| viXra.org > Quantitative Biology > 2501 |
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| viXra.org > Quantitative Biology > 2501 |
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[2] viXra:2501.0169 [pdf] submitted on 2025-01-30 14:19:29
Authors: Richard Murdoch Montgomery
Comments: 24 Pages.
Random matrix theory has played a pivotal role in understanding the complexity of biological systems, especially in elucidating the stability and coexistence of species in ecological communities. In this study, we apply random matrix theory at a trophic level consisting of four species with different initial populations. We incorporate varying interaction probabilities, denoted as p, to explore how the structure and strength of interspecific interactions affect species persistence and extinction rates. By modeling the system’s dynamics through a suite of mathematically derived equations and generating adjacency matrices under different values of p, we produce multiple scenarios that highlight the interplay between cooperation and competition. Our numerical simulations yield a series of graphs illustrating the likelihood of coexistence, extinction trajectories, and the effect of interaction intensity. The results underscore the delicate balance between competition and mutual benefit, shedding light on conditions in which biodiversity is maintained or lost. In our ensuing discussion, we reflect on theoretical implications, potential applications in conservation biology, limitations of our approach, and directions for future research.
Category: Quantitative Biology
[1] viXra:2501.0120 [pdf] submitted on 2025-01-21 21:36:09
Authors: Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Alexandre Vetcher, Daniel Siqueira de Oliveira, Max V. Myakishev-Rempel
Comments: 10 Pages. (Note by viXra Admin: Authors' names should be listed right after the title - Please conform)
Background: Transposable elements constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. Methods: This study computationally investigates the density patterns of transposons around chromatin contact points identified from public Micro-C chromatin conformation data from human cell culture. The density peak patterns of various transposable families and subfamilies were studied within a 100kb window centered on contact points. The analysis was focused on the most abundant transposons, such as Alu and LINE-1. Results: The computational analysis revealed highly pronounced, non-random density patterns of transposons around the chromatin contact points. The patterns were produced by aligning all ligation points and plotting the average density around them. The patterns were strikingly different between transposable element families and substantially different between the members of the families. The patterns were found to be reproducible across independent studies and biological replicates. Among major families and subfamilies there were no members that didn't have reproducible density patterns around the contact points. Randomly generated coordinates produced less pronounced patterns, which were not correlated between replicates as expected for the negative control. Some families showed enrichment and some - depletion at contact points, while 100Kb window-wide patterns remained correlated between biological replicates. The patterns were asymmetric relative to the chromosomal orientation. Additionally, the patterns were oriented relative to the transposon sequence direction. Conclusion: This is an indication of the existence of a chromosome-scale sequence structure. The overall study results strengthen the functional importance of TEs in chromatin folding.
Category: Quantitative Biology
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