Detailed Chemical Abundances in NGC 5824: Another Metal-Poor Globular Cluster with Internal Heavy Element Abundance Variations

We present radial velocities, stellar parameters, and detailed abundances of 39 elements derived from high-resolution spectroscopic observations of red giant stars in the luminous, metal-poor globular cluster NGC 5824. We observe 26 stars in NGC 5824 using the Michigan/Magellan Fiber System (M2FS) and two stars using the Magellan Inamori Kyocera Echelle (MIKE) spectrograph. We derive a mean metallicity of [Fe/H]=-1.94+/-0.02 (statistical) +/-0.10 (systematic). The metallicity dispersion of this sample of stars, 0.08 dex, is in agreement with previous work and does not exceed the expected observational errors. Previous work suggested an internal metallicity spread only when fainter samples of stars were considered, so we cannot exclude the possibility of an intrinsic metallicity dispersion in NGC 5824. The M2FS spectra reveal a large internal dispersion in [Mg/Fe], 0.28 dex, which is found in a few other luminous, metal-poor clusters. [Mg/Fe] is correlated with [O/Fe] and anti-correlated with [Na/Fe] and [Al/Fe]. There is no evidence for internal dispersion among the other alpha- or Fe-group abundance ratios. Twenty-five of the 26 stars exhibit a n-capture enrichment pattern dominated by r-process nucleosynthesis ([Eu/Fe]=+0.11+/-0.12; [Ba/Eu]=-0.66+/-0.05). Only one star shows evidence of substantial s-process enhancement ([Ba/Fe]=+0.56+/-0.12; [Ba/Eu]=+0.38+/-0.14), but this star does not exhibit other characteristics associated with s-process enhancement via mass-transfer from a binary companion. The Pb and other heavy elements produced by the s-process suggest a timescale of no more than a few hundred Myr for star formation and chemical enrichment, like the complex globular clusters M2, M22, and NGC 5286.Comment: Accepted for publication in MNRAS. (26 pages, 18 figures, 9 tables including online data

Data Exploration, Quality Control and Testing in Single-Cell qPCR-Based Gene Expression Experiments

Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arrays combined with multiplexed quantitative polymerase chain reactions (qPCR) now enables high-throughput single-cell gene expression measurement, allowing assessment of cellular heterogeneity. However very little analytic tools have been developed specifically for the statistical and analytical challenges of single-cell qPCR data. We present a statistical framework for the exploration, quality control, and analysis of single-cell gene expression data from microfluidic arrays. We assess accuracy and within-sample heterogeneity of single-cell expression and develop quality control criteria to filter unreliable cell measurements. We propose a statistical model accounting for the fact that genes at the single-cell level can be on (and for which a continuous expression measure is recorded) or dichotomously off (and the recorded expression is zero). Based on this model, we derive a combined likelihood-ratio test for differential expression that incorporates both the discrete and continuous components. Using an experiment that examines treatment-specific changes in expression, we show that this combined test is more powerful than either the continuous or dichotomous component in isolation, or a t-test on the zero-inflated data. While developed for measurements from a specific platform (Fluidigm), these tools are generalizable to other multi-parametric measures over large numbers of events.Comment: 9 pages, 5 figure

Detailed Chemical Abundances in the r-Process-Rich Ultra-Faint Dwarf Galaxy Reticulum 2

The ultra-faint dwarf galaxy Reticulum 2 (Ret 2) was recently discovered in images obtained by the Dark Energy Survey. We have observed the four brightest red giants in Ret 2 at high spectral resolution using the Michigan/Magellan Fiber System. We present detailed abundances for as many as 20 elements per star, including 12 elements heavier than the Fe group. We confirm previous detection of high levels of r-process material in Ret 2 (mean [Eu/Fe]=+1.69+/-0.05) found in three of these stars (mean [Fe/H]=-2.88+/-0.10). The abundances closely match the r-process pattern found in the well-studied metal-poor halo star CS22892-052. Such r-process-enhanced stars have not been found in any other ultra-faint dwarf galaxy, though their existence has been predicted by at least one model. The fourth star in Ret 2 ([Fe/H]=-3.42+/-0.20) contains only trace amounts of Sr ([Sr/Fe]=-1.73+/-0.43) and no detectable heavier elements. One r-process enhanced star is also enhanced in C (natal [C/Fe]=+1.1). This is only the third such star known, which suggests that the nucleosynthesis sites leading to C and r-process enhancements are decoupled. The r-process-deficient star is enhanced in Mg ([Mg/Fe]=+0.81+/-0.14), and the other three stars show normal levels of alpha-enhancement (mean [Mg/Fe]=+0.34+/-0.03). The abundances of other alpha and Fe-group elements closely resemble those in ultra-faint dwarf galaxies and metal-poor halo stars, suggesting that the nucleosynthesis that led to the large r-process enhancements either produced no light elements or produced light-element abundance signatures indistinguishable from normal supernovae.Comment: Accepted for publication in the Astronomical Journal. 12 pages, 6 figures, 8 table

Superior T memory stem cell persistence supports long-lived T cell memory

Long-lived memory T cells are able to persist in the host in the absence of antigen; however, the mechanism by which they are maintained is not well understood. Recently, a subset of human T cells, stem cell memory T cells (TSCM cells), was shown to be self-renewing and multipotent, thereby providing a potential reservoir for T cell memory throughout life. However, their in vivo dynamics and homeostasis still remain to be defined due to the lack of suitable animal models. We identified T cells with a TSCM phenotype and stem cell–like properties in nonhuman primates. These cells were the least-differentiated memory subset, were functionally distinct from conventional memory cells, and served as precursors of central memory. Antigen-specific TSCM cells preferentially localized to LNs and were virtually absent from mucosal surfaces. They were generated in the acute phase of viral infection, preferentially survived in comparison with all other memory cells following elimination of antigen, and stably persisted for the long term. Thus, one mechanism for maintenance of long-term T cell memory derives from the unique homeostatic properties of TSCM cells. Vaccination strategies designed to elicit durable cellular immunity should target the generation of TSCM cells

Identification of human viral protein-derived ligands recognized by individual MHCI-restricted T-cell receptors

Evidence indicates that autoimmunity can be triggered by virus-specific CD8+ T cells that crossreact with self-derived peptide epitopes presented on the cell surface by major histocompatibility complex class I (MHCI) molecules. Identification of the associated viral pathogens is challenging because individual T-cell receptors can potentially recognize up to a million different peptides. Here, we generate peptide length-matched combinatorial peptide library (CPL) scan data for a panel of virus-specific CD8+ T-cell clones spanning different restriction elements and a range of epitope lengths. CPL scan data drove a protein database search limited to viruses that infect humans. Peptide sequences were ranked in order of likelihood of recognition. For all anti-viral CD8+ T-cell clones examined in this study, the index peptide was either the top-ranked sequence or ranked as one of the most likely sequences to be recognized. Thus, we demonstrate that anti-viral CD8+ T-cell clones are highly focused on their index peptide sequence and that ‘CPL-driven database searching’ can be used to identify the inciting virus-derived epitope for a given CD8+ T-cell clone. Moreover, to augment access to CPL-driven database searching, we have created a publicly accessible webtool. Application of these methodologies in the clinical setting may clarify the role of viral pathogens in the etiology of autoimmune diseases

Alpha and lambda interferon together mediate suppression of CD4 T cells induced by respiratory syncytial virus

The mechanism by which respiratory syncytial virus (RSV) suppresses T-cell proliferation to itself and other antigens is poorly understood. We used monocyte-derived dendritic cells (MDDC) and CD4 T cells and measured [(3)H]thymidine incorporation to determine the factors responsible for RSV-induced T-cell suppression. These two cell types were sufficient for RSV-induced suppression of T-cell proliferation in response to cytomegalovirus or Staphylococcus enterotoxin B. Suppressive activity was transferable with supernatants from RSV-infected MDDC and was not due to transfer of live virus or RSV F (fusion) protein. Supernatants from RSV-infected MDDC, but not MDDC exposed to UV-killed RSV or mock conditions, contained alpha interferon (IFN-alpha; median, 43 pg/ml) and IFN-lambda (approximately 1 to 20 ng/ml). Neutralization of IFN-alpha with monoclonal antibody (MAb) against one of its receptor chains, IFNAR2, or of IFN-lambda with MAb against either of its receptor chains, IFN-lambdaR1 (interleukin 28R [IL-28R]) or IL-10R2, had a modest effect. In contrast, blocking the two receptors together markedly reduced or completely blocked the RSV-induced suppression of CD4 T-cell proliferation. Defining the mechanism of RSV-induced suppression may guide vaccine design and provide insight into previously uncharacterized human T-cell responses and activities of interferons

Identification, isolation and in vitro expansion of human and nonhuman primate T stem cell memory cell

The T cell compartment is phenotypically and functionally heterogeneous; subsets of naive and memory cells have different functional properties, and also differ with respect to homeostatic potential and the ability to persist in vivo. Human stem cell memory T (TSCM) cells, which possess superior immune reconstitution and antitumor response capabilities, can be identified by polychromatic flow cytometry on the basis of the simultaneous expression of several naive markers together with the memory marker CD95. We describe here a protocol based on the minimum set of markers required for optimal identification of human and nonhuman primate (NHP) TSCM cells with commonly available flow cytometers. By using flow sorters, TSCM cells can thereby be isolated efficiently at high yield and purity. With the use of the 5.5-h isolation procedure, depending on the number of cells needed, the sorting procedure can last for 2-15 h. We also indicate multiple strategies for their efficient expansion in vitro at consistent numbers for functional characterization or adoptive transfer experiments

The Simian Immunodeficiency Virus Targets Central Cell Cycle Functions through Transcriptional Repression In vivo

A massive and selective loss of CD4+ memory T cells occurs during the acute phase of immunodeficiency virus infections. The mechanism of this depletion is poorly understood but constitutes a key event with implications for progression. We assessed gene expression of purified T cells in Rhesus Macaques during acute SIVmac239 infection in order to define mechanisms of pathogenesis. We observe a general transcriptional program of over 1,600 interferon-stimulated genes induced in all T cells by the infection. Furthermore, we identify 113 transcriptional changes that are specific to virally infected cells. A striking downregulation of several key cell cycle regulator genes was observed and shared promotor-region E2F binding sites in downregulated genes suggested a targeted transcriptional control of an E2F regulated cell cycle program. In addition, the upregulation of the gene for the fundamental regulator of RNA polymerase II, TAF7, demonstrates that viral interference with the cell cycle and transcriptional regulation programs may be critical components during the establishment of a pathogenic infection in vivo