| 1. |
- Cho, Nam-Hyuk, et al.
(författare)
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The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:19, s. 7981-7986
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Tidskriftsartikel (refereegranskat)abstract
- Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi (previously called Rickettsia tsutsugamushi). The bacterium is maternally inherited in trombicuid mites and transmitted to humans by feeding larvae. We report here the 2,127,051-bp genome of the Boryong strain, which represents the most highly repeated bacterial genome sequenced to date. The repeat density of the scrub typhus pathogen is 200-fold higher than that of its close relative Rickettsia prowazekii, the agent of epidemic typhus. A total of 359 tra genes for components of conjugative type IV secretion systems were identified at 79 sites in the genome. Associated with these are >200 genes for signaling and host–cell interaction proteins, such as histidine kinases, ankyrin-repeat proteins, and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi genome contains >400 transposases, 60 phage integrases, and 70 reverse transcriptases. Deletions and rearrangements have yielded unique gene combinations as well as frequent pseudogenization in the tra clusters. A comparative analysis of the tra clusters within the genome and across strains indicates sequence homogenization by gene conversion, whereas complexity, diversity, and pseudogenization are acquired by duplications, deletions, and transposon integrations into the amplified segments. The results suggest intragenomic duplications or multiple integrations of a massively proliferating conjugative transfer system. Diversifying selection on host–cell interaction genes along with repeated population bottlenecks may drive rare genome variants to fixation, thereby short-circuiting selection for low complexity in bacterial genomes.
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| 2. |
- Kim, Kwangwoo, et al.
(författare)
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High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci
- 2015
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 74:3
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Tidskriftsartikel (refereegranskat)abstract
- Objective A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data. Methods We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45 790 European case-control samples. Results We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5x10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs. Conclusions This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases.
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| 3. |
- Tung, Cao, et al.
(författare)
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Capture of iodine and organic iodides using silica zeolites and the semiconductor behaviour of iodine in a silica zeolite
- 2016
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Ingår i: Energy & Environmental Science. - : Royal Society of Chemistry (RSC). - 1754-5692 .- 1754-5706. ; 9:3, s. 1050-1062
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Tidskriftsartikel (refereegranskat)abstract
- During the reprocessing of spent nuclear fuel rods, a highly moist off-gas mixture containing various volatile radioactive species, such as iodine (I-2), organic iodides and nitric acid, is produced. Efforts have been made to devise materials, which can effectively capture radioactive iodine (I-2) and organic iodides from the off-gas mixture without being damaged by moisture, nitric acid, and I-2. In the investigation described herein, we observed that all-silica zeolites, such as silicalite-1 and Si-BEA, are stable in 5 M nitric acid and adsorb I-2, CH3I, and CH3CH2I from highly acidic off-gas mixture to much greater extents than activated carbon does. In particular, the hydrophobicity-intensified silicalite-1 performs best. We further found that I-2 forms a unique semiconducting three-dimensional supramolecular network within the silicalite-1 channels. The conductivity of the fully I-2 loaded silicalite-1 is observed to be ca. 10(4) S m(-1), which is ca. 10(8)-fold higher than that of solid I-2.
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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Alef, Walter, et al.
(författare)
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Geodetic data analysis of VGOS experiments
- 2021
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Ingår i: 2021 34th General Assembly and Scientific Symposium of the International Union of Radio Science, URSI GASS 2021.
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Konferensbidrag (refereegranskat)abstract
- Very Long Baseline Interferometry (VLBI) serves as one of the common geodetic methods to define the global reference frames and monitor Earth's orientation variations. The technical upgrade of the VLBI method known as the VLBI Global Observing System (VGOS) includes a critical re-design of the observed frequencies from the dual band mode (S and X band, i.e. 2 GHz and 8 GHz) to observations in a broadband (2-14 GHz). Since 2019 the first VGOS experiments are available for the geodetic analysis in free access at the International VLBI service for Geodesy and Astrometry (IVS). Also regional-only subnetworks such as European VLBI stations have succeeded already in VGOS mode. Based on these brand-new observations we review the current geodetic data analysis workflow to build a bridge between geodetic observed delays derived from different bands.
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| 6. |
- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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