Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis

Abstract Background In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. A more holistic view of this molecular interplay will help in the further study of the regulatory mechanisms controlling seed storage compound accumulation. Results We identified gene coexpression networks in the transcriptome of developing Arabidopsis (Arabidopsis thaliana) seeds from the globular to mature embryo stages by analyzing publicly accessible microarray datasets. Genes encoding the known enzymes in the fatty acid biosynthesis pathway were found in one coexpression subnetwork (or cluster), while genes encoding oleosins and seed storage proteins were identified in another subnetwork with a distinct expression profile. In the triacylglycerol assembly pathway, only the genes encoding diacylglycerol acyltransferase 1 (DGAT1) and a putative cytosolic "type 3" DGAT exhibited a similar expression pattern with genes encoding oleosins. We also detected a large number of putative cis-acting regulatory elements in the promoter regions of these genes, and promoter motifs for LEC1 (LEAFY COTYLEDON 1), DOF (DNA-binding-with-One-Finger), GATA, and MYB transcription factors (TF), as well as SORLIP5 (Sequences Over-Represented in Light-Induced Promoters 5), are overrepresented in the promoter regions of fatty acid biosynthetic genes. The conserved CCAAT motifs for B3-domain TFs and binding sites for bZIP (basic-leucine zipper) TFs are enriched in the promoters of genes encoding oleosins and seed storage proteins. Conclusions Genes involved in the accumulation of seed storage reserves are expressed in distinct patterns and regulated by different TFs. The gene coexpression clusters and putative regulatory elements presented here provide a useful resource for further experimental characterization of protein interactions and regulatory networks in this process.</p

清涼飮料税論

The production of J/\).psi\) and $\psi(2S)$ was measured with the ALICE detector in Pb-Pb collisions at the LHC. The measurement was performed at forward rapidity 2.5 < y < 4 \() down to zero transverse momentum \(p_{\rm T} in the dimuon decay channel. Inclusive J/\).psi\) yields were extracted in different centrality classes and the centrality dependence of the average $p_{\rm T}$ is presented. The J/\).psi\) suppression, quantified with the nuclear modification factor $R_{\rm AA}$ , was studied as a function of centrality, transverse momentum and rapidity. Comparisons with similar measurements at lower collision energy and theoretical models indicate that the J/\).psi\) production is the result of an interplay between color screening and recombination mechanisms in a deconfined partonic medium, or at its hadronization. Results on the $\psi(2S)$ suppression are provided via the ratio of $\psi(2S)$ over J/\).psi\) measured in pp and Pb-Pb collisions

Multiplicity dependence of pion, kaon, proton and lambda production in p–Pb collisions at √sNN = 5.02 TeV

Inthis Letter, comprehensive results on π±,K±,K0S, p(pbar) and Λ(Λbar) production at mid-rapidity (0< yCMS < 0.5) in p–Pb collisions at √sNN = 5.02 TeV, measured by the ALICE detector at the LHC, are reported. The transverse momentum distributions exhibit a hardening as a function of event multiplicity, which is stronger for heavier particles. This behavior is similar to what has been observed in pp and Pb–Pb collisions at the LHC. The measured pT distributions are compared to d–Au, Au–Au and Pb–Pb results at lower energy and with predictions based on QCD-inspired and hydrodynamic models

Production of charged pions, kaons and protons at large transverse momenta in pp and Pb–Pb collisions at sNN=2.76\sqrt{s_{NN}}=2.76 TeV

Transverse momentum spectra of pi(+/-), K-+/- and p((p) over bar) up to p(T) = 20 GeV/c at mid-rapidity in pp, peripheral (60-80%) and central (0-5%) Pb-Pb collisions at v root s(NN) = 2.76 TeV have been measured using the ALICE detector at the Large Hadron Collider. The proton-to-pion and the kaon-to-pionratios both show a distinct peak at p(T) approximate to 3 GeV/c in central Pb-Pb collisions. Below the peak, p(T) 10 GeV/c particle ratios in pp and Pb-Pb collisions are in agreement and the nuclear modification factors for pi(+/-), K-+/- and p((p) over bar) indicate that, within the systematic and statistical uncertainties, the suppression is the same. This suggests that the chemical composition of leading particles from jets in the medium is similar to that of vacuum jets

Production of charged pions, kaons and protons at large transverse momenta in pp and Pb–Pb collisions at sNN=2.76\sqrt{s_{NN}}=2.76 TeV

Transverse momentum spectra of pi(+/-), K-+/- and p((p) over bar) up to p(T) = 20 GeV/c at mid-rapidity in pp, peripheral (60-80%) and central (0-5%) Pb-Pb collisions at v root s(NN) = 2.76 TeV have been measured using the ALICE detector at the Large Hadron Collider. The proton-to-pion and the kaon-to-pionratios both show a distinct peak at p(T) approximate to 3 GeV/c in central Pb-Pb collisions. Below the peak, p(T) 10 GeV/c particle ratios in pp and Pb-Pb collisions are in agreement and the nuclear modification factors for pi(+/-), K-+/- and p((p) over bar) indicate that, within the systematic and statistical uncertainties, the suppression is the same. This suggests that the chemical composition of leading particles from jets in the medium is similar to that of vacuum jets

Measurement of charged jet suppression in Pb-Pb collisions at sNN\sqrt{s_{NN}}=2.76TeV

A measurement of the transverse momentum spectra of jets in Pb-Pb collisions at $\sqrt{s_{NN}}$=2.76TeV is reported. Jets are reconstructed from charged particles using the anti-$k_T$ jet algorithm with jet resolution parameters R of 0.2 and 0.3 in pseudo-rapidity |$\eta$|<0.5. The transverse momentum p_T of charged particles is measured down to 0.15 GeV/c which gives access to the low p_T fragments of the jet. Jets found in heavy-ion collisions are corrected event-by-event for average background density and on an inclusive basis (via unfolding) for residual background fluctuations and detector effects. A strong suppression of jet production in central events with respect to peripheral events is observed. The suppression is found to be similar to the suppression of charged hadrons, which suggests that substantial energy is radiated at angles larger than the jet resolution parameter R=0.3 considered in the analysis. The fragmentation bias introduced by selecting jets with a high p_T leading particle, which rejects jets with a soft fragmentation pattern, has a similar effect on the jet yield for central and peripheral events. The ratio of jet spectra with R=0.2 and R=0.3 is found to be similar in Pb-Pb and simulated PYTHIA pp events, indicating no strong broadening of the radial jet structure in the reconstructed jets with R<0.3.A measurement of the transverse momentum spectra of jets in Pb-Pb collisions at $\sqrt{s_{\rm NN}}=2.76$ TeV is reported. Jets are reconstructed from charged particles using the anti-$k_{\rm T}$ jet algorithm with jet resolution parameters $R$ of $0.2$ and $0.3$ in pseudo-rapidity $|\eta|<0.5$. The transverse momentum $p_{\rm T}$ of charged particles is measured down to $0.15$ GeV/$c$ which gives access to the low $p_{\rm T}$ fragments of the jet. Jets found in heavy-ion collisions are corrected event-by-event for average background density and on an inclusive basis (via unfolding) for residual background fluctuations and detector effects. A strong suppression of jet production in central events with respect to peripheral events is observed. The suppression is found to be similar to the suppression of charged hadrons, which suggests that substantial energy is radiated at angles larger than the jet resolution parameter $R=0.3$ considered in the analysis. The fragmentation bias introduced by selecting jets with a high $p_{\rm T}$ leading particle, which rejects jets with a soft fragmentation pattern, has a similar effect on the jet yield for central and peripheral events. The ratio of jet spectra with $R=0.2$ and $R=0.3$ is found to be similar in Pb-Pb and simulated PYTHIA pp events, indicating no strong broadening of the radial jet structure in the reconstructed jets with $R<0.3$

J/psi Elliptic Flow in Pb-Pb Collisions at root s(NN)=5.02 TeV

We report a precise measurement of the J/psi elliptic flow in Pb-Pb collisions at root s(NN) = 5.02 TeV with the ALICE detector at the LHC. The J/psi mesons are reconstructed at midrapidity (|y| < 0.9) in the dielectron decay channel and at forward rapidity (2.5 < y < 4.0) in the dimuon channel, both down to zero transverse momentum. At forward rapidity, the elliptic flow v(2) of the J/psi is studied as a function of the transverse momentum and centrality. A positive v(2) is observed in the transverse momentum range 2<p(T)<8GeV/c in the three centrality classes studied and confirms with higher statistics our earlier results at root s(NN) = 2.76 TeV in semicentral collisions. At midrapidity, the J/psi v(2) is investigated as a function of the transverse momentum in semicentral collisions and found to be in agreement with the measurements at forward rapidity. These results are compared to transport model calculations. The comparison supports the idea that at low p(T) the elliptic flow of the J/psi originates from the thermalization of charm quarks in the deconfined medium but suggests that additional mechanisms might be missing in the models

Long-range angular correlations of pi, K and p in p-Pb collisions at root s(NN)=5.02 TeV

Angular correlations between unidentified charged trigger particles and various species of charged associated particles (unidentified particles, pions, kaons, protons and antiprotons) are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV in the transverse-momentum range 0.3 < p(T) < 4 GeV/c. The correlations expressed as associated yield per trigger particle are obtained in the pseudorapidity range vertical bar n(lab)vertical bar < 0.8. Fourier coefficients are extracted from the long-range correlations projected onto the azimuthal angle difference and studied as a function of p(T) and in intervals of event multiplicity. In high-multiplicity events, the second-order coefficient for protons, 4, is observed to be smaller than that for pions, v(2)(pi), up to about p(T) = 2 GeV/c. To reduce correlations due to jets, the per-trigger yield measured in low-multiplicity events is subtracted from that in high-multiplicity events. A two-ridge structure is obtained for all particle species. The Fourier decomposition of this structure shows that the second-order coefficients for pions and kaons are similar. The v(2)(p) is found to be smaller at low P-T and larger at higher p(T) than v(2)(pi), with a crossing occurring at about 2 GeV/c. This is qualitatively similar to the elliptic-flow pattern observed in heavy-ion collisions. A mass ordering effect at low transverse momenta is consistent with expectations from hydrodynamic model calculations assuming a collectively expanding system. (C) 2013 CERN. Published by Elsevier B.V. All rights reserved.7264169916417