Ústav biomedicínského inženýrství

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Now showing 1 - 5 of 141
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    Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis
    (American Society for Microbiology, 2023-11-30) Schwarzerová, Jana; Zeman, Michal; Babák, Vladimír; Jurečková, Kateřina; Nykrýnová, Markéta; Varga, Margaret; Weckwerth, Wolfram; Dolejská, Monika; Provazník, Valentine; Rychlík, Ivan; Čejková, Darina
    The study presents an innovative pipeline for detecting horizontal gene transfer (HGT) among a collection of sequenced genomes from gut microbiota. Herein, chicken and porcine gut microbiota were analyzed. Based on statistical analysis, we propose that nearly identical genes co-shared between distinct genera can be evidence for a previous event of mobilization of that gene from genome to genome via HGT. Data mining, computational analysis, and network analysis were used to investigate genomes of 452 isolates of chicken or porcine origin to detect genes involved in HGT. The proposed pipeline is user-friendly and includes network visualization. The study highlights that different species and strains of the same genera typically carry different cargo of mobilized genes. The pipeline is capable of identifying not yet characterized genes, as well as genes that are usually co-transferred with genes involved in resistance, virulence, and/or mobilization. Among the analyzed genome collection, the main reservoirs of the HGT genes were found in Phocaeicola spp. (Bacteroidaceae) and UBA9475 spp. (early Pseudoflavonifractor, Oscillospiraceae). Altogether, over 6,000 genes suspected of HGT were identified. Genes associated with intracellular trafficking and secretion and DNA repair were enriched, while genes of unknown and general functions were dominant but not enriched. Only 15 genes were co-shared between Gram-positive and Gram-negative bacteria, mostly genes directly associated with mobilome or antibiotic resistance. However, most HGTs were identified among different genera of the same phylum. Therefore, we suggest that a significant selection pressure exists on gene variants at the phylum level.
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    High prevalence and genetic diversity of Treponema paraluisleporidarum isolates in European lagomorphs
    (American Society for Microbiology, 2023-11-26) Knauf, Sascha; Hisgen, Linda; Agren, Erik O.; Barlow, Alexander M.; Faehndrich, Marcus; Voigt, Ulrich; Fischer, Luisa; Grillová, Linda; Hallmaier-Wacker, Luisa K.; Kik, Marja J. L.; Klink, Jana C.; Křenová, Jitka; Lavazza, Antonio; Lueert, Simone; Nováková, Markéta; Čejková, Darina; Pacioni, Carlo; Trogu, Tiziana; Šmajs, David; Roos, Christian
    The bacterium Treponema paraluisleporidarum causes syphilis in lagomorphs. In a set of 1,095 samples from four species—European brown hare, mountain hare, Corsican hare, and European rabbit—we tested for infection and genotyped the strains that infect wild lagomorphs. Samples originate from Sweden, the Netherlands, the United Kingdom, Germany, the Czech Republic, and Italy. The phylogenetic analyses of two informative gene targets (tp0488 and tp0548) showed high genetic diversity among the lagomorph-infecting treponemes. More specifically, we found a high number of nucleotide variants and various short repeat units in the tp0548 locus that have not been described for human syphilis and primate yaws causing Treponema pallidum. While the functional aspect of these short repeat units remains subject to ongoing investigations, it likely enables the pathogen to better survive in its lagomorph host. Our data did not support any geographic clustering, which is equally reflected in the host population genetics as shown by mitochondrial genome data corresponding to the sampled lagomorph populations. This is unexpected and in contrast with what has been shown for nonhuman primate infection with T. pallidum. In the future, the combination of multi-locus sequence typing and whole genome data from modern and ancient samples from a wide geographic range and multiple lagomorph species will contribute to a better understanding of the epidemiology and evolutionary path of lagomorph-infecting treponemes. In conclusion, our current study demonstrates widespread infection and a high genetic variation of the syphilis-causing pathogen in a higher number of positively PCR-tested European lagomorphs (n = 302/1,095).
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    A Brief Review of Bone Cell Function and Importance
    (MDPI, 2023-11-05) Šromová, Veronika; Sobola, Dinara; Kaspar, Pavel
    This review focuses on understanding the macroscopic and microscopic characteristics of bone tissue and reviews current knowledge of its physiology. It explores how these features intricately collaborate to maintain the balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption, which plays a pivotal role in shaping not only our physical framework but also overall health. In this work, a comprehensive exploration of microscopic and macroscopic features of bone tissue is presented.
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    A minireview on the bioinformatics analysis of mobile gene elements in microbiome research
    (Frontiers, 2023-10-11) Schwarzerová, Jana; Labanava, Anastasiya; Rychlík, Ivan; Varga, Margaret; Čejková, Darina
    The horizontal transfer of mobile gene elements between bacteria plays a crucial role in their evolutionary dynamics. Additionally, it enables the accumulation and dissemination of genes conferring antibiotic and heavy-metal resistance, and thus contributes to the worldwide emergence and spread of drug-resistance pathogens. This process is instrumental in maintaining genetic diversity within bacterial populations and facilitates their adaptation to novel environments. It allows bacteria to acquire genes responsible for the synthesis of enzymes that utilize alternative energy sources and substrates. Furthermore, bacteria can acquire genes associated with toxin production and increased virulence. Horizontal gene transfer serves as a pivotal mechanism in bacterial evolution, enabling the acquisition of novel genetic information and enhancing their capabilities. However, the proper detection and identification of horizontally transferred genes at the microbiome scale is challenging, whether using wet-lab experime
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    Synthesis, characterization and In-vitro studies of CNT/Gd 2 O 3 hybrid structure
    (Elsevier, 2023-06-01) Paul, Rima; Chatterjee, Dipanwita; Das Ghosh, Lopamudra; Narayanswamy, Venkatesha; Pratap Singh, Mahander; Agarwal, Manish; Ghosh, Deepshikha; Radhakrishna, Mithun; Sekhar Tiwary, Chandra; Provazník, Valentine; Chattopadhyay, Kamanio
    Carbon nanotubes have been explored in various fields of science and technology due to their unique properties. However, their toxic nature put limitations to its consideration for the bio-medical applications. In our work, we report the synthesis of paramagnetic CNT/Gd 2 O 3 hybrid nanostructures through easily scalable electrochemical deposition technique. The nanostructure has shown significant longitudinal relaxivity of 18.93 mM 1 s 1 for water protons indicating its possibility to be used as an MRI contrast agent. The in-vitro cytotoxicity test on the normal (HaCaT) and cancerous (HeLa) cells reveal that CNT/Gd 2 O 3 hybrid nanostructure is bio-compatible in comparison to the pure CNTs, which is further supported by our theoretical studies using MD simulations.