94 research outputs found
The Chandra Source Catalog
The Chandra Source Catalog (CSC) is a general purpose virtual X-ray
astrophysics facility that provides access to a carefully selected set of
generally useful quantities for individual X-ray sources, and is designed to
satisfy the needs of a broad-based group of scientists, including those who may
be less familiar with astronomical data analysis in the X-ray regime. The first
release of the CSC includes information about 94,676 distinct X-ray sources
detected in a subset of public ACIS imaging observations from roughly the first
eight years of the Chandra mission. This release of the catalog includes point
and compact sources with observed spatial extents <~ 30''. The catalog (1)
provides access to the best estimates of the X-ray source properties for
detected sources, with good scientific fidelity, and directly supports
scientific analysis using the individual source data; (2) facilitates analysis
of a wide range of statistical properties for classes of X-ray sources; and (3)
provides efficient access to calibrated observational data and ancillary data
products for individual X-ray sources, so that users can perform detailed
further analysis using existing tools. The catalog includes real X-ray sources
detected with flux estimates that are at least 3 times their estimated 1 sigma
uncertainties in at least one energy band, while maintaining the number of
spurious sources at a level of <~ 1 false source per field for a 100 ks
observation. For each detected source, the CSC provides commonly tabulated
quantities, including source position, extent, multi-band fluxes, hardness
ratios, and variability statistics, derived from the observations in which the
source is detected. In addition to these traditional catalog elements, for each
X-ray source the CSC includes an extensive set of file-based data products that
can be manipulated interactively.Comment: To appear in The Astrophysical Journal Supplement Series, 53 pages,
27 figure
Statistical Characterization of the Chandra Source Catalog
The first release of the Chandra Source Catalog (CSC) contains ~95,000 X-ray
sources in a total area of ~0.75% of the entire sky, using data from ~3,900
separate ACIS observations of a multitude of different types of X-ray sources.
In order to maximize the scientific benefit of such a large, heterogeneous
data-set, careful characterization of the statistical properties of the
catalog, i.e., completeness, sensitivity, false source rate, and accuracy of
source properties, is required. Characterization efforts of other, large
Chandra catalogs, such as the ChaMP Point Source Catalog (Kim et al. 2007) or
the 2 Mega-second Deep Field Surveys (Alexander et al. 2003), while
informative, cannot serve this purpose, since the CSC analysis procedures are
significantly different and the range of allowable data is much less
restrictive. We describe here the characterization process for the CSC. This
process includes both a comparison of real CSC results with those of other,
deeper Chandra catalogs of the same targets and extensive simulations of
blank-sky and point source populations.Comment: To be published in the Astrophysical Journal Supplement Series (Fig.
52 replaced with a version which astro-ph can convert to PDF without issues.
Murid herpesvirus-4 lacking thymidine kinase reveals route-dependent requirements for host colonization
Gammaherpesviruses infect at least 90 % of the world's population. Infection control is difficult, in part because some fundamental features of host colonization remain unknown, for example whether normal latency establishment requires viral lytic functions. Since human gammaherpesviruses have narrow species tropisms, answering such questions requires animal models. Murid herpesvirus-4 (MuHV-4) provides one of the most tractable. MuHV-4 genomes delivered to the lung or peritoneum persist without lytic replication. However, they fail to disseminate systemically, suggesting that the outcome is inoculation route-dependent. After upper respiratory tract inoculation, MuHV-4 infects mice without involving the lungs or peritoneum. We examined whether host entry by this less invasive route requires the viral thymidine kinase (TK), a gene classically essential for lytic replication in terminally differentiated cells. MuHV-4 TK knockouts delivered to the lung or peritoneum were attenuated but still reached lymphoid tissue. In contrast, TK knockouts delivered to the upper respiratory tract largely failed to establish a detectable infection. Therefore TK, and by implication lytic replication, is required for MuHV-4 to establish a significant infection by a non-invasive route
Involvement of a specificity proteins-binding element in regulation of basal and estrogen-induced transcription activity of the BRCA1 gene
INTRODUCTION:Increased estrogen level has been regarded to be a risk factor for breast cancer. However, estrogen has also been shown to induce the expression of the tumor suppressor gene, BRCA1. Upregulation of BRCA1 is thought to be a feedback mechanism for controlling DNA repair in proliferating cells. Estrogens enhance transcription of target genes by stimulating the association of the estrogen receptor (ER) and related coactivators to estrogen response elements or to transcription complexes formed at activator protein (AP)-1 or specificity protein (Sp)-binding sites. Interestingly, the BRCA1 gene lacks a consensus estrogen response element. We previously reported that estrogen stimulated BRCA1 transcription through the recruitment of a p300/ER-alpha complex to an AP-1 site harbored in the proximal BRCA1 promoter. The purpose of the study was to analyze the contribution of cis-acting sites flanking the AP-1 element to basal and estrogen-dependent regulation of BRCA1 transcription.METHODS:Using transfection studies with wild-type and mutated BRCA1 promoter constructs, electromobility binding and shift assays, and DNA-protein interaction and chromatin immunoprecipitation assays, we investigated the role of Sp-binding sites and cAMP response element (CRE)-binding sites harbored in the proximal BRCA1 promoter.RESULTS:We report that in the BRCA1 promoter the AP-1 site is flanked upstream by an element (5'-GGGGCGGAA-3') that recruits Sp1, Sp3, and Sp4 factors, and downstream by a half CRE-binding motif (5'-CGTAA-3') that binds CRE-binding protein. In ER-alpha-positive MCF-7 cells and ER-alpha-negative Hela cells expressing exogenous ER-alpha, mutation of the Sp-binding site interfered with basal and estrogen-induced BRCA1 transcription. Conversely, mutation of the CRE-binding element reduced basal BRCA1 promoter activity but did not prevent estrogen activation. In combination with the AP-1/CRE sites, the Sp-binding domain enhanced the recruitment of nuclear proteins to the BRCA1 promoter. Finally, we report that the MEK1 (mitogen-activated protein kinase kinase-1) inhibitor PD98059 attenuated the recruitment of Sp1 and phosphorylated ER-alpha, respectively, to the Sp and AP-1 binding element.CONCLUSION:These cumulative findings suggest that the proximal BRCA1 promoter segment comprises cis-acting elements that are targeted by Sp-binding and CRE-binding proteins that contribute to regulation of BRCA1 transcription.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]
The Death Effector Domains of Caspase-8 Induce Terminal Differentiation
The differentiation and senescence programs of metazoans play key roles in regulating normal development and preventing aberrant cell proliferation, such as cancer. These programs are intimately associated with both the mitotic and apoptotic pathways. Caspase-8 is an apical apoptotic initiator that has recently been appreciated to coordinate non-apoptotic roles in the cell. Most of these functions are attributed to the catalytic domain, however, the amino-terminal death effector domains (DED)s, which belong to the death domain superfamily of proteins, can also play key roles during development. Here we describe a novel role for caspase-8 DEDs in regulating cell differentiation and senescence. Caspase-8 DEDs accumulate during terminal differentiation and senescence of epithelial, endothelial and myeloid cells; genetic deletion or shRNA suppression of caspase-8 disrupts cell differentiation, while re-expression of DEDs rescues this phenotype. Among caspase-8 deficient neuroblastoma cells, DED expression attenuated tumor growth in vivo and proliferation in vitro via disruption of mitosis and cytokinesis, resulting in upregulation of p53 and induction of differentiation markers. These events occur independent of caspase-8 catalytic activity, but require a critical lysine (K156) in a microtubule-binding motif in the second DED domain. The results demonstrate a new function for the DEDs of caspase-8, and describe an unexpected mechanism that contributes to cell differentiation and senescence
Murid Herpesvirus-4 Exploits Dendritic Cells to Infect B Cells
Dendritic cells (DCs) play a central role in initiating immune responses. Some persistent viruses infect DCs and can disrupt their functions in vitro. However, these viruses remain strongly immunogenic in vivo. Thus what role DC infection plays in the pathogenesis of persistent infections is unclear. Here we show that a persistent, B cell-tropic gamma-herpesvirus, Murid Herpesvirus-4 (MuHV-4), infects DCs early after host entry, before it establishes a substantial infection of B cells. DC-specific virus marking by cre-lox recombination revealed that a significant fraction of the virus latent in B cells had passed through a DC, and a virus attenuated for replication in DCs was impaired in B cell colonization. In vitro MuHV-4 dramatically altered the DC cytoskeleton, suggesting that it manipulates DC migration and shape in order to spread. MuHV-4 therefore uses DCs to colonize B cells
The Physics of the B Factories
This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C
Mutational analysis of the β-subunit of yeast geranylgeranyl transferase I
The gene CAL1 (also known as CDC43 ) of Saccharomyces cerevisiae encodes the β subunit of geranylgeranyl transferase I (GGTase I), which modifies several small GTPases. Biochemical analyses of the mutant-enzymes encoded by cal1 , and cdc43-2 to cdc43-7 , expressed in bacteria, have hown that all of the mutant enzymes possess reduced activity, and that none shows temerature-sensitive enzymatic activities. Nonetheless, all of the cal1/cdc43 mutants show temperature-sensitive growth phenotypes. Increase in soluble pools of the small GTPases was observed in the yeast mutant cells at the restrictive temperature in vivo, suggesting that the yeast prenylation pathway itself is temperative sensitive. The cal-1 mutation, located most proximal to the C-terminus of the protein, differs from the other cdc43 mutations in several respects. An increase in soluble Rholp was observed in the cal-1 strain grown at the restrictive temperature. The temperature-sensitive phenotype of cal-1 is most efficiently suppressed by overproduction of Rholp. Overproduction of the other essential target, Cdc42p, in contrast, is deleterious in cal-1 cells, but not in other cdc43 mutants or the wild-type strains. The cdc43-5 mutant cells accumulate Cdc42p in soluble pools and cdc43-5 is suppressed by overproduction of Cdc42p. Thus, several phenotypic differences are observed among the cal1/cdc43 mutations, possibly due to alterations in substrate specificity caused by the mutations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42258/1/438-252-1-2-1_62520001.pd
Developmental roadmap for antimicrobial susceptibility testing systems
Antimicrobial susceptibility testing (AST) technologies help to accelerate the initiation of targeted antimicrobial therapy for patients with infections and could potentially extend the lifespan of current narrow-spectrum antimicrobials. Although conceptually new and rapid AST technologies have been described, including new phenotyping methods, digital imaging and genomic approaches, there is no single major, or broadly accepted, technological breakthrough that leads the field of rapid AST platform development. This might be owing to several barriers that prevent the timely development and implementation of novel and rapid AST platforms in health-care settings. In this Consensus Statement, we explore such barriers, which include the utility of new methods, the complex process of validating new technology against reference methods beyond the proof-of-concept phase, the legal and regulatory landscapes, costs, the uptake of new tools, reagent stability, optimization of target product profiles, difficulties conducting clinical trials and issues relating to quality and quality control, and present possible solutions
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