New evidence fortrans-species evolution of theH-2 class I polymorphism

A serological survey using alloantisera specific for the H-2 class I antigens in Japanese wild mice,Mus musculus molossinus, revealed a high frequency of the H-2K^f antigen. This antigen has also been found in European wild mice,M. m. domesticus andM. m. musculus. In this survey, the H-2K^f antigen was characterized through the use of ten newly isolated monoclonal antibodies raised against cells of a Japanese wild mouse, and by Southern blot analysis using anH-2K locus-specific probe which hybridizes with the 3′ end of the gene. The serologically identified H-2K^f antigens revealed several minor variations in reactivities to the monoclonal antibodies. However, all the antigens examined could be clearly separated into two types with respect to the restriction fragment length polymorphism (RFLP) pattern. The first type, found together with a single, characteristic RFLP pattern, was always associated with the presence of reactivity to one particular monoclonal antibody, MS54. The second type, found to represent different RFLP patterns, is associated with the absence of reactivity to MS54. This concordance between the presence of an antigenic determinant and a particular RFLP was observed not only withinMus musculus subspecies but also in a different species:M. spretus, carrying the same antigenic determinant, gave an identical RFLP to that of the other MS54-positiveMus musculus subspecies. The data suggest that the antigenic determinant specific for MS54 is an ancient polymorphic structure which has survived the long period of diversification ofMus species (approximately 2–3 million years) without alteration, and is associated with a stable DNA structure at the 3′ end of theH-2K gene.     

Are there pitfalls to pitfalls? Dung beetle sampling in French Guiana

Dung beetles have widely been accepted as cost-effective indicator taxa for biodiversity assessment; thus, standard protocols have been created to examine their species richness and diversity in many habitats. However, the vast majority of studies adopt short-term sampling protocols; few studies have quantified sampling efficiency at longer time scales or tested the efficacy of species richness estimates. Here we present long- and short-term sampling data from two regions of French Guiana: the Nouragues Tropical Forest Research Station and Kaw Mountain. We examine species richness and diversity, and use these data to make suggestions for future biodiversity assessments of dung beetles using dung baited pitfall transects. Species richness estimates based on short-term samples strongly underestimate the actual species richness by approximately 40?%. Duration of trapping was found to be more important than the number of traps and length of transects; by setting a second transect (4-day sample period) in the same habitat of Nouragues, thereby increasing the sample duration, the number of species increased by 14?%.     

What Will It Take to Eliminate Pediatric HIV? Reaching WHO Target Rates of Mother-to-Child HIV Transmission in Zimbabwe: A Model-Based Analysis

Background

The World Health Organization (WHO) has called for the “virtual elimination” of pediatric HIV: a mother-to-child HIV transmission (MTCT) risk of less than 5%. We investigated uptake of prevention of MTCT (PMTCT) services, infant feeding recommendations, and specific drug regimens necessary to achieve this goal in Zimbabwe.

Methods and Findings

We used a computer model to simulate a cohort of HIV-infected, pregnant/breastfeeding women (mean age, 24 y; mean CD4, 451/µl; breastfeeding duration, 12 mo). Three PMTCT regimens were evaluated: (1) single-dose nevirapine (sdNVP), (2) WHO 2010 guidelines'' “Option A” (zidovudine in pregnancy, infant nevirapine throughout breastfeeding for women without advanced disease, lifelong combination antiretroviral therapy for women with advanced disease), and (3) WHO “Option B” (pregnancy/breastfeeding-limited combination antiretroviral drug regimens without advanced disease; lifelong antiretroviral therapy with advanced disease). We examined four levels of PMTCT uptake (proportion of pregnant women accessing and adhering to PMTCT services): reported rates in 2008 and 2009 (36% and 56%, respectively) and target goals in 2008 and 2009 (80% and 95%, respectively). The primary model outcome was MTCT risk at weaning.The 2008 sdNVP-based National PMTCT Program led to a projected 12-mo MTCT risk of 20.3%. Improved uptake in 2009 reduced projected risk to 18.0%. If sdNVP were replaced by more effective regimens, with 2009 (56%) uptake, estimated MTCT risk would be 14.4% (Option A) or 13.4% (Option B). Even with 95% uptake of Option A or B, projected transmission risks (6.1%–7.7%) would exceed the WHO goal of less than 5%. Only if the lowest published transmission risks were used for each drug regimen, or breastfeeding duration were shortened, would MTCT risks at 95% uptake fall below 5%.

Conclusions

Implementation of the WHO PMTCT guidelines must be accompanied by efforts to improve access to PMTCT services, retain women in care, and support medication adherence throughout pregnancy and breastfeeding, to approach the “virtual elimination” of pediatric HIV in Zimbabwe. Please see later in the article for the Editors'' Summary     

An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs

We present a new flexible, simple, and powerful genome-scan method (flexible intercross analysis, FIA) for detecting quantitative trait loci (QTL) in experimental line crosses. The method is based on a pure random-effects model that simultaneously models between- and within-line QTL variation for single as well as epistatic QTL. It utilizes the score statistic and thereby facilitates computationally efficient significance testing based on empirical significance thresholds obtained by means of permutations. The properties of the method are explored using simulations and analyses of experimental data. The simulations showed that the power of FIA was as good as, or better than, Haley-Knott regression and that FIA was rather insensitive to the level of allelic fixation in the founders, especially for pedigrees with few founders. A chromosome scan was conducted for a meat quality trait in an F(2) intercross in pigs where a mutation in the halothane (Ryanodine receptor, RYR1) gene with a large effect on meat quality was known to segregate in one founder line. FIA obtained significant support for the halothane-associated QTL and identified the base generation allele with the mutated allele. A genome scan was also performed in a previously analyzed chicken F(2) intercross. In the chicken intercross analysis, four previously detected QTL were confirmed at a 5% genomewide significance level, and FIA gave strong evidence (P < 0.01) for two of these QTL to be segregating within the founder lines. FIA was also extended to account for epistasis and using simulations we show that the method provides good estimates of epistatic QTL variance even for segregating QTL. Extensions of FIA and its applications on other intercross populations including backcrosses, advanced intercross lines, and heterogeneous stocks are also discussed.     

Laminar-to-turbulent transition in pulsatile flow through a stenosis

Laminar-to-turbulent transition in pulsatile flow through a stenosis is studied by means of three-dimensional numerical simulations. The flow transition is associated with the occurrence of a flow instability initiating in the stenosis region. The instability is manifested by a three-dimensional symmetry-breaking and leads to asymmetric separation and intense swirling motion downstream of the stenosis. The above have profound effects on the wall shear stress (WSS). The simulations reveal that the asymmetric separation is extended several radii downstream of the stenosis with substantial WSS fluctuations, in both space and time, occurring in the poststenotic region.     

Electroaddressed immobilization of recombinant HIV-1 P24 capsid protein onto screen-printed arrays for serological testing

A serological chemiluminescent biochip was designed based on screen-printed electrode arrays composed of nine 1-mm(2) electrodes. Arrays were shown to be produced with good batch-to-batch reproducibility (standard deviations of 4.4 and 12.0% for ferricyanide oxidation potential and current, respectively) and very good reproducibility within a particular array (2.0 and 7.5% standard deviations for the same controls). Electrode arrays were used to electroaddress various bioconjugate structures comprising a recombinant HIV-1 P24 capsid protein (RH24K) in polypyrrole film. Entrapment of RH24K preimmobilized onto maleic anhydride-alt-methyl vinyl ether copolymer was shown to be the more efficient immobilization procedure. This addressed sensing layer enabled the detection of anti-P24 antibodies at a concentration of 3.5 ng/ml through peroxidase-labeled anti-human immunoglobulin G reaction. The biochip was used to perform an HIV-1 serological test in human sera. HIV-1 seropositive and seronegative sera were easily discriminated using serum dilutions greater than 1/10,000.     

Immunoreactivity in mammals of two typical plant glyco-epitopes,core alpha(1,3)-fucose and core xylose

The presence of nonmammalian core alpha(1,3)-fucose and core xylose glyco-epitopes on glycans N-linked to therapeutic glycoproteins produced in plants has raised the question of their immunogenicity in human therapy. We address this question by studying the distribution of these N-glycans in pea, rice, and maize (which are the crops intended for the production of therapeutic proteins) and by reinvestigating their immunogenicity in rodents. We found that immunization with a model glycoprotein, horseradish peroxidase, elicits in C57BL/6 mice and rats the production of antibodies (Abs) specific for core alpha(1,3)-fucose and core xylose epitopes. Furthermore, we demonstrated that about 50% of nonallergic blood donors contains in their sera Abs specific for core xylose, whereas 25% have Abs against core alpha(1,3)-fucose. These Abs probably result from sensitization to environmental antigens. Although the immunological significance of these data is too speculative at the moment, the presence of such Abs might introduce some limitations to the use of plant-derived biopharmaceutical glycoproteins, such as an accelerated clearance during human therapy.     

Distribution of greenhouse gases in hyper-arid and arid areas of northern Chile and the contribution of the high altitude wetland microbiome (Salar de Huasco,Chile)

Northern Chile harbors different bioclimatic zones including hyper-arid and arid ecosystems and hotspots of microbial life, such as high altitude wetlands, which may contribute differentially to greenhouse gases (GHG) such as carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). In this study, we explored ground level GHG distribution and the potential role of a wetland situated at 3800 m.a.s.l, and characterized by high solar radiation <?1600 W m^?2, extreme temperature ranges (?12 to 24 °C) and wind stress (<?17 m s^?1). The water source of the wetland is mainly groundwater springs, which generates streams and ponds surrounded by peatlands. These sites support a rich microbial aquatic life including diverse bacteria and archaea communities, which transiently form more complex structures, such as microbial mats. In this study, GHG were measured in the water and above ground level air at the wetland site and along an elevation gradient in different bioclimatic areas from arid to hyper-arid zones. The microbiome from the water and sediments was described by high-throughput sequencing 16S rRNA and rDNA genes. The results indicate that GHG at ground level were variable along the elevation gradient potentially associated with different bioclimatic zones, reaching high values at the high Andean steppe and variable but lower values in the Atacama Desert and at the wetland. The water areas of the wetland presented high concentrations of CH₄ and CO₂, particularly at the spring areas and in air bubbles below microbial mats. The microbial community was rich (>?40 phyla), including archaea and bacteria potentially active in the different matrices studied (water, sediments and mats). Functional microbial groups associated with GHG recycling were detected at low frequency, i.e., <?2.5% of total sequences. Our results indicate that hyper-arid and arid areas of northern Chile are sites of GHG exchange associated with various bioclimatic zones and particularly in aquatic areas of the wetland where this ecosystem could represent a net sink of N₂O and a source for CH₄ and CO₂.     

Adhesion properties of mutants of Staphylococcus aureus defective in fibronectin-binding proteins and studies on the expression of fnb genes

Staphylococcus aureus 8325-4 has the potential to express two distinct cell wall-associated fibronectin-binding proteins called FnBPA and FnBPB. In order to test if both proteins are expressed in S. aureus and if both are required for promoting bacterial adhesion to fibronectin-coated surfaces, insertion mutations were isolated in each gene. A DNA fragment encoding tetracycline resistance was inserted into fnbA and a fragment encoding erythromycin resistance was inserted into fnbB . A double fnbA fnbB mutant was also constructed. The fnbA and fnbB single mutants showed no significant reduction in their adhesion to polymethylmethacrylate coverslips that had been coated in vitro with fibronectin. However, the double mutant was completely defective in adhesion. Monospecific antibodies directed against the non-conserved N-terminal regions of both proteins confirmed the lack of expression of FnBPs in the mutant strains. Wild-type fnbA and fnbB genes cloned seperately on a multicopy plasmid were each able to restore fully the adhesion-defective phenotype of the 8325-4 fnbA fnbB mutant. This demonstrates that both fnb genes are expressed in S. aureus and that both contribute to the ability of strain 8325-4 to adhere to fibronectin-coated surfaces. The double mutant was also defective in adhesion to coverslips that had been removed from tissue cages implanted subcutaneously in guinea-pigs, which suggests that fibronectin is important in promoting attachment of S. aureus to biomaterial in vivo .