Life Sciences Commons^™

Genomics Education Partnership F Element Annotation Report, Amanda Moy

Honors Projects

The Genomics Education Partnership (GEP), headquartered at the University of Alabama, is a collection of over 100 universities that provide training and resources in order to provide students experiential learning in bioinformatics and genomics. The GEP hosts numerous research projects, including the F element project. The F element project has the main focus of annotating the F element genes of the fruit fly species D. ananassae, D. bipectinata, D. kikkawai, and D. takahashii. The Muller F element is the smallest chromosome in Drosophila species. However, the four species listed above have a notably larger F element than other …

Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste

School of Biological Sciences: Dissertations, Theses, and Student Research

The family Luteoviridae consists of three genera: Luteovirus, Enamovirus, and Polerovirus. The genus Polerovirus contains 32 virus species. All are transmitted by aphids and can infect a wide variety of crops from cereals and wheat to cucurbits and peppers. However, little is known about how this wide range of hosts and vectors developed. In poleroviruses, aphid transmission and virion formation is mediated by the coat protein read-through domain (CPRT) while silencing suppression and phloem limitation is mediated by Protein 0 (P0)—a protein unique to poleroviruses. P0 gives poleroviruses a great advantage amongst plant viruses and diversifies polerovirus species, but the …

Characterizing The Behavior Of Mutated Proteins With Emcap: The Energy Minimization Curve Analysis Pipeline, Matthew Lee, Bodi Van Roy, Filip Jagodzinski

WWU Honors College Senior Projects

Studies of protein mutants in wet laboratory experiments are expensive and time consuming. Computational experiments that simulate the motions of protein with amino acid substitutions can complement wet lab experiments for studying the effects of mutations. In this work we present a computational pipeline that performs exhaustive single-point amino acid substitutions in silico. We perform energy minimization as part of molecular dynamics (MD) of our generated mutant proteins, and the wild type, and log the energy potentials for each step of the simulations. We motivate several metrics that rely on the energy minimization curves of the wild type and mutant, …

Ontogeny Related Changes In The Pediatric Liver Metabolome., Christopher M. Wilson, Qian Li, R Gaedigk, Chengpeng Bi, Saskia N. De Wildt, J Steven Leeder, Brooke L. Fridley

Manuscripts, Articles, Book Chapters and Other Papers

Background: A major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent.

Methods: Metabolites …

Functional, Proteomic And Bioinformatic Analyses Of Nrf2- And Keap1- Null Skeletal Muscle, Lie Gao, Vikas Kumar, Neetha Nanoth Vellichirammal, Song-Young Park, Tara L. Rudebush, Li Yu, Won-Mok Son, Elizabeth J. Pekas, Ahmed M. Wafi, Juan Hong, Peng Xiao, Chittibabu Guda, Han-Jun Wang, Harold D. Scultz, Irving H. Zucker

Health and Kinesiology Faculty Publications

Key points

• Nrf2 is a master regulator of endogenous cellular defences, governing the expression of more than 200 cytoprotective proteins, including a panel of antioxidant enzymes.
• Nrf2 plays an important role in redox haemostasis of skeletal muscle in response to the increased generation of reactive oxygen species during contraction.
• Employing skeletal muscle-specific transgenic mouse models with unbiased-omic approaches, we uncovered new target proteins, downstream pathways and molecular networks of Nrf2 in skeletal muscle following Nrf2 or Keap1 deletion.
• Based on the findings, we proposed a two-way model to understand Nrf2 function: a tonic effect through a Keap1-independent mechanism under basal …

Exploration Of The Role Of Microbiome Structure, Metabolism, And Modification In Black Band Disease Etiology, Patricia Waikel

FIU Electronic Theses and Dissertations

The coral microbiome plays an integral role in coral health. Modification of the microbiome is thought to alter susceptibility to disease. Black Band Disease (BBD), is polymicrobial, mat forming, and affects reef building coral globally. Dominated by the cyanobacterium Roseofilum reptotaenium, it has been noted to increase in virulence with increasing temperatures, making BBD of particular concern in the face of climate change-induced warming seas. The active sulfur cycle of BBD makes dimethylsulfoniopropionate (DMSP), a widely available source of sulfur in the marine environment, of particular interest in the study of BBD. Traditional infection studies require field collection and …

Integrate Structural Analysis, Isoform Diversity, And Interferon-Inductive Propensity Of Ace2 To Predict Sars-Cov2 Susceptibility In Vertebrates, Eric R. Sang, Yun Tian, Yuanying Gong, Laura C. Miller, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

The current new coronavirus disease (COVID-19) has caused globally over 0.4/6 million confirmed deaths/infected cases across more than 200 countries. As the etiological coronavirus (a.k.a. SARS-CoV2) may putatively have a bat origin, our understanding about its intermediate reservoir between bats and humans, especially its tropism in wild and domestic animals are mostly unknown. This constitutes major concerns in public health for the current pandemics and potential zoonosis. Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. …

Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Novel foods and Genetically Engineered (GE) organisms are being developed for nutritional, industrial, and environmental applications. Dietary interventions have been used recently to mitigate methane emissions in ruminants. In this project, bioinformatics tools have been used to answer two main questions. The first question is the potential allergy risks for consumption of novel foods and GE organisms. The second question is the effects of dietary interventions on microbiome functionality related to methane production in ruminants.

To answer the first question, regulatory authorities in the United States and Europe now expect an evaluation of new proteins in novel foods or genetically …

Adaptations Of Interferon Regulatory Factor 3 During Transition From Terrestrial To Aquatic Life, Monica Angeletti

Honors Theses

Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and play a major role in the induction of interferons, which are a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of these IRFs to the environment. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned …

A Phylogenomic Approach Reveals A Low Somatic Mutation Rate In A Long-Lived Plant., Adam J Orr, Amanda Padovan, David Kainer, Carsten Kulheim, Lindell Bromham, Carlos Bustos-Segura, William Foley, Tonya Haff, Ji-Fan Hsieh, Alejandro Morales-Suarez, Reed A Cartwright, Robert Lanfear

Michigan Tech Publications

Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a …

10th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The Annual Postdoctoral Science Symposium (APSS) was initiated on August 4, 2011, by the MD Anderson Postdoctoral Association to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience.

APSS is a scientific symposium organized by postdoctoral fellows from The University of Texas MD Anderson Cancer Center that welcomes submissions and presentations from postdoctoral fellows from all Texas Medical Center affiliated institutions and other Houston area institutions. The APSS provides a professional venue for postdoctoral scientists to develop, clarify and refine their research as result of formal reviews and critiques …