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61.
Background
The Mycobacterium tuberculosis 19-kDa lipoprotein has been reported to stimulate both T and B cell responses as well as induce a number of Th1 cytokines. In order to evaluate the Mycobacterium avium subsp. paratuberculosis (M. avium subsp. paratuberculosis) 19-kDa lipoprotein as an immunomodulator in cattle with Johne's disease, the gene encoding the 19-kDa protein (MAP0261c) was analyzed. 相似文献62.
Intraspecific gene genealogies: trees grafting into networks 总被引:1,自引:0,他引:1
Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena. 相似文献
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Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1) 总被引:1,自引:0,他引:1
The blind use of models of nucleotide substitution in evolutionary analyses is a common practice in the viral community. Typically, a simple model of evolution like the Kimura two-parameter model is used for estimating genetic distances and phylogenies, either because other authors have used it or because it is the default in various phylogenetic packages. Using two statistical approaches to model fitting, hierarchical likelihood ratio tests and the Akaike information criterion, we show that different viral data sets are better explained by different models of evolution. We demonstrate our results with the analysis of HIV-1 sequences from a hierarchy of samples; sequences within individuals, individuals within subtypes, and subtypes within groups. We also examine results for three different gene regions: gag, pol, and env. The Kimura two-parameter model was not selected as the best-fit model for any of these data sets, despite its widespread use in phylogenetic analyses of HIV-1 sequences. Furthermore, the model complexity increased with increasing sequence divergence. Finally, the molecular-clock hypothesis was rejected in most of the data sets analyzed, throwing into question clock-based estimates of divergence times for HIV-1. The importance of models in evolutionary analyses and their repercussions on the derived conclusions are discussed. 相似文献
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Pérez-Losada M Jobes DV Sinangil F Crandall KA Arenas M Posada D Berman PW 《PloS one》2011,6(3):e16902
Background
In 2003, a phase III placebo-controlled trial (VAX003) was completed in Bangkok, Thailand. Of the 2,546 individuals enrolled in the trial based on high risk for infection through injection drug use (IDU), we obtained clinical samples and HIV-1 sequence data (envelope glycoprotein gene gp120) from 215 individuals who became infected during the trial. Here, we used these data in combination with other publicly available gp120 sequences to perform a molecular surveillance and phylodynamic analysis of HIV-1 in Thailand.Methodology and Findings
Phylogenetic and population genetic estimators were used to assess HIV-1 gp120 diversity as a function of vaccination treatment, viral load (VL) and CD4+ counts, to indentify transmission clusters and to investigate the timescale and demographics of HIV-1 in Thailand. Three HIV-1 subtypes were identified: CRF01_AE (85% of the infections), subtype B (13%) and CRF15_AE (2%). The Bangkok IDU cohort showed more gp120 diversity than other Asian IDU cohorts and similar diversity to that observed in sexually infected individuals. Moreover, significant differences (P<0.02) in genetic diversity were observed in CRF01_AE IDU with different VL and CD4+ counts. No phylogenetic structure was detected regarding any of the epidemiological and clinical factors tested, although high proportions (35% to 50%) of early infections fell into clusters, which suggests that transmission chains associated with acute infection play a key role on HIV-1 spread among IDU. CRF01_AE was estimated to have emerged in Thailand in 1984.5 (1983–1986), 3–6 years before the first recognition of symptomatic patients (1989). The relative genetic diversity of the HIV-1 population has remained high despite decreasing prevalence rates since the mid 1990s.Conclusions
Our study and recent epidemiological reports indicate that HIV-1 is still a major threat in Thailand and suggest that HIV awareness and prevention needs to be strengthened to avoid AIDS resurgence. 相似文献68.
Lore T. Verryckt David S. Ellsworth Sara Vicca Leandro Van Langenhove Josep Peñuelas Philippe Ciais Juan M. Posada Clément Stahl Sabrina Coste Elodie A. Courtois Michael Obersteiner Jérôme Chave Ivan A. Janssens 《Biotropica》2020,52(6):1183-1193
Leaf-level net photosynthesis (An) estimates and associated photosynthetic parameters are crucial for accurately parameterizing photosynthesis models. For tropical forests, such data are poorly available and collected at variable light conditions. To avoid over- or underestimation of modeled photosynthesis, it is critical to know at which photosynthetic photon flux density (PPFD) photosynthesis becomes light-saturated. We studied the dependence of An on PPFD in two tropical forests in French Guiana. We estimated the light saturation range, including the lowest PPFD level at which Asat (An at light saturation) is reached, as well as the PPFD range at which Asat remained unaltered. The light saturation range was derived from photosynthetic light-response curves, and within-canopy and interspecific differences were studied. We observed wide light saturation ranges of An. Light saturation ranges differed among canopy heights, but a PPFD level of 1,000 µmol m−2 s−1 was common across all heights, except for pioneer trees species that did not reach light saturation below 2,000 µmol m−2 s−1. A light intensity of 1,000 µmol m−2 s−1 sufficed for measuring Asat of climax species at our study sites, independent of the species or the canopy height. Because of the wide light saturation ranges, results from studies measuring Asat at higher PPFD levels (for upper canopy leaves up to 1,600 µmol m−2 s−1) are comparable with studies measuring at 1,000 µmol m−2 s−1. 相似文献
69.
Laia Ventura-Garcia Maria Roura Christopher Pell Elisabeth Posada Joaquim Gascón Edelweis Aldasoro Jose Mu?oz Robert Pool 《PLoS neglected tropical diseases》2013,7(9)
Background
Globally, more than 10 million people are infected with Trypanosoma cruzi, which causes about 20 000 annual deaths. Although Chagas disease is endemic to certain regions of Latin America, migratory flows have enabled its expansion into areas where it was previously unknown. Economic, social and cultural factors play a significant role in its presence and perpetuation. This systematic review aims to provide a comprehensive overview of qualitative research on Chagas disease, both in endemic and non-endemic countries.Methodology/Principal Findings
Searches were carried out in ten databases, and the bibliographies of retrieved studies were examined. Data from thirty-three identified studies were extracted, and findings were analyzed and synthesized along key themes. Themes identified for endemic countries included: socio-structural determinants of Chagas disease; health practices; biomedical conceptions of Chagas disease; patient''s experience; and institutional strategies adopted. Concerning non-endemic countries, identified issues related to access to health services and health seeking.Conclusions
The emergence and perpetuation of Chagas disease depends largely on socio-cultural aspects influencing health. As most interventions do not address the clinical, environmental, social and cultural aspects jointly, an explicitly multidimensional approach, incorporating the experiences of those affected is a potential tool for the development of long-term successful programs. Further research is needed to evaluate this approach. 相似文献70.
Posada JM Sievänen R Messier C Perttunen J Nikinmaa E Lechowicz MJ 《Annals of botany》2012,110(3):731-741