eLife

Latest preprint reviews

1. A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

   This article has 2 authors:

   1. Krishna Rijal
   2. Pankaj Mehta

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces a fully differentiable variant of the Gillespie algorithm as an approximate stochastic simulation scheme for complex chemical reaction networks, allowing kinetic parameters to be inferred from empirical measurements of network outputs using gradient descent. The concept and algorithm design are convincing and innovative. While the proofs of concept are promising, some questions are left open about implications for more complex systems that cannot be addressed by existing methods. This work has the potential to be of significant interest to a broad audience of quantitative and synthetic biologists.

   Reviewed by eLife

2. Maintenance of neuronal TDP-43 expression requires axonal lysosome transport

   This article has 20 authors:

   1. Veronica H Ryan
   2. Sydney Lawton
   3. Joel F Reyes
   4. James Hawrot
   5. Ashley M Frankenfield
   6. Sahba Seddighi
   7. Daniel M Ramos
   8. Jacob Epstein
   9. Faraz Faghri
   10. Nicholas L Johnson
   11. Jizhong Zou
   12. Martin Kampmann
   13. John Replogle
   14. Yue Andy Qi
   15. Hebao Yuan
   16. Kory Johnson
   17. Dragan Maric
   18. Ling Hao
   19. Mike A Nalls
   20. Michael Emmerson Ward

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this important manuscript, Ryan et al perform a genome-wide CRISPR based screen to identify genes that modulate TDP-43 levels in neurons. They identify a number of genes and pathways and highlight the BORC complex, which is required for anterograde lysosome transport as one such regulator of TDP-43 protein levels. Overall, this is a convincing study, which opens the door for additional future investigations on the regulation of TDP-43.

   Reviewed by eLife, PREreview

3. Peripheral glia and neurons jointly regulate activity-induced synaptic remodeling at the Drosophila neuromuscular junction

   This article has 5 authors:

   1. Yen-Ching Chang
   2. Yi-Jheng Peng
   3. Joo Yeun Lee
   4. Annie Wen
   5. Karen T Chang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on a new role of glia in activity-dependent synaptic remodeling using the Drosophila NMJ as a model system. The evidence supporting the claims of the authors is convincing. The authors have addressed most of the reviewers' concerns and help to further clarify the claims. The work will be of interest to neuroscientists working on glia-neuron interaction and synaptic remodeling.

   Reviewed by eLife

4. Transcriptional antitermination integrates the expression of loci of diverse phage origin in the chimeric Bartonella Gene Transfer Agent BaGTA

   This article has 4 authors:

   1. Aleksandr Korotaev
   2. Quirin Niggli
   3. Valeria Congedi
   4. Christoph Dehio

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript describes an important finding of the transcriptional control of a chimeric gene transfer agents (GTA) cluster in Bartonella by a processive anti-termination factor (BrrG). The evidence provided is convincing. This manuscript will interest researchers working on transcriptional regulation, horizontal gene transfer, and phages.

   Reviewed by eLife

5. The eduWOSM: a benchtop advanced microscope for education and research

   This article has 4 authors:

   1. Nicholas J Carter
   2. Douglas S Martin
   3. Justin E Molloy
   4. Robert A Cross

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a valuable study and a promising development for the field of open-source microscopy for educational purposes. The strengths include the low cost of constructing the microscope, impressive performance and detailed resources including a dedicated website and YouTube channel. The claims are generally supported by solid evidence, however, the manuscript would be strengthened by inclusion of further details on standard performance metrics (e.g. signal to noise ratio etc.) compared to existing systems and further details and clarification on the microscope, construction and operation.

   Reviewed by eLife

6. Function and firing of the Streptomyces coelicolor contractile injection system requires the membrane protein CisA

   This article has 8 authors:

   1. Bastien Casu
   2. Joseph W Sallmen
   3. Peter E Haas
   4. Govind Chandra
   5. Pavel Afanasyev
   6. Jingwei Xu
   7. Martin Pilhofer
   8. Susan Schlimpert

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

   Reviewed by eLife

7. A pair of congenic mice for imaging of transplants by positron emission tomography using anti-transferrin receptor nanobodies

   This article has 12 authors:

   1. Thomas Balligand
   2. Claire Carpenet
   3. Sergi Olivé Palau
   4. Tom Jaspers
   5. Pavana Suresh
   6. Xin Liu
   7. Himadri Medhi
   8. Yoon Ho Lee
   9. Mohammad Rashidian
   10. Bart De Strooper
   11. Hidde L Ploegh
   12. Maarten Dewilde

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this highly innovative study, Carpenet C et al explore the use of nanobody-based PET imaging to track proliferative cells after in vivo transplantation in mice, in a fully immunocompetent setting. The development of a unique set of PET tracers and mouse strains to track genetically-unmodified transplanted cells in vivo is an important novel asset that could potentially facilitate cell tracking in different research fields. The evidence provided is compelling as the new method proposed might facilitate overcoming certain limitations of alternative approaches, such as full sized immunoglobulins and small molecules.

   Reviewed by eLife

8. Reactive Oxygen Detoxification Contributes to Mycobacterium abscessus Antibiotic Survival

   This article has 6 authors:

   1. Nicholas A Bates
   2. Ronald Rodriguez
   3. Rama Drwich
   4. Abigail Ray
   5. Sarah A Stanley
   6. Bennett H Penn

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Using a transposon sequencing (TN-seq) approach, the authors identified key genetic determinants of drug tolerance in Mycobacterium abscessus. Given that M. abscessus is inherently resistant to multiple antibiotics, this valuable study makes a significant contribution by uncovering how antibiotic tolerance is linked to reactive oxygen species (ROS) in this non-tuberculous mycobacterial (NTM) species. The solid findings further strengthen the growing evidence that ROS play a central role in the mechanism of antibiotic action and tolerance in mycobacteria. However, the use of words persistence or tolerance should follow the consensus definition given in the Balaban 2019 Nat Rev Micro paper.

   Reviewed by eLife

9. Early experience affects foraging behavior of wild fruit bats more than their original behavioral predispositions

   This article has 7 authors:

   1. Adi Rachum
   2. Lee M Harten
   3. Reut Assa
   4. Aya Goldshtein
   5. Xing Chen
   6. Nesim Gonceer
   7. Yossi Yovel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper provides important insight into how early life experience shapes adult behavior in fruit bats. The authors raised juvenile bats either in an impoverished or enriched environment and studied their foraging behaviors. The evidence is convincing that bats raised in enriched environments are more active, bold, and exploratory. The work will be of interest to ethologists and developmental psychologists.

   Reviewed by eLife

10. The electrogenicity of the Na+/K+-ATPase poses challenges for computation in highly active spiking cells

    This article has 3 authors:

    1. Liz Weerdmeester
    2. Jan-Hendrik Schleimer
    3. Susanne Schreiber

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study provides new insights into the lesser-known effects of the sodium-potassium pump on how nerve cells process signals, particularly in highly active cells like those of weakly electric fish. The computational methods used to establish the claims in this work are compelling and can be used as a starting point for further studies.

    Reviewed by eLife