The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromosomes are presented graphically in an intuitive way. It is also possible to relax structure with short molecular dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu.pl/.
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http://dx.doi.org/10.1093/nar/gky511 | DOI Listing |
J Math Biol
January 2025
Institut universitaire de France (IUF), Paris, France.
We build and study an individual based model of the telomere length's evolution in a population across multiple generations. This model is a continuous time typed branching process, where the type of an individual includes its gamete mean telomere length and its age. We study its Malthusian's behaviour and provide numerical simulations to understand the influence of biologically relevant parameters.
View Article and Find Full Text PDFBMC Genomics
January 2025
Henan Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, 453003, China.
Background: The Sec14 domain is an ancient lipid-binding domain that evolved from yeast Sec14p and performs complex lipid-mediated regulatory functions in subcellular organelles and intracellular traffic. The Sec14 family is characterized by a highly conserved Sec14 domain, and is ubiquitously expressed in all eukaryotic cells and has diverse functions. However, the number and characteristics of Sec14 homologous genes in soybean, as well as their potential roles, remain understudied.
View Article and Find Full Text PDFBMC Cancer
January 2025
Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
Background: Gastric cancer peritoneal metastasis lacks effective predictive indices. This article retrospectively explored predictive values of DNA ploidy, stroma, and nucleotyping in gastric cancer peritoneal metastasis.
Methods: A comprehensive analysis was conducted on specimens obtained from 80 gastric cancer patients who underwent gastric resection at the Department of Gastrointestinal Surgery of Wuhan University Renmin Hospital.
Sci Data
January 2025
Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon Tong, Hong Kong.
Black carp (Mylopharyngodon piceus) is one of the "four famous domestic fishes" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies.
View Article and Find Full Text PDFNat Commun
January 2025
Sorbonne Université, CNRS, Laboratory of Computational and Quantitative Biology, LCQB, Paris, France.
Telomere shortening ultimately causes replicative senescence. However, identifying the mechanisms driving replicative senescence in cell populations is challenging due to the heterogeneity of telomere lengths and the asynchrony of senescence onset. Here, we present a mathematical model of telomere shortening and replicative senescence in Saccharomyces cerevisiae which is quantitatively calibrated and validated using data of telomerase-deficient single cells.
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