Podcasts about genomic dna

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.29.534749v1?rss=1 Authors: van Soest, D. M. K., Polderman, P. E., den Toom, W. T., Zwakenberg, S., De Henau, S., Burgering, B. M. T., Dansen, T. B. Abstract: Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of genomic DNA damage and subsequent mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondrial can directly damage nuclear DNA under (patho)physiological conditions has been largely lacking. In this study we modeled the effects of mitochondrial H2O2 release and compared this to H2O2 production at the nucleosomes in an untransformed human cell line. We used a chemogenetic approach to produce localized H2O2 and combined it with a new method we developed to directly quantify the amount of H2O2 produced. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2 generation. Nuclear H2O2 production gives rise to DNA strand breaks, subsequent activation of the DNA damage response, cell cycle arrest and eventually senescence. Release of H2O2 from mitochondria on the other hand shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. Artificially high levels of mitochondrial H2O2 release do result in DNA strand breaks, but in parallel invariably cause ferroptosis-mediated cell death, preventing propagation of DNA damage-induced mutations. This study shows that H2O2 released from mitochondria is unlikely to directly damage genomic DNA, limiting its contribution to oncogenic transformation and aging. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Neste programa vamos entender como a genética traz heranças dos antepassados e como podem ter influência nos dias de hoje. Vem participar dessa sessão de fofocas históricas! ARTE DA VITRINE: Randall Random GENERA Confira o Blog Genera: https://jovemnerd.page.link/Genera-descubra-ou-nao-o-samurai-dentro-de-voce https://jovemnerd.page.link/Genera-arqueologos-e-geneticistas-presenca-viking-na-inglaterra SAIBA MAIS GOUT: A Disease of Kings – Karger Genomica dos Vikins - Population genomics of the Viking world Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes Lessons From History  Royal blood: Queen Victoria and the legacy of hemophilia in European royalty Bubonic plague had long-term effect on human immunity, study suggests OUÇA TAMBÉM Playlist do GeneraCast: https://bit.ly/3H7rEnn Playlist do GeneraCast no Spotify: https://spoti.fi/3LPxmxS GeneraCast 10 - Genes, cheiros e encontros E-MAILS Mande suas críticas, elogios, sugestões e caneladas para nerdcast@jovemnerd.com.br EDIÇÃO COMPLETA POR RADIOFOBIA PODCAST E MULTIMÍDIA http://radiofobia.com.br

Neste programa vamos entender como a genética traz heranças dos antepassados e como podem ter influência nos dias de hoje. Vem participar dessa sessão de fofocas históricas! ARTE DA VITRINE: Randall Random GENERA Confira o Blog Genera: https://jovemnerd.page.link/Genera-descubra-ou-nao-o-samurai-dentro-de-voce https://jovemnerd.page.link/Genera-arqueologos-e-geneticistas-presenca-viking-na-inglaterra SAIBA MAIS GOUT: A Disease of Kings – Karger Genomica dos Vikins - Population genomics of the Viking world Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes Lessons From History  Royal blood: Queen Victoria and the legacy of hemophilia in European royalty Bubonic plague had long-term effect on human immunity, study suggests OUÇA TAMBÉM Playlist do GeneraCast: https://bit.ly/3H7rEnn Playlist do GeneraCast no Spotify: https://spoti.fi/3LPxmxS GeneraCast 10 - Genes, cheiros e encontros E-MAILS Mande suas críticas, elogios, sugestões e caneladas para nerdcast@jovemnerd.com.br EDIÇÃO COMPLETA POR RADIOFOBIA PODCAST E MULTIMÍDIA http://radiofobia.com.br

Neste programa vamos entender como a genética traz heranças dos antepassados e como podem ter influência nos dias de hoje. Vem participar dessa sessão de fofocas históricas! ARTE DA VITRINE: Randall Random GENERA Confira o Blog Genera: https://jovemnerd.page.link/Genera-descubra-ou-nao-o-samurai-dentro-de-voce https://jovemnerd.page.link/Genera-arqueologos-e-geneticistas-presenca-viking-na-inglaterra SAIBA MAIS GOUT: A Disease of Kings – Karger Genomica dos Vikins - Population genomics of the Viking world Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes Lessons From History  Royal blood: Queen Victoria and the legacy of hemophilia in European royalty Bubonic plague had long-term effect on human immunity, study suggests OUÇA TAMBÉM Playlist do GeneraCast: https://bit.ly/3H7rEnn Playlist do GeneraCast no Spotify: https://spoti.fi/3LPxmxS GeneraCast 10 - Genes, cheiros e encontros E-MAILS Mande suas críticas, elogios, sugestões e caneladas para nerdcast@jovemnerd.com.br EDIÇÃO COMPLETA POR RADIOFOBIA PODCAST E MULTIMÍDIA http://radiofobia.com.br

Die beiden wichtigsten Regeln für einen Podcast sind wohl Erstens: einfach machen, und Zweitens: durchhalten. Da wir selbst nicht so ganz fassen können, dass wir uns mit biophon bereits ein ganzes Jahr an diese Regeln halten, feiern wir diesen Umstand gemeinsam mit unserem Geburtstag und dem Jahreswechsel in einer experimentellen Sonderfolge. Und die ist antizyklisch, uncut, persönlich, perspektivisch, retrospektiv, und natürlich wissenschaftlich. Wir schauen auf das Jahr zurück, geben Einblicke in unseren Arbeitsprozess und nehmen uns an einem eigentlich folgenlosen Freitag ganz viele folgenreiche Dinge vor. Nachdem wir in der ersten Hälfte also unterm Strich ganz viel Quatsch machen, gibt es in der zweiten Hälfte auch noch Biologie. Anders als sonst müssen wir dabei diesmal beide arbeiten und konfrontieren uns abwechselnd mit Aussagen, die entweder in die Kategorie "Biologie" oder "Quatsch" einzusortieren sind. Ausladende Erklärungen gehören dabei genauso dazu wie dumme Wortwitze, und dazu könnte man nach einem Jahr biophon durchaus sagen: alles wie immer.  LiebhaberInnen von Laber- und Faktenpodcasts, vereinigt euch (oder hört euch nur den wissenschaftlichen Teil an - schaut in die Kapitelmarken!) und feiert mit uns den Jahreswechsel in der Gewissheit, dass ihr, liebe Hörerinnen und Hörer, das Beste seid, was diesem Podcast je passiert ist. QuellenMilben im Gesicht, Bakterien im Darm:Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS biology, https://doi.org/10.1371/journal.pbio.1002533Verwandtschaftsverhältnisse:Rohland, N. et al. (2010). Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS biology, https://doi.org/10.1371/journal.pbio.1000564Meyer, M. et al. (2017). Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. Elife, https://doi.org/10.7554/eLife.25413Trauernde Elefanten:Goldenberg, S. Z., & Wittemyer, G. (2020). Elephant behavior toward the dead: A review and insights from field observations. Primates, https://doi.org/10.1007/s10329-019-00766-5Gesichtsbremse:Beseris, E. A., Naleway, S. E., & Carrier, D. R. (2020). Impact protection potential of mammalian hair: Testing the pugilism hypothesis for the evolution of human facial hair. Integrative Organismal Biology, https://doi.org/10.1093/iob/obaa005Arthropoden zum Abendbrot:https://www.scientificamerican.com/article/fact-or-fiction-people-swallow-8-spiders-a-year-while-they-sleep1/Erbliche Vorlieben:Callaway, E. (2012). Soapy taste of coriander linked to genetic variants. Nature News. https://doi.org/10.1038/nature.2012.11398Eriksson, N. et al. (2012). A genetic variant near olfactory receptor genes influences cilantro preference. Flavour, https://doi.org/10.1186/2044-7248-1-22

All too often, genomic testing in patients with undiagnosed disorders results in the finding of variants of unknown significance (VUS). This leaves the health-care provider and patient in a quandary, not knowing whether that variant is disease causing or not. On this month’s GenePod, Bekim Sadikovic, PhD, director of the Clinical Genomic Center and head of the molecular diagnostics program at Canada’s Western University, discusses the implementation of genomic DNA methylation testing in patients with rare disorders – a diagnostic tool that may help sort out the impact of VUS by identifying the signals of DNA methylation. See acast.com/privacy for privacy and opt-out information.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.27.267153v1?rss=1 Authors: Gombolay, A., Storici, F. Abstract: Ribose-Map is a user-friendly, standardized bioinformatics toolkit for the comprehensive analysis of ribonucleotide sequencing experiments. It allows researchers to map the locations of ribonucleotides in DNA to single-nucleotide resolution and identify biological signatures of ribonucleotide incorporation. In addition, it can be applied to data generated using any currently available high-throughput ribonucleotide sequencing technique, thus standardizing the analysis of ribonucleotide sequencing experiments and allowing direct comparisons of results. This protocol describes in detail how to use Ribose-Map to analyze raw ribonucleotide sequencing data, including preparing the reads for analysis, locating the genomic coordinates of ribonucleotides, exploring the genome-wide distribution of ribonucleotides, determining the nucleotide sequence context of ribonucleotides, and identifying hotspots of ribonucleotide incorporation. Ribose-Map does not require background knowledge of ribonucleotide sequencing analysis and assumes only basic command-line skills. The protocol requires less than 3 hr of computing time for most datasets and about 30 min of hands-on time. Copy rights belong to original authors. Visit the link for more info

Your DNA can help identify many underlying issues that may need to be addressed to help you achieve optimal health. In this episode, Dr. Mercola interviews Bob Miller who explains many pathways, enzymes and health issues that your DNA can affect, and also talk about how this information can be used to help you feel better. Feel free to contact me at gary@naturalcompounder.com or 781-893-3870 x111 if you would like more information about how Genomic DNA testing may help you.

Genome-wide association studies identified the autophagy gene IRGM to be strongly associated with Crohn's disease (CD) but its impact in ulcerative colitis (UC), its phenotypic effects and potential epistatic interactions with other IBD susceptibility genes are less clear which we therefore analyzed in this study. Genomic DNA from 2060 individuals including 817 CD patients, 283 UC patients, and 961 healthy, unrelated controls (all of Caucasian origin) was analyzed for six IRGM single nucleotide polymorphisms (SNPs) (rs13371189, rs10065172 = p.Leu105Leu, rs4958847, rs1000113, rs11747270, rs931058). In all patients, a detailed genotype-phenotype analysis and testing for epistasis with the three major CD susceptibility genes NOD2, IL23R and ATG16L1 were performed. Our analysis revealed an association of the IRGM SNPs rs13371189 (p = 0.02, OR 1.31 [95% CI 1.05-1.65]), rs10065172 = p.Leu105Leu (p = 0.016, OR 1.33 [95% CI 1.06-1.66]) and rs1000113 (p = 0.047, OR 1.27 [95% CI 1.01-1.61]) with CD susceptibility. There was linkage disequilibrium between these three IRGM SNPs. In UC, several IRGM haplotypes were weakly associated with UC susceptibility (p

Genome-wide association studies identified PTPN2 (protein tyrosine phosphatase, non-receptor type 2) as susceptibility gene for inflammatory bowel diseases (IBD). However, the exact role of PTPN2 in Crohn's disease (CD) and ulcerative colitis (UC) and its phenotypic effect are unclear. We therefore performed a detailed genotype-phenotype and epistasis analysis of PTPN2 gene variants. Genomic DNA from 2131 individuals of Caucasian origin (905 patients with CD, 318 patients with UC, and 908 healthy, unrelated controls) was analyzed for two SNPs in the PTPN2 region (rs2542151, rs7234029) for which associations with IBD were found in previous studies in other cohorts. Our analysis revealed a significant association of PTPN2 SNP rs2542151 with both susceptibility to CD (p = 1.95×10⁻⁵; OR 1.49 [1.34-1.79]) and UC (p = 3.87×10⁻², OR 1.31 [1.02-1.68]). Moreover, PTPN2 SNP rs7234029 demonstrated a significant association with susceptibility to CD (p = 1.30×10⁻³; OR 1.35 [1.13-1.62]) and a trend towards association with UC (p = 7.53×10⁻²; OR 1.26 [0.98-1.62]). Genotype-phenotype analysis revealed an association of PTPN2 SNP rs7234029 with a stricturing disease phenotype (B2) in CD patients (p = 6.62×10⁻³). Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and PTPN2 SNP rs2542151 (p = 0.024) in CD and between ATG16L1 SNP rs4663396 and PTPN2 SNP rs7234029 (p = 4.68×10⁻³) in UC. There was no evidence of epistasis between PTPN2 and NOD2 and PTPN2 and IL23R. In silico analysis revealed that the SNP rs7234029 modulates potentially the binding sites of several transcription factors involved in inflammation including GATA-3, NF-κB, C/EBP, and E4BP4. Our data confirm the association of PTPN2 variants with susceptibility to both CD and UC, suggesting a common disease pathomechanism for these diseases. Given recent evidence that PTPN2 regulates autophagosome formation in intestinal epithelial cells, the potential link between PTPN2 and ATG16L1 should be further investigated.

Osteopontin represents a multifunctional molecule playing a pivotal role in chronic inflammatory and autoimmune diseases. Its expression is increased in inflammatory bowel disease (IBD). The aim of our study was to analyze the association of osteopontin (OPN/SPP1) gene variants in a large cohort of IBD patients. Genomic DNA from 2819 Caucasian individuals (n = 841 patients with Crohn's disease (CD), n = 473 patients with ulcerative colitis (UC), and n = 1505 healthy unrelated controls) was analyzed for nine OPN SNPs (rs2728127, rs2853744, rs11730582, rs11739060, rs28357094, rs4754 = p.Asp80Asp, rs1126616 = p.Ala236Ala, rs1126772 and rs9138). Considering the important role of osteopontin in Th17-mediated diseases, we performed analysis for epistasis with IBD-associated IL23R variants and analyzed serum levels of the Th17 cytokine IL-22. For four OPN SNPs (rs4754, rs1126616, rs1126772 and rs9138), we observed significantly different distributions between male and female CD patients. rs4754 was protective in male CD patients (p = 0.0004, OR = 0.69). None of the other investigated OPN SNPs was associated with CD or UC susceptibility. However, several OPN haplotypes showed significant associations with CD susceptibility. The strongest association was found for a haplotype consisting of the 8 OPN SNPs rs2728127-rs2853744-rs11730582-rs11439060-rs28357094-rs112661-rs1126772-rs9138 (omnibus p-value = 2.07×10⁻⁸). Overall, the mean IL-22 secretion in the combined group of OPN minor allele carriers with CD was significantly lower than that of CD patients with OPN wildtype alleles (p = 3.66×10⁻⁵). There was evidence for weak epistasis between the OPN SNP rs28357094 with the IL23R SNP rs10489629 (p = 4.18×10⁻²) and between OPN SNP rs1126616 and IL23R SNP rs2201841 (p = 4.18×10⁻²) but none of these associations remained significant after Bonferroni correction. Our study identified OPN haplotypes as modifiers of CD susceptibility, while the combined effects of certain OPN variants may modulate IL-22 secretion.

Recent evidence suggests a crucial role of the endocannabinoid system, including the cannabinoid 1 receptor (CNR1), in intestinal inflammation. We therefore investigated the influence of the CNR1 1359 G/A (p.Thr453Thr; rs1049353) single nucleotide polymorphism (SNP) on disease susceptibility and phenotype in patients with ulcerative colitis (UC) and Crohn's disease (CD). Genomic DNA from 579 phenotypically well-characterized individuals was analyzed for the CNR1 1359 G/A SNP. Amongst these were 166 patients with UC, 216 patients with CD, and 197 healthy controls. Compared to healthy controls, subjects A/A homozygous for the CNR1 1359 G/A SNP had a reduced risk to develop UC (p = 0.01, OR 0.30, 95% CI 0.12-0.78). The polymorphism did not modulate CD susceptibility, but carriers of the minor A allele had a lower body mass index than G/G wildtype carriers (p = 0.0005). In addition, homozygous carriers of the G allele were more likely to develop CD before 40 years of age (p = 5.9x10(-7)) than carriers of the A allele. The CNR1 p.Thr453Thr polymorphism appears to modulate UC susceptibility and the CD phenotype. The endocannabinoid system may influence the manifestation of inflammatory bowel diseases, suggesting endocannabinoids as potential target for future therapies.

Background: The aims were to analyze two novel NOD2 variants (rs2066843 and rs2076756) in a large cohort of patients with inflammatory bowel disease and to elucidate phenotypic consequences. Methodology/Principal Findings: Genomic DNA from 2700 Caucasians including 812 patients with Crohn's disease (CD), 442 patients with ulcerative colitis (UC), and 1446 healthy controls was analyzed for the NOD2 SNPs rs2066843 and rs2076756 and the three main CD-associated NOD2 variants p.Arg702Trp (rs2066844), p.Gly908Arg (rs2066847), and p.Leu1007fsX1008 (rs2066847). Haplotype and genotype-phenotype analyses were performed. The SNPs rs2066843 (p = 3.01×10−5, OR 1.48, [95% CI 1.23-1.78]) and rs2076756 (p = 4.01×10−6; OR 1.54, [95% CI 1.28-1.86]) were significantly associated with CD but not with UC susceptibility. Haplotype analysis revealed a number of significant associations with CD susceptibility with omnibus p values

Recent studies demonstrated an association of STAT4 variants with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), indicating that multiple autoimmune diseases share common susceptibility genes. We therefore investigated the influence of STAT4 variants on the susceptibility and phenotype of inflammatory bowel diseases (IBD) in a large patient and control cohort. Genomic DNA from 2704 individuals of Caucasian origin including 857 patients with Crohn's disease (CD), 464 patients with ulcerative colitis (UC), and 1383 healthy, unrelated controls was analyzed for seven SNPs in the STAT4 gene (rs11889341, rs7574865, rs7568275, rs8179673, rs10181656, rs7582694, rs10174238). In addition, a detailed genotype-phenotype analysis was performed. Our analysis revealed an association of the STAT4 SNP rs7574865 with overall decreased susceptibility to CD (p = 0.047, OR 0.86 [95% CI 0.74-0.99]). However, compared to CD patients carrying the wild type genotype, the STAT4 SNP rs7574865 was significantly associated with early CD onset (p = 0.021) and colonic CD (p = 0.008; OR = 4.60, 95% CI 1.63-12.96). For two other STAT4 variants, there was a trend towards protection against CD susceptibility (rs7568275, p = 0.058, OR 0.86 [95% CI 0.74-1.00]; rs10174238, p = 0.057, OR 0.86 [95% CI 0.75-1.00]). In contrast, we did not observe any association with UC susceptibility. Evidence for weak gene-gene interaction of STAT4 with the IL23R SNP rs11209026 was lost after Bonferroni correction. Our results identified the STAT4 SNP rs7574865 as a disease-modifying gene variant in colonic CD. However, in contrast to SLE and RA, the effect of rs7574865 on CD susceptibility is only weak.

Bacterial interactions play a major role in nature, but are poorly understood, because of the lack of adequate model systems. Phototrophic consortia represent the most highly developed type of interspecific bacterial association due to the precise spatial arrangement of phototrophic green sulfur bacteria (GSB) around a heterotrophic central bacterium. Therefore, they are valuable model systems for the study of symbiosis, signal transduction, and coevolution between different bacteria. This thesis summarizes a series of laboratory experiments with the objective of elucidating the molecular, physiological and phylogenetical properties of the two bacterial partners in the symbiotic phototrophic consortium "Chlorochromatium aggregatum". The central bacterium of “C. aggregatum” had been identified as a Betaproteobacterium, however, it could not be characterized further due to the low amount of consortia in enrichment cultures. In this work a suitable method for enrichment and isolation of DNA of the central bacterium of "C. aggregatum" has been established using cesium chloride-bisbenzimidazole equilibrium density gradient centrifugation (Chapter 3). In density gradients, genomic DNA of the central bacterium of “C. aggregatum” formed a distinct band, which could be detected by real-time PCR. Using this method, the GC-content of the central bacterium was estimated to be 55.6%. Furthermore, its precise phylogenetic position was determined and it was shown to represent a novel and phylogenetically isolated lineage of the Comamonadaceae within the -subgroup of the Proteobacteria. Chapter 4 describes the detection of a new, highly diverse subcluster of Betaproteobacteria, which contains several central bacteria of phototrophic consortia. Genomic DNA of the central bacterium of “C. aggregatum” was enriched several hundred fold by employing a selective method for growth of consortia in a monolayer biofilm followed by a purification of the central bacterial genome by density gradient centrifugation. A combination of molecular methods revealed that two rrn operons of the central bacterium are arranged in a tandem fashion. This rare gene order was exploited to screen various natural microbial communities. A diverse and previously unknown subgroup of Betaproteobacteria was discovered in the chemocline of Lake Dagow, Eastern Germany. All 16S rRNA gene sequences recovered are related to that of the central bacterium of “C. aggregatum”. Phylogenetic analyses showed, that the central, chemotrophic symbionts of phototrophic consortia have a polyphyletic origin, just like their phototrophic counterparts. This indictates that not only different GSB but also different Betaproteobacteria have adapted to life in this type of symbiosis. Chapter 5 focuses on the isolation of the epibiont of “C. aggregatum” from a consortia enrichment culture and its description as Chlorobium chlorochromatii strain CaD. It represents a novel species within the genus Chlorobium and is characterized by physiological properties typical for GSB. However, the symbiotic strain differs from free-living GSB in the distribution of its chlorosomes and the presence of a conspicuous additional structure at the attachment-site to the central bacterium. Its capability to grow in pure culture indicates that it is not obligately symbiotic. The natural habitat of GSB and phototrophic consortia is the chemocline of stratified lakes. Therefore, the physiological response to oxygen exposure of the epibiont and the free-living GSB Chlorobium limicola has been investigated (Chapter 6). It was shown that GSB are able to survive oxygen exposure and have developed several strategies for oxygen detoxification. Genome annotation revealed the presence of several enzymes involved in oxygen detoxification in all currently sequenced GSB genomes. Phylogenetic analyses showed that most of these enzymes likely were present in the common ancestor of this group. The activity of some of those enzymes could be confirmed. Since carotenoids also act as antioxidants, the carotenoid composition of the epibiont was investigated. In contrast to all other GSB it lacks chlorobactene, the major carotenoid in green-coloured GSB. In addition, 7,8-dihydro--carotene has been identified in the epibiont as a novel carotenoid in nature. Substantial progress has been made in the course of this study not only with the establishment of a method facilitating genome sequencing of the central bacterium of “C. aggregatum”, but also with the developement of a molecular screening tool for central bacteria of phototrophic consortia. The resulting sequences will enable the direct comparison of the phylogeny of both bacterial partners in different phototrophic consortia and hence will provide the unique opportunity to assess for the first time the process of the coevolution of a bacteria-bacteria-symbiosis.

The IL23R gene has been identified as a susceptibility gene for inflammatory bowel disease (IBD) in the North American population. The aim of our study was to test this association in a large German IBD cohort and to elucidate potential interactions with other IBD genes as well as phenotypic consequences of IL23R variants. Genomic DNA from 2670 Caucasian individuals including 833 patients with Crohn's disease (CD), 456 patients with ulcerative colitis (UC), and 1381 healthy unrelated controls was analyzed for 10 IL23R SNPs. Genotyping included the NOD2 variants p.Arg702Trp, p.Gly908Arg, and p.Leu1007fsX1008 and polymorphisms in SLC22A4/OCTN1 (1672 C-->T) and SLC22A5/OCTN2 (-207 G-->C). All IL23R gene variants analyzed displayed highly significant associations with CD. The strongest association was found for the SNP rs1004819 [P = 1.92x10(-11); OR 1.56; 95 % CI (1.37-1.78)]. 93.2% of the rs1004819 TT homozygous carriers as compared to 78% of CC wildtype carriers had ileal involvement [P = 0.004; OR 4.24; CI (1.46-12.34)]. The coding SNP rs11209026 (p.Arg381Gln) was protective for CD [P = 8.04x10(-8); OR 0.43; CI (0.31-0.59)]. Similar, but weaker associations were found in UC. There was no evidence for epistasis between the IL23R gene and the CD susceptibility genes CARD15 and SLC22A4/5. IL23R is an IBD susceptibility gene, but has no epistatic interaction with CARD15 and SLC22A4/5. rs1004819 is the major IL23R variant associated with CD in the German population, while the p.Arg381Gln IL23R variant is a protective marker for CD and UC.

Orbital and pretibial fibroblasts are targets of autoimmune attack in Graves' ophthalmopathy (GO) and pretibial dermopathy (PTD). The fibroblast autoantigen involved in these peripheral manifestations of Graves' disease and the reason for the association of GO and PTD with hyperthyroidism are unknown. RNA encoding the full-length extracellular domain of the TSH receptor has been demonstrated in orbital and dermal fibroblasts from patients with GO and normal subjects, suggesting a possible antigenic link between fibroblasts and thyrocytes. RNA was isolated from cultured orbital, pretibial, and abdominal fibroblasts obtained from patients with severe GO (n = 22) and normal subjects (n = 5). RNA was reverse transcribed, and the resulting cDNA was amplified by the polymerase chain reaction, using primers spanning overlapping regions of the entire extracellular domain of the TSH receptor. Nucleotide sequence analysis showed an A for C substitution in the first position of codon 52 in 2 of the patients, both of whom had GO, PTD, and acropachy. Genomic DNA isolated from the 2 affected patients, and not from an additional 12 normal subjects, revealed the codon 52 mutation by direct sequencing and AciI restriction enzyme digestions. In conclusion, we have demonstrated the presence of a genomic point mutation, leading to a threonine for proline amino acid shift in the predicted peptide, in the extracellular domain of the TSH receptor in two patients with severe GO, PTD, acropachy, and high thyroid-stimulating immunoglobulin levels. RNA encoding this mutant product was demonstrated in the fibroblasts of these patients. We suggest that the TSH receptor may be an important fibroblast autoantigen in GO and PTD, and that this mutant form of the receptor may have unique immunogenic properties.

Sat, 1 Jan 1994 12:00:00 +0100 https://epub.ub.uni-muenchen.de/7387/1/7387.pdf Becker, Peter B.; Quivy, J.-P. ddc:610, Medizin

Fri, 1 Jan 1993 12:00:00 +0100 https://epub.ub.uni-muenchen.de/9406/1/9406.pdf Speicher, Michael R.; Ried, Thomas; Scherthan, Harry; Lengauer, Christoph; Joos, Stefan; Manoir, Stanislas du; Jauch, Anna; Schröck, Evelin; Popp, Susanne; Lichter, Peter; Cremer, Thomas

The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb.

G-Proteins are membrane-bound heterotrimeric polypeptides that couple receptor signals to second messenger systems such as cAMP. Recently, point mutations at 2 codons of the highly preserved alpha-chain of Gs, the adenyl cyclase-stimulating G-protein, were found in GH-secreting pituitary tumors. These mutations resulted in constitutively activated Gs alpha and high intracellular cAMP levels. In addition, point mutations at similar codons of a different G-protein, G(i) alpha 2, were reported in adrenocortical neoplasms, suggesting a potential role of this isoform in the genesis of these tumors. We reevaluated the frequency of constitutively activating point mutations in the alpha- chain of the stimulatory (Gs alpha) and inhibitory (G(i) alpha 2) G- proteins in human adrenocortical tumors. Seven adrenocortical carcinomas, 2 human adrenocortical tumor cell lines, and 11 adrenocortical adenomas were studied. Genomic DNA was purified from either frozen tumor tissue or paraffin-embedded sections. Using specific primers and the polymerase chain reaction, DNA fragments surrounding codons 201 and 227 (Gs alpha) and 179 and 205 (G(i) alpha 2) were amplified and visualized on a 2% agarose gel. In a second asymmetric polymerase chain reaction, using nested primers, single stranded DNA was generated using 1-10 microL of the initial amplification mixture and directly sequenced using the dideoxy chain termination method of Sanger. We found no mutations at codons 201, 227 and 179, 205 of Gs alpha and G(i) alpha 2, respectively, in the tumors studied. We conclude that previously identified oncogenic point mutations in the stimulatory and inhibitory alpha-chain of G-proteins do not appear to be present at high frequency in adrenal neoplasms. Thus, the mechanism(s) of tumorigenesis in these tumors is different from that in GH-secreting adenomas and may involve oncogenic mutations of other cell constituents.