1,146 research outputs found
Spo0A∼P Imposes a Temporal Gate for the Bimodal Expression of Competence in Bacillus subtilis
ComK transcriptionally controls competence for the uptake of transforming DNA in Bacillus subtilis. Only 10%–20% of the cells in a clonal population are randomly selected for competence. Because ComK activates its own promoter, cells exceeding a threshold amount of ComK trigger a positive feedback loop, transitioning to the competence ON state. The transition rate increases to a maximum during the approach to stationary phase and then decreases, with most cells remaining OFF. The average basal rate of comK transcription increases transiently, defining a window of opportunity for transitions and accounting for the heterogeneity of competent populations. We show that as the concentration of the response regulator Spo0A∼P increases during the entry to stationary phase it first induces comK promoter activity and then represses it by direct binding. Spo0A∼P activates by antagonizing the repressor, Rok. This amplifies an inherent increase in basal level comK promoter activity that takes place during the approach to stationary phase and is a general feature of core promoters, serving to couple the probability of competence transitions to growth rate. Competence transitions are thus regulated by growth rate and temporally controlled by the complex mechanisms that govern the formation of Spo0A∼P. On the level of individual cells, the fate-determining noise for competence is intrinsic to the comK promoter. This overall mechanism has been stochastically simulated and shown to be plausible. Thus, a deterministic mechanism modulates an inherently stochastic process
Heavy Quarks and Heavy Quarkonia as Tests of Thermalization
We present here a brief summary of new results on heavy quarks and heavy
quarkonia from the PHENIX experiment as presented at the "Quark Gluon Plasma
Thermalization" Workshop in Vienna, Austria in August 2005, directly following
the International Quark Matter Conference in Hungary.Comment: 8 pages, 5 figures, Quark Gluon Plasma Thermalization Workshop
(Vienna August 2005) Proceeding
Deuteron and antideuteron production in Au+Au collisions at sqrt(s_NN)=200 GeV
The production of deuterons and antideuterons in the transverse momentum
range 1.1 < p_T < 4.3 GeV/c at mid-rapidity in Au + Au collisions at
sqrt(s_NN)=200 GeV has been studied by the PHENIX experiment at RHIC. A
coalescence analysis comparing the deuteron and antideuteron spectra with those
of protons and antiprotons, has been performed. The coalescence probability is
equal for both deuterons and antideuterons and increases as a function of p_T,
which is consistent with an expanding collision zone. Comparing (anti)proton
yields p_bar/p = 0.73 +/- 0.01, with (anti)deuteron yields: d_bar/d = 0.47 +/-
0.03, we estimate that n_bar/n = 0.64 +/- 0.04.Comment: 326 authors, 6 pages text, 5 figures, 1 Table. Submitted to PRL.
Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Mid-Rapidity Direct-Photon Production in p+p Collisions at sqrt(s) = 200 GeV
A measurement of direct photons in p+p collisions at sqrt(s)=200 GeV is
presented. A photon excess above background from pi^0 --> gamma+gamma, eta -->
gamma+gamma, and other decays is observed in the transverse momentum range 5.5
< p_T < 7 GeV/c. The result is compared to a next-to-leading-order perturbative
QCD calculation. Within errors, good agreement is found between the QCD
calculation and the measured result.Comment: 330 authors, 7 pages text, RevTeX, 2 figures, 2 tables. Submitted to
Physical Review D. Plain text data tables for the points plotted in figures
for this and previous PHENIX publications are (or will be) publicly available
at http://www.phenix.bnl.gov/papers.htm
Suppressed pi^0 Production at Large Transverse Momentum in Central Au+Au Collisions at sqrt(s_NN) = 200 GeV
Transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c
have been measured at mid-rapidity by the PHENIX experiment at RHIC in Au+Au
collisions at sqrt(s_NN) = 200 GeV. The pi^0 multiplicity in central reactions
is significantly below the yields measured at the same sqrt(s_NN) in peripheral
Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For
the most central bin, the suppression factor is ~2.5 at p_T = 2 GeV/c and
increases to ~4-5 at p_T ~= 4 GeV/c. At larger p_T, the suppression remains
constant within errors. The deficit is already apparent in semi-peripheral
reactions and increases smoothly with centrality.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 2 tables. Submitted to
PRL. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Scaling properties of proton and anti-proton production in sqrt(s_NN) = 200 GeV Au + Au collisions
We report on the yield of protons and anti-protons, as a function of
centrality and transverse momentum, in Au+Au collisions at sqrt(s_NN) = 200 GeV
measured at mid-rapidity by the PHENIX experiment at RHIC. In central
collisions at intermediate transverse momenta (1.5 < p_T < 4.5 GeV/c) a
significant fraction of all produced particles are protons and anti-protons.
They show a centrality-scaling behavior different from that of pions. The
p-bar/pion and p/pion ratios are enhanced compared to peripheral Au+Au, p+p,
and electron+positron collisions. This enhancement is limited to p_T < 5 GeV/c
as deduced from the ratio of charged hadrons to pi^0 measured in the range 1.5
< p_T < 9 GeV/c.Comment: 325 authors, 6 pages text, 4 figures, RevTeX 4. Minor changes to text
and figures to meet PRL length restrictions; no changes to figures;
resubmitted to PRL. Plain text data tables for the points plotted in figures
for this and previous PHENIX publications are (or will be) publicly available
at http://www.phenix.bnl.gov/papers.htm
J/Psi Production in Au-Au Collisions at sqrt(s_NN) = 200 GeV at the Relativistic Heavy Ion Collider
First results on charm quarkonia production in heavy ion collisions at the
Relativistic Heavy Ion Collider (RHIC) are presented. The yield of J/Psi's
measured in the PHENIX experiment via electron-positron decay pairs at
mid-rapidity for Au-Au reactions at sqrt(s_NN) = 200 GeV are analyzed as a
function of collision centrality. For this analysis we have studied 49.3
million minimum bias Au-Au reactions. We present the J/Psi invariant yield
dN/dy for peripheral and mid-central reactions. For the most central collisions
where we observe no signal above background, we quote 90% confidence level
upper limits. We compare these results with our J/Psi measurement from
proton-proton reactions at the same energy. We find that our measurements are
not consistent with models that predict strong enhancement relative to binary
collision scaling.Comment: 325 authors, 11 pages text, 6 figures, 4 tables, RevTeX 4. Accepted
for publication as a regular article in Physical Review C. This version has
minor changes to respond to referee suggestions. Plain text data tables for
the points plotted in figures for this and previous PHENIX publications are
publicly available at http://www.phenix.bnl.gov/papers.htm
Understanding mixed sequence DNA recognition by novel designed compounds: the kinetic and thermodynamic behavior of azabenzimidazole diamidines
Sequence-specific recognition of DNA by small organic molecules offers a potentially effective approach for the external regulation of gene expression and is an important goal in cell biochemistry. Rational design of compounds from established modules can potentially yield compounds that bind strongly and selectively with specific DNA sequences. An initial approach is to start with common A·T bp recognition molecules and build in G·C recognition units. Here we report on the DNA interaction of a synthetic compound that specifically binds to a G·C bp in the minor groove of DNA by using an azabenzimidazole moiety. The detailed interactions were evaluated with biosensor-surface plasmon resonance (SPR), isothermal calorimetric (ITC), and mass spectrometry (ESI-MS) methods. The compound, DB2277, binds with single G·C bp containing sequences with subnanomolar potency and displays slow dissociation kinetics and high selectivity. A detailed thermodynamic and kinetic study at different experimental salt concentrations and temperatures shows that the binding free energy is salt concentration dependent but essentially temperature independent under our experimental conditions, and binding enthalpy is temperature dependent but salt concentration independent. The results show that in the proper compound structural context novel heterocyclic cations can be designed to strongly recognize complex DNA sequences
Measurement of Single Muons at Forward Rapidity in p+p Collisions at sqrt(s) = 200 GeV and Implications for Charm Production
Muon production at forward rapidity (1.5 < |\eta| < 1.8) has been measured by
the PHENIX experiment over the transverse momentum range 1 < p_T \le 3 GeV/c in
sqrt(s) = 200 GeV p+p collisions at the Relativistic Heavy Ion Collider. After
statistically subtracting contributions from light hadron decays an excess
remains which is attributed to the semileptonic decays of hadrons carrying
heavy flavor, i.e. charm quarks or, at high p_T, bottom quarks. The resulting
muon spectrum from heavy flavor decays is compared to PYTHIA and a
next-to-leading order perturbative QCD calculation. PYTHIA is used to determine
the charm quark spectrum that would produce the observed muon excess. The
corresponding differential cross section for charm quark production at forward
rapidity is determined to be d\sigma_(c c^bar)/dy|_(y=1.6)=0.243 +/- 0.013
(stat.) +/- 0.105 (data syst.) ^(+0.049)_(-0.087) (PYTHIA syst.) mb.Comment: 329 authors, pages text, 18 figures, tables. Submitted to Physical
Review D. Plain text data tables for the points plotted in figures for this
and previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
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