360 research outputs found
Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5’D2-RS – 3’D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response
Precise tracking of vaccine-responding T-cell clones reveals convergent and personalized response in identical twins
T-cell receptor (TCR) repertoire data contain information about infections
that could be used in disease diagnostics and vaccine development, but
extracting that information remains a major challenge. Here we developed a
statistical framework to detect TCR clone proliferation and contraction from
longitudinal repertoire data. We applied this framework to data from three
pairs of identical twins immunized with the yellow fever vaccine. We identified
500-1500 responding TCRs in each donor and validated them using three
independent assays. While the responding TCRs were mostly private, albeit with
higher overlap between twins, they could be well predicted using a classifier
based on sequence similarity. Our method can also be applied to samples
obtained post-infection, making it suitable for systematic discovery of new
infection-specific TCRs in the clinic
Azimuthal Angle Correlations for Rapidity Separated Hadron Pairs in d+Au Collisions at sqrt(s_NN) = 200 GeV
We report on two-particle azimuthal angle correlations between charged
hadrons at forward/backward (deuteron/gold going direction) rapidity and
charged hadrons at mid-rapidity in deuteron-gold (d+Au) and proton-proton (p+p)
collisions at sqrt(s_NN) = 200 GeV. Jet structures are observed in the
correlations which we quantify in terms of the conditional yield and angular
width of away side partners. The kinematic region studied here samples partons
in the gold nucleus carrying nucleon momentum fraction x~0.1 to x~0.01. Within
this range, we find no x dependence of the jet structure in d+Au collisions.Comment: 330 authors, 6 pages text, 4 figures, no tables. Submitted to Phys.
Rev. Lett. 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
Dilepton mass spectra in p+p collisions at sqrt(s)= 200 GeV and the contribution from open charm
The PHENIX experiement has measured the electron-positron pair mass spectrum
from 0 to 8 GeV/c^2 in p+p collisions at sqrt(s)=200 GeV. The contributions
from light meson decays to e^+e^- pairs have been determined based on
measurements of hadron production cross sections by PHENIX. They account for
nearly all e^+e^- pairs in the mass region below 1 GeV/c^2. The e^+e^- pair
yield remaining after subtracting these contributions is dominated by
semileptonic decays of charmed hadrons correlated through flavor conservation.
Using the spectral shape predicted by PYTHIA, we estimate the charm production
cross section to be 544 +/- 39(stat) +/- 142(syst) +/- 200(model) \mu b, which
is consistent with QCD calculations and measurements of single leptons by
PHENIX.Comment: 375 authors from 57 institutions, 18 pages, 4 figures, 2 tables.
Submitted to Physics Letters B. v2 fixes technical errors in matching authors
to institutions. 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
Inclusive cross section and double helicity asymmetry for \pi^0 production in p+p collisions at sqrt(s)=200 GeV: Implications for the polarized gluon distribution in the proton
The PHENIX experiment presents results from the RHIC 2005 run with polarized
proton collisions at sqrt(s)=200 GeV, for inclusive \pi^0 production at
mid-rapidity. Unpolarized cross section results are given for transverse
momenta p_T=0.5 to 20 GeV/c, extending the range of published data to both
lower and higher p_T. The cross section is described well for p_T < 1 GeV/c by
an exponential in p_T, and, for p_T > 2 GeV/c, by perturbative QCD. Double
helicity asymmetries A_LL are presented based on a factor of five improvement
in uncertainties as compared to previously published results, due to both an
improved beam polarization of 50%, and to higher integrated luminosity. These
measurements are sensitive to the gluon polarization in the proton, and exclude
maximal values for the gluon polarization.Comment: 375 authors, 7 pages, 3 figures. Submitted to Phys. Rev. D, Rapid
Communications. 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
Centrality dependence of charged hadron production in deuteron+gold and nucleon+gold collisions at sqrt(s_NN)=200 GeV
We present transverse momentum (p_T) spectra of charged hadrons measured in
deuteron-gold and nucleon-gold collisions at \sqrts = 200 GeV for four
centrality classes. Nucleon-gold collisions were selected by tagging events in
which a spectator nucleon was observed in one of two forward rapidity
detectors. The spectra and yields were investigated as a function of the number
of binary nucleon-nucleon collisions, \nu, suffered by deuteron nucleons. A
comparison of charged particle yields to those in p+p collisions show that the
yield per nucleon-nucleon collision saturates with \nu for high momentum
particles. We also present the charged hadron to neutral pion ratios as a
function of p_T.Comment: 330 authors, 15 pages text, 16 figures, 3 tables. Submitted to Phys.
Rev. Lett. v2 has minor changes to reflect revisions during review process.
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
Cross sections and double-helicity asymmetries of midrapidity inclusive charged hadrons in p+p collisions at sqrt(s)=62.4 GeV
Unpolarized cross sections and double-helicity asymmetries of
single-inclusive positive and negative charged hadrons at midrapidity from p+p
collisions at sqrt(s)=62.4 GeV are presented. The PHENIX measurements for 1.0 <
p_T < 4.5 GeV/c are consistent with perturbative QCD calculations at
next-to-leading order in the strong coupling constant, alpha_s. Resummed pQCD
calculations including terms with next-to-leading-log accuracy, yielding
reduced theoretical uncertainties, also agree with the data. The
double-helicity asymmetry, sensitive at leading order to the gluon polarization
in a momentum-fraction range of 0.05 ~< x_gluon ~< 0.2, is consistent with
recent global parameterizations disfavoring large gluon polarization.Comment: PHENIX Collaboration. 447 authors, 12 pages, 5 figures, 5 tables.
Submitted to Physical Review
Inclusive cross section and single-transverse-spin asymmetry for very forward neutron production in polarized p+p collisions at sqrt(s)=200 GeV
The energy dependence of the single-transverse-spin asymmetry, A_N, and the
cross section for neutron production at very forward angles were measured in
the PHENIX experiment at RHIC for polarized p+p collisions at sqrt(s)=200 GeV.
The neutrons were observed in forward detectors covering an angular range of up
to 2.2 mrad. We report results for neutrons with momentum fraction of x_F=0.45
to 1.0. The energy dependence of the measured cross sections were consistent
with x_F scaling, compared to measurements by an ISR experiment which measured
neutron production in unpolarized p+p collisions at sqrt(s)=30.6--62.7 GeV. The
cross sections for large x_F neutron production for p+p collisions, as well as
those in e+p collisions measured at HERA, are described by a pion exchange
mechanism. The observed forward neutron asymmetries were large, reaching
A_N=-0.08+/-0.02 for x_F=0.8; the measured backward asymmetries, for negative
x_F, were consistent with zero. The observed asymmetry for forward neutron
production is discussed within the pion exchange framework, with interference
between the spin-flip amplitude due to the pion exchange and nonflip amplitudes
from all Reggeon exchanges. Within the pion exchange description, the measured
neutron asymmetry is sensitive to the contribution of other Reggeon exchanges
even for small amplitudes.Comment: 383 authors, 16 pages, 18 figures, 6 tables. Submitted to Phys. Rev.
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
Nuclear Modification Factors for Hadrons At Forward and Backward Rapidities in Deuteron-Gold Collisions at sqrt(s_NN) = 200 GeV
We report on charged hadron production in deuteron-gold reactions at
sqrt(s_NN) = 200 GeV. Our measurements in the deuteron-direction cover 1.4 <
eta < 2.2, referred to as forward rapidity, and in the gold-direction -2.0 <
eta < -1.4, referred to as backward rapidity, and a transverse momentum range
p_T = 0.5-4.0 GeV/c. We compare the relative yields for different deuteron-gold
collision centrality classes. We observe a suppression relative to binary
collision scaling at forward rapidity, sensitive to low momentum fraction (x)
partons in the gold nucleus, and an enhancement at backward rapidity, sensitive
to high momentum fraction partons in the gold nucleus.Comment: 330 authors, 6 pages text, 4 figures, REVTeX4. Published in Physical
Review Letters. Minor changes over previous version in response to referee
and editor comments, plus updating of references. 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
J/psi suppression at forward rapidity in Au+Au collisions at sqrt(s_NN)=39 and 62.4 GeV
We present measurements of the J/psi invariant yields in sqrt(s_NN)=39 and
62.4 GeV Au+Au collisions at forward rapidity (1.2<|y|<2.2). Invariant yields
are presented as a function of both collision centrality and transverse
momentum. Nuclear modifications are obtained for central relative to peripheral
Au+Au collisions (R_CP) and for various centrality selections in Au+Au relative
to scaled p+p cross sections obtained from other measurements (R_AA). The
observed suppression patterns at 39 and 62.4 GeV are quite similar to those
previously measured at 200 GeV. This similar suppression presents a challenge
to theoretical models that contain various competing mechanisms with different
energy dependencies, some of which cause suppression and others enhancement.Comment: 365 authors, 10 pages, 11 figures, 4 tables. Submitted to Phys. Rev.
C. 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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