ABSTRACT: Evolutionary Genomics and Anthropological Approaches on the Endangered Malaysian Orang Asli Populations: Towards Ensuring Their Sustainability
Project description:The largest of the tuna species, Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely through overfishing. Thus, the development of aquaculture practices independent of wild resources can provide an important contribution towards ensuring security and sustainability of this species in the longer-term. In order to provide a resource for ongoing studies, we have used 454 pyrosequencing technology to sequence a mixed-tissue normalized cDNA library, derived from adult individuals. Transcript sequences were used to develop a novel 15K Agilent oligo microarray for T. thynnus and comparative tissue gene expression profiles were inferred for gill, heart, liver, ovaries and testes.
Project description:Purpose: Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Methods: Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. Results: We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa. Conclusions: There is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.
Project description:We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver.
Project description:Comparative-genomic studies have reported widespread variation in levels of gene expression within and between species. In the vast majority of cases, the phenotypic and evolutionary relevance of regulatory change is unknown. We haveu sed a wild Malaysian population of S. cerevisiae as a testbed in the search to identify organismal correlates of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Analysis of differential gene expression between three Malaysian and two Wine/European isolates and allele-specific expression within three Malaysian x Wine/European hybrids.
Project description:Comparative-genomic studies have reported widespread variation in levels of gene expression within and between species. In the vast majority of cases, the phenotypic and evolutionary relevance of regulatory change is unknown. We haveu sed a wild Malaysian population of S. cerevisiae as a testbed in the search to identify organismal correlates of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron.
Project description:Background: Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria.Results: Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching.
