Timothy D. Arthur's research while affiliated with University of California, San Diego and other places

... Gene expression has long been known to be regulated in a spatial (organ, tissue, or cell type) and temporal (fetal-like and adult) specific manner [15][16][17][18][19][20][21][22] , indicating that cardiac regulatory variants function, and hence affect, the expression of a gene and its associated cardiac traits and disease, across a range of developmental stages and in different cellular contexts [15][16][17][23][24][25][26] . With the development of cell type deconvolution techniques 27,28 , bulk RNA-seq enables the characterization of cell type-specific gene expression as well as the expression of both genes and associated isoforms 24,29,30 . Furthermore, the GTEx consortium has generated bulk RNA-seq from hundreds of adult cardiac samples from multiple tissue types and whole genome-sequenced the donors 25 . ...

... GTEx and the eQTL catalogue provided us with the unique opportunity to investigate the associations among genotype and gene expression [29]. Through eQTL analysis, we associated these aTRH related SNPs with the genes they could potentially regulate [30]. Three candidate genes: SDC3, LAPTM5, and UGT2B4 were identified that were regulated by SNPs in 1p53 and 4q13.2-21.1 locus. ...

... Schmiedel et al. found several genes whose expression in specific immune cell types and tissues, including resting and activated naive CD4 + cells, influenced and colocalized with genetic determinants of COVID-19 outcomes (Schmiedel et al. 2021). D'Antonio et al. found genes that colocalized with COVID-19 loci in whole blood, including ABO and IFNAR2, and identified the causal variants using fine-mapping (D'Antonio et al. 2021). ...

... Bile acids are eventually resorbed in the intestine and returned to the liver through enterohepatic circulation where they can be re-conjugated or repaired in the hepatocyte [6]. influenced in part by the chemical identity of the amino acid that is conjugated to the sterol core [9,11]. ...

... These commensal bacteria utilize host lipids as an energy source and metabolize some lipids to new isoforms to enhance mucosal barrier function. Conversely, gut bacteria have also been associated with detrimental changes to dietary lipids, as demonstrated by studies of the microbiome associated with irritable bowel syndrome (69,70). These studies begin to shed light on the potential circular relationship between dietary lipids, changes in the local host environment, and selection for bacteria that metabolize those same nutrients and benefit from changes to the environment (71). ...

... The library generation was carried out with a miniaturised version of the Kapa HyperPlus Illuminacompatible library prep kit (Kapa Biosystems) [73]. The DNA extracts were normalized to 5 ng total input per sample using an Echo 550 acoustic liquid-handling robot (Labcyte Inc). ...

... 21,25 Indeed, the participation of microbial components (including bacterial-derived lipids) in maintenance of host's health has been described for several species of the Bacteroidetes and Verrucomicrobia families. 21,[25][26][27][28] Undoubtedly, the involvement of bacterio-lipids in host's gut homeostasis is driving a strong scientific interest. ...

... We note that a locus here could be a nucleotide, gene, or gene set --any contiguous or non-contiguous stretch of DNA in which multiple mutations interact with strong antagonism (e.g. two mutations in the same locus would be just as beneficial as only one of these). We next use equation (7) to obtain a formula for d N /d S that has only three free parameters when a single value for is chosen: µ [43]). Invertible promoters are restricted out of the genome and re-ligated in the opposite direction to turn gene expression on or off. ...

... longum, B. breve, and B. pseudocatenulatum [4,5]. In infant cohort studies, associations between HMO degradation, enrichment of select Bifidobacterium species, higher fecal acetate and lactate, and advantageous health outcomes have been observed [6][7][8][9][10][11]. As such, robust colonization of Bifidobacterium during infancy has been linked with improved markers for type 1 diabetes [12], reduced likelihood of obesity [13,14], robust vaccine responses [15], and lower antimicrobial resistance gene carriage [8,16,17]. ...

... The lack of persistent Lactobacillus after supplementation was consistent with a recent infant probiotic study that showed that following treatment with Bifidobacteriumand Lactobacillus-based probiotics, some Bifidobacterium persisted but no Lactobacillus persisted in the infant gut (Beck et al., 2022). Bifidobacterium was noticeably more abundant than Lactobacillus in the cohort studied here, which is supported by previous studies (Vatanen et al., 2018). ...