Biology subjects

Sedat, J. W.

Publications and source records attributed to Sedat, J. W..

3 recordsLinked to original sources

bioRxiv2025

Deconvolution to restore cryo-EM maps with anisotropic resolution

With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single particle cryo-EM is premised on randomly orientated particles embedded in a thin layer of vitreous ice to resolve high-resolution structure in all directions. In practice, preferentially distributed particle orientations and/or other imperfections in imaging and data processing deteriorate quality of obtained cryo-EM map. Here we present a deconvolution approach, named AR-Decon, that computationally improves the quality of cryo-EM maps. We tested and validated the procedure, compared its performance with that of machine learning based density modification method, and benchmarked its performance with a wide range of deposited maps. Our results show that AR-Decon is robust and is a generally applicable post-processing procedure for single particle cryo-EM.

biophysics↗

bioRxiv2024

Helical Coiled Nucleosome Chromosome Architectures during Cell Cycle Progression

Recent studies showed an interphase chromosome architecture, --- a specific coiled nucleosome structure, --- derived from cryo-preserved EM tomograms, and dispersed throughout the nucleus. The images were computationally processed to fill in the missing wedges of data caused by incomplete tomographic tilts. The resulting structures increased z-resolution enabling an extension of the proposed architecture to that of mitotic chromosomes. Here we provide additional insights and details into the coiled nucleosome chromosome architectures. We build on the defined chromosomes time-dependent structures in an effort to probe their dynamics. Variants of the coiled chromosome structures, possibly further defining specific regions, are discussed. We propose, based on generalized specific uncoiling of mitotic chromosomes in telophase, large-scale re-organization of interphase chromosomes. Chromosome territories, organized as micron-sized small patches, are constructed, satisfying complex volume considerations. Finally, we unveiled the structures of replicated coiled chromosomes, still attached to centromeres, as part of chromosome architecture. Significance StatementThis study places all 46 sequenced human chromosomes, --- correctly filled with nucleosomes and in micron sized chromosome territories -- into 10micron (average sized) nuclei. The chromosome architecture used a helical nucleosome coiled structure discerned from cryo-EM tomography, as was recently published (https://doi.org/10.1073/pnas.2119101119). This chromosome architecture was further modeled to dynamic structures, structure variations and chromosome replication centromere complications. Finally, this chromosome architecture was modified to allow seamless transition through the cell cycle.

cell biology↗

bioRxiv2021

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

We have developed "Microscope-Cockpit" (Cockpit), a highly adaptable open source user-friendly Python-based GUI environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near-instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses "Python-Microscope" (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging. HighlightsO_LIUser-friendly setup and use for simple to complex bespoke microscopes. C_LIO_LIFacilitates collaborations between biomedical scientists and microscope technologists. C_LIO_LITouchscreen for near-instantaneous navigation of specimen landscape. C_LIO_LIUses Python-Microscope, for abstracted open source hardware device control. C_LIO_LIWell-suited for user training of AI-algorithms for automated microscopy. C_LI

biophysics↗