Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection

Distribution of black flies (Diptera: Simuliidae) in the State of Espírito Santo, Brazil

Entre os anos de 2004 e 2008 foram realizadas coletas de Simuliidae em várias localidades no Estado do Espírito Santo, Brasil. No total, 66 córregos e rios das doze principais bacias hidrográficas do estado foram amostrados. Dezessete espécies foram coletadas, sendo que nove delas representam ocorrências novas para o estado (Simulium pertinax, S. jujuyense, S. rubrithorax, S. subnigrum, S. travassosi, S. spinibranchium, S. hirtipupa, S. lutzianum e S. anamariae), duplicando o número de espécies conhecidas no estado.We conducted a freshwater survey from 2004 to 2008 in several localities of Espírito Santo, Brazil. In total, 66 streams and rivers were sampled in the 12 hydrographic basins of the state. We collected and identified 17 species of which nine represent new records (Simulium pertinax, S. jujuyense, S. rubrithorax, S. subnigrum, S. travassosi, S. spinibranchium, S. hirtipupa, S. lutzianum e S. anamariae). These findings doubled the number of records of black fly species to the State of Espírito Santo, Brazil

Blockade of CD40 ligand for intercellular communication reduces hypertension, placental oxidative stress, and AT1-AA in response to adoptive transfer of CD4(+) T lymphocytes from RUPP rats

Preeclampsia (PE) is associated with altered immune activation during pregnancy. We have previously shown that adoptive transfer of CD4+ T cells from the reduced uterine perfusion pressure (RUPP) rat model of PE increases blood pressure, oxidative stress (ROS), and inflammation in normal pregnant recipient rats. The objective of this study was to determine if blockade of communication via the CD40-CD40 ligand (CD40L) interaction between placental ischemia-induced CD4+ T cells with endogenous normal pregnant (NP) cells would improve pathophysiology that was previously observed in NP recipient rats of RUPP CD4+ T cells. Splenic CD4+ T lymphocytes were magnetically separated, incubated with 2.5 {mu}g/ml anti-CD40 ligand ({alpha}CD40L) overnight, and transferred into NP rats on day 12 of gestation (NP+RUPP CD4+ T+anti-CD40L). On day 19 of gestation, blood pressure (MAP), blood, and tissues were collected. MAP was 99 +/- 2 in NP (n = 13), 116 +/- 4 in NP+RUPP CD4+ T cells (n = 7; P < 0.01); MAP only increased to 104 +/- 2 in NP+RUPP CD4+ T cells+CD40L (n = 24) (P < 0.05 vs. NP+RUPP CD4+ T cells). Mechanisms of hypertension in response to RUPP CD4+ T cells include endothelin-1 (ET-1), ROS, and angiotensin II type I receptor (AT1-AA) were analyzed. Inhibition of CD40L binding reduced placental ET-1 to 2.3-fold above NP rats and normalized placental ROS from 318.6 +/- 89 in NP+RUPP CD4+ T cells (P < 0.05) to 118.7 +/- 24 in NP+RUPP CD4+ T+anti-CD40L (P < 0.05). AT1-AA was also normalized with inhibition of CD40L. These data suggest that placental ischemia-induced T-cell communication via the CD40L is one important mechanism leading to much of the pathophysiology of PE

α-intercalated cells defend the urinary system from bacterial infection

{alpha}–Intercalated cells (A-ICs) within the collecting duct of the kidney are critical for acid-base homeostasis. Here, we have shown that A-ICs also serve as both sentinels and effectors in the defense against urinary infections. In a murine urinary tract infection model, A-ICs bound uropathogenic E. coli and responded by acidifying the urine and secreting the bacteriostatic protein lipocalin 2 (LCN2; also known as NGAL). A-IC–dependent LCN2 secretion required TLR4, as mice expressing an LPS-insensitive form of TLR4 expressed reduced levels of LCN2. The presence of LCN2 in urine was both necessary and sufficient to control the urinary tract infection through iron sequestration, even in the harsh condition of urine acidification. In mice lacking A-ICs, both urinary LCN2 and urinary acidification were reduced, and consequently bacterial clearance was limited. Together these results indicate that A-ICs, which are known to regulate acid-base metabolism, are also critical for urinary defense against pathogenic bacteria. They respond to both cystitis and pyelonephritis by delivering bacteriostatic chemical agents to the lower urinary system

Search for the Flavor-Changing Neutral Current Decay D0→μ+μ−D^0 \to \mu^+\mu^- with the HERA-B Detector

We report on a search for the flavor-changing neutral current decay $D^0 \to \mu^+\mu^-$ using $50 \times 10^6$ events recorded with a dimuon trigger in interactions of 920 GeV protons with nuclei by the HERA-B experiment. We find no evidence for such decays and set a 90% confidence level upper limit on the branching fraction $Br(D^0 \to \mu^+\mu^-) <2.0 \times 10^{-6}$.Comment: 17 pages, 4 figures (of which 1 double), paper to be submitted to Physics Letters

Measurement of the J/Psi Production Cross Section in 920 GeV/c Fixed-Target Proton-Nucleus Interactions

The mid-rapidity (dsigma_(pN)/dy at y=0) and total sigma_(pN) production cross sections of J/Psi mesons are measured in proton-nucleus interactions. Data collected by the HERA-B experiment in interactions of 920 GeV/c protons with carbon, titanium and tungsten targets are used for this analysis. The J/Psi mesons are reconstructed by their decay into lepton pairs. The total production cross section obtained is sigma_(pN)(J/Psi) = 663 +- 74 +- 46 nb/nucleon. In addition, our result is compared with previous measurements

Measurement of the partial widths of the Z into up- and down-type quarks

Using the entire OPAL LEP1 on-peak Z hadronic decay sample, Z -> qbarq gamma decays were selected by tagging hadronic final states with isolated photon candidates in the electromagnetic calorimeter. Combining the measured rates of Z -> qbarq gamma decays with the total rate of hadronic Z decays permits the simultaneous determination of the widths of the Z into up- and down-type quarks. The values obtained, with total errors, were Gamma u = 300 ^{+19}_{-18} MeV and Gamma d = 381 ^{+12}_{-12} MeV. The results are in good agreement with the Standard Model expectation.Comment: 22 pages, 5 figures, Submitted to Phys. Letts.

Search for R-Parity Violating Decays of Scalar Fermions at LEP

A search for pair-produced scalar fermions under the assumption that R-parity is not conserved has been performed using data collected with the OPAL detector at LEP. The data samples analysed correspond to an integrated luminosity of about 610 pb-1 collected at centre-of-mass energies of sqrt(s) 189-209 GeV. An important consequence of R-parity violation is that the lightest supersymmetric particle is expected to be unstable. Searches of R-parity violating decays of charged sleptons, sneutrinos and squarks have been performed under the assumptions that the lightest supersymmetric particle decays promptly and that only one of the R-parity violating couplings is dominant for each of the decay modes considered. Such processes would yield final states consisting of leptons, jets, or both with or without missing energy. No significant single-like excess of events has been observed with respect to the Standard Model expectations. Limits on the production cross- section of scalar fermions in R-parity violating scenarios are obtained. Constraints on the supersymmetric particle masses are also presented in an R-parity violating framework analogous to the Constrained Minimal Supersymmetric Standard Model.Comment: 51 pages, 24 figures, Submitted to Eur. Phys. J.

Measurement of Rb in e+e- Collisions at 182 - 209 GeV

Measurements of Rb, the ratio of the bbbar cross-section to the qqbar cross- section in e+e- collisions, are presented. The data were collected by the OPAL experiment at LEP at centre-of-mass energies between 182 GeV and 209 GeV. Lepton, lifetime and event shape information is used to tag events containing b quarks with high efficiency. The data are compatible with the Standard Model expectation. The mean ratio of the eight measurements reported here to the Standard Model prediction is 1.055+-0.031+-0.037, where the first error is statistical and the second systematic.Comment: 21 pages, 5 figures, Submitted to Phys. Letts