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111.
Mathematical models in biology are powerful tools for the study and exploration of complex dynamics. Nevertheless, bringing theoretical results to an agreement with experimental observations involves acknowledging a great deal of uncertainty intrinsic to our theoretical representation of a real system. Proper handling of such uncertainties is key to the successful usage of models to predict experimental or field observations. This problem has been addressed over the years by many tools for model calibration and parameter estimation. In this article we present a general framework for uncertainty analysis and parameter estimation that is designed to handle uncertainties associated with the modeling of dynamic biological systems while remaining agnostic as to the type of model used. We apply the framework to fit an SIR-like influenza transmission model to 7 years of incidence data in three European countries: Belgium, the Netherlands and Portugal. 相似文献
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113.
Supriya Khedkar Georgy Smyshlyaev Ivica Letunic Oleksandr
M Maistrenko Luis
Pedro Coelho Askarbek Orakov Sofia K Forslund Falk Hildebrand Mechthild Luetge Thomas S B Schmidt Orsolya Barabas Peer Bork 《Nucleic acids research》2022,50(6):3155
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal. 相似文献
114.
Natlia Marins Bastos Juliana Germano Ferst Rodrigo Silva Goulart Juliano Coelho da Silveira 《Animal Reproduction》2022,19(1)
The oviduct is an important reproductive structure that connects the ovary to the uterus and takes place to important events such as oocyte final maturation, fertilization and early embryonic development. Thus, gametes and embryo can be directly influenced by the oviductal microenvironment composed by epithelial cells such secretory and ciliated cells and oviductal fluid. The oviduct composition is anatomically dynamic and is under ovarian hormones control. The oviductal fluid provides protection, nourishment and transport to gametes and embryo and allows interaction to oviductal epithelial cells. All these functions together allows the oviduct to provides the ideal environment to the early reproductive events. Extracellular vesicles (EVs) are biological nanoparticles that mediates cell communication and are present at oviductal fluid and plays an important role in gametes/embryo - oviductal cells communication. This review will present the ability of the oviducts based on its dynamic and systemic changes during reproductive events, as well as the contribution of EVs in this process. 相似文献
115.
Ayako Sano Reiko Tanaka Kazuko Nishimura Cilmery S. Kurokawa Kunie labuki R. Coelho Marcello Franco Mario Rubens Montenegro Makoto Miyaji 《Mycoscience》1997,38(2):117-122
We have studied the physiological and morphological features of 17 isolates ofParacoccidioides brasiliensis in order to define their phenotypes. The isolates were cultured at room temperature on potato dextrose agar (PDA, Difco)
slants for mycelial growth and in 1% dextrose brain heart infusion agar (BHIA, Difco) at 37°C for the study of yeast forms.
Most mycelial and yeast forms grew well between pH 5.6–9.4. In their response to osmotic pressure the isolates were separated
in three groups: intolerant, intermediate and tolerant. They also varied in carbohydrate assimilation tests, which indicated
important metabolic variation. No clear differences were observed in phenol oxidase tests, KNO3, starch, casein and arbutin assimilation tests. Only 1 of the isolates, Bt-19, had gelatinase activity. No correlation was
observed between the above differences and virulence. Two patterns of growth were observed in the mycelial cultures, glabrous
and cottonous, the latter being correlated with increased virulence for ddY mice. Most yeast forms grew as cerebriform colonies,
but Pb-HC and Bt-19 colonies had a cobblestone-like surface. 相似文献
116.
José Carlos Gonçalves Graça Diogo Maria Teresa Coelho Nieves Vidal Sara Amâncio 《In vitro cellular & developmental biology. Plant》2008,44(5):412-418
Endogenous levels of indole-3-acetic acid (IAA), indole-3-acetylaspartic acid (IAAsp) and indole-3-butyric acid (IBA) were
measured during the first 8 d of in vitro rooting of rootstock from the chestnut ‘M3’ hybrid by high performance liquid chromatography (HPLC). Rooting was induced
either by dipping the basal ends of the shoots into a 4.92-mM IBA solution for 1 min or by sub-culturing the shoots on solid
rooting medium supplemented with 14.8-μM IBA for 5 d. For root development, the induced shoots were transferred to auxin-free
solid medium. Auxins were measured in the apical and basal parts of the shoots by means of HPLC. Endogenous levels of IAA
and IAAsp were found to be greater in IBA-treated shoots than in control shoots. In extracts of the basal parts of the shoots,
the concentration of free IAA showed a significant peak 2 d after either root inductive method and a subsequent gradual decrease
for the remainder of the time course. The concentration of IAAsp peaked at day 6 in extracts of the basal parts of shoots
induced with 14.8-μM IBA for 5 d, whereas shoots induced by dipping showed an initial increase until day 2 and then remained
stable. In extracts from basal shoot portions induced by dipping, IBA concentration showed a transient peak at day 1 and a
plateau between day 2 and 4, in contrast to the profile of shoots induced on auxin-containing medium, which showed a significant
reduction between 4 and 6 d after transferred to auxin-free medium. All quantified auxins remained at a relatively low level,
virtually constant, in extracts from apical shoot portions, as well as in extracts from control non-rooting shoots. In conclusion,
the natural auxin IAA is the signal responsible for root induction, although it is driven by exogenous IBA independently of
the adding conditions. 相似文献
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Coelho ER Urményi TP Franco da Silveira J Rondinelli E Silva R 《International journal for parasitology》2003,33(8):853-858
The dodecamer universal minicircle sequence is a conserved sequence present in minicircles of trypanosomatid kinetoplast DNA studied so far. This sequence is recognised by a protein named universal minicircle sequence binding protein, described for Crithidia fasciculata, involved in minicircle DNA replication. We have identified a Trypanosoma cruzi gene homologue of the Crithidia fasciculata universal minicircle sequence binding protein. Similar to the Crithidia fasciculata universal minicircle sequence binding protein, the Trypanosoma cruzi protein, named PDZ5, contains five zinc finger motifs. Pulsed field gel electrophoresis indicated that the pdz5 gene is located in the chromosomal band XX of the Trypanosoma cruzi genome. The predicted amino acid sequence of PDZ5 shows a high degree of similarity with several trypanosomatid zinc finger proteins. Specific antibody raised against Crithidia fasciculata universal minicircle sequence binding protein recognises both the recombinant and endogenous PDZ5. The complete pdz5 coding sequence cloned in bacteria expresses a recombinant PDZ5 protein that binds specifically to the universal minicircle sequence dodecamer. These data strongly suggest that PDZ5 represents a Trypanosoma cruzi universal minicircle sequence binding protein. 相似文献
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120.
Regina Coeli Elio H. Baba Neusa Araujo Paulo M. Z. Coelho Guilherme Oliveira 《PLoS neglected tropical diseases》2013,7(12)