| 11. |
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| 12. |
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| 13. |
- Kirby, Andrew, et al.
(författare)
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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:3, s. 299-303
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Tidskriftsartikel (refereegranskat)abstract
- Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (similar to 1.5-5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.
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| 14. |
- Nilsson, Christina, et al.
(författare)
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An enzymatic ruler modulates Lewis antigen glycosylation of Helicobacter pylori LPS during persistent infection
- 2006
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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. ; 103:8, s. 2863-2868
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Helicobacter pylori persistently colonizes about half the human population and contributes to the development of peptic ulcer disease and gastric cancer. This organism has evolved means to structurally alter its surface characteristics to evade innate and adaptive immune responses. H. pylori produces LPS O-antigen units that can be posttranslationally fucosylated to generate Lewis antigens, structures also found on human epithelial cells. We demonstrate an extensive diversity of Lewis x and Lewis y expression in LPS O-antigen units, occurring over time and in different regions of the human stomach. Lewis expression patterns were correlated with the on/off status of the three fucosyltransferases (FucT), FutA, FutB, and FutC, which are regulated via slipped-strand mispairing in intragenic polyC tract regions of the corresponding genes. The alpha1,3-FucT, FutA and FutB, each contain a C-terminal heptad repeat region, consisting of a variable number of DD/NLRV/INY tandem repeats. Variations in the number of heptad repeats correlated to the sizes of O-antigen polymers to become decorated by fucose residues. Our data support a molecular ruler mechanism for how H. pylori varies its LPS fucosylation pattern, where one heptad repeat in the enzyme corresponds to one N-acetyl-beta-lactosamine unit in the O-antigen polysaccharide.
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| 15. |
- Nilsson, Hans-Olof, et al.
(författare)
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High prevalence of Helicobacter Species detected in laboratory mouse strains by multiplex PCR-denaturing gradient gel electrophoresis and pyrosequencing.
- 2004
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Ingår i: Journal of Clinical Microbiology. - 1098-660X. ; 42:8, s. 3781-3788
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Tidskriftsartikel (refereegranskat)abstract
- Rodent models have been developed to study the pathogenesis of diseases caused by Helicobacter pylori, as well as by other gastric and intestinal Helicobacter spp., but some murine enteric Helicobacter spp. cause hepatobiliary and intestinal tract diseases in specific inbred strains of laboratory mice. To identify these murine Helicobacter spp., we developed an assay based on PCR-denaturing gradient gel electrophoresis and pyrosequencing. Nine strains of mice, maintained in four conventional laboratory animal houses, were assessed for Helicobacter sp. carriage. Tissue samples from the liver, stomach, and small intestine, as well as feces and blood, were collected; and all specimens (n = 210) were screened by a Helicobacter genus-specific PCR. Positive samples were identified to the species level by multiplex denaturing gradient gel electrophoresis, pyrosequencing, and a H. ganmani-specific PCR assay. Histologic examination of 30 tissue samples from 18 animals was performed. All mice of eight of the nine strains tested were Helicobacter genus positive; H. bilis, H. hepaticus, H. typhlonius, H. ganmani, H. rodentium, and a Helicobacter sp. flexispira-like organism were identified. Helicobacter DNA was common in fecal (86%) and gastric tissue (55%) specimens, whereas samples of liver tissue (21%), small intestine tissue (17%), and blood (14%) were less commonly positive. Several mouse strains were colonized with more than one Helicobacter spp. Most tissue specimens analyzed showed no signs of inflammation; however, in one strain of mice, hepatitis was diagnosed in livers positive for H. hepaticus, and in another strain, gastric colonization by H. typhlonius was associated with gastritis. The diagnostic setup developed was efficient at identifying most murine Helicobacter spp.
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| 16. |
- Taneera, Jalal, et al.
(författare)
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Influence of activated charcoal, porcine gastric mucin and beta-cyclodextrin on the morphology and growth of intestinal and gastric Helicobacter spp.
- 2002
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Ingår i: Microbiology. - 1465-2080. ; 148:3, s. 677-684
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Tidskriftsartikel (refereegranskat)abstract
- Bile-tolerant Helicobacter spp. are emerging human and animal pathogens. However, due to their fastidious nature, which requires nutrient-rich complex media to grow, infection with these bacteria may be underestimated. The accumulation of toxic metabolites in cultures may be one of the main obstacles for successful culture of these organisms. The present study examined various potential growth-enhancing substances for Helicobacter spp. and, furthermore, how they may affect spiral to coccoid conversion. Five Helicobacter spp. were cultured on agar and in broth media supplemented with activated charcoal, beta-cyclodextrin, or porcine gastric mucin. Growth was determined by estimating the numbers of colony-forming units and colony diameter, as well as bacterial cell mass. Coccoid transformation was estimated every 24 h by both Gram and acridine-orange staining. Activated charcoal was superior in supporting growth and increased cell mass on agar and in broth media. beta-Cyclodextrin delayed spiral to coccoid conversion by Helicobacter pylori and Helicobacter canis, whereas activated charcoal delayed the conversion to coccoid forms of Helicobacter hepaticus and Helicobacter bilis. The progression to coccoid forms by Helicobacter pullorum on agar media was not influenced by any growth supplement. The spiral to coccoid conversion was more rapid in broth media than on agar media. The growth enhancement observed is probably related to the capacity of activated charcoal to remove toxic compounds in culture media.
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