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A Coarse-Grained Simulation Approach for Protein Molecular Conformation Dynamics.
J Phys Chem A
January 2025
Computer Modelling Group, 3710 33 St NW, Calgary, Alberta T2L 2M1, Canada.
Coarse-grained molecular dynamics simulation is widely accepted for assessment of a large complex biological system, but it may also lead to a misleading conclusion. The challenge is to simulate protein structural dynamics (such as folding-unfolding behavior) due to the lack of a necessary backbone flexibility. This study developed a standard coarse-grained model directly from the protein atomic structure and amino acid coarse-grained FF (such as MARTINI FF v2.
View Article and Find Full Text PDFTranscriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes.
BMC Mol Cell Biol
January 2025
Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
Background: During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known to be essential for developmental competence of the oocyte, less is known about the accompanying molecular changes. Here we examine the changes in the transcriptome and DNA methylation during the NSN to SN transition in mouse oocytes.
View Article and Find Full Text PDFAdvancing therapeutic strategies for graft-versus-host disease by targeting gut microbiome dynamics in allogeneic hematopoietic stem cell transplantation: current evidence and future directions.
Mol Med
January 2025
Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, No. 8 Dianli Road, Zhenjiang, 212002, Jiangsu, People's Republic of China.
Hematopoietic stem cell transplantation (HSCT) is a highly effective therapy for malignant blood illnesses that pose a high risk, as well as diseases that are at risk due to other variables, such as genetics. However, the prevalence of graft-versus-host disease (GVHD) has impeded its widespread use. Ensuring the stability of microbial varieties and associated metabolites is crucial for supporting metabolic processes, preventing pathogen intrusion, and modulating the immune system.
View Article and Find Full Text PDFCytoskeleton-functionalized synthetic cells with life-like mechanical features and regulated membrane dynamicity.
Nat Chem
January 2025
Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
The cytoskeleton is a crucial determinant of mammalian cell structure and function, providing mechanical resilience, supporting the cell membrane and orchestrating essential processes such as cell division and motility. Because of its fundamental role in living cells, developing a reconstituted or artificial cytoskeleton is of major interest. Here we present an approach to construct an artificial cytoskeleton that imparts mechanical support and regulates membrane dynamics.
View Article and Find Full Text PDFSpatiotemporal analysis of land surface temperature and land cover changes in Prešov city using downscaling approach and machine learning algorithms.
Environ Monit Assess
January 2025
Institute of Geography, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04001, Košice, Slovak Republic.
In recent decades, global climate change and rapid urbanization have aggravated the urban heat island (UHI) effect, affecting the well-being of urban citizens. Although this significant phenomenon is more pronounced in larger metropolitan areas due to extensive impervious surfaces, small- and medium-sized cities also experience UHI effects, yet research on UHI in these cities is rare, emphasizing the importance of land surface temperature (LST) as a key parameter for studying UHI dynamics. Therefore, this paper focuses on the evaluation of LST and land cover (LC) changes in the city of Prešov, Slovakia, a typical medium-sized European city that has recently undergone significant LC changes.
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