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  • 1
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 2
    In: Mammalian Genome, Springer Science and Business Media LLC, Vol. 22, No. 9-10 ( 2011-10), p. 530-543
    Type of Medium: Online Resource
    ISSN: 0938-8990 , 1432-1777
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 1459397-X
    SSG: 12
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  • 3
    In: Genetics, Oxford University Press (OUP), Vol. 220, No. 1 ( 2022-01-04)
    Abstract: While direct additive and dominance effects on complex traits have been mapped repeatedly, additional genetic factors contributing to the heterogeneity of complex traits have been scarcely investigated. To assess genetic background effects, we investigated transmission ratio distortions (TRDs) of alleles from parent to offspring using an advanced intercross line (AIL) of an initial cross between the mouse inbred strains C57BL/6NCrl (B6N) and BFMI860-12 [Berlin Fat Mouse Inbred (BFMI)]. A total of 341 males of generation 28 and their respective 61 parents and 66 grandparents were genotyped using Mega Mouse Universal Genotyping Arrays. TRDs were investigated using allele transmission asymmetry tests, and pathway overrepresentation analysis was performed. Sequencing data were used to test for overrepresentation of nonsynonymous SNPs (nsSNPs) in TRD regions. Genetic incompatibilities were tested using the Bateson–Dobzhansky–Muller two-locus model. A total of 62 TRD regions were detected, many in close proximity to the telocentric centromere. TRD regions contained 44.5% more nsSNPs than randomly selected regions (182 vs 125.9 ± 17.0, P  & lt; 1 × 10−4). Testing for genetic incompatibilities between TRD regions identified 29 genome-wide significant incompatibilities between TRD regions [P(BF)  & lt; 0.05]. Pathway overrepresentation analysis of genes in TRD regions showed that DNA methylation, epigenetic regulation of RNA, and meiotic/meiosis regulation pathways were affected independent of the parental origin of the TRD. Paternal BFMI TRD regions showed overrepresentation in the small interfering RNA biogenesis and in the metabolism of lipids and lipoproteins. Maternal B6N TRD regions harbored genes involved in meiotic recombination, cell death, and apoptosis pathways. The analysis of genes in TRD regions suggests the potential distortion of protein–protein interactions influencing obesity and diabetic retinopathy as a result of disadvantageous combinations of allelic variants in Aass, Pgx6, and Nme8. Using an AIL significantly improves the resolution at which we can investigate TRD. Our analysis implicates distortion of protein–protein interactions as well as meiotic drive as the underlying mechanisms leading to the observed TRD in our AIL. Furthermore, genes with large amounts of nsSNPs located in TRD regions are more likely to be involved in pathways that are related to the phenotypic differences between the parental strains. Genes in these TRD regions provide new targets for investigating genetic adaptation, protein–protein interactions, and determinants of complex traits such as obesity.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2012
    In:  BMC Genomics Vol. 13, No. 1 ( 2012-12)
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2012-12)
    Abstract: Genomic imprinting refers to parent-of-origin dependent gene expression caused by differential DNA methylation of the paternally and maternally derived alleles. Imprinting is increasingly recognized as an important source of variation in complex traits, however, its role in explaining variation in muscle and physiological traits, especially those of commercial value, is largely unknown compared with genetic effects. Results We investigated both genetic and genomic imprinting effects on key muscle traits in mice from the Berlin Muscle Mouse population, a key model system to study muscle traits. Using a genome scan, we first identified loci with either imprinting or genetic effects on phenotypic variation. Next, we established the proportion of phenotypic variation explained by additive, dominance and imprinted QTL and characterized the patterns of effects. In total, we identified nine QTL, two of which show large imprinting effects on glycogen content and potential, and body weight. Surprisingly, all imprinting patterns were of the bipolar type, in which the two heterozygotes are different from each other but the homozygotes are not. Most QTL had pleiotropic effects and explained up to 40% of phenotypic variance, with individual imprinted loci accounting for 4-5% of variation alone. Conclusion Surprisingly, variation in glycogen content and potential was only modulated by imprinting effects. Further, in contrast to general assumptions, our results show that genomic imprinting can impact physiological traits measured at adult stages and that the expression does not have to follow the patterns of paternal or maternal expression commonly ascribed to imprinting effects.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2041499-7
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  • 5
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 6
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2013-12)
    Abstract: This study is aimed at the analysis of genetic and physiological effects of myostatin on economically relevant meat quality traits in a genetic background of high muscularity. For this purpose, we generated G 3 populations of reciprocal crosses between the two hypermuscular mouse lines BMMI866, which carries a myostatin mutation and is lean, and BMMI806, which has high intramuscular and body fat content. To assess the relationship between muscle mass, body composition and muscle quality traits, we also analysed intramuscular fat content (IMF), water holding capacity (WHC), and additional physiological parameters in M. quadriceps and M. longissimus in 308 G 3 -animals. Results We found that individuals with larger muscles have significantly lower total body fat (r = −0.28) and IMF (r = −0.64), and in females, a lower WHC (r = −0.35). In males, higher muscle mass was also significantly correlated with higher glycogen contents (r = 0.2) and lower carcass pH-values 24 hours after dissection (r = −0.19). Linkage analyses confirmed the influence of the myostatin mutation on higher lean mass (1.35 g), reduced body fat content (−1.15%), and lower IMF in M. longissimus (−0.13%) and M. quadriceps (−0.07%). No effect was found for WHC. A large proportion of variation of intramuscular fat content of the M. longissimus at the myostatin locus could be explained by sex (23%) and direction-of-cross effects (26%). The effects were higher in males (+0.41%). An additional locus with negative over-dominance effects on total fat mass (−0.55 g) was identified on chromosome 16 at 94 Mb (86–94 Mb) which concurs with fat related QTL in syntenic regions on SSC13 in pigs and BTA1 in cattle. Conclusion The data shows QTL effects on mouse muscle that are similar to those previously observed in livestock, supporting the mouse model. New information from the mouse model helps to describe variation in meat quantity and quality, and thus contribute to research in livestock.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
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  • 7
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2023
    In:  Cancer Research Vol. 83, No. 7_Supplement ( 2023-04-04), p. 2187-2187
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 2187-2187
    Abstract: Human gamma delta T cells (γδ-T cells) are non-conventional T lymphocytes expressing a TCR heterodimer comprised of gamma (γ) and delta (δ) chains. They constitute an essential part of the innate immune system playing a pivotal role at the front line of the host's defense against pathogens. γδ-T cells have received particular attention as they exert multiple functions under non-infectious settings, most notably in carcinogenesis, where they can initiate a potent HLA-independent anti-tumor activity. Owing to these attributes, γδ-T cells appear to be a promising target for designing cell-based anti-cancer immunotherapies. For such strategies - which involve manipulation of γδ-T cells, e.g. by activation, tumor-targeting, or genetic modification - accurate and quantitative cell-counting tools are indispensable. The gold standard for immune cell quantification to date is still flow cytometry (FCM), although this technology is associated with demanding sample logistics as it requires suspensions of viable cells and presents challenges to standardization amongst different sites, cytometers and operators. In recent years, a huge body of evidence has been accumulated demonstrating epigenetic qPCR (Epiontis ID®) as a powerful and FCM-equivalent methodology for cell quantification and immune monitoring, which is not affected with such limitations. Here we present a DNA methylation-specific, real-time PCR-based assay for the precise quantification of γδ-T cells in blood, tissues and formalin fixed and paraffin embedded (FFPE) samples. The qPCR assay targets a differentially methylated region in the gene encoding the constant region of the T cell receptor gamma chain (TRGC2). This marker region was shown being entirely unmethylated in γδ-T cells, but appearing fully methylated in conventional CD4+ and CD8+ T cells, in CD56+ NK and CD19+ B cells, in CD14+ monocytes and CD15+ granulocytes. Validation of the assay according to ICH guidelines and ISO17025 standards demonstrated a robust performance and stability, linear measurements in the operational range (between 0% and 100% methylation), a definite target cell type specificity and a good correlation to paralleled flow cytometric analyses. The intra- and inter-assay precision is below 15% and 20%, respectively and the lower limit of quantification, above where standard precision of measurements can be achieved, lies at 74 unmethylated target molecules. Cell type-specificity was shown using blood from heathy donors, the applicability in cancerous samples still has to be confirmed.In summary the epigenetic, γδ-T cell-specific assay posted here may represent a useful tool for immune monitoring in clinical settings assisting the development of innovative γδ-T cell-based immunotherapies. Citation Format: Sven Olek, Udo Baron, Isabell Janack, Kati Bourquain, Stefan Kärst, Deborah Phippard, Laura Lozza, Ciro Novaes Lino Rosa. Epigenetic monitoring of gamma delta T-cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2187.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2008
    In:  Nucleic Acids Research Vol. 36, No. suppl_2 ( 2008-07-01), p. W460-W464
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 36, No. suppl_2 ( 2008-07-01), p. W460-W464
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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