The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

<p>Abstract</p> <p>Background</p> <p>Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (<it>Phaseolus vulgaris</it>) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the <it>Phaseolus vulgaris </it>EST database. The diversity, degree of transferability and polymorphism of these markers were tested.</p> <p>Results</p> <p>From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the <it>Phaseolus </it>(63.7%), <it>Vigna </it>(25.9%), <it>Glycine </it>(19.8%), <it>Medicago </it>(10.2%), <it>Dipterix </it>(6%) and <it>Arachis </it>(1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM.</p> <p>Conclusions</p> <p>A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of <it>Phaseolus vulgaris</it>. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to genomic SSRs, and they were incorporated in the common bean reference genetic map, which constitutes an important contribution to and advance in <it>Phaseolus vulgaris </it>genomic research.</p

Infection by the hepatitis C virus in chronic renal failure patients undergoing hemodialysis in Mato Grosso state, central Brazil: a cohort study

BACKGROUND: Hepatitis C virus (HCV) is a significant problem for patients undergoing hemodialysis therapy. This situation has never been studied in Mato Grosso state, central Brazil. This study was conducted aiming to estimate the prevalence of the anti-HCV and the incidence of seroconversion in the main metropolitan region of the state. METHODS: 433 patients from the six hemodialysis units were interviewed and anti-HCV was tested by a third-generation enzyme immunoassay. An open cohort of patients who tested negative for anti-HCV at the entry of the study was created and seroconversions was assessed monthly. The staff responsible for the units were interviewed to assess whether the infection control measures were being followed. Logistic and Cox regression analysis were performed in order to assess risk factor to HCV. RESULTS: The entry on the study took place between January 2002 and June 2005. 73 out of 433 (16.9%, CI95%: 13.3–20.8) was found to be anti-HCV reactive. The multivariate analysis indicated as risk factors associated to anti-HCV the duration of the hemodialysis treatment, the number of transfusions received, and the unit of treatment. An open cohort of 360 patients who tested negative for anti-HCV was created, with a following average of 24 (± 15) months. Forty seroconversions were recorded corresponding to an incidence density of 4.6/1000 patient-months, ranges 0 to 30 among the units. Cox regression indicated the time of hemodialysis (RR = 2.2; CI95%: 1.1–4.6; p < 0.05) and the unit where treatment was performed (RR = 42.4; CI95%: 9.9–180.5; p < 0.05) as risk factors for seroconversion. The three units with highest anti-HCV prevalence and incidence were identified as those that more frequently failed to apply control measures. CONCLUSION: The study demonstrated high prevalence and incidence of anti-HCV in some of the hemodialysis units. Time on hemodialysis therapy was an independent factor associated to HCV. Blood transfusion was associated with anti-HCV in initial survey but was not important in incident cases. Failure of applying control meaures was more evident in units with the highest HCV prevalence and incidence. The results suggest that nosocomial transmission was the main spread factor of HCV in the studied population

Predictability of evolutionary trajectories in fitness landscapes

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.Comment: 14 pages, 7 figure

SOIL FAUNA ALONG THE PROCESS OF ECOLOGICAL SUCCESSION IN GULLIES REVEGETATED IN THE MUNICIPALITY OF PINHEIRAL \u2013 RJ

O objetivo do trabalho foi avaliar a diversidade, riqueza e composi\ue7\ue3o da comunidade da fauna do solo ep\uedgea em uma vo\ue7oroca revegetada no ano de 2000 com diferentes esp\ue9cies de leguminosas arb\uf3reas. A vo\ue7oroca est\ue1 localizada no Instituto Federal de Educa\ue7\ue3o (IFRJ) campus Nilo Pe\ue7anha no munic\uedpio de Pinheiral \u2013 RJ. Foram avaliadas as seguintes \ue1reas: plantio de Acacia mangium Willd. (PA), plantio de Mimosa caesalpiniifolia Benth. (PM), plantio de leguminosas arb\uf3reas no ter\ue7o superior da encosta (PTS), plantio de leguminosas no interior da vo\ue7oroca (IVR2000). Os plantios de A. mangium e M. caesalpiniifolia foram realizados antes da revegeta\ue7\ue3o. Para efeito comparativo tamb\ue9m foi avaliada uma \ue1rea de floresta secund\ue1ria com 20 anos, pr\uf3xima ao local de coleta. Na coleta da fauna do solo ep\uedgea foram utilizadas 10 armadilhas do tipo pitfall (MOLDENKE, 1994) por \ue1rea. Foram realizadas tr\ueas coletas, uma no in\uedcio da revegeta\ue7\ue3o, em maio de 2000, em junho de 2006 e abril de 2008. Houve um aumento no n\ufamero de grupos e na diversidade da fauna do solo no plantio no ter\ue7o superior, no interior da vo\ue7oroca, e no plantio de Mimosa caesalpiniifolia ap\uf3s 6 anos da interven\ue7\ue3o. Nas coletas realizadas em 2000 e 2006, a APC mostrou que a maioria dos grupos estava associada ao ano de 2006, mostrando total antagonismo com o ano de 2000. O plantio de Acacia mangium foi a \ue1rea com o menor n\ufamero de grupos. Na coleta realizada em 2008, a pastagem foi a \ue1rea com menor n\ufamero m\ue9dio de grupos coletados e na an\ue1lise de componentes principais (ACP) do interior da vo\ue7oroca os grupos estavam associados ao ano de 2008 com total antagonismo com os anos de 2000 e 2006. Os grupos Formicidae e Collembola (Entomobryomorpha) foram os mais dominantes em todas as \ue1reas amostradas no ano de 2000 e 2008 e no interior da vo\ue7oroca ano de 2006.The diversity, richness and composition of the soil epigeous fauna community were evaluated in a revegetated gully at the Instituto Federal de Educa\ue7\ue3o (IFRJ) campus Nilo Pe\ue7anha, in the municipality of Pinheiral, Rio de Janeiro state. Revegetation was performed in 2000, and consisted of four different strategies involving N-fixing trees: planting Acacia mangium Willd. (PA); planting Mimosa caesalpiniifolia Benth. (PM); on the outer edges of the gully head (PTS); and planting a mix of legume tree species into the gully (IVR2000). Acacia mangium and Mimosa caesalpiniifolia were planted above the gully head. A nearby 20-year secondary forest remnant was used as a reference site. Ten pitfall traps were used for the sampling of epigeous fauna at each one of the five areas (MOLDENKE, 1994). Sampling was performe in May 2000, June 2006, and April 2008. Six years after revegetation has started, fauna group richness and diversity increased both into the gully and in Mimosa caesalpiniifolia plantation. For the 2000 and 2006 samplings a PCA showed that groups were mostly associated to 2006, and completely opposite to 2000. Acacia mangium plantation had the lowest group richness. In the 2008 sampling, pasture showed the lowest group richness, and according to the PCA groups into the gully were associated to 2008, and completely opposite to 2000 and 2006. Formicidae and Collembola (Entomobryomorpha) were dominant in all sampled areas, both in 2000 and 2008, and into the gully in 2006 as well

Sequestration of free cholesterol in cell membranes by prions correlates with cytoplasmic phospholipase A2 activation

<p>Abstract</p> <p>Background</p> <p>The transmissible spongiform encephalopathies (TSEs), otherwise known as the prion diseases, occur following the conversion of the normal cellular prion protein (PrP^C) to an alternatively folded isoform (PrP^Sc). The accumulation of PrP^Scwithin the brain leads to neurodegeneration through an unidentified mechanism. Since many neurodegenerative disorders including prion, Parkinson's and Alzheimer's diseases may be modified by cholesterol synthesis inhibitors, the effects of prion infection on the cholesterol balance within neuronal cells were examined.</p> <p>Results</p> <p>We report the novel observation that prion infection altered the membrane composition and significantly increased total cholesterol levels in two neuronal cell lines (ScGT1 and ScN2a cells). There was a significant correlation between the concentration of free cholesterol in ScGT1 cells and the amounts of PrP^Sc. This increase was entirely a result of increased amounts of free cholesterol, as prion infection reduced the amounts of cholesterol esters in cells. These effects were reproduced in primary cortical neurons by the addition of partially purified PrP^Sc, but not by PrP^C. Crucially, the effects of prion infection were not a result of increased cholesterol synthesis. Stimulating cholesterol synthesis via the addition of mevalonate, or adding exogenous cholesterol, had the opposite effect to prion infection on the cholesterol balance. It did not affect the amounts of free cholesterol within neurons; rather, it significantly increased the amounts of cholesterol esters. Immunoprecipitation studies have shown that cytoplasmic phospholipase A₂(cPLA₂) co-precipitated with PrP^Scin ScGT1 cells. Furthermore, prion infection greatly increased both the phosphorylation of cPLA₂and prostaglandin E₂production.</p> <p>Conclusion</p> <p>Prion infection, or the addition of PrP^Sc, increased the free cholesterol content of cells, a process that could not be replicated by the stimulation of cholesterol synthesis. The presence of PrP^Scincreased solubilisation of free cholesterol in cell membranes and affected their function. It increased activation of the PLA₂pathway, previously implicated in PrP^Scformation and in PrP^Sc-mediated neurotoxicity. These observations suggest that the neuropathogenesis of prion diseases results from PrP^Scaltering cholesterol-sensitive processes. Furthermore, they raise the possibility that disturbances in membrane cholesterol are major triggering events in neurodegenerative diseases.</p

Interpreting malaria age-prevalence and incidence curves: a simulation study of the effects of different types of heterogeneity

ABSTRACT: BACKGROUND: Individuals in a malaria endemic community differ from one another. Many of these differences, such as heterogeneities in transmission or treatment-seeking behaviour, affect malaria epidemiology. The different kinds of heterogeneity are likely to be correlated. Little is known about their impact on the shape of age-prevalence and incidence curves. In this study, the effects of heterogeneity in transmission, treatment-seeking and risk of co-morbidity were simulated. METHODS: Simple patterns of heterogeneity were incorporated into a comprehensive individual-based model of Plasmodium falciparum malaria epidemiology. The different types of heterogeneity were systematically simulated individually, and in independent and co-varying pairs. The effects on age-curves for parasite prevalence, uncomplicated and severe episodes, direct and indirect mortality and first-line treatments and hospital admissions were examined. RESULTS: Different heterogeneities affected different outcomes with large effects reserved for outcomes which are directly affected by the action of the heterogeneity rather than via feedback on acquired immunity or fever thresholds. Transmission heterogeneity affected the age-curves for all outcomes. The peak parasite prevalence was reduced and all age-incidence curves crossed those of the reference scenario with a lower incidence in younger children and higher in older age-groups. Heterogeneity in the probability of seeking treatment reduced the peak incidence of first-line treatment and hospital admissions. Heterogeneity in co-morbidity risk showed little overall effect, but high and low values cancelled out for outcomes directly affected by its action. Independently varying pairs of heterogeneities produced additive effects. More variable results were produced for co-varying heterogeneities, with striking differences compared to independent pairs for some outcomes which were affected by both heterogeneities individually. CONCLUSIONS: Different kinds of heterogeneity both have different effects and affect different outcomes. Patterns of co-variation are also important. Alongside the absolute levels of different factors affecting age-curves, patterns of heterogeneity should be considered when parameterizing or validating models, interpreting data and inferring from one outcome to anothe

What zinc supplementation does and does not achieve in diarrhea prevention: a systematic review and meta-analysis

<p>Abstract</p> <p>Background</p> <p>Prevention of diarrhea has presented indomitable challenges. A preventive strategy that has received significant interest is zinc supplementation. Existing literature including quantitative meta-analyses and systematic reviews tend to show that zinc supplementation is beneficial however evidence to the contrary is augmenting. We therefore conducted an updated and comprehensive meta-analytical synthesis of the existing literature on the effect of zinc supplementation in prevention of diarrhea.</p> <p>Methods</p> <p>EMBASE^®, MEDLINE ^®and CINAHL^®databases were searched for published reviews and meta-analyses on the use of zinc supplementation for the prevention childhood diarrhea. Additional RCTs published following the meta-analyses were also sought. Effect of zinc supplementation on the following five outcomes was studied: incidence of diarrhea, prevalence of diarrhea, incidence of persistent diarrhea, incidence of dysentery and incidence of mortality. The published RCTs were combined using random-effects meta-analyses, subgroup meta-analyses, meta-regression, cumulative meta-analyses and restricted meta-analyses to quantify and characterize the role of zinc supplementation with the afore stated outcomes.</p> <p>Results</p> <p>We found that zinc supplementation has a modest beneficial association (9% reduction) with incidence of diarrhea, a stronger beneficial association (19% reduction) with prevalence of diarrhea and occurrence of multiple diarrheal episodes (28% reduction) but there was significant unexplained heterogeneity across the studies for these associations. Age, continent of study origin, zinc salt and risk of bias contributed significantly to between studies heterogeneity. Zinc supplementation did not show statistically significant benefit in reducing the incidence of persistent diarrhea, dysentery or mortality. In most instances, the 95% prediction intervals for summary relative risk estimates straddled unity.</p> <p>Conclusions</p> <p>Demonstrable benefit of preventive zinc supplementation was observed against two of the five diarrhea-related outcomes but the prediction intervals straddled unity. Thus the evidence for a preventive benefit of zinc against diarrhea is inconclusive. Continued efforts are needed to better understand the sources of heterogeneity. The outcomes of zinc supplementation may be improved by identifying subgroups that need zinc supplementation.</p