352 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
Challenges in QCD matter physics - The Compressed Baryonic Matter experiment at FAIR
Substantial experimental and theoretical efforts worldwide are devoted to
explore the phase diagram of strongly interacting matter. At LHC and top RHIC
energies, QCD matter is studied at very high temperatures and nearly vanishing
net-baryon densities. There is evidence that a Quark-Gluon-Plasma (QGP) was
created at experiments at RHIC and LHC. The transition from the QGP back to the
hadron gas is found to be a smooth cross over. For larger net-baryon densities
and lower temperatures, it is expected that the QCD phase diagram exhibits a
rich structure, such as a first-order phase transition between hadronic and
partonic matter which terminates in a critical point, or exotic phases like
quarkyonic matter. The discovery of these landmarks would be a breakthrough in
our understanding of the strong interaction and is therefore in the focus of
various high-energy heavy-ion research programs. The Compressed Baryonic Matter
(CBM) experiment at FAIR will play a unique role in the exploration of the QCD
phase diagram in the region of high net-baryon densities, because it is
designed to run at unprecedented interaction rates. High-rate operation is the
key prerequisite for high-precision measurements of multi-differential
observables and of rare diagnostic probes which are sensitive to the dense
phase of the nuclear fireball. The goal of the CBM experiment at SIS100
(sqrt(s_NN) = 2.7 - 4.9 GeV) is to discover fundamental properties of QCD
matter: the phase structure at large baryon-chemical potentials (mu_B > 500
MeV), effects of chiral symmetry, and the equation-of-state at high density as
it is expected to occur in the core of neutron stars. In this article, we
review the motivation for and the physics programme of CBM, including
activities before the start of data taking in 2022, in the context of the
worldwide efforts to explore high-density QCD matter.Comment: 15 pages, 11 figures. Published in European Physical Journal
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
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
Jet Structure from Dihadron Correlations in d+Au collisions at sqrt(s_NN) = 200 GeV
Dihadron correlations at high transverse momentum in d+Au collisions at
sqrt(s_NN) = 200 GeV at midrapidity are measured by the PHENIX experiment at
the Relativistic Heavy Ion Collider (RHIC). From these correlations we extract
several structural characteristics of jets; the root-mean-squared (RMS)
transverse momentum of fragmenting hadrons with respect to the jet
sqrt(), the mean sine-squared angle between the scattered partons
, and the number of particles produced within the dijet that are
associated with a high-p_T particle (dN/dx_E distributions). We observe that
the fragmentation characteristics of jets in d+Au collisions are very similar
to those in p+p collisions and that there is also little dependence on the
centrality of the d+Au collision. This is consistent with the nuclear medium
having little influence on the fragmentation process. Furthermore, there is no
statistically significant increase in the value of from p+p to
d+Au collisions. This constrains the amount of multiple scattering that partons
undergo in the cold nuclear medium before and after a hard-collision.Comment: 330 authors, 30 pages text, RevTeX4, 42 figures, 20 tables. Submitted
to Physical Review 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
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
Double Helicity Asymmetry in Inclusive Mid-Rapidity neutral pion Production for Polarized p+p Collisions at sqrt(s)=200 GeV
We present a measurement of the double longitudinal spin asymmetry in
inclusive pi^0 production in polarized proton-proton collisions at sqrt(s)=200
GeV. The data were taken at the Relativistic Heavy Ion Collider with average
beam polarizations of 26%. The measurements are the first of a program to study
the longitudinal spin structure of the proton, using strongly interacting
probes, at collider energies. The asymmetry is presented for transverse momenta
1-5 GeV/c at mid-rapidity, where next-to-leading order perturbative quantum
chromodynamic (NLO pQCD) calculations describe the unpolarized cross section
well. The observed asymmetry is small and is compared with a NLO pQCD
calculation with a range of polarized gluon distributions.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 1 table. To be
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
Transverse-energy distributions at midrapidity in , Au, and AuAu collisions at --200~GeV and implications for particle-production models
Measurements of the midrapidity transverse energy distribution, d\Et/d\eta,
are presented for , Au, and AuAu collisions at
GeV and additionally for AuAu collisions at
and 130 GeV. The d\Et/d\eta distributions are first
compared with the number of nucleon participants , number of
binary collisions , and number of constituent-quark participants
calculated from a Glauber model based on the nuclear geometry. For
AuAu, \mean{d\Et/d\eta}/N_{\rm part} increases with , while
\mean{d\Et/d\eta}/N_{qp} is approximately constant for all three energies.
This indicates that the two component ansatz, , which has been used to represent
distributions, is simply a proxy for , and that the term
does not represent a hard-scattering component in distributions. The
distributions of AuAu and Au are then calculated from
the measured distribution using two models that both reproduce
the AuAu data. However, while the number-of-constituent-quark-participant
model agrees well with the Au data, the additive-quark model does not.Comment: 391 authors, 24 pages, 19 figures, and 15 Tables. Submitted to Phys.
Rev. C. 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
High transverse momentum eta meson production in p+p, d+Au and Au+Au collisions at sqrt(s_NN) = 200 GeV
Inclusive transverse momentum spectra of eta mesons in the range p_T~2-12
GeV/c have been measured at mid-rapidity (|\eta| < 0,35) by the PHENIX
experiment at RHIC in p+p, d+Au and Au+Au collisions at sqrt(s_NN) = 200 GeV.
The eta mesons are reconstructed through their eta--> \gamma\gamma channel for
the three colliding systems as well as through the eta-->pi^0 pi+ pi- decay
mode in p+p and d+Au collisions. The nuclear modification factor in d+Au
collisions, R_dAu(p_T~1.0-1.1, suggests at most only modest p_T broadening
("Cronin enhancement"). In central Au+Au reactions, the eta yields are
significantly suppressed, with R_AuAu(pT)~0.2. The ratio of eta to pi^0 yields
is approximately constant as a function of p_T for the three colliding systems
in agreement with the high-p_T world average of R_eta/pi^0 \approx 0.5 in
hadron-hadron, hadron-nucleus, and nucleus-nucleus collisions for a wide range
of center-of-mass energies [sqrt(s_NN)~3-1800 GeV] as well as, for high scaled
momentum x_p, in e+e- annihilations at sqrt(s)=91.2 GeV. These results are
consistent with a scenario where high-p_T eta production in nuclear collisions
at RHIC is largely unaffected by initial-state effects, but where light-quark
mesons (pi^0;eta) are equally suppressed due to final-state interactions of the
parent partons in the dense medium produced in Au+Au reactions.Comment: 391 authors, NN pages text, RevTeX4, figures, tables. Submitted to
Physical Review 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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