Digital Commons Network^™

Cultivating Ecosystems: Microbial Communities In Recirculating Aquaculture Systems, Ryan Bartelme

Theses and Dissertations

Intensive cultivation of fish is necessary to meet future global market demands. Recirculating aquaculture systems (RAS) enable dense growth of fish, while occupying less space than traditional aquaculture farms. However, RAS often experience complications and high fish mortalities due to disease and improper waste management. In properly functioning systems, the microorganisms associated with fish (gut, scales) as well as those found in the system environment (water, component surfaces) remove waste and maintain fish health by discouraging growth of opportunistic pathogens. Previous RAS microbiome studies are small in scope, utilize coarse methods, and contain limited long-term spatial or temporal data. With …

Mining The Red Sea Metagenomics Libraries For Betaine Pathways, Sherouk Allam

Theses and Dissertations

Glycine Betaine (GB) is a fundamental solute for salinity tolerance in many organisms. Our aim in this study was to identify the GB pathway in highly complex natural community inhabiting brine pool and Red Sea column in Atlantis II Red Sea. Environmental genomics is a powerful tool for collecting information on microbial communities. Knowledge can be collected about highly complex natural communities. Microbial community living in extreme conditions evolved divers molecular mechanisms to withstand these conditions. Metagenomic libraries from Atlantic II samples were used to study betaine biosynthetic pathway that is more abundant. Betaine is synthesized independently from two different …

Discovering Driver Mutations In Biological Data, Yahya Bokhari

Theses and Dissertations

Background

Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. …