eLife

Latest preprint reviews

1. Granger causality analysis for calcium transients in neuronal networks, challenges and improvements

   This article has 6 authors:

   1. Xiaowen Chen
   2. Faustine Ginoux
   3. Martin Carbo-Tano
   4. Thierry Mora
   5. Aleksandra M Walczak
   6. Claire Wyart

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript provides a solid and valuable analysis of the advantages and potential pitfalls of the application of Granger Causality to calcium imaging data that should be of interest to a wide range of neuroscience researchers. Granger Causality is a key tool in assessing the temporal relationships between variables, but one that is susceptible to many types of artifacts. The rigor of the authors' application of the methodology to calcium imaging data in particular leads to a more robust understanding of the effects of measurement artifacts and analysis choices on the results. There was some concern, however, about whether all of the findings would apply outside feedforward neural circuits and it was unclear how some of the results relate to others that currently exist in the literature.

   Reviewed by eLife

2. Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules

   This article has 3 authors:

   1. Yufeng Zhou
   2. John H Lewis
   3. Zhe Lu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper presents a single-molecule polarization microscopy study aimed at monitoring the arginine/agmatine antiporter AdiC as it transiently exchanges between conformational states. This approach measures how a bis-TMR fluorophore anchored onto helix 6a changes its orientation in the microscope, and the authors identify four states that they propose correspond to the key steps in the transport cycle (inward-open, inward occluded, outward occluded and outward open). This is a cutting-edge and challenging approach that sets the stage for direct measurements of conformational equilibria and will thus be of interest to anyone studying transport mechanisms. However, additional investigation is required to validate the robustness of the post-processing of the single-molecule data to yield the four-state model compared to alternate models, to test the robustness of the data with transport mutants/conditions that would slow or eliminate states, and to consolidate transitions that are observed that conflict with previous observations of obligatory coupling in AdiC.

   Reviewed by eLife

3. State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels

   This article has 5 authors:

   1. Yein Christina Park
   2. Bharat Reddy
   3. Navid Bavi
   4. Eduardo Perozo
   5. José D Faraldo-Gómez

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript reports a new structure of the small conductance mechanosensitive channel MscS from E. coli in the open state, together with coarse-grained and atomistic molecular dynamics simulations of MscS and the related channel MSL1 of plant mitochondria in closed and open states. The important finding is that the surrounding lipid bilayer is severely distorted in the closed state only, with the protein inducing high curvature in the inner leaflet due to the membrane protruding into the cytoplasm. The authors argue convincingly that the role of membrane tension is to increase the energy of the protein-membrane system in this closed state compared to the relatively flat-membrane open state, in contrast to the previous proposal that tension-induced gating is driven by expansion of the in-plane area of the protein. The finding may be relevant for the understanding of ion channel mechano-sensation more generally, including of the PIEZO1 channel.

   Reviewed by eLife

4. Rapid learning of predictive maps with STDP and theta phase precession

   This article has 4 authors:

   1. Tom M George
   2. William de Cothi
   3. Kimberly L Stachenfeld
   4. Caswell Barry

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This article presents a model that uses spike timing-dependent plasticity and theta phase precession of spiking neurons to generate representations similar to those learned by temporal difference learning to form successor representations. This work is important for bridging between biologically detailed mechanisms shown in experimental data and the more abstract models in the reinforcement framework literature. The simulations are compelling, but several aspects may rely on unrealistic assumptions, so further work is necessary to determine whether such a learning process could actually occur in the brain.

   Reviewed by eLife

5. Molecular characterization of cell types in the squid Loligo vulgaris

   This article has 9 authors:

   1. Jules Duruz
   2. Marta Sprecher
   3. Jenifer C Kaldun
   4. Al-Sayed Al-Soudy
   5. Heidi EL Lischer
   6. Geert van Geest
   7. Pamela Nicholson
   8. Rémy Bruggmann
   9. Simon G Sprecher

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript describes cell types in the head of the squid, Loligo vulgaris, through expression patterns of key genes identified in single cell transcriptomics. This topic is generally of great comparative interest. It will contribute to a better understanding of the cephalopod nervous and sensory systems, providing a basis for future comparative and evolutionary research.

   Reviewed by eLife

6. The impact of task context on predicting finger movements in a brain-machine interface

   This article has 10 authors:

   1. Matthew J Mender
   2. Samuel R Nason-Tomaszewski
   3. Hisham Temmar
   4. Joseph T Costello
   5. Dylan M Wallace
   6. Matthew S Willsey
   7. Nishant Ganesh Kumar
   8. Theodore A Kung
   9. Parag Patil
   10. Cynthia A Chestek

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides valuable findings about how brain machine interfaces cope with changes in context, an important consideration for deploying such devices in the real world. The evidence supporting the claims is solid although increasing the number and range of contexts investigated would have strengthened the study. The work will be of interest to motor neuroscientists and engineers developing brain machine interfaces and will be useful for future development of such devices.

   Reviewed by eLife

7. Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses

   This article has 16 authors:

   1. Rituparna Chakrabarti
   2. Lina María Jaime Tobón
   3. Loujin Slitin
   4. Magdalena Redondo Canales
   5. Gerhard Hoch
   6. Marina Slashcheva
   7. Elisabeth Fritsch
   8. Kai Bodensiek
   9. Özge Demet Özçete
   10. Mehmet Gültas
   11. Susann Michanski
   12. Felipe Opazo
   13. Jakob Neef
   14. Tina Pangrsic
   15. Tobias Moser
   16. Carolin Wichmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is an important and methodologically compelling paper that reports the first application of optogenetics to inner hair cell ribbon exocytosis mechanisms in the inner ear and rapid flash-and-freeze techniques to a ribbon synapse. The conclusions of the paper are mostly well supported by the data and it will capture the interests of a broad audience of neurobiologists and sensory physiologists. Paired recordings of inner hair cells and afferents validate the optogenetic protocols of stimulation. A surprising finding is the nearly complete absence of docked vesicles at rest and after stimulation, but upon stimulation vesicles rapidly associate with the ribbon. The reviewers agreed that this is a high-quality study, but that some additional work is needed to address certain pitfalls of the methods used and to rule out alternative explanations of the data.

   Reviewed by eLife

8. Ultrafast (400 Hz) network oscillations induced in mouse barrel cortex by optogenetic activation of thalamocortical axons

   This article has 3 authors:

   1. Hang Hu
   2. Rachel E Hostetler
   3. Ariel Agmon

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript provides a successful model to study the ultrafast brain oscillation-mediated brain circuitry and cellular mechanisms in sensory processing. Utilizing this model, the authors studied potential cellular mechanisms that generate ultrafast oscillations (250-600Hz) in the cortex. These oscillations correlate with sensory stimulation and might be relevant for perceiving relevant sensory inputs. The data reasonably support most of the claims by the authors in this manuscript.

   Reviewed by eLife

9. Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases

   This article has 4 authors:

   1. Joan Gizzio
   2. Abhishek Thakur
   3. Allan Haldane
   4. Ronald M Levy

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important paper provides a convincing mechanism for relative binding specificity of Type II inhibitors to kinases. The combination of a sequence-derived Potts-model with experimental dissociation constants and calculated free energies of binding to the DFG-out state is highly compelling and goes beyond the current state of the art. Given the importance of kinases in pathophysiological processes, the results will be of interest to a broad audience and, in addition, the combination of computational methods can be applicable to a wide variety of other biophysical processes that involve conformational rearrangements.

   Reviewed by eLife

10. Cholecystokinin-expressing (CCK+) basket cells are key controllers of theta-gamma coupled rhythms in the hippocampus

    This article has 4 authors:

    1. Alexandra P Chatzikalymniou
    2. Spandan Sengupta
    3. Jeremie Lefebvre
    4. Frances K Skinner

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This paper reports a useful set of results that uses a reduced network model based on a previously published large-scale network model to explain the generation of theta-gamma rhythms in the hippocampus. Combining the detailed and reduced models and comparing their results is a powerful approach. However, the evidence for the main claim that CCK+ basket cells play a key role in theta-gamma coupling in the hippocampus is currently incomplete.

    Reviewed by eLife