222 research outputs found
First case of Chlamydia trachomatis L2b proctitis in a woman
AbstractSince 2003, outbreaks of lymphogranuloma venereum (LGV) have been reported in European countries, North America, and Australia. Current LGV cases have been caused by Chlamydia trachomatis serovar L2. This sexually transmitted infection is predominantly found among men who have sex with men, specifically men who are seropositive for human immunodeficiency virus and have clinical signs of proctitis. The current outbreak has been almost exclusively attributed to a new variant, designated L2b. Although urogenital cases of LGV have been described in the heterosexual population, we report the first case of C. trachomatis L2b proctitis in a woman
Comparison of the properties of two fossil groups of galaxies with the normal group NGC 6034 based on multiband imaging and optical spectroscopy
We collected multiband imaging and spectroscopy for two fossil groups (RX
J1119.7+2126 and 1RXS J235814.4+150524) and one normal group (NGC 6034). We
computed photometric redshifts in the central zones of each group, combining
previous data with the SDSS five-band data. For each group we investigated the
red sequence (RS) of the color-magnitude relation and computed the luminosity
functions, stellar population ages and distributions of the group members.
Spectroscopy allowed us to investigate the large-scale surroundings of these
groups and the substructure levels in 1RXS J235814.4+150524 and NGC 6034. The
large-scale environment of 1RXS J235814.4+150524 is poor, though its galaxy
density map shows a clear signature of the surrounding cosmic web. RX
J1119.7+2126 appears to be very isolated, while the cosmic environment of NGC
6034 is very rich. At the group scale, 1RXS J235814.4+150524 shows no
substructure. Galaxies with recent stellar populations seem preferentially
located in the group outskirts. A RS is discernable for all three groups in a
color-magnitude diagram. The luminosity functions based on photometric redshift
selection and on statistical background subtraction have comparable shapes, and
agree with the few points obtained from spectroscopic redshifts. These
luminosity functions show the expected dip between first and second brightest
galaxies for the fossil groups only. Their shape is also regular and relatively
flat at faint magnitudes down to the completeness level for RX J1119.7+2126 and
NGC 6034, while there is a clear lack of faint galaxies for 1RXS
J235814.4+150524. RX J1119.7+2126 is definitely classified as a fossil group;
1RXS J235814.4+150524 also has properties very close to those of a fossil
group, while we confirm that NGC 6034 is a normal group.Comment: Accepted in A&A, english-improved, 5 jpeg figures, and shortened
abstrac
The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment
The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in
operation since July 2014. This paper describes the second data release from
this phase, and the fourteenth from SDSS overall (making this, Data Release
Fourteen or DR14). This release makes public data taken by SDSS-IV in its first
two years of operation (July 2014-2016). Like all previous SDSS releases, DR14
is cumulative, including the most recent reductions and calibrations of all
data taken by SDSS since the first phase began operations in 2000. New in DR14
is the first public release of data from the extended Baryon Oscillation
Spectroscopic Survey (eBOSS); the first data from the second phase of the
Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2),
including stellar parameter estimates from an innovative data driven machine
learning algorithm known as "The Cannon"; and almost twice as many data cubes
from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous
release (N = 2812 in total). This paper describes the location and format of
the publicly available data from SDSS-IV surveys. We provide references to the
important technical papers describing how these data have been taken (both
targeting and observation details) and processed for scientific use. The SDSS
website (www.sdss.org) has been updated for this release, and provides links to
data downloads, as well as tutorials and examples of data use. SDSS-IV is
planning to continue to collect astronomical data until 2020, and will be
followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14
happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov
2017 (this is the "post-print" and "post-proofs" version; minor corrections
only from v1, and most of errors found in proofs corrected
Distinct Genetic Loci Control Plasma HIV-RNA and Cellular HIV-DNA Levels in HIV-1 Infection: The ANRS Genome Wide Association 01 Study
Previous studies of the HIV-1 disease have shown that HLA and Chemokine receptor genetic variants influence disease progression and early viral load. We performed a Genome Wide Association study in a cohort of 605 HIV-1-infected seroconverters for detection of novel genetic factors that influence plasma HIV-RNA and cellular HIV-DNA levels. Most of the SNPs strongly associated with HIV-RNA levels were localised in the 6p21 major histocompatibility complex (MHC) region and were in the vicinity of class I and III genes. Moreover, protective alleles for four disease-associated SNPs in the MHC locus (rs2395029, rs13199524, rs12198173 and rs3093662) were strikingly over-represented among forty-five Long Term HIV controllers. Furthermore, we show that the HIV-DNA levels (reflecting the HIV reservoir) are associated with the same four SNPs, but also with two additional SNPs on chromosome 17 (rs6503919; intergenic region flanked by the DDX40 and YPEL2 genes) and chromosome 8 (rs2575735; within the Syndecan 2 gene). Our data provide evidence that the MHC controls both HIV replication and HIV reservoir. They also indicate that two additional genomic loci may influence the HIV reservoir
Identification and Structural Characterization of a New Three-Finger Toxin Hemachatoxin from Hemachatus haemachatus Venom
10.1371/journal.pone.0048112PLoS ONE710
Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue
The discovery of expression quantitative trait loci (“eQTLs”) can
help to unravel genetic contributions to complex traits. We identified genetic
determinants of human liver gene expression variation using two independent
collections of primary tissue profiled with Agilent
(n = 206) and Illumina (n = 60)
expression arrays and Illumina SNP genotyping (550K), and we also incorporated
data from a published study (n = 266). We found that
∼30% of SNP-expression correlations in one study failed to replicate
in either of the others, even at thresholds yielding high reproducibility in
simulations, and we quantified numerous factors affecting reproducibility. Our
data suggest that drug exposure, clinical descriptors, and unknown factors
associated with tissue ascertainment and analysis have substantial effects on
gene expression and that controlling for hidden confounding variables
significantly increases replication rate. Furthermore, we found that
reproducible eQTL SNPs were heavily enriched near gene starts and ends, and
subsequently resequenced the promoters and 3′UTRs for 14 genes and tested
the identified haplotypes using luciferase assays. For three genes, significant
haplotype-specific in vitro functional differences correlated
directly with expression levels, suggesting that many bona fide
eQTLs result from functional variants that can be mechanistically isolated in a
high-throughput fashion. Finally, given our study design, we were able to
discover and validate hundreds of liver eQTLs. Many of these relate directly to
complex traits for which liver-specific analyses are likely to be relevant, and
we identified dozens of potential connections with disease-associated loci.
These included previously characterized eQTL contributors to diabetes, drug
response, and lipid levels, and they suggest novel candidates such as a role for
NOD2 expression in leprosy risk and
C2orf43 in prostate cancer. In general, the work presented
here will be valuable for future efforts to precisely identify and functionally
characterize genetic contributions to a variety of complex traits
Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages
Background: HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. Methodology/Principal Findings: Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16×10-5). While the association was not genome-wide significant (p<1×10-7), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84×10-6). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). Conclusions/Significance: These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo. © 2011 Bol et al
Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus
The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed
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