Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

Nanochromics: old materials, new structures and architectures for high performance devices

Due to the development of nanoscience, the interest in electrochromism has increased and new assemblies of electrochromic materials at nanoscale leading to higher efficiencies and chromatic contrasts, low switching times and the possibility of color tuning have been developed. These advantages are reached due to the extensive surface area found in nanomaterials and the large amount of organic electrochromic molecules that can be easily attached onto inorganic nanoparticles, as TiO2 or SiO2. Moreover, the direct contact between electrolyte and nanomaterials produces high ionic transfer rates, leading to fast charge compensation, which is essential for high performance electrochromic electrodes. Recently, the layer-by-layer technique was presented as an interesting way to produce different architectures by the combination of both electrochromic nanoparticles and polymers. The present paper shows some of the newest insights into nanochromic science.

High genetic diversity in field isolates of Trypanosoma theileri assessed by analysis of cathepsin L-like sequences disclosed multiple and new genotypes infecting cattle in Thailand

In this study, we describe the first survey in Thailand of Trypanosoma theileri, a widespread and prevalent parasite of cattle that is transmitted by tabanid flies. Investigation of 210 bovine blood samples of Thai cattle from six farms by hematocrit centrifuge technique (HCT) revealed 14 samples with trypanosomes morphologically compatible to T. theileri. Additional animals were positive for T. theileri by PCR based on the Cathepsin L-like sequence (TthCATL-PCR) despite negative by HCT, indicating cryptic infections. Results revealed a prevalence of 26 +/- 15% (95% CI) of T. theileri infection. Additionally, 12 samples positive for T. theileri were detected in cattle from other 11 farms. From a total of 30 blood samples positive by HCT and/or PCR from 17 farms, seven were characterized to evaluate the genetic polymorphism of T. theileri through sequence analysis of PCR-amplified CATL DNA sequences. All CATL sequences of T. theileri from Thai cattle clustered with sequences of the previously described phylogenetic lineages TthI and TthII, supporting only two major lineages of T. theileri in cattle around the world. However, 11 of the 29 CATL sequences analyzed showed to be different, disclosing an unexpectedly large polymorphic genetic repertoire, with multiple genotypes of T. theileri not previously described in other countries circulating in Thai cattle. (C) 2011 Elsevier B.V. All rights reserved.

New treatment of cellulite with infrared-LED illumination applied during high-intensity treadmill training

Phototherapy improves cellular activation which is an important factor for the treatment of cellulite. The objective of this research was to develop and evaluate the effects of a new (noninvasive and nonpharmacological) clinical procedure to improve body aesthetics: infrared-LED (850 nm) plus treadmill training. Twenty women (25-55 years old) participated in this study. They were separated in two groups: the control group, which carried out only the treadmill training (n = 10), and the LED group, with phototherapy during the treadmill training (n - 10). The training was performed for 45 minutes twice a week over 3 months at intensities between 85% and 90% maximal heart rate (HR(max)). The irradiation parameters were 39 mW/cm(2) and a fluence of 106 J/cm(2). The treatment was evaluated by interpreting body composition parameters, photographs and thermography. This was primarily a treatment for cellulite with a reduction of saddlebag and thigh circumference. At the same time, the treadmill training prevented an increase of body fat, as well as the loss of lean mass. Moreover, thermal images of the temperature modification of the thighs are presented. These positive effects can result in a further improvement of body aesthetics using infrared-LED together with treadmill training.

Predicting and characterizing new molecular species at a high-level theoretical approach: HSeCl, HClSe, and SeCl

New molecular species HSeCl, HClSe, and SeCl were investigated at a high level of theory, CCSD(T), with a series of correlation consistent basis sets with extrapolation to the CBS limit. Account has been taken for valence-only and core-valence correlation effects, and of anharmonic effects on the vibrational frequencies. HSeCl is 43.25 kcal mol (1) more stable than HClSe. A barrier (Delta G(#)) of 47.20 kcal mol (1) separates these species. Internuclear distances are generally overestimated by 0.008 angstrom in the valence-only correlation calculations. Inclusion of anharmonicity leads to much improved vibrational frequencies. For SeCl, we estimate Delta H(f) (0 K) = 23.96 and Delta H(f) (298.15 K) = 24.64 kcal mol (1); for HSeCl, we had 4.20 and 4.97 kcal mol (1), respectively. (C) 2010 Elsevier B.V. All rights reserved.

Inbreeding levels in Northeast Brazil: strategies for the prospecting of new genetic disorders

A new autosomal recessive genetic condition, the SPOAN syndrome (an acronym for spastic paraplegia, optic atrophy and neuropathy syndrome), was recently discovered in an isolated region of the State of Rio Grande do Norte in Northeast Brazil, in a population that was identified by the IBGE (Brazilian Institute of Geography and Statistics) as belonging to the Brazilian communities with the highest rates of "deficiencies" (Neri, 2003), a term used to describe diseases, malformations, and handicaps in general. This prompted us to conduct a study of consanguinity levels in five of its municipal districts by directly interviewing their inhabitants. Information on 7,639 couples (corresponding to about 40% of the whole population of the studied districts) was obtained. The research disclosed the existence of very high frequencies of consanguineous marriages, which varied from about 9% to 32%, suggesting the presence of a direct association between genetic diseases such as the SPOAN syndrome, genetic drift and inbreeding levels. This fact calls for the introduction of educational programs for the local populations, as well as for further studies aiming to identify and characterize other genetic conditions. Epidemiological strategies developed to collect inbreeding data, with the collaboration of health systems available in the region, might be very successful in the prospecting of genetic disorders.

A new species of Trichogenes from the rio Itapemirim drainage, southeastern Brazil, with comments on the monophyly of the genus (Siluriformes: Trichomycteridae)

A new species of the formerly monotypic genus Trichogenes is described from a high-altitude stream of the rio Itapemirim system, an isolated Atlantic drainage in the State of Espírito Santo, southeastern Brazil. Trichogenes claviger, new species, differs from all other trichomycterids by the sexually dimorphic posterior process of the opercle, much elongated in males; the terminal mouth; the deeply bifurcated anterior neural spines and the presence of a large anterodorsal claw-like process on the neural arches of the anterior four free vertebrae. The new species also differs from its only congener, T. longipinnis, by a number of additional traits, including the the lack of branched anal-fin rays in specimens of any size; the broader than long posterior nostril; the deeper head (head depth 72.9-86.6% HL); the presence of a fine dark line along the base of the anal fin; the lack of dark spots on cheeks; the shape of the interopercle; the presence of odontodes on a bony expansion on the posterodorsal margin of the interopercle; the fewer vertebrae (35); the absence of an antorbital; and the fewer pleural ribs (eight). Small juveniles of the new species are also strikingly different from those of all other Trichomycteridae, including T. longipinnis, having a very large lateral eye, an upturned mouth, and compressed head. Trichogenes claviger occurs in shaded sectors of a blackwater sluggish stream with sandy substrate and patchy accumulations of vegetable debris, a habitat markedly different from the rocky torrential environment known for T. longipinnis. A comparison of the internal anatomy of the two species provides the basis for a hypothesis of a monophyletic Trichogenes. Data from the new species further support a sister-group relationship between Trichogeninae and Copionodontinae, as well as the position of that clade as sister group to all remaining Trichomycteridae.

Redescription of Anopheles (Nyssorhynchus) antunesi Galvão & Amaral and description of a new species of the Myzorhynchella Section (Diptera: Culicidae) from Serra da Mantiqueira, Brazil

Anopheles (Nyssorhynchus) pristinus Nagaki & Sallum, n. sp. of the Myzorhynchella Section is described based on morphological characters of adult females, males, fourth-instar larvae, pupae and male genitalia. Anopheles (Nyssorhynchus) antunesi Galvão & Amaral is characterized to fix its identity and distinguish it from An. pristinus. The eggs of An. antunesi are described for the first time. Molecular characterization employing sequences of the COI mitochondrial gene and the ITS2 region of ribosomal DNA are provided for each species. An. antunesi and An. pristinus are compared with morphologically similar species of the Myzorhynchella Section. The results of the present study suggest that the new species has been misidentified as both An. antunesi and Anopheles lutzii Cruz. An. antunesi and An. pristinus are sympatric, occurring at high altitudes in Serra da Mantiqueira, southeastern Brazil

Plasmodium vivax circumsporozoite genotypes: a limited variation or new subspecies with major biological consequences?

Background: Plasmodium vivax circumsporozoite variants have been identified in several geographical areas. The real implication of the genetic variation in this region of the P. vivax genome has been questioned for a long time. Although previous studies have observed significant association between VK210 and the Duffy blood group, we present here that evidences of this variation are limited to the CSP central portion. Methods: The phylogenetic analyses were accomplished starting from the amplification of conserved domains of 18 SSU RNAr and Cyt B. The antibodies responses against the CSP peptides, MSP-1, AMA-1 and DBP were detected by ELISA, in plasma samples of individuals infected with two P. vivax CS genotypes: VK210 and P. vivax-like. Results: These analyses of the two markers demonstrate high similarity among the P. vivax CS genotypes and surprisingly showed diversity equal to zero between VK210 and P. vivax-like, positioning these CS genotypes in the same clade. A high frequency IgG antibody against the N- and C-terminal regions of the P. vivax CSP was found as compared to the immune response to the R- and V-repetitive regions (p = 0.0005, Fisher's Exact test). This difference was more pronounced when the P. vivax-like variant was present in the infection (p = 0.003, Fisher's Exact test). A high frequency of antibody response against MSP-1 and AMA-1 peptides was observed for all P. vivax CS genotypes in comparison to the same frequency for DBP. Conclusions: This results target that the differences among the P. vivax CS variants are restrict to the central repeated region of the protein, mostly nucleotide variation with important serological consequences.

ABO genotyping in leukemia patients reveals new ABO variant alleles

The ABO blood group is the most important blood group system in transfusion medicine and organ transplantation. To date, more than 160 ABO alleles have been identified by molecular investigation. Almost all ABO genotyping studies have been performed in blood donors and families and for investigation of ABO subgroups detected serologically. The aim of the present study was to perform ABO genotyping in patients with leukemia. Blood samples were collected from 108 Brazilian patients with chronic myeloid leukemia (N = 69), chronic lymphoid leukemia (N = 13), acute myeloid leukemia (N = 15), and acute lymphoid leukemia (N = 11). ABO genotyping was carried out using allele specific primer polymerase chain reaction followed by DNA sequencing. ABO*001 was the most common allele found, followed by ABO*022 and by ABO*A103. We identified 22 new ABO*(variants) in the coding region of the ABO gene in 25 individuals with leukemia (23.2%). The majority of ABO variants was detected in O alleles (15/60.0%). In 5 of 51 samples typed as blood group O (9.8%), we found non-deletional ABO*O alleles. Elucidation of the diversity of this gene in leukemia and in other diseases is important for the determination of the effect of changes in an amino acid residue on the specificity and activity of ABO glycosyltransferases and their function. In conclusion, this is the first report of a large number of patients with leukemia genotyped for ABO. The findings of this study indicate that there is a high level of recombinant activity in the ABO gene in leukemia patients, revealing new ABO variants.

Evaluation of Primary Resistance to HIV Entry Inhibitors Among Brazilian Patients Failing Reverse Transcriptase/Protease Inhibitors Treatment Reveal High Prevalence of Maraviroc Resistance-Related Mutations

Entry inhibitor is a new class of drugs that target the viral envelope protein. This region is variable; hence resistance to these drugs may be present before treatment. The aim of this study was to analyze the frequency of patients failing treatment with transcriptase reverse and protease inhibitors that would respond to the entry inhibitors Enfuvirtide, Maraviroc, and BMS-806. The study included 100 HIV-1 positive patients from one outpatient clinic in the city of Sao Paulo, for whom a genotype test was requested due to treatment failure. Proviral DNA was amplified and sequenced for regions of gp120 and gp41. A total of 80 could be sequenced and from those, 73 (91.3%), 5 (6.3%) and 2 (2.5%) were classified as subtype B, F, and recombinants (B/F and B/C), respectively. CXCR4 co-receptor use was predicted in 30% of the strains. Primary resistance to Enfuvirtide was found in 1.3%, following the AIDS Society consensus list, and 10% would be considered resistant if a broader criterion was used. Resistance to BMS-806 was higher; 6 (7.5%), and was associated to non-B strains. Strikingly, 27.5% of samples harbored one or more mutation among A316T, I323V, and S405A, which have been related to decreased susceptibility of Maraviroc; 15% of them among viruses predictive to be R5. A more common mutation was A316T, which was associated to the Brazilian B strain harboring the GWGR motif at the tip of V3 loop and their derivative sequences. These results may be impact guidelines for genotype testing and treatment in Brazil.

CAN OLD GALAXIES AT HIGH REDSHIFTS AND BARYON ACOUSTIC OSCILLATIONS CONSTRAIN H(0)?

A new age-redshift test is proposed in order to constrain H(0) on the basis of the existence of old high-redshift galaxies (OHRGs). In the flat Lambda cold dark matter model, the value of H(0) is heavily dependent on the mass density parameter Omega(M) = 1- Omega(Lambda). Such a degeneracy can be broken through a joint analysis involving the OHRG and baryon acoustic oscillation signature. By assuming a galaxy incubation time, t(inc) = 0.8 +/- 0.4 Gyr, our joint analysis yields a value of H(0) = 71 +/- 4 km s(-1) Mpc(-1) (1 sigma) with the best-fit density parameter Omega(M) = 0.27 +/- 0.03. Such results are in good agreement with independent studies from the Hubble Space Telescope key project and recent estimates of the Wilkinson Microwave Anisotropy Probe, thereby suggesting that the combination of these two independent phenomena provides an interesting method to constrain the Hubble constant.

New constraints on the chemical evolution of the solar neighbourhood and Galactic disc(s) Improved astrophysical parameters for the Geneva-Copenhagen Survey

We present a re-analysis of the Geneva-Copenhagen survey, which benefits from the infrared flux method to improve the accuracy of the derived stellar effective temperatures and uses the latter to build a consistent and improved metallicity scale. Metallicities are calibrated on high-resolution spectroscopy and checked against four open clusters and a moving group, showing excellent consistency. The new temperature and metallicity scales provide a better match to theoretical isochrones, which are used for a Bayesian analysis of stellar ages. With respect to previous analyses, our stars are on average 100 K hotter and 0.1 dex more metal rich, which shift the peak of the metallicity distribution function around the solar value. From Stromgren photometry we are able to derive for the first time a proxy for [alpha/Fe] abundances, which enables us to perform a tentative dissection of the chemical thin and thick disc. We find evidence for the latter being composed of an old, mildly but systematically alpha-enhanced population that extends to super solar metallicities, in agreement with spectroscopic studies. Our revision offers the largest existing kinematically unbiased sample of the solar neighbourhood that contains full information on kinematics, metallicities, and ages and thus provides better constraints on the physical processes relevant in the build-up of the Milky Way disc, enabling a better understanding of the Sun in a Galactic context.

PFLEIDERER 2: IDENTIFICATION OF A NEW GLOBULAR CLUSTER IN THE GALAXY

We provide evidence that indicates the star cluster Pfleiderer 2, which is projected in a rich field, as a newly identified Galactic globular cluster. Since it is located in a crowded field, core extraction and decontamination tools were applied to reveal the cluster sequences in B, V, and I color-magnitude diagrams (CMDs). The main CMD features of Pfleiderer 2 are a tilted red giant branch and a red horizontal branch, indicating a high metallicity around solar. The reddening is E(B - V) = 1.01. The globular cluster is located at a distance of d(circle dot) = 16 +/- 2 kpc from the Sun. The cluster is located 2.7 kpc above the Galactic plane and at a distance of R(GC) = 9.7 kpc from the Galactic center, which is unusual for a metal-rich globular cluster.

Beryllium abundances along the evolutionary sequence of the open cluster IC 4651-A new test for hydrodynamical stellar models

Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims. Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods. Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results. Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the Li and Be behavior along the color-magnitude diagram of this intermediate-age cluster for stars more massive than 1.2 M(circle dot).