Biophysics

Biophysics of microRNA-34a targeting and its influence on down-regulation

1. Lara Sweetapple
2. David M Kosek
3. Elnaz Banijamali
4. Walter Becker
5. Juliane Müller
6. Christina Karadiakos
7. Lorenzo Baronti
8. Ileana Guzzetti
9. Dimitri Schritt
10. Alan Chen
11. Emma R Andersson
12. Katja Petzold

Reviewed by Review Commons

Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern

1. Callum M Ives
2. Linh Nguyen
3. Carl A Fogarty
4. Aoife M Harbison
5. Yves Durocher
6. John Klassen
7. Elisa Fadda

• Curated by eLife

  eLife assessment

  This study presents an important finding on the structural role of glycosylation at position N343 of the SARS-CoV-2 spike protein's receptor-binding domain in maintaining its stability, with implications across different variants of concern. The evidence supporting the claims of the authors is convincing, since appropriate and validated methodology in line with current state-of-the-art has been approached. The work will be of interest to evolutionary virologists.

Reviewed by eLife

Potassium-mediated bacterial chemotactic response

1. Chi Zhang
2. Rongjing Zhang
3. Junhua Yuan

• Curated by eLife

  eLife assessment

  In this important study, the authors report a novel measurement of the Escherichia coli chemotactic response and demonstrate that these bacteria display an attractant response to potassium, which is connected to intracellular pH level. The experimental evidence provided is convincing and the work will be of interest to microbiologists studying chemotaxis.

Reviewed by eLife

Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion

1. Tianyu Yuan
2. Hao Yan
3. Kevin C. Li
4. Ivan Surovtsev
5. Megan C. King
6. Simon G. J. Mochrie

Reviewed by Review Commons

PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more

1. Mélina Baheux Blin
2. Vincent Loreau
3. Frank Schnorrer
4. Pierre Mangeol

Reviewed by Review Commons

Diffusive lensing as a mechanism of intracellular transport and compartmentalization

1. Achuthan Raja Venkatesh
2. Kathy H Le
3. David M Weld
4. Onn Brandman

• Curated by eLife

  eLife assessment

  The authors discuss an effect, "diffusive lensing", by which particles would accumulate in high-viscosity regions – for instance in the intracellular medium. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention. The "lensing effect" discussed is a direct consequence of the choice of the Ito convention without spurious drift which has been discussed before and its adequacy for the intracellular medium is insufficiently discussed and relatively doubtful. Consequently, the relevance of the presented results for biology remain unclear and based on incomplete evidence.

Reviewed by eLife

Active mechanics of sea star oocytes

1. Peter J. Foster
2. Sebastian Fürthauer
3. Nikta Fakhri

Reviewed by PREreview

Automated multiconformer model building for X-ray crystallography and cryo-EM

1. Stephanie A Wankowicz
2. Ashraya Ravikumar
3. Shivani Sharma
4. Blake Riley
5. Akshay Raju
6. Daniel W Hogan
7. Jessica Flowers
8. Henry van den Bedem
9. Daniel A Keedy
10. James S Fraser

• Curated by eLife

  eLife assessment

  This work describes important updates to qFit, the state-of-the art tool for modeling alternative conformations of protein molecules based on high resolution X-ray diffraction or Cryo-EM data. The authors provide some convincing analyses of qFit's performance in selected test cases. This manuscript will be of interest to structural biologists and protein biochemists, since the adoption of qFit in structural refinement may lead to new mechanistic insights into protein function.

Reviewed by eLife

Amyloid Accelerator Polyphosphate Implicated as the Mystery Density in α-Synuclein Fibrils

1. Philipp Huettemann
2. Pavithra Mahadevan
3. Justine Lempart
4. Eric Tse
5. Budheswar Dehury
6. Brian F. P. Edwards
7. Daniel R. Southworth
8. Bikash R. Sahoo
9. Ursula Jakob

Reviewed by Arcadia Science

Ion channel thermodynamics studied with temperature jumps measured at the cell membrane

1. Carlos A.Z. Bassetto
2. Bernardo I. Pinto
3. Ramon Latorre
4. Francisco Bezanilla

• Curated by Biophysics Colab

  Evaluation statement (17 January 2024)

  The study by Bassetto Jr. et al. presents an elegant and pioneering technique to rapidly manipulate membrane temperature by up to 10 ºC in less than 1.5 ms, thereby enabling high temporal resolution of the temperature dependence of ion channel currents. The approach combines the cut-open oocyte voltage clamp technique with laser illumination to heat the sub-membrane melanosome layer. Temperature is quantified from observed changes in membrane capacitance. Recordings of Kir1.1, TRPM8, and TRPV1 channels are used to validate the effectiveness of the technique. A limitation is that, in its current form, the technique can be used only on melanosome-containing Xenopus oocyte membranes.

  Biophysics Colab recommends this study to scientists working on the temperature dependence of ion channels and other membrane proteins.

  Biophysics Colab has evaluated this study as one that meets the following criteria:

  • Rigorous methodology
  • Transparent reporting
  • Appropriate interpretation

  (This evaluation refers to the version of record for this work, which is linked to and has been revised from the original preprint following peer review.)

Reviewed by Biophysics Colab