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

УСЛОВИЯ И ОРГАНИЗАЦИЯ ПЕРЕХОДА К БАЗОВЫМ ТЕХНОЛОГИЯМ НОВОГО ТЕХНОЛОГИЧЕСКОГО УКЛАДА

With due account for the coming new (VI-th) world technological structure, future creation of new types of industrial production is both possible and necessary. Economic environment conditions favorable for such development are designated. In reference to Russian technologicalenvironment particulars, self-developing economic-technological microenvironment of a new quality level should be created in zones where controlled «technological chains» function. Possibilities of creation of the VI-th technological structure level basic technologies are shown for industrial and household waste processing techniques as an example.В перспективе возможно, а с учетом формирующегося в мире нового (VI-го) технологического уклада необходимо создание новых промышленных производств. Обозначены условия экономической среды, благоприятствующие такому развитию. Применительно к российским особенностям технологической среды необходимым является создание саморазвивающейся экономико-технологической макросреды нового уровня качества в зонах функционирования управляемых «технологических цепочек». Показаны возможности создания базовых технологий VI-го технологического уклада на примере переработки промышленных и бытовых отходов

Разработка тест-системы для анализа эффекта «смены матрицы» при обратной транскрипции in vitro

We investigated an in vitro system for the analysis of template switching effect of RNA-dependent DNA-polymerase during reverse transcription reaction. An RT-PCR-based approach was realized. An RNA sample was used as a template. The RNA contains a region with a stable secondary structure flanked by two homologous sequences. The described system can find use for testing overall performance of new and existing forms of the reverse transcriptase.Предложена система in vitro для анализа эффекта «смены матрицы» РНК-зависимой ДНК-полимеразой в ходе реакции обратной транскрипции. Реализуется подход, основанный на ступенчатой обратной транскрипции - полимеразной цепной реакции (ОТ-ПЦР). В качестве матрицы используется РНК, имеющая участок со стабильной вторичной структурой, который фланкирован короткими гомологичными фрагментами. Описанная система может найти применение при тестировании эффективности работы новых и существующих мутантных форм обратных транскриптаз, предназначенных для решения исследовательских и генноинженерных задач

Landau theory applied to phase transitions in calcium orthotungstate and isostructural compounds

The pressure-driven tetragonal-to-monoclinic phase transition in CaWO4 and related scheelite-structured orthotungstates is analysed in terms of spontaneous strains. Based upon our previous high-pressure x-ray diffraction results and the Landau theory, it is suggested that the scheelite-to-fergusonite transition is of second order in nature.Comment: 14 pages, 3 figure

УСЛОВИЯ И ОРГАНИЗАЦИЯ ПЕРЕХОДА К БАЗОВЫМ ТЕХНОЛОГИЯМ НОВОГО ТЕХНОЛОГИЧЕСКОГО УКЛАДА

With due account for the coming new (VI-th) world technological structure, future creation of new types of industrial production is both possible and necessary. Economic environment conditions favorable for such development are designated. In reference to Russian technological environment particulars, self-developing economic-technological microenvironment of a new quality level should be created in zones where controlled «technological chains» function. Possibilities of creation of the VI-th technological structure level basic technologies are shown for industrial and household waste processing techniques as an example.В перспективе возможно, а с учетом формирующегося в мире нового (VI-го) технологического уклада необходимо создание новых промышленных производств. Обозначены условия экономической среды, благоприятствующие такому развитию. Применительно к российским особенностям технологической среды необходимым является создание саморазвивающейся экономико-технологической макросреды нового уровня качества в зонах функционирования управляемых «технологических цепочек». Показаны возможности создания базовых технологий VI-го технологического уклада на примере переработки промышленных и бытовых отходов

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

Effect of Dopants on Zirconia Stabilization—An X-ray Absorption Study: III, Charge-Compensating Dopants

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66100/1/j.1151-2916.1994.tb05404.x.pd

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

Measurements of double-helicity asymmetries in inclusive J/ψJ/\psi production in longitudinally polarized p+pp+p collisions at s=510\sqrt{s}=510 GeV

We report the double helicity asymmetry, $A_{LL}^{J/\psi}$, in inclusive $J/\psi$ production at forward rapidity as a function of transverse momentum $p_T$ and rapidity $|y|$. The data analyzed were taken during $\sqrt{s}=510$ GeV longitudinally polarized $p$$+$$p$ collisions at the Relativistic Heavy Ion Collider (RHIC) in the 2013 run using the PHENIX detector. At this collision energy, $J/\psi$ particles are predominantly produced through gluon-gluon scatterings, thus $A_{LL}^{J/\psi}$ is sensitive to the gluon polarization inside the proton. We measured $A_{LL}^{J/\psi}$ by detecting the decay daughter muon pairs $\mu^+ \mu^-$ within the PHENIX muon spectrometers in the rapidity range $1.2<|y|<2.2$. In this kinematic range, we measured the $A_{LL}^{J/\psi}$ to be $0.012 \pm 0.010$~(stat)~$\pm$~$0.003$(syst). The $A_{LL}^{J/\psi}$ can be expressed to be proportional to the product of the gluon polarization distributions at two distinct ranges of Bjorken $x$: one at moderate range $x \approx 0.05$ where recent RHIC data of jet and $\pi^0$ double helicity spin asymmetries have shown evidence for significant gluon polarization, and the other one covering the poorly known small-$x$ region $x \approx 2\times 10^{-3}$. Thus our new results could be used to further constrain the gluon polarization for $x< 0.05$.Comment: 335 authors, 10 pages, 4 figures, 3 tables, 2013 data. Version accepted for publication by 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