4,520 research outputs found
Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates
Protein kinase (PK) genes comprise the third largest superfamily that occupy ∼2% of the human genome. They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood.Our comparative analysis demonstrates that genomic organization of regulatory PK genes differs from organization of other protein coding genes. PK genes occupy larger genomic loci, have longer introns, spacer regions, and encode larger proteins. The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages. On average, PK genes evolve slower than other protein coding genes. Breadth of PK expression negatively correlates with rate of non-synonymous substitutions in protein coding regions. This rate is lower for high expression and ubiquitous PKs, relative to low expression PKs, and correlates with divergence in untranslated regions. Conversely, rate of silent mutations is uniform in different PK groups, indicating that differing rates of non-synonymous substitutions reflect variations in selective pressure. Brain and testis employ a considerable number of tissue-specific PKs, indicating high complexity of phosphorylation-dependent regulatory network in these organs. There are considerable differences in genomic organization between PKs up-regulated in the testis and brain. PK genes up-regulated in the highly proliferative testicular tissue are fast evolving and small, with short introns and transcribed regions. In contrast, genes up-regulated in the minimally proliferative nervous tissue carry long introns, extended transcribed regions, and evolve slowly.PK genomic architecture, the size of gene functional domains and evolutionary rates correlate with the pattern of gene expression. Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed. Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution
Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases
Background: The secondary structure and complexity of mRNA influences its
accessibility to regulatory molecules (proteins, micro-RNAs), its stability and
its level of expression. The mobile elements of the RNA sequence, the wobble
bases, are expected to regulate the formation of structures encompassing coding
sequences.
Results: The sequence/folding energy (FE) relationship was studied by
statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found
that the FE (dG) associated with coding sequences is significant and negative
(407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able
to form structures. However, the FE has only a small free component, less than
10% of the total. The contribution of the 1st and 3rd codon bases to the FE is
larger than the contribution of the 2nd (central) bases. It is possible to
achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous
codons. The sequence/FE relationship can be described with a simple algorithm,
and the total FE can be predicted solely from the sequence composition of the
nucleic acid. The contributions of different synonymous codons to the FE are
additive and one codon cannot replace another. The accumulated contributions of
synonymous codons of an amino acid to the total folding energy of an mRNA is
strongly correlated to the relative amount of that amino acid in the translated
protein.
Conclusion: Synonymous codons are not interchangable with regard to their
role in determining the mRNA FE and the relative amounts of amino acids in the
translated protein, even if they are indistinguishable in respect of amino acid
coding.Comment: 14 pages including 6 figures and 1 tabl
Measurements of differential cross sections of Z/gamma*+jets+X events in proton anti-proton collisions at sqrt{s}=1.96 TeV
We present cross section measurements for Z/gamma*+jets+X production,
differential in the transverse momenta of the three leading jets. The data
sample was collected with the D0 detector at the Fermilab Tevatron proton
anti-proton collider at a center-of-mass energy of 1.96 TeV and corresponds to
an integrated luminosity of 1 fb-1. Leading and next-to-leading order
perturbative QCD predictions are compared with the measurements, and agreement
is found within the theoretical and experimental uncertainties. We also make
comparisons with the predictions of four event generators. Two
parton-shower-based generators show significant shape and normalization
differences with respect to the data. In contrast, two generators combining
tree-level matrix elements with a parton shower give a reasonable description
of the the shapes observed in data, but the predicted normalizations show
significant differences with respect to the data, reflecting large scale
uncertainties. For specific choices of scales, the normalizations for either
generator can be made to agree with the measurements.Comment: Published in PLB. 11 pages, 3 figure
Measurement of the Boson Mass
A measurement of the mass of the boson is presented based on a sample of
5982 decays observed in collisions at
= 1.8~TeV with the D\O\ detector during the 1992--1993 run. From a
fit to the transverse mass spectrum, combined with measurements of the
boson mass, the boson mass is measured to be .Comment: 12 pages, LaTex, style Revtex, including 3 postscript figures
(submitted to PRL
Search for Top Squark Pair Production in the Dielectron Channel
This report describes the first search for top squark pair production in the
channel stop_1 stopbar_1 -> b bbar chargino_1 chargino_1 -> ee+jets+MEt using
74.9 +- 8.9 pb^-1 of data collected using the D0 detector. A 95% confidence
level upper limit on sigma*B is presented. The limit is above the theoretical
expectation for sigma*B for this process, but does show the sensitivity of the
current D0 data set to a particular topology for new physics.Comment: Five pages, including three figures, submitted to PRD Brief Report
Simultaneous measurement of the ratio B(t->Wb)/B(t->Wq) and the top quark pair production cross section with the D0 detector at sqrt(s)=1.96 TeV
We present the first simultaneous measurement of the ratio of branching
fractions, R=B(t->Wb)/B(t->Wq), with q being a d, s, or b quark, and the top
quark pair production cross section sigma_ttbar in the lepton plus jets channel
using 0.9 fb-1 of ppbar collision data at sqrt(s)=1.96 TeV collected with the
D0 detector. We extract R and sigma_ttbar by analyzing samples of events with
0, 1 and >= 2 identified b jets. We measure R = 0.97 +0.09-0.08 (stat+syst) and
sigma_ttbar = 8.18 +0.90-0.84 (stat+syst)} +/-0.50 (lumi) pb, in agreement with
the standard model prediction.Comment: submitted to Phys.Rev.Letter
Search for Squarks and Gluinos in Events Containing Jets and a Large Imbalance in Transverse Energy
Using data corresponding to an integrated luminosity of 79 pb-1, D0 has
searched for events containing multiple jets and large missing transverse
energy in pbar-p collisions at sqrt(s)=1.8 TeV at the Fermilab Tevatron
collider. Observing no significant excess beyond what is expected from the
standard model, we set limits on the masses of squarks and gluinos and on the
model parameters m_0 and m_1/2, in the framework of the minimal low-energy
supergravity models of supersymmetry. For tan(beta) = 2 and A_0 = 0, with mu <
0, we exclude all models with m_squark < 250 GeV/c^2. For models with equal
squark and gluino masses, we exclude m < 260 GeV/c^2.Comment: 10 pages, 3 figures, Submitted to PRL, Fixed typo on page bottom of
p. 6 (QCD multijet background is 35.4 events
Measurement of the B0_s semileptonic branching ratio to an orbitally excited D_s** state, Br(B0_s -> Ds1(2536) mu nu)
In a data sample of approximately 1.3 fb-1 collected with the D0 detector
between 2002 and 2006, the orbitally excited charm state D_s1(2536) has been
observed with a measured mass of 2535.7 +/- 0.6 (stat) +/- 0.5 (syst) MeV via
the decay mode B0_s -> D_s1(2536) mu nu X. A first measurement is made of the
branching ratio product Br(b(bar) -> D_s1(2536) mu nu X).Br(D_s1(2536)->D*
K0_S). Assuming that D_s1(2536) production in semileptonic decay is entirely
from B0_s, an extraction of the semileptonic branching ratio Br(B0_s ->
D_s1(2536) mu nu X) is made.Comment: 7 pages, 2 figures, LaTeX, version with minor changes as accepted by
Phys. Rev. Let
Search for First Generation Scalar Leptoquark Pairs in ppbar Collisions at sqrt(s)=1.8 TeV
We have searched for first generation scalar leptoquark (LQ) pairs in the
enu+jets channel using ppbar collider data (integrated luminosity= 115 pb^-1)
collected by the DZero experiment at the Fermilab Tevatron during 1992-96. The
analysis yields no candidate events. We combine the results with those from the
ee+jets and nunu+jets channels to obtain 95% confidence level (CL) upper limits
on the LQ pair production cross section as a function of mass and of beta, the
branching fraction to a charged lepton. Comparing with the next-to-leading
order theory, we set 95% CL lower limits on the LQ mass of 225, 204, and 79
GeV/c^2 for beta=1, 1/2, and 0, respectively.Comment: 14 pages, 4 figures, submitted to Physical Review Letters Replaced to
correct visitor addresse
Journal Staff
We present the first measurements of the differential cross section d sigma/dp(T)(gamma) for the production of an isolated photon in association with at least two b-quark jets. The measurements consider photons with rapidities vertical bar y(gamma)vertical bar < 1.0 and transverse momenta 30 < p(T)(gamma) < 200 GeV. The b-quark jets are required to have p(T)(jet) > 15 GeVand vertical bar y(jet)vertical bar < 1.5. The ratio of differential production cross sections for gamma + 2 b-jets to gamma + b-jet as a function of p(T)(gamma) is also presented. The results are based on the proton-antiproton collision data at root s = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. The measured cross sections and their ratios are compared to the next- to- leading order perturbative QCD calculations as well as predictions based on the k(T)- factorization approach and those from the sherpa and pythia Monte Carlo event generators
- …