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Biochemistry, Genetics and Molecular Biology

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Biophysics

The application of physical principles and methods to understand biological systems, including biomolecular structure and dynamics, membrane biophysics, cellular mechanics, and the development of biophysical techniques

5 papers in this specialization

Paperzilla Papers in Biophysics

Acoustic modulation of mechanosensitive genes and adipocyte differentiation

This study in mouse cells found that acoustic waves can influence gene expression and suppress adipocyte (fat cell) differentiation. The study suggests a pathway involving focal adhesions, FAK phosphorylation, Ptgs2 activity, and PGE2 production, but acknowledges other pathways likely exist.

Time-deterministic cryo-optical microscopy

Researchers developed a technique to rapidly freeze cells during live observation with optical microscopy, allowing for high-resolution snapshots of dynamic processes. This method, coupled with time-deterministic freezing, enables researchers to observe fast reactions such as calcium waves and combine super resolution microscopy with Raman microscopy. Changes in the fluorescence intensity or spectrum shapes of some indicators under cryogenic conditions compared to those under room temperature, requiring careful analysis and interpretation.

Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules

This multi-lab study established guidelines for conducting and analyzing DEER/PELDOR experiments on nitroxide-labeled biomolecules. It provides recommendations for sample preparation, data acquisition, processing, and interpretation, aiming to improve the reliability and reproducibility of distance measurements using pulsed dipolar EPR spectroscopy.

CellProfiler 4: improvements in speed, utility and usability

CellProfiler 4, the latest version of the open-source image analysis software, boasts significant performance improvements, particularly in complex workflows like 3D segmentation and Cell Painting assays. User interface refinements and new modules, including object merging and integration with ImageJ macros, enhance usability and expand functionality. These updates make CellProfiler 4 a more efficient and versatile tool for high-throughput microscopy image analysis.

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s12859-021-04344-9.pdf

Jul 14, 11:17 AM

DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data

DeerLab, an open-source Python-based software package, is introduced for analyzing dipolar EPR spectroscopy data. It implements a variety of methods including one-step analysis, multi-pathway models, and global analysis to improve accuracy and reliability in distance distribution determination.