
   4. Jan Dobeš
   5. Ondřej Ballek
   6. Martina Dobešová
   7. Jasper Manning
   8. Richard S Blumberg
   9. Dominik Filipp

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to immunologists studying mechanisms of thymic central tolerance. The study elegantly makes use of multiple genetic mouse models to generate data supporting the conclusion that different dendritic cell subsets in the thymus capture self-antigens from distinct subsets of thymic epithelial cells. However, some key conclusions are not entirely novel, and the final model, as currently presented, draws from only selective analyses and thus may not accurately reflect the antigen transfer between thymic epithelial cell and dendritic cell subsets that promote central tolerance.

     (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. Proton transfer pathway in anion channelrhodopsin-1

   This article has 5 authors:

   1. Masaki Tsujimura
   2. Keiichi Kojima
   3. Shiho Kawanishi
   4. Yuki Sudo
   5. Hiroshi Ishikita

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors report continuum electrostatics, molecular dynamics and QM/MM simulations to probe the protonation pattern of key residues in anion channelrhodopsin (GtACR1). The findings provide new mechanistic insights into the gating mechanism of GtACR1, and the study will be of potential interest for the community focused on biophysical chemistry, protein simulations and optogenetics. More generally, the study helps highlight that due to potential compensatory effects, care needs to be exercised when interpreting absorption spectra of mutant proteins.

     (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. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis

   This article has 20 authors:

   1. Andreas Hober
   2. Khue Hua Tran-Minh
   3. Dominic Foley
   4. Thomas McDonald
   5. Johannes PC Vissers
   6. Rebecca Pattison
   7. Samantha Ferries
   8. Sigurd Hermansson
   9. Ingvar Betner
   10. Mathias Uhlén
   11. Morteza Razavi
   12. Richard Yip
   13. Matthew E Pope
   14. Terry W Pearson
   15. Leigh N Andersson
   16. Amy Bartlett
   17. Lisa Calton
   18. Jessica J Alm
   19. Lars Engstrand
   20. Fredrik Edfors

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study describes the addition of peptide immunoprecipitation by means of SISCAPA technology to the Sars-Cov2 mass spectrometry-based diagnostics toolbox. While MS-based viral detection has been described by several other groups, the presented method enriches SARS-CoV-2 peptides from clinical samples, thus enhancing the sensitivity and addressing one of the major limitations of this new method for viral diagnostics. The work is straightforward and of potentially great importance to the field. It shows beyond any doubt that mass spectrometry can become a clinically applied diagnostic instrument to detect (viral) infection.

     (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, ScreenIT

5. Remote immune processes revealed by immune-derived circulating cell-free DNA

   This article has 22 authors:

   1. Ilana Fox-Fisher
   2. Sheina Piyanzin
   3. Bracha Lea Ochana
   4. Agnes Klochendler
   5. Judith Magenheim
   6. Ayelet Peretz
   7. Netanel Loyfer
   8. Joshua Moss
   9. Daniel Cohen
   10. Yaron Drori
   11. Nehemya Friedman
   12. Michal Mandelboim
   13. Marc E Rothenberg
   14. Julie M Caldwell
   15. Mark Rochman
   16. Arash Jamshidi
   17. Gordon Cann
   18. David Lavi
   19. Tommy Kaplan
   20. Benjamin Glaser
   21. Ruth Shemer
   22. Yuval Dor

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide significant support for the utility of their assay for immune monitoring in health and disease.

     (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. Suppression weakens unwanted memories via a sustained reduction of neural reactivation

   This article has 2 authors:

   1. Ann-Kristin Meyer
   2. Roland G Benoit

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The goal of this study was to test whether multiple attempts at suppressing the retrieval of an (emotional) memory is associated with degradation of the representation of information in the brain about such memories. A combination of sophisticated computational modelling in fMRI reveals that neural representations of previously suppressed memories are sustainably weakened during memory retrieval attempts. This manuscript is of interest for neuroscientists in the field of motivated forgetting and memory control.

     (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

7. Correlative all-optical quantification of mass density and mechanics of subcellular compartments with fluorescence specificity

   This article has 13 authors:

   1. Raimund Schlüßler
   2. Kyoohyun Kim
   3. Martin Nötzel
   4. Anna Taubenberger
   5. Shada Abuhattum
   6. Timon Beck
   7. Paul Müller
   8. Shovamaye Maharana
   9. Gheorghe Cojoc
   10. Salvatore Girardo
   11. Andreas Hermann
   12. Simon Alberti
   13. Jochen Guck

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this interesting study, the authors combined Brillouin microscopy with Optical Diffraction Tomography and epi-fluorescence imaging to investigate physical properties of biological materials including nucleoplasm, cytoplasm, phase-separated organelles, and adipocytes. The results are largely convincing and offer interesting insights into the material properties of these subcellular structures.

     (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. Presynaptic stochasticity improves energy efficiency and helps alleviate the stability-plasticity dilemma

   This article has 3 authors:

   1. Simon Schug
   2. Frederik Benzing
   3. Angelika Steger

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In large nervous systems such as mammalian cortex excitatory synapses are stochastic and the probability of release of neurotransmitter can be modulated by plasticity and neural activity. This paper presents a simple biologically plausible mechanism that regulates the probability of release during learning. Using network simulations the authors show that this can result in more energy efficient processing of learned stimuli by enhancing the reliability of important connections, with lower expected rates of transmission at less important synapses.

     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

9. Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection

   This article has 2 authors:

   1. Vishwa Patel
   2. Nishad Matange

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper investigates the evolutionary path of Escherichia coli resistance to the antibiotic trimethoprim. The authors show that adaptive mutations that accumulate early are often not in the drug target itself, but rather mutations that lead to transcriptional up-regulation of the drug target. Higher-level resistance can then evolve due to the addition of mutations in the drug target; however, at lower drug concentrations, cells are more likely to accumulate mutations that reverse the fitness defect associated with the initially acquired mutations. Overall, this study shows that regulatory mutations can play a major role in the evolution of antibiotic resistance in bacterial populations, and that the evolutionary path is influenced by the level of drug exposure.

     (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. Reviewers #1 , #2, and #3 agreed to share their names with the authors.)

   Reviewed by eLife

10. METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance

    This article has 13 authors:

    1. Eriko Matsuura-Suzuki
    2. Tadahiro Shimazu
    3. Mari Takahashi
    4. Kaoru Kotoshiba
    5. Takehiro Suzuki
    6. Kazuhiro Kashiwagi
    7. Yoshihiro Sohtome
    8. Mai Akakabe
    9. Mikiko Sodeoka
    10. Naoshi Dohmae
    11. Takuhiro Ito
    12. Yoichi Shinkai
    13. Shintaro Iwasaki

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This work examines how METTLL18-mediated RPL3 histidine methylation on 245 position regulates translation elongation and protects cells from cellular aggregation of Tyr-rich proteins. The study hints at the existence of a "ribosome code" and how posttranslational modification of ribosomal proteins could affect translation.

      (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