Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases

Copy number variation at leptin receptor gene locus associated with metabolic traits and the risk of type 2 diabetes mellitus

<p>Abstract</p> <p>Background</p> <p>Recent efforts have been made to link complex human traits and disease susceptibility to DNA copy numbers. The leptin receptor (LEPR) has been implicated in obesity and diabetes. Mutations and genetic variations of <it>LEPR </it>gene have been discovered in rodents and humans. However, the association of DNA copy number variations at the <it>LEPR </it>gene locus with human complex diseases has not been reported. In an attempt to study DNA copy number variations associated with metabolic traits and type 2 diabetes mellitus (T2DM), we targeted the <it>LEPR </it>gene locus in DNA copy number analyses.</p> <p>Results</p> <p>We identified DNA copy number variations at the <it>LEPR </it>gene locus among a Korean population using genome-wide SNP chip data, and then quantified copy numbers of the E2 DNA sequence in the first two exons overlapped between <it>LEPR </it>and <it>LEPROT </it>genes by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method. Among the non-diabetic subjects (n = 1,067), lower E2 DNA copy numbers were associated with higher fasting glucose levels in men (<it>p </it>= 1.24 × 10^-7) and women (<it>p </it>= 9.45 × 10^-5), as well as higher total cholesterol levels in men (<it>p </it>= 9.96 × 10^-7). In addition, the significant association between lower E2 DNA copy numbers and lower level of postprandial 2hr insulin was evident only in non-diabetic women, whereas some obesity-related phenotypes and total cholesterol level exhibited significant associations only in non-diabetic men. Logistic regression analysis indicated that lower E2 DNA copy numbers were associated with T2DM (odds ratio, 1.92; 95% CI, 1.26~2.96; p < 0.003) in our nested case-control study. Interestingly, the E2 DNA copy number exhibited a negative correlation with LEPR gene expression, but a positive correlation with LEPROT gene expression.</p> <p>Conclusions</p> <p>This work suggests that a structural variation at the <it>LEPR </it>gene locus is functionally associated with complex metabolic traits and the risk of T2DM.</p

A More Appropriate Cardiac Troponin T Level That Can Predict Outcomes in End-Stage Renal Disease Patients with Acute Coronary Syndrome

Purpose: Cardiac troponin T (cTnT), a useful marker for diagnosing acute myocardial infarction (AMI) in the general population, is significantly higher than the usual cut-off value in many end-stage renal disease (ESRD) patients without clinically apparent evidence of AMI. The aim of this study was to evaluate the clinical usefulness of cTnT in ESRD patients with acute coronary syndrome (ACS). Materials and methods: Two hundred eighty-four ESRD patients with ACS were enrolled between March 2002 and February 2008. These patients were followed until death or June 2009. Medical records were reviewed retrospectively. The cut-off value of cTnT for AMI was evaluated using a receiver operating characteristic (ROC) curve. We calculated Kaplan-Meier survival curves, and potential outcome predictors were determined by Cox proportional hazard analysis. Results: AMIs were diagnosed in 40 patients (14.1%). The area under the curve was 0.98 in the ROC curve (p<0.001; 95% CI, 0.95-1.00). The summation of sensitivity and specificity was highest at the initial cTnT value of 0.35 ng/mL (sensitivity, 0.95; specificity, 0.97). Survival analysis showed a statistically significant difference in all-cause and cardiovascular mortalities for the group with an initial cTnT ≥0.35 ng/mL compared to the other groups. Initial serum cTnT concentration was an independent predictor for mortality. Conclusion: Because ESRD patients with an initial cTnT concentration ≥0.35 ng/mL have a poor prognosis, it is suggested that urgent diagnosis and treatment be indicated in dialysis patients with ACS when the initial cTnT levels are ≥0.35 ng/mL.ope

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or between species can give clues about phenotypic differences. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases

Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1

Aminoacyl-tRNA synthetases possess unique domains. In this study the structure of the vertebrate IARS1 and EARS1 complex reveals that vertebrate IARS1 protects the DNA repair factor BRCA1 from proteolytic degradation via its UBX-fold domain. Aminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I. Here, we present the crystal structure of the chicken IARS1 UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1). UNE-I consists of tandem ubiquitin regulatory X (UBX) domains that interact with a distinct hairpin loop on EARS1 and protect its neighboring proteins in the multi-synthetase complex from degradation. Phosphomimetic mutation of the two serine residues in the hairpin loop releases IARS1 from the complex. IARS1 interacts with BRCA1 in the nucleus, regulates its stability by inhibiting ubiquitylation via the UBX domains, and controls DNA repair function

Measurement of the rapidity and transverse momentum distributions of Z bosons in pp collisions at √(s)=7 TeV

Measurements of the normalized rapidity (y) and transverse-momentum (qT) distributions of Drell–Yan muon and electron pairs in the Z-boson mass region (60<Mℓℓ<120  GeV) are reported. The results are obtained using a data sample of proton-proton collisions at a center-of-mass energy of 7 TeV, collected by the CMS experiment at the Large Hadron Collider (LHC), corresponding to an integrated luminosity of 36  pb-1. The distributions are measured over the ranges |y|<3.5 and qT<600  GeV and compared with quantum chromodynamics (QCD) calculations using recent parton distribution functions to model the momenta of the quarks and gluons in the protons. Overall agreement is observed between the models and data for the rapidity distribution, while no single model describes the Z transverse-momentum distribution over the full range

Measurement of the differential cross section for isolated prompt photon production in pp collisions at 7 TeV

A measurement of the differential cross section for the inclusive production of isolated prompt photons in proton-proton collisions at a center-of-mass energy of 7 TeV is presented. The data sample corresponds to an integrated luminosity of 36 pb(-1) recorded by the CMS detector at the LHC. The measurement covers the pseudorapidity range vertical bar eta vertical bar < 2.5 and the transverse energy range 25 < E-T < 400 GeV, corresponding to the kinematic region 0.007 < x(T) < 0.114. Photon candidates are identified with two complementary methods, one based on photon conversions in the silicon tracker and the other on isolated energy deposits in the electromagnetic calorimeter. The measured cross section is presented as a function of E-T in four pseudorapidity regions. The next-to-leading-order perturbative QCD calculations are consistent with the measured cross section

Long-range and short-range dihadron angular correlations in central PbPb collisions at √sNN=2.76 TeV

This is the pre-print version of the Published Article, which can be accessed from the link below.First measurements of dihadron correlations for charged particles are presented for central PbPb collisions at a nucleon-nucleon center-of-mass energy of 2.76TeV over a broad range in relative pseudorapidity ( ) and the full range of relative azimuthal angle ( ). The data were collected with the CMS detector, at the LHC. A broadening of the away-side ( ) azimuthal correlation is observed at all , as compared to the measurements in pp collisions. Furthermore, long-range dihadron correlations in are observed for particles with similar values. This phenomenon, also known as the \ridge", persists up to at least j j = 4. For particles with transverse momenta (pT) of 2-4 GeV/c, the ridge is found to be most prominent when these particles are correlated with particles of pT = 2-6 GeV/c, and to be much reduced when paired with particles of pT = 10-12 GeV/c

Search for supersymmetry in events with b jets and missing transverse momentum at the LHC

A search for supersymmetry is presented using a sample of events with b jets and missing transverse momentum. The search uses a data sample of proton-proton collisions at a centre-of-mass energy of 7TeV, corresponding to an integrated luminosity of 35 pb(-1), collected with the CMS detector. A total of 0.33(-0.33)(+0.43) (stat.) +/- 0.13 (syst.) events is predicted, using control samples in the data, to arise from standard model processes, and one event is observed in the data. Upper limits are set at the 95% confidence level on the cross sections of benchmark supersymmetric models