2011 lAAF World Championships in Daegu: blood tests for all athletes in the framework of the Athlete Biological Passport.

The 2011 International Association of Athletics Federation (IAAF) World Championships took place in Daegu, Korea. For the first time, all athletes were blood tested prior to the competition in order to give a clear signal to the world athletic community of the wish to enter into the era of the Athlete Biological Passport and fight against doping in their sport. The hematological parameters were measured on site. Thus, a mobile-accredited laboratory for blood testing was created in Daegu. Two serum tubes were collected for clinical chemistry and hormonal analyses in order to build the bases of the endocrine and the androgen (steroid) modules of the Athlete Biological Passport in blood. This paper describes some of the main challenges the project faced with regard to the large number of athletes, competing in different disciplines, and the logistic problems that had to be solved for smart implementation of one of the most complex operations organized in the last decade in the fight against doping.

Isozymic variability in a Brazilian collection of annatto (Bixa orellana L.)

The objectives of this work were to optimize the isozyme electrophoresis technique for Bixa orellana, and use isozyme markers for a preliminary survey on the genetic variability in Brazilian annatto germplasm accessions. Collection consisted of seed samples from sixty open pollinated trees, representing two Northern and four Southern geographic provenances. The extraction, electrophoresis, and interpretation of annatto isozymes are described. Three out of the twenty-one identified isozyme loci were polymorphic in the collection. The percentage of polymorphic loci (P = 21.05) and the expected heterozygosity in annatto (H T = 0.064) were low, compared to other tropical woody species. A UPGMA phenogram, constructed with Nei's genetic distances, clearly separated the germplasm provenant from North and Central Brazil. Variability was significantly higher among the accessions from Maranhão. A sharp genetic differentiation was detected between accessions from Maranhão and Pará States, despite their geographical proximity. The distinctive isozyme polymorphism, observed in the accessions from Maranhão, together with reports on local morphological heterogeneity in annatto fruit shape, color, and pubescence, calls for more detailed genetic and taxonomic investigation.

The effect of a period of intensive exercise on the isoform test to detect growth hormone doping in sports.

OBJECTIVE: The major objective of this study was to investigate the effects of several days of intense exercise on growth hormone (hGH) testing using the World Anti-Doping Agencies hGH isoform differential immunoassays. Additionally the effects of circadian variation and exercise type on the isoform ratios were also investigated. STUDY DESIGN: 15 male athletes performed a simulated nine day cycling stage race. Blood samples were collected twice daily over a period of 15days (stage race+three days before and after). hGH isoforms were analysed by the official WADA immunoassays (CMZ Assay GmbH). RESULTS: All measured isoform ratios were far below the WADA decision limits for an adverse analytical finding. Changes in the isoform ratios could not be clearly connected to circadian variation, exercise duration or intensity. CONCLUSIONS: The present study demonstrates that the hGH isoform ratios are not significantly affected by exercise or circadian variation. We demonstrated that heavy, long term exercise does not interfere with the decision limits for an adverse analytical finding.

Herbicidas aplicados na soja e produtividade do milho em sucessão

O objetivo deste trabalho foi avaliar o efeito residual de herbicidas aplicados na cultura da soja sobre a produtividade do milho em semeadura subseqüente. Foram instalados cinco experimentos na safra agrícola 2002/2003, com delineamento em blocos ao acaso e quatro repetições. Cada experimento correspondeu ao período decorrido entre a aplicação dos herbicidas e a semeadura do milho: zero (semeadura no mesmo dia da aplicação), 30, 60, 90 e 120 dias após aplicação (daa). Os experimentos foram compostos por oito tratamentos (herbicidas diclosulan, sulfentrazone, imazaquin, imazethapyr, fomesafen, lactofen, e chlorimuron-ethyl e um tratamento testemunha), e o efeito dos herbicidas sobre a cultura do milho foi avaliado pela fitotoxicidade e a produtividade. O efeito da fitotoxicidade foi acentuado a zero e 30 daa, e apresentou correlação direta com a redução da produtividade de milho, principalmente quanto aos herbicidas diclosulan e imazaquin. Aos 60 daa não houve correlação direta entre a fitotoxicidade e a produtividade, demonstrando que a cultura do milho apresentou boa capacidade de recuperação. Aos 90 e 120 daa não ocorreram sintomas de fitotoxicidade em nenhum dos tratamentos. Os produtos utilizados apresentaram efeito residual sobre a cultura do milho, principalmente quando foi semeado até 60 dias após aplicação dos herbicidas.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio omega. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the omega ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to similar to 80%) and low GC (similar to 30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test.

Detection of Leishmania RNA virus in Leishmania parasites.

BACKGROUND: Patients suffering from cutaneous leishmaniasis (CL) caused by New World Leishmania (Viannia) species are at high risk of developing mucosal (ML) or disseminated cutaneous leishmaniasis (DCL). After the formation of a primary skin lesion at the site of the bite by a Leishmania-infected sand fly, the infection can disseminate to form secondary lesions. This metastatic phenotype causes significant morbidity and is often associated with a hyper-inflammatory immune response leading to the destruction of nasopharyngeal tissues in ML, and appearance of nodules or numerous ulcerated skin lesions in DCL. Recently, we connected this aggressive phenotype to the presence of Leishmania RNA virus (LRV) in strains of L. guyanensis, showing that LRV is responsible for elevated parasitaemia, destructive hyper-inflammation and an overall exacerbation of the disease. Further studies of this relationship and the distribution of LRVs in other Leishmania strains and species would benefit from improved methods of viral detection and quantitation, especially ones not dependent on prior knowledge of the viral sequence as LRVs show significant evolutionary divergence. METHODOLOGY/PRINCIPAL FINDINGS: This study reports various techniques, among which, the use of an anti-dsRNA monoclonal antibody (J2) stands out for its specific and quantitative recognition of dsRNA in a sequence-independent fashion. Applications of J2 include immunofluorescence, ELISA and dot blot: techniques complementing an arsenal of other detection tools, such as nucleic acid purification and quantitative real-time-PCR. We evaluate each method as well as demonstrate a successful LRV detection by the J2 antibody in several parasite strains, a freshly isolated patient sample and lesion biopsies of infected mice. CONCLUSIONS/SIGNIFICANCE: We propose that refinements of these methods could be transferred to the field for use as a diagnostic tool in detecting the presence of LRV, and potentially assessing the LRV-related risk of complications in cutaneous leishmaniasis.

Dexamethasone intravitreal implant for noninfectious intermediate or posterior uveitis.

OBJECTIVE: To evaluate the safety and efficacy of 2 doses of dexamethasone intravitreal implant (DEX implant) for treatment of noninfectious intermediate or posterior uveitis. METHODS: In this 26-week trial, eyes with noninfectious intermediate or posterior uveitis were randomized to a single treatment with a 0.7-mg DEX implant (n = 77), 0.35-mg DEX implant (n = 76), or sham procedure (n = 76). MAIN OUTCOME MEASURE: The main outcome measure was the proportion of eyes with a vitreous haze score of 0 at week 8. RESULTS: The proportion of eyes with a vitreous haze score of 0 at week 8 was 47% with the 0.7-mg DEX implant, 36% with the 0.35-mg DEX implant, and 12% with the sham (P < .001); this benefit persisted through week 26. A gain of 15 or more letters from baseline best-corrected visual acuity was seen in significantly more eyes in the DEX implant groups than the sham group at all study visits. The percentage of eyes with intraocular pressure of 25 mm Hg or more peaked at 7.1% for the 0.7-mg DEX implant, 8.7% for the 0.35-mg DEX implant, and 4.2% for the sham (P > .05 at any visit). The incidence of cataract reported in the phakic eyes was 9 of 62 (15%) with the 0.7-mg DEX implant, 6 of 51 (12%) with the 0.35-mg DEX implant, and 4 of 55 (7%) with the sham (P > .05). CONCLUSIONS: In patients with noninfectious intermediate or posterior uveitis, a single DEX implant significantly improved intraocular inflammation and visual acuity persisting for 6 months. Application to Clinical Practice Dexamethasone intravitreal implant may be used safely and effectively for treatment of intermediate and posterior uveitis. Trial Registration clinicaltrials.gov Identifier: NCT00333814.

Diurnal and exercise-related variability of haemoglobin and reticulocytes in athletes.

Haemoglobin (Hb) and Reticulocytes (Ret) are measured as indirect markers of doping in athletes. We studied the diurnal variation, the impact of exercise, fluid intake and ambient temperature in athletes on these parameters. Hourly venous blood samples were obtained from 36 male athletes of different disciplines (endurance (END) and non-endurance (NON-END)) over 12 h during a typical training day. Seven inactive subjects served as controls (CON). Hb and Ret were determined. A mixed model procedure was used to analyse the data. At baseline, Hb was similar for all groups, END showed lower Ret than NON-END and CON. Exercise showed a significant impact on Hb (+0.46 g/dl, p<0.001), the effect disappeared approximately 2 h after exercise. Hb decreased over the day by approximately 0.55 g/dl (p<0.01). There was no relevant effect on Ret. Fluid intake and ambient temperature had no significant effect. Hb shows significant diurnal- and exercise related variations. In an anti-doping context, most of these variations are in favour of the athlete. Blood samples taken after exercise might therefore provide reliable results and thus be used for the longitudinal monitoring of athletes if a timeframe for the re-equilibration of vascular volumes is respected.

Comparison of "Live High-Train Low" in Normobaric versus Hypobaric Hypoxia.

We investigated the changes in both performance and selected physiological parameters following a Live High-Train Low (LHTL) altitude camp in either normobaric hypoxia (NH) or hypobaric hypoxia (HH) replicating current "real" practices of endurance athletes. Well-trained triathletes were split into two groups (NH, n = 14 and HH, n = 13) and completed an 18-d LHTL camp during which they trained at 1100-1200 m and resided at an altitude of 2250 m (PiO2  = 121.7±1.2 vs. 121.4±0.9 mmHg) under either NH (hypoxic chamber; FiO2 15.8±0.8%) or HH (real altitude; barometric pressure 580±23 mmHg) conditions. Oxygen saturations (SpO2) were recorded continuously daily overnight. PiO2 and training loads were matched daily. Before (Pre-) and 1 day after (Post-) LHTL, blood samples, VO2max, and total haemoglobin mass (Hbmass) were measured. A 3-km running test was performed near sea level twice before, and 1, 7, and 21 days following LHTL. During LHTL, hypoxic exposure was lower for the NH group than for the HH group (220 vs. 300 h; P<0.001). Night SpO2 was higher (92.1±0.3 vs. 90.9±0.3%, P<0.001), and breathing frequency was lower in the NH group compared with the HH group (13.9±2.1 vs. 15.5±1.5 breath.min-1, P<0.05). Immediately following LHTL, similar increases in VO2max (6.1±6.8 vs. 5.2±4.8%) and Hbmass (2.6±1.9 vs. 3.4±2.1%) were observed in NH and HH groups, respectively, while 3-km performance was not improved. However, 21 days following the LHTL intervention, 3-km run time was significantly faster in the HH (3.3±3.6%; P<0.05) versus the NH (1.2±2.9%; ns) group. In conclusion, the greater degree of race performance enhancement by day 21 after an 18-d LHTL camp in the HH group was likely induced by a larger hypoxic dose. However, one cannot rule out other factors including differences in sleeping desaturations and breathing patterns, thus suggesting higher hypoxic stimuli in the HH group.

A fast automated screening method for the detection of blood transfusion in sports.

Currently, there is no simple direct screening method for the misuse of blood transfusions in sports. In this study, we investigated whether the measurement of iron in EDTA-plasma can serve as biomarker for such purpose. Our results revealed an increase of the plasma iron level up to 25-fold 6 h after blood re-infusion. The variable remained elevated 10-fold one day after the procedure. A specificity of 100% and a sensitivity of 93% were obtained with a proposed threshold at 45 µg/dL of plasma iron. Therefore, our test could be used as a simple, cost effective biomarker for the screening for blood transfusion misuse in sports. Copyright © 2014 John Wiley & Sons, Ltd.

Componentes genéticos aditivos e não aditivos em maracujazeiro-azedo

O objetivo deste trabalho foi avaliar os componentes genéticos aditivos e não aditivos em caracteres qualitativos e produtivos de maracujazeiro, para determinar a ocorrência de efeitos genéticos dominantes. Foram estudados 12 híbridos F1, obtidos entre duas populações distintas, com uso do delineamento II de Comstock e Robinson. Durante o primeiro e o segundo ano (safrinha e primeira safra, respectivamente), foram avaliados os seguintes caracteres: número de frutos por planta, produção estimada, massa de fruto, massa de casca, massa de polpa, comprimento longitudinal, diâmetro equatorial, espessura de casca, teor de sólidos solúveis totais, acidez titulável total e coloração da polpa. A produção do biênio 2004/2005 foi estimada a partir do número total de frutos, multiplicado pela massa média dos frutos. Foram observados efeitos de dominância e, portanto, de heterose, no primeiro ano, para massa de matéria fresca, massa de polpa, massa de casca e diâmetro equatorial do fruto e, no segundo ano, para diâmetro equatorial do fruto e coloração da polpa. Houve predominância dos efeitos aditivos para número de frutos e massa de fruto. Os valores de herdabilidade são indicativos de que a população avaliada pode ser utilizada para a formação da população-base, para promover seleção recorrente.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.