Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Signals for CP violation in scalar tau pair production at muon colliders

We discuss signals for CP violation in μ + μ - → Τ̃ i - Τ̃ j +, where i, j = 1, 2 label the two scalar Τ mass eigenstates. We assume that these reactions can proceed through the production and decay of the heavy neutral Higgs bosons present in supersymmetric models. CP violation in the Higgs sector can be probed through a rate asymmetry even with unpolarized beams, while the CP-odd phase associated with the Τ̃ mass matrix can be probed only if the polarization of at least one beam can be varied. These asymmetries might be O (1).

Effective pair potentials and structure of water

Classical Monte Carlo calculations have been performed in order to investigate the ability of the TIP4P, SPC, and SPCE water models to reproduce the structural features of liquid water. The simulations were carried out in the NPT ensemble at 4 thermodynamic conditions. The results are compared with recent neutron diffraction data. Essentially, the three models capture equally well the thermodynamic and structural features of water. Although they were parametrized to reproduce the water properties at ambient conditions, the agreement with the experimental pair correlation functions was even better at supercritical conditions. This is because the effective pair potentials have some difficulty to reproduce cooperative interactions, like hydrogen bonds. These interactions are less effective at supercritical conditions, where the liquid behaves roughly like a gas.

Supersymmetric Higgs boson pair production at hadron colliders

We study the pair production of neutral Higgs bosons through gluon fusion at hadron colliders in the framework of the minimal supersymmetric standard model. We present analytical expressions for the relevant amplitudes, including both quark and squark loop contributions, and allowing for mixing between the superpartners of left- and right-handed quarks. Squark loop contributions can increase the cross section for the production of two CP-even Higgs bosons by more than two orders of magnitude, if the relevant trilinear soft breaking parameter is large and the mass of the lighter squark eigenstate is not too far above its current lower bound. In the region of large tan β, neutral Higgs boson pair production might even be observable in the 4b final state during the next run of the Fermilab Tevatron collider. ©1999 The American Physical Society.

Strong-interaction effects in stop pair production at e+e- colliders

We discuss perturbative and non-perturbative strong-interaction effects in the pair production of stop squarks (t̃1) at e+e- colliders. Events with an additional hard gluon allow to detect or exclude t̃1t̃*1 production even in scenarios with very small mass splitting between ti and an invisible lightest supersymmetric particle (LSP). Such events can also help to establish that t̃1 transforms as a triplet under SU(3)C. We also carefully study non-perturbative t̃1 fragmentation, which is currently not well understood: not only is the t̃1 fragmentation function not known very well, but also there are ambiguities in the algorithm employed to model fragmentation. We present numerical results both for CERN LEP-183 and for a proposed future e+e- collider operating at center-of-mass energy s1/2 = 500 GeV.

Bose-Einstein correlations in W-pair decays

Bose-Einstein correlations are studied in semileptonic (WW → qq̄lv) and fully hadronic (WW → qq̄qq̄) W-pair decays with the ALEPH detector at LEP at centre-of-mass energies of 172, 183 and 189 GeV. They are compared with those made at the Z peak after correction for the different flavour compositions. A Monte Carlo model of Bose-Einstein correlations based on the JETSET hadronization scheme was tuned to the Z data and reproduces the correlations in the WW → qq̄lv events. The same Monte Carlo reproduces the correlations in the WW → qq̄qq̄ channel assuming independent fragmentation of the two W's. A variant of this model with Bose-Einstein correlations between decay products of different W's is disfavoured. (C) 2000 Published by Elsevier Science B.V.

Supersymmetric Higgs boson pair production: Discovery prospects at hadron colliders

We study the potential of hadron colliders in the search for the pair production of neutral Higgs bosons in the framework of the minimal supersymmetric standard model. We perform a detailed signal and background analysis, working out efficient kinematical cuts for the extraction of the signal. The important role of squark loop contributions to the signal is re-emphasized. If the signal is sufficiently enhanced by these contributions, it could even be observable at the next run of the upgraded Tevatron collider in the near future. At the LHC the pair production of light and heavy Higgs bosons might be detectable simultaneously.

Taxonomic importance of the prefemoral process of the first pair of legs in males of the genus Pseudonannolene (Diplopoda, Spirostreptida)

The first pair of legs in males of some groups of diplopods is modified, having a large coxa and oral projecting prefemoral process; in the family Spirostreptidae (Spirostreptida) this structure has relevance on the genus level. This paper discusses the shape, presence, and absence of the prefemoral process in the genus Pseudonannolene (Pseudonannolenidae, Spirostreptida) and suggests that this structure is an important taxonomic character in this genus and can be used for distinguishing some species.

Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1) locus in Brazil and Vietnam

Background: Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods: We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed: Polyα, TA42 (only for Brazilian samples), TA81, TA1, TA87, TA109 (only for Brazilian samples), 2490, ARAII, PfG377, PfPK2, and TA60. Results: The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion: Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

ZmPUMP encodes a fully functional monocot plant uncoupling mitochondrial protein whose affinity to fatty acid is increased with the introduction of a His pair at the second matrix loop

Uncoupling proteins (UCPs) are specialized mitochondrial transporter proteins that uncouple respiration from ATP synthesis. In this study, cDNA encoding maize uncoupling protein (ZmPUMP) was expressed in Escherichia coli and recombinant ZmPUMP reconstituted in liposomes. ZmPUMP activity was associated with a linoleic acid (LA)-mediated H+ efflux with Km of 56.36 ± 0.27 μM and Vmax of 66.9 μmol H+ min-1 (mg prot)-1. LA-mediated H+ fluxes were sensitive to ATP inhibition with Ki of 2.61 ± 0.36 mM (at pH 7.2), a value similar to those for dicot UCPs. ZmPUMP was also used to investigate the importance of a histidine pair present in the second matrix loop of mammalian UCP1 and absent in plant UCPs. ZmPUMP with introduced His pair (Lys155His and Ala157His) displayed a 1.55-fold increase in LA-affinity while its activity remained unchanged. Our data indicate conserved properties of plant UCPs and suggest an enhancing but not essential role of the histidine pair in proton transport mechanism. © 2006 Elsevier Inc. All rights reserved.

Search for resonant pair production of neutral long-lived particles decaying to bb̄ in pp̄ collisions at s=1.96TeV

We report on a first search for resonant pair production of neutral long-lived particles (NLLP) which each decay to a bb̄ pair, using 3.6fb-1 of data recorded with the D0 detector at the Fermilab Tevatron collider. We search for pairs of displaced vertices in the tracking detector at radii in the range 1.6-20cm from the beam axis. No significant excess is observed above background, and upper limits are set on the production rate in a hidden-valley benchmark model for a range of Higgs boson masses and NLLP masses and lifetimes. © 2009 The American Physical Society.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Zeros of Jacobi-Sobolev orthogonal polynomials following non-coherent pair of measures

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Search for violation of Lorentz invariance in top quark pair production and decay

Using data collected with the D0 detector at the Fermilab Tevatron Collider, corresponding to 5.3fb -1 of integrated luminosity, we search for violation of Lorentz invariance by examining the tt̄ production cross section in lepton+jets final states. We quantify this violation using the standard-model extension framework, which predicts a dependence of the tt̄ production cross section on sidereal time as the orientation of the detector changes with the rotation of the Earth. Within this framework, we measure components of the matrices (c Q) μν33 and (c U) μν33 containing coefficients used to parametrize violation of Lorentz invariance in the top quark sector. Within uncertainties, these coefficients are found to be consistent with zero. © 2012 American Physical Society.