5 results on '"Emily R Davenport"'
Search Results
2. The relationship between the gut microbiome and host gene expression: a review
- Author
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Robert G. Nichols and Emily R. Davenport
- Subjects
ved/biology.organism_classification_rank.species ,Regulator ,Gene Expression ,Review ,Computational biology ,Biology ,03 medical and health sciences ,0302 clinical medicine ,RNA, Ribosomal, 16S ,Gene expression ,Genetics ,Humans ,Epigenetics ,Microbiome ,Model organism ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,ved/biology ,Human genetics ,Gastrointestinal Microbiome ,Chromatin ,Gene Expression Regulation ,RNA splicing ,Energy Metabolism ,030217 neurology & neurosurgery - Abstract
Despite the growing knowledge surrounding host–microbiome interactions, we are just beginning to understand how the gut microbiome influences—and is influenced by—host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health. Electronic supplementary material The online version of this article (10.1007/s00439-020-02237-0) contains supplementary material, which is available to authorized users.
- Published
- 2020
3. Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations
- Author
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Andrew G. Clark, Dehai Wang, Xiaoling Gong, and Emily R. Davenport
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0106 biological sciences ,0301 basic medicine ,education.field_of_study ,Panmixia ,Population ,Zoology ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Japonica ,03 medical and health sciences ,030104 developmental biology ,Genetic variation ,Genetic structure ,Genetics ,Microsatellite ,Japanese eel ,Temporal isolation ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Japanese eel (Anguilla japonica) is an important food source in East Asia whose population has dramatically declined since the 1970s. Despite past analysis with DNA sequencing, microsatellite and isozyme methods, management decisions remain hampered by contradictory findings. For example, it remains unresolved whether Japanese eels are a single panmictic population or whether they harbor significant substructure. Accurate assessment of population genetic substructure, both spatial and temporal, is essential for determining the relevant number of distinct management units appropriate for this species. In the present study, we assayed genetic variation genome-wide using Restriction Site Associated DNA Sequencing (RAD-seq) technology to analyze the population genetic structure of Japanese eels. For analysis of temporal isolation, five “cohort” samples were collected yearly from 2005 to 2009 in the Yangtze River Estuary. For analysis of spatial structure, five “arrival wave” samples were collected in China in 2009, and two arrival wave samples were collected in Japan in 2001. In each cohort of each arrival wave, five individuals were collected for a total of 55 eels sampled. In total, 214,210 loci were identified from these individuals, 106,652 of which satisfied quality checks and were retained for further analysis. There was relatively little population differentiation between arrival waves and cohorts collected either at different locations during the same year (Fst = 0.077) or at the same location collected over subsequent years (Fst = 0.082), and locations displayed no consistent isolation-by-distance.
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- 2019
4. Heritable components of the human fecal microbiome are associated with visceral fat
- Author
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Michelle Beaumont, Massimo Mangino, Matthew A. Jackson, Tess Pallister, Julia K. Goodrich, Jordana T. Bell, Sara Vieira-Silva, Rob Knight, Idil Yet, Andrew G. Clark, Ruth E. Ley, Jeroen Raes, Justine W. Debelius, Emily R. Davenport, and Tim D. Spector
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0301 basic medicine ,Aging ,Bioinformatics ,Population ,Twins ,Gut flora ,Cardiovascular ,Oral and gastrointestinal ,Heritability ,03 medical and health sciences ,fluids and secretions ,0302 clinical medicine ,Clinical Research ,Information and Computing Sciences ,Genetics ,medicine ,2.1 Biological and endogenous factors ,Obesity ,Visceral fat ,Microbiome ,Aetiology ,education ,Metabolic and endocrine ,Nutrition ,Cancer ,Genetic association ,2. Zero hunger ,education.field_of_study ,biology ,Prevention ,Research ,Human Genome ,Biological Sciences ,medicine.disease ,biology.organism_classification ,3. Good health ,Stroke ,030104 developmental biology ,Cohort ,Fecal microbiome ,Body mass index ,Environmental Sciences ,030217 neurology & neurosurgery - Abstract
Background Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures. Results We profile six adiposity measures in 3666 twins and estimate their heritability, finding novel evidence for strong genetic effects underlying visceral fat and android/gynoid ratio. We confirm the association of lower diversity of the fecal microbiome with obesity and adiposity measures, and then compare the association between fecal microbial composition and the adiposity phenotypes in a discovery subsample of twins. We identify associations between the relative abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures. Most of these results involve visceral fat associations, with the strongest associations between visceral fat and Oscillospira members. Using BMI as a surrogate phenotype, we pursue replication in independent samples from three population-based cohorts including American Gut, Flemish Gut Flora Project and the extended TwinsUK cohort. Meta-analyses across the replication samples indicate that 8 OTUs replicate at a stringent threshold across all cohorts, while 49 OTUs achieve nominal significance in at least one replication sample. Heritability analysis of the adiposity-associated microbial OTUs prompted us to assess host genetic-microbe interactions at obesity-associated human candidate loci. We observe significant associations of adiposity-OTU abundances with host genetic variants in the FHIT, TDRG1 and ELAVL4 genes, suggesting a potential role for host genes to mediate the link between the fecal microbiome and obesity. Conclusions Our results provide novel insights into the role of the fecal microbiota in cardio-metabolic disease with clear potential for prevention and novel therapies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1052-7) contains supplementary material, which is available to authorized users.
- Published
- 2016
5. Epigenetic modifications are associated with inter-species gene expression variation in primates
- Author
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Emily R. Davenport, Katelyn Michelini, Yoav Gilad, Jonathan K. Pritchard, Carolyn E. Cain, Matthew Stephens, Xiang Zhou, Noah Lewellen, and Marsha Myrthil
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Primates ,Genomics ,RNA polymerase II ,Cell Line ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,biology.animal ,Gene expression ,Animals ,Humans ,Primate ,Lymphocytes ,RNA, Messenger ,Epigenetics ,030304 developmental biology ,Epigenesis ,Genetics ,Regulation of gene expression ,0303 health sciences ,biology ,Sequence Analysis, RNA ,Research ,Chromatin ,Histone ,Gene Expression Regulation ,Evolutionary biology ,biology.protein ,H3K4me3 ,030217 neurology & neurosurgery - Abstract
Background Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species. Results To begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution. Conclusions Our observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0547-3) contains supplementary material, which is available to authorized users.
- Published
- 2014
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