Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

<p>Abstract</p> <p>Background</p> <p>Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones.</p> <p>In this paper we introduce Factor Analysis for Multiple Testing (FAMT) to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF) on chromosome 5 distal region around 168 cM.</p> <p>Results</p> <p>Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region.</p> <p>Conclusion</p> <p>Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.</p

Implications of the polymorphism of HLA-G on its function, regulation, evolution and disease association

The HLA-G gene displays several peculiarities that are distinct from those of classical HLA class I genes. The unique structure of the HLA-G molecule permits a restricted peptide presentation and allows the modulation of the cells of the immune system. Although polymorphic sites may potentially influence all biological functions of HLA-G, those present at the promoter and 3′ untranslated regions have been particularly studied in experimental and pathological conditions. The relatively low polymorphism observed in the MHC-G coding region both in humans and apes may represent a strong selective pressure for invariance, whereas, in regulatory regions several lines of evidence support the role of balancing selection. Since HLA-G has immunomodulatory properties, the understanding of gene regulation and the role of polymorphic sites on gene function may permit an individualized approach for the future use of HLA-G for therapeutic purposes

Search for radiative penguin decays B+->rho(+)gamma, B-0 ->rho(0)gamma, and B-0 ->omega gamma

A search for the decays B-->rho(770)gamma and B-0-->omega(782)gamma is performed on a sample of 211x10(6) Y(4S)-->B (B) over bar events collected by the BABAR detector at the SLAC PEP-II asymmetric-energy e(+)e(-) storage ring. No evidence for the decays is seen. We set the following limits on the individual branching fractions: B(B+-->rho(+)gamma)rho(0)gamma)omegagamma)(rho/omega)gamma]<1.2x10(-6), from which we determine a constraint on the ratio of Cabibbo-Kobayashi-Maskawa matrix elements |V-td|/|V-ts|

Search for the decay B+-> K+ v(v)over-bar

We search for the rare flavor-changing neutral-current decay B+ -> K+ v (v) over tilde in a data sample of 82 fb(-1) collected with the BABAR detector at the PEP-II B-factory. Signal events are selected by examining the properties of the system recoiling against either a reconstructed hadronic or semileptonic charged-B decay. Using these two independent samples we obtain a combined limit of B(B+ -> K+ v (v) over bar) pi(+) v (v) over bar) < 1.0 x 10(-4) using only the hadronic B reconstruction method

Search for the rare leptonic decay B-->tau(-)nu(tau)

We present a search for the decay B- -> tau(-)(tau) in a sample of 88.9 x 10(6) B (B) over bar pairs recorded with the BABAR detector at the Stanford Linear Accelerator Center B factory. One of the two B mesons from the Upsilon(4S) is reconstructed in a hadronic or a semileptonic final state, and the decay products of the other B in the event are analyzed for consistency with a B- -> tau(-)(tau) decay. We find no evidence of a signal and set an upper limit on the branching fraction of B((B) over bar -> tau(-)(tau)) < 4.2 x 10(-4) at the 90% confidence level

Non-Invasive whole-body detection of complement activation using radionuclide imaging in a mouse model of myocardial ischaemia-reperfusion injury

Abstract Complement activation is a recognised mediator of myocardial ischaemia-reperfusion-injury (IRI) and cardiomyocytes are a known source of complement proteins including the central component C3, whose activation products can mediate tissue inflammation, cell death and profibrotic signalling. We investigated the potential to detect and quantify the stable covalently bound product C3d by external body imaging, as a marker of complement activation in heart muscle in a murine model of myocardial IRI. We used single-photon-emission-computed-tomography (SPECT) in conjunction with 99mTechnecium-labelled recombinant complement receptor 2 (99mTc-rCR2), which specifically detects C3d at the site of complement activation. Compared to control imaging with an inactive CR2 mutant (99mTc-K41E CR2) or an irrelevant protein (99mTc-PSMA) or using 99mTc-rCR2 in C3-deficient mice, the use of 99mTc-rCR2 in complement-intact mice gave specific uptake in the reperfused myocardium. The heart to skeletal muscle ratio of 99mTc-rCR2 was significantly higher than in the three control groups. Histological analysis confirmed specific uptake of 99mTc-rCR2. Following therapeutic inhibition of complement C3 activation, we found reduced myocardial uptake of 99mTc-rCR2. We conclude, therefore that 99mTc-rCR2 imaging can be used for non-invasive detection of activated complement and in future could be exploited to quantify the severity of myocardial damage due to complement activation