Biophysics

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

Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

1. Ai Nguyen
2. Huaying Zhao
3. Dulguun Myagmarsuren
4. Sanjana Srinivasan
5. Di Wu
6. Jiji Chen
7. Grzegorz Piszczek
8. Peter Schuck

• Curated by eLife

  eLife assessment

  This important manuscript provides new insights into the biophysics of the SARS-CoV-2 nucleocapsid. The evidence, which relies on a convincing combination of genetic and biophysical data, nicely supports the conclusions.

Reviewed by eLife

Divergent mechanisms of steroid inhibition in the human ρ1 GABA _A receptor

1. Chen Fan
2. John Cowgill
3. Rebecca J. Howard
4. Erik Lindahl

Reviewed by PREreview

High-throughput discovery of inhibitory protein fragments with AlphaFold

1. Andrew Savinov
2. Sebastian Swanson
3. Amy E. Keating
4. Gene-Wei Li

Reviewed by PREreview

Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness

1. Ning Liu
2. Wenan Qiang
3. Philip Jordan
4. John Marko
5. Huanyu Qiao

• Curated by eLife

  eLife assessment

  This valuable paper describes the stiffness of meiotic chromosomes in both oocytes and spermatocytes. The authors identify differences in stiffness between meiosis I and II chromosomes, as well as an age-dependent increase in stiffness in meiosis I (and meiosis II) chromosomes, results that are highly significant for the field of chromosome biology. The mechanisms underlying age-dependent changes in chromosome stiffness remain unclear, and the evidence to suggest that changes in stiffness are independent of cohesin, which is known to deteriorate with age, is incomplete.

Reviewed by eLife