The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes

Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair

Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger

We have isolated 78 microsatellite loci from the Eurasian badger (Meles meles). Of the 52 loci characterized, 39 were found to be polymorphic. A fluorescently labelled primer set was developed to enable individual-specific 17-locus genotypes to be obtained efficiently

Strategies for Achieving Healthy Energy Balance Among African Americans in the Mississippi Delta

IntroductionLow-income African Americans who live in rural areas of the Deep South are particularly vulnerable to diseases associated with unhealthy energy imbalance. The Centers for Disease Control and Prevention (CDC) has suggested various physical activity strategies to achieve healthy energy balance. Our objective was to conduct formal, open-ended discussions with low-income African Americans in the Mississippi Delta to determine 1) their dietary habits and physical activity levels, 2) their attitudes toward CDC’s suggested physical activity strategies, and 3) their suggestions on how to achieve CDC’s strategies within their own environment. MethodsA qualitative method (focus groups) was used to conduct the study during 2005. Prestudy meetings were held with African American lay health workers to formulate a focus group topic guide, establish inclusion criteria for focus group participants, select meeting sites and times, and determine group segmentation guidelines. Focus groups were divided into two phases.ResultsAll discussions and focus group meetings were held in community centers within African American neighborhoods in the Mississippi Delta and were led by trained African American moderators. Phase I focus groups identified the following themes: overeating, low self-esteem, low income, lack of physical exercise, unhealthy methods of food preparation, a poor working definition of healthy energy balance, and superficial knowledge of strategies for achieving healthy energy balance. Phase 2 focus groups identified a preference for social support-based strategies for increasing physical activity levels. ConclusionEnergy balance strategies targeting low-income, rural African Americans in the Deep South may be more effective if they emphasize social interaction at the community and family levels and incorporate the concept of community volunteerism

Fiber-based wavelength-swept spontaneous Raman spectroscopy for brain tissue classification

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Modelling Anopheles gambiae s.s. Population Dynamics with Temperature- and Age-Dependent Survival

Climate change and global warming are emerging as important threats to human health, particularly through the potential increase in vector- and water-borne diseases. Environmental variables are known to affect substantially the population dynamics and abundance of the poikilothermic vectors of disease, but the exact extent of this sensitivity is not well established. Focusing on malaria and its main vector in Africa, Anopheles gambiae sensu stricto, we present a set of novel mathematical models of climate-driven mosquito population dynamics motivated by experimental data suggesting that in An. gambiae, mortality is temperature and age dependent. We compared the performance of these models to that of a “standard” model ignoring age dependence. We used a longitudinal dataset of vector abundance over 36 months in sub-Saharan Africa for comparison between models that incorporate age dependence and one that does not, and observe that age-dependent models consistently fitted the data better than the reference model. This highlights that including age dependence in the vector component of mosquito-borne disease models may be important to predict more reliably disease transmission dynamics. Further data and studies are needed to enable improved fitting, leading to more accurate and informative model predictions for the An. gambiae malaria vector as well as for other disease vectors

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses

Adhesion Evaluation of Duplex Paint System for Sustainable Infrastructure

Organic paints are applied to galvanized or metalized steel surfaces in a duplex system, which is potentially more sustainable than the zinc-rich primer/steel system. A series of experimental tests were performed to measure and investigate adhesion strengths on three different types of roughened zinc surfaces. The contact angles were also measured for freshly formulated liquid paints on the roughened zinc surfaces to test if there is a correlation between the paint wetting property and the adhesive strengths. By comparing duplex system and zinc-rich primer/steel qualified North East Protective Coating (NEPCOAT) panels, it was found that the paint adhesion of the duplex system is as strong as the zinc primer/steel panels test results. The results also showed that adhesive strengths depend on the match between the paint and type of roughened zinc surfaces. The measurement of liquid paint wetting properties indicates small contact angles correlate with stronger pull-off adhesive strength. The authors of this study suggest that contact angle/strength correlation could be useful as a tool for optimizing the match between the paints and the profiled zinc surface