Biophysics

Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription

1. Yi-Che Chang
2. Sofia A. Quinodoz
3. Clifford P. Brangwynne

• Curated by eLife

  eLife assessment

  This valuable study establishes a method for live-cell imaging, tracking, and quantification of Alu elements marking euchromatic regions of the nucleus. The method will help characterize the relationship between chromatin dynamics and transcriptional activity. While the findings are largely consistent with previous reports, characterization of the technique is incomplete and could benefit from additional controls.

Reviewed by eLife

Intracellular mechanical fingerprint reveals cell type specific mechanical tuning

1. Till M. Muenker
2. Bart E. Vos
3. Timo Betz

• Curated by eLife

  eLife assessment

  Münker and colleagues use an optical tweezer setup to apply oscillatory forces to endocytosed/phagocytosed glass beads over a wide frequency range (from ~1 to 1000 Hz) and probe cytoplasmic material properties at multiple time scales in six different cell types. Using statistical methods and principal component analysis, they find that the active and passive mechanical properties of cells can be described by 6 parameters (from power law fits) that allow characterizing the viscous and elastic nature of the cytoplasmic material as well as an effective active energy driven by cellular metabolism. Overall, this is very well done and important work, using convincing and state-of-the-art methods, albeit with some limitations related to the way the beads are internalized.

Reviewed by eLife

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