A history of chagas disease transmission, control, and re-emergence in peri-rural La Joya, Peru

Background

The history of Chagas disease control in Peru and many other nations is marked by scattered and poorly documented vector control campaigns. The complexities of human migration and sporadic control campaigns complicate evaluation of the burden of Chagas disease and dynamics of Trypanosoma cruzi transmission.

Methodology/Principal Findings

We conducted a cross-sectional serological and entomological study to evaluate temporal and spatial patterns of T. cruzi transmission in a peri-rural region of La Joya, Peru. We use a multivariate catalytic model and Bayesian methods to estimate incidence of infection over time and thereby elucidate the complex history of transmission in the area. Of 1,333 study participants, 101 (7.6%; 95% CI: 6.2–9.0%) were confirmed T. cruzi seropositive. Spatial clustering of parasitic infection was found in vector insects, but not in human cases. Expanded catalytic models suggest that transmission was interrupted in the study area in 1996 (95% credible interval: 1991–2000), with a resultant decline in the average annual incidence of infection from 0.9% (95% credible interval: 0.6–1.3%) to 0.1% (95% credible interval: 0.005–0.3%). Through a search of archival newspaper reports, we uncovered documentation of a 1995 vector control campaign, and thereby independently validated the model estimates.

Conclusions/Significance

High levels of T. cruzi transmission had been ongoing in peri-rural La Joya prior to interruption of parasite transmission through a little-documented vector control campaign in 1995. Despite the efficacy of the 1995 control campaign, T. cruzi was rapidly reemerging in vector populations in La Joya, emphasizing the need for continuing surveillance and control at the rural-urban interface.     

Towards an accurate identification of mosaic genes and partial horizontal gene transfers

Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution.     

The dissipation of wind wave energy across a fringing reef at Ipan,Guam

Field observations over a fringing reef at Ipan, Guam, during trade wind and tropical storm conditions are used to assess the transformation of sea and swell energy from the fore reef to the shoreline. Parameterizations of wave breaking and bottom friction developed for sandy beaches are found to represent the observed decay in wave energy with an increased friction coefficient. These parameterizations are incorporated into the one-dimensional energy flux balance, which is integrated across the reef to assess the effects of varying tidal range, incident wave height and reef bathymetry on the sea and swell band wave height and wave setup near the shoreline. Wave energy on the reef is strongly depth-limited and controlled by the reef submergence level. Shoreline wave energy increases with incident wave height largely due to the increase in water level from breaking wave setup. Increased tidal levels result in increased shoreline energy, since wave setup is only weakly reduced. The wave height at the shore is shown to be inversely proportional to the width of the reef flat due to dissipation.     

Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations

In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations. A number of important phylogenetic and general bioinformatics tools have been included in the first software release. As Armadillo is an open-source project, it allows scientists to develop their own modules as well as to integrate existing computer applications. Using our workflow platform, different complex phylogenetic tasks can be modeled and presented in a single workflow without any prior knowledge of programming techniques. The first version of Armadillo was successfully used by professors of bioinformatics at Université du Quebec à Montreal during graduate computational biology courses taught in 2010-11. The program and its source code are freely available at: .     

Expression of soluble Saccharomyces cerevisiae alcohol dehydrogenase in Escherichia coli applicable to oxido-reduction bioconversions

Six-carbon aldehydes and alcohols belong to flavours and fragrances with wide application in the food, feed, cosmetic, chemical and pharmaceutical sectors. In the present study, we prepared the expression system for production of recombinant yeast alcohol dehydrogenase 1 (YADH1) from Saccharomyces cerevisiae which is suitable also for catalysis of the interconversion of C-6 aldehydes and alcohols. We have demonstrated that an effective three-step strategy can overcome the insolubility problems during YADH1 production in Escherichia coli. We used trxB and gor deficient expression strain, decreased concentration of isopropyl β-D-1-thiogalactopyranoside and lowered temperature to 20°C during induction. Finally, kinetic parameters of recombinant YADH1 were determined and we concluded it is a promising enzyme also for the interconversion of C-6 alcohols/aldehydes in green note volatile production.     

Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees

Background  

Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data [1] and, as such, it has become a common method for assessing tree confidence in phylogenetics [2]. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.