Time-lapse atomic force microscopy (AFM) is widely used for direct visualization of the nanoscale dynamics of various biological systems. The advent of high-speed AFM instrumentation made it possible to image the dynamics of proteins and protein-DNA complexes within millisecond time range. This chapter describes protocols for studies of structure and dynamics of nucleosomes with time-lapse AFM including the high-speed AFM instrument. The necessary specifics for the preparation of chromatin samples for imaging with AFM including the protocols for the surface preparation are provided.
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http://dx.doi.org/10.1007/978-1-4939-2474-5_3 | DOI Listing |
Sci Rep
May 2024
Department of Dental Radiology and Radiation Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
Diffusing alpha-emitters radiation therapy (Alpha-DaRT) is a unique method, in which interstitial sources carrying Ra release a chain of short-lived daughter atoms from their surface. Although DNA damage response (DDR) is crucial to inducing cell death after irradiation, how the DDR occurs during Alpha-DaRT treatment has not yet been explored. In this study, we temporo-spatially characterized DDR such as kinetics of DNA double-strand breaks (DSBs) and cell cycle, in two-dimensional (2D) culture conditions qualitatively mimicking Alpha-DaRT treatments, by employing HeLa cells expressing the Fucci cell cycle-visualizing system.
View Article and Find Full Text PDFJ Am Chem Soc
April 2024
Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.
Hydrothermal methods are widely used to synthesize functional inorganic materials. The interplay between the reactive species, solution chemistry, and the nanoscale product makes it challenging to control the reaction pathway to achieve a uniform product. Here, we resolve the heterogeneity that arises during hydrothermal synthesis across different length scales.
View Article and Find Full Text PDFSci Adv
January 2024
Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
Invading microbes face a myriad of cidal mechanisms of phagocytes that inflict physical damage to microbial structures. How intracellular bacterial pathogens adapt to these stresses is not fully understood. Here, we report the discovery of a virulence mechanism by which changes to the mechanical stiffness of the mycobacterial cell surface confer refraction to killing during infection.
View Article and Find Full Text PDFExtremophiles
December 2023
Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
Topoisomerases are crucial enzymes in genome maintenance that modulate the topological changes during DNA metabolism. Deinococcus radiodurans, a Gram-positive bacterium is characterized by its resistance to many abiotic stresses including gamma radiation. Its multipartite genome encodes both type I and type II topoisomerases.
View Article and Find Full Text PDFBiophys J
December 2023
The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, Florida. Electronic address:
Vascular endothelial cells (ECs) form a semipermeable barrier separating vascular contents from the interstitium, thereby regulating the movement of water and molecular solutes across small intercellular gaps, which are continuously forming and closing. Under inflammatory conditions, however, larger EC gaps form resulting in increased vascular leakiness to circulating fluid, proteins, and cells, which results in organ edema and dysfunction responsible for key pathophysiologic findings in numerous inflammatory disorders. In this study, we extend our earlier work examining the biophysical properties of EC gap formation and now address the role of lamellipodia, thin sheet-like membrane projections from the leading edge, in modulating EC spatial-specific contractile properties and gap closure.
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