The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

PTEN Directly Activates the Actin Depolymerization Factor Cofilin-1 During PGE(2)-Mediated Inhibition of Phagocytosis of Fungi

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genomic Strategy Identifies a Missense Mutation in WD-Repeat Domain 65 (WDR65) in an Individual With Van der Woude Syndrome

Genetic variation in the transcription factor interferon regulatory factor 6 (IRF6) causes and contributes risk for oral clefting disorders. We hypothesized that genes regulated by IRF6 are also involved in oral clefting disorders. We used five criteria to identify potential IRF6 target genes; differential gene expression in skin taken from wild-type and Irf6-deficient murine embryos, localization to the Van der Woude syndrome 2 (VWS2) locus at 1p36-1p32, overlapping expression with Irf6, presence of a conserved predicted-binding site in the promoter region, and a mutant murine phenotype that was similar to the Irf6 mutant mouse. Previously, we observed altered expression for 573 genes; 13 were located in the murine region syntenic to the VWS2 locus. Two of these genes, Wdr65 and Stratifin, met 4 of 5 criteria. Wdr65 was a novel gene that encoded a predicted protein of 1,250 amino acids with two WD domains. As potential targets for Irf6 regulation, we hypothesized that disease-causing mutations will be found in WDR65 and Stratifin in individuals with VWS or VWS-like syndromes. We identified a potentially etiologic missense mutation in WDR65 in a person with VWS who does not have an exonic mutation in IRF6. The expression and mutation data were consistent with the hypothesis that WDR65 was a novel gene involved in oral clefting. (C) 2011 Wiley-Liss, Inc.

Oral cleft prevention program (OCPP)

Background: Oral clefts are one of the most common birth defects with significant medical, psychosocial, and economic ramifications. Oral clefts have a complex etiology with genetic and environmental risk factors. There are suggestive results for decreased risks of cleft occurrence and recurrence with folic acid supplements taken at preconception and during pregnancy with a stronger evidence for higher than lower doses in preventing recurrence. Yet previous studies have suffered from considerable design limitations particularly non-randomization into treatment. There is also well-documented effectiveness for folic acid in preventing neural tube defect occurrence at 0.4 mg and recurrence with 4 mg. Given the substantial burden of clefting on the individual and the family and the supportive data for the effectiveness of folic acid supplementation as well as its low cost, a randomized clinical trial of the effectiveness of high versus low dose folic acid for prevention of cleft recurrence is warranted.Methods/design: This study will assess the effect of 4 mg and 0.4 mg doses of folic acid, taken on a daily basis during preconception and up to 3 months of pregnancy by women who are at risk of having a child with nonsyndromic cleft lip with/without palate (NSCL/P), on the recurrence of NSCL/P. The total sample will include about 6,000 women (that either have NSCL/P or that have at least one child with NSCL/P) randomly assigned to the 4 mg and the 0.4 mg folic acid study groups. The study will also compare the recurrence rates of NSCL/P in the total sample of subjects, as well as the two study groups (4mg, 0.4 mg) to that of a historical control group. The study has been approved by IRBs (ethics committees) of all involved sites. Results will be disseminated through publications and presentations at scientific meetings.Discussion: The costs related to oral clefts are high, including long term psychological and socio-economic effects. This study provides an opportunity for huge savings in not only money but the overall quality of life. This may help establish more specific clinical guidelines for oral cleft prevention so that the intervention can be better tailored for at-risk women.

Measurement of inclusive differential cross sections for Upsilon(1S) production in p(p)over-bar collisions at root s=1.96 TeV

We present measurements of the inclusive production cross sections of the Upsilon(1S) bottomonium state in p (p) over bar collisions at root s=1.96 TeV. Using the Upsilon(1S)->mu(+)mu(-) decay mode for a data sample of 159 +/- 10 pb(-1) collected by the D0 detector at the Fermilab Tevatron collider, we determine the differential cross sections as a function of the Upsilon(1S) transverse momentum for three ranges of the Upsilon(1S) rapidity: 0 <\y(Upsilon)\<= 0.6, 0.6 <\y(Upsilon)\<= 1.2, and 1.2 <\y(Upsilon)\<= 1.8.

Measurement of the ratio of B+ and B-0 meson lifetimes

The ratio of the B+ and B-0 meson lifetimes was measured using data collected in 2002-2004 by the D0 experiment in Run II of the Fermilab Tevatron Collider. These mesons were reconstructed in B&RARR;μ(+)ν D*-X decays, which are dominated by B-0 and B&RARR;μ(+)ν(D) over bar X-0 decays, which are dominated by B+. The ratio of lifetimes is measured to be τ(+)/τ(0)=1.080&PLUSMN; 0.016(stat)&PLUSMN; 0.014(syst).

Search for the flavour-changing neutral current B-s(0)->mu+mu- in p(p)over-bar collisions at root s=1.96 TeV with the D0 dectector

We present the results of a search for the flavor-changing neutral current decay B-s(0)-->mu(+)mu(-) using a data set with integrated luminosity of 240 pb(-1) of p (p) over bar collisions at roots=1.96 TeV collected with the D0 detector in run II of the Fermilab Tevatron collider. We find the upper limit on the branching fraction to be B(B-s(0)-->mu(+)mu(-))less than or equal to5.0x10(-7) at the 95% C.L. assuming no contributions from the decay B-d(0)-->mu(+)mu(-) in the signal region. This limit is the most stringent upper bound on the branching fraction B-s(0)-->mu(+)mu(-) to date.

Search for first-generation scalar leptoquarks in p(p)over-bar collisions at root s=1.96 TeV

We report on a search for pair production of first-generation scalar leptoquarks (LQ) in p (p) over bar collisions at root s=1.96 TeV using an integrated luminosity of 252 pb(-1) collected at the Fermilab Tevatron collider by the D0 detector. We observe no evidence for LQ production in the topologies arising from LQ(LQ) over bar -> eqeq and LQ(LQ) over bar -> eq nu q, and derive 95% C.L. lower limits on the LQ mass as a function of beta, where beta is the branching fraction for LQ -> eq. The limits are 241 and 218 GeV/c(2) for beta=1 and 0.5, respectively. These results are combined with those obtained by D0 at root s=1.8 TeV, which increases these LQ mass limits to 256 and 234 GeV/c(2).

Measurement of the B-s(0) lifetime in the exclusive decay channel B-s(0)-> J/psi phi

Using the exclusive decay B-s(0)-->J/psi(mu(+)mu(-))phi(K+K-), we report the most precise single measurement of the B-s(0) lifetime. The data sample corresponds to an integrated luminosity of approximately 220 pb(-1) collected with the D0 detector at the Fermilab Tevatron Collider in 2002-2004. We reconstruct 337 signal candidates, from which we extract the B-s(0) lifetime, tau(B-s(0))=1.444(-0.090)(+0.098)(stat)+/-0.020(sys) ps. We also report a measurement for the lifetime of the B-0 meson using the exclusive decay B-0-->J/psi(mu(+)mu(-))K-*0(892)(K(+)pi(-)). We reconstruct 1370 signal candidates, obtaining tau(B-0)=1.473(-0.050)(+0.052)(stat)+/-0.023(sys) ps, and the ratio of lifetimes, tau(B-s(0))/tau(B-0)=0.980(-0.071)(+0.076)(stat)+/-0.003(sys).

Measurement of the WW production cross section in p(p)over-bar collisions at root(s)over-bar=1.96 TeV

We present a measurement of the W boson pair-production cross section in p(p) over bar collisions at a center-of-mass energy of root s=1.96 TeV. The data, collected with the Run II D0 detector at Fermilab, correspond to an integrated luminosity of 224-252 pb(-1) depending on the final state (ee, e mu, or mu mu). We observe 25 candidates with a background expectation of 8.1 +/- 0.6(stat)+/- 0.6(syst)+/- 0.5(lum) events. The probability for an upward fluctuation of the background to produce the observed signal is 2.3x10(-7), equivalent to 5.2 standard deviations. The measurement yields a cross section of 13.8(-3.8)(+4.3)(stat)(-0.9)(+1.2)(syst)+/- 0.9(lum) pb, in agreement with predictions from the standard model.

The upgraded DO detector

The DO experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid -argon calorimeters and central muon detector, remaining from Run 1, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DO. (c) 2006 Elsevier B.V. All rights reserved.

Search for anomalous heavy-flavor quark production in association with W bosons

We search for anomalous production of heavy-flavor quark jets in association with W bosons at the Fermilab Tevatron p(p) over bar Collider in final states in which the heavy-flavor quark content is enhanced by requiring at least one tagged jet in an event. Jets are tagged using one algorithm based on semileptonic decays of b/c hadrons, and another on their lifetimes. We compare e+jets (164 pb(-1)) and mu+jets (145 pb(-1)) channels collected with the D0 detector at root s = 1.96 TeV to expectations from the standard model and set upper limits on anomalous production of such events.

Measurement of dijet azimuthal decorrelations at central rapidities in p(p)over-bar collisions at root s=1.96 TeV

Correlations in the azimuthal angle between the two largest transverse momentum jets have been measured using the D0 detector in p (p) over bar collisions at a center-of-mass energy root s=1.96 TeV. The analysis is based on an inclusive dijet event sample in the central rapidity region corresponding to an integrated luminosity of 150 pb(-1). Azimuthal correlations are stronger at larger transverse momenta. These are well described in perturbative QCD at next-to-leading order in the strong coupling constant, except at large azimuthal differences where contributions with low transverse momentum are significant.

Observation and properties of the X(3872) decaying to J/psi pi(+)pi(-) in p(p)over-bar collisions at root s=1.96 TeV

We report the observation of the X(3872) in the J/psipi(+)pi(-) channel, with J/psi decaying to mu(+)mu(-), in p (p) over bar collisions at roots=1.96 TeV. Using approximately 230 pb(-1) of data collected with the Run II D0 detector, we observe 522+/-100 X(3872) candidates. The mass difference between the X(3872) state and the J/psi is measured to be 774.9+/-3.1(stat)+/-3.0(syst) MeV/c(2). We have investigated the production and decay characteristics of the X(3872) and find them to be similar to those of the psi(2S) state.

Search for Wbb(-) and WH production in pp(-) collisions at root s=1.96 TeV

We present a search for Wb (b) over bar production in p (p) over bar collisions at root s=1.96 TeV in events containing one electron, an imbalance in transverse momentum, and two b-tagged jets. Using 174 pb(-1) of integrated luminosity accumulated by the D0 experiment at the Fermilab Tevatron collider, and the standard-model description of such events, we set a 95% C.L. upper limit on Wb (b) over bar production of 6.6 pb for b quarks with transverse momenta p(T)(b)> 20 GeV and b (b) over bar separation in pseudorapidity-azimuth space Delta R-bb> 0.75. Restricting the search to optimized b (b) over bar mass intervals provides upper limits on WH production of 9.0-12.2 pb for Higgs-boson masses of 105-135 GeV.