Systems Biology Commons^™

Genetic Predictors Of Metabolic Side Effects Of Diuretic Therapy, Jorge L. Del Aguila

Dissertations and Theses (Open Access)

Thiazide diuretics are a recommended first-line monotherapy for hypertension (i.e.SBP>140 mmHg or DBP>90 mmHg). Even so, diuretics are associated with adverse metabolic side effects, such as hyperlipidemia, hyperglycemia and hypokalemia which increase the risk of developing type II diabetes. This thesis used three analytical strategies to identify and quantify genetic factors that contribute to the development of adverse metabolic effects due to thiazide diuretic treatment. I performed a genome-wide association study (GWAS) and meta-analysis of the change in fasting plasma glucose and triglycerides in response to HCTZ from two different clinical trials: the Pharmacogenomic Evaluation of Antihypertensive Responses …

A Quantitative Analysis Of Kalandars And Captive Bears In Pakistan, Thomas P. Rooney, Kendra C. Millam

Biological Sciences Faculty Publications

In 2013, the Bioresource Research Centre (Islamabad, Pakistan) conducted a comprehensive census of the remaining dancing and bear-baiting bears in Pakistan. This involved locating and counting the actual involved bears and bear keepers (kalandars), collecting detailed socio-economic data from the bear-keepers, and identifying attitudes and key drivers behind this livelihood. This report summarizes the findings from the census, reveals relationships in the data that are not immediately apparent, and identifies potential leverage points for ongoing campaign efforts.

White-Tailed Deer Are A Biotic Filter During Community Assembly, Reducing Species And Phylogenetic Diversity, Danielle R. Begley-Miller, Andrew L. Hipp, Bethany H. Brown, Marlene Hahn, Thomas P. Rooney

Biological Sciences Faculty Publications

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H′), richness (SR), phylogenetic community structure and phylogenetic diversity in paired …

Expression Pattern And Biochemical Properties Of Zebrafish N-Acetylglutamate Synthase, Ljubica Caldovic, Nantaporn Haskins, Amy Mumo, Himani Majumdar, Mary Pinter, Mendel Tuchman, Alison Krufka

Genomics and Precision Medicine Faculty Publications

The urea cycle converts ammonia, a waste product of protein catabolism, into urea. Because fish dispose ammonia directly into water, the role of the urea cycle in fish remains unknown. Six enzymes, N-acetylglutamate synthase (NAGS), carbamylphosphate synthetase III, ornithine transcarbamylase, argininosuccinate synthase, argininosuccinate lyase and arginase 1, and two membrane transporters, ornithine transporter and aralar, comprise the urea cycle. The genes for all six enzymes and both transporters are present in the zebrafish genome. NAGS (EC 2.3.1.1) catalyzes the formation of N-acetylglutamate from glutamate and acetyl coenzyme A and in zebrafish is partially inhibited by L-arginine. NAGS and other urea …

Piwi Homologs Mediate Histone H4 Mrna Localization To Planarian Chromatoid Bodies, Labib Rouhana, Jennifer A. Weiss, Ryan S. King, Phillip A. Newmark

Biological Sciences Faculty Publications

The well-known regenerative abilities of planarian flatworms are attributed to a population of adult stem cells called neoblasts that proliferate and differentiate to produce all cell types. A characteristic feature of neoblasts is the presence of large cytoplasmic ribonucleoprotein granules named chromatoid bodies, the function of which has remained largely elusive. This study shows that histone mRNAs are a common component of chromatoid bodies. Our experiments also demonstrate that accumulation of histone mRNAs, which is typically restricted to the S phase of eukaryotic cells, is extended during the cell cycle of neoblasts. The planarian PIWI homologs SMEDWI-1 and SMEDWI-3 are …

Sampling Local Fungal Diversity In An Undergraduate Laboratory Using Dna Barcoding, A. H. Harrington, A. F. Bigott, B. W. Anderson, M. J. Boone, S. M. Brick, J. F. Delsol, R. A. Hotchkiss, R. A. Huddleston, E. H. Kasper, J. J. Mcgrady, M. L. Mckinnie, M. V. Ottenlips, N. E. Skinner, K. C. Spatz, A. J. Steinberg, F. Van Den Broek, C. N. Wilson, A. M. Wofford, A. M. Willyard

Journal of the Arkansas Academy of Science

Traditional methods for fungal species identification require diagnostic morphological characters and are often limited by the availability of fresh fruiting bodies and local identification resources. DNA barcoding offers an additional method of species identification and is rapidly developing as a critical tool in fungal taxonomy. As an exercise in an undergraduate biology course, we identified 9 specimens collected from the Hendrix College campus in Conway, Arkansas, USA to the genus or species level using morphology. We report that DNA barcoding targeting the internal transcribed spacer (ITS) region supported several of our taxonomic determinations and we were able to contribute 5 …

A Systems Biology Approach To Detect Eqtls Associated With Mirna And Mrna Co-Expression Networks In The Nucleus Accumbens Of Chronic Alcoholic Patients, Mohammed Mamdani

Theses and Dissertations

Alcohol Dependence (AD) is a chronic substance use disorder with moderate heritability (60%). Linkage and genome-wide association studies (GWAS) have implicated a number of loci; however, the molecular mechanisms underlying AD are unclear. Advances in systems biology allow genome-wide expression data to be integrated with genetic data to detect expression quantitative trait loci (eQTL), polymorphisms that regulate gene expression levels, influence phenotypes and are significantly enriched among validated genetic signals for many commonly studied traits including AD.

We integrated genome-wide mRNA and miRNA expression data with genotypic data from the nucleus accumbens (NAc), a major addiction-related brain region, of 36 …

Wolves Facilitate The Recovery Of Browse-Sensitive Understory Herbs In Wisconsin Forests, Krystle Bouchard, Jane E. Wiedenhoeft, Adrian P. Wydeven, Thomas P. Rooney

Biological Sciences Faculty Publications

We asked whether wolf re-colonization would facilitate increased growth and reproduction of three browse-sensitive plant species. We hypothesized plant size and the proportion of reproductive individuals would be lowest in areas with no wolves, intermediate where wolves had been present for 4-6 years, and highest where wolves had been present for 12-13 years. Two plant species exhibited significantly greater reproduction where wolves were present for 12-13 years. Mean leaf size of indicator plants was significantly greater in areas where wolves were present for 12-13 years, as compared with that in areas where wolves were not present or were present for …

Tossing The Coin For Half Life, William L. Romine

Biological Sciences Faculty Publications

No abstract provided.

The Science (And Pseudoscience) Of Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Reproductive Isolation In The Elegans-Group Of Caenorhabditis, Scott Everet Baird, Sara Rose Seibert

Biological Sciences Faculty Publications

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus Caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of Caenorhabditis is poised to become an important experimental …

Food Limitation As A Potentially Emerging Contributor To The Asian Vulture Crisis, Fakhar -I- Abbas, Thomas P. Rooney, Jibran Haider, Afsar Mian

Biological Sciences Faculty Publications

It was believed that the reason for decline in Asian vulture population is the drug, Diclofenac sodium (DFS), used in livestock. Even after declaring the DFS use banned by the government, apparent decrease in the population of vultures was reported. Alternate hypothesis was suggested that food limitation may be a cause of Asian vulture crisis in Pakistan. Very recent shifts in livestock utilization observed in Pakistan may present a significant barrier to vulture recovery. Increased livestock utilization is translated to fewer carcasses. Since 2005, no livestock carcasses were found in 1650 km transect in the habitat of vultures. Carcasses recorded …

Game-Based Curricula In Biology Classes: Multi-Level Assessment Of Science Learning, Troy D. Sadler, William L. Romine, Parker E. Stuart

Biological Sciences Faculty Publications

Video games played on computers, game consoles, tablets and smart phones have become a very popular medium in our society. A growing body of scholarship suggests that video games can support substantial learning (for reviews see Gee, 2007; Honey & Hilton, 2011; Squire, 2011). Research has documented ways in which games engage students deeply in thinking, learning, and collaboration (Gee, 2005). Evidence suggests that games can support development of critical thinking (Squire, 2006), creativity (Annetta, Cheng, & Holmes, 2010), and mastery and application of target concepts (Squire, 2011).

Artifacts And Noise In Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Dna Technology In Court, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Statistical Weights Of Single Source Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Generating Forensic Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

What Can Go Wrong With Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Observer Effects In Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Statistical Weights Of Mixed Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

Presentation recording from December 2012 can be found at http://youtu.be/daRBTopFA1A.

Part of the Forensic DNA Profiling Video Series.

Implications Of Database Searches For Dna Profiling Statistics, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Differential Activity Of The Kras Oncogene By Method Of Activation: Implications For Signaling And Therapeutic Intervention, Nathan Ihle

Dissertations and Theses (Open Access)

Despite having been identified over thirty years ago and definitively established as having a critical role in driving tumor growth and predicting for resistance to therapy, the KRAS oncogene remains a target in cancer for which there is no effective treatment. KRas is activated b y mutations at a few sites, primarily amino acid substitutions at codon 12 which promote a constitutively active state. I have found that different amino acid substitutions at codon 12 can activate different KRas downstream signaling pathways, determine clonogenic growth potential and determine patient response to molecularly targeted therapies. Computer modeling of the KRas structure …

Effects Of Moderate Swim Exercise On Adiposity And Metabolic Function In Mice, Roberta L. Pohlman, Ana Carneiro, Vera Farah, Lynn K. Hartzler, Mariana Morris

Biological Sciences Faculty Publications

No abstract provided.

Heterogeneity In Genetic Diversity Among Non-Coding Loci Fails To Fit Neutral Coalescent Models Of Population History, Jeffrey L. Peters, Trina E. Roberts, Kevin Winker, Kevin G. Mccracken

Biological Sciences Faculty Publications

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two …

Distribution, Population Size, And Structure Of Himalayan Grey Goral Naemorhedus Goral Bedfordi (Cetartiodactyla: Bovidae) In Pakistan, Fakhar -I- Abbas, Kathreen E. Ruckstuhl, Afsar Mian, Tanveer Akhtar, Thomas P. Rooney

Biological Sciences Faculty Publications

Himalayan grey goral (Naemorhedus goral bedfordi) is a Red List (Near Threatened) member of Caprinae endemic to Asia, occupying the south-facing slopes of the Himalaya Mountains. The species is listed as Vulnerable on the National Pakistan Red List, but the distribution and abundance of the species within the nation is poorly known. We conducted a national census of Himalayan grey goral in Pakistan during 2002 – 2004, with the objective of documenting the geographic locations of populations, estimating population size, and describing group sizes and sex ratios. We conducted a direct count census in 98 sites distributed over …

Time Of Day Regulates Subcellular Trafficking, Tripartite Synaptic Localization, And Polyadenylation Of The Astrocytic Fabp7 Mrna, Jason R. Gerstner, William M. Vanderheyden, Timothy Lavaute, Cara J. Westmark, Labib Rouhana, Allan I. Pack, Marvin Wickens, Charles F. Landry

Biological Sciences Faculty Publications

The astrocyte brain fatty acid binding protein (Fabp7) has previously been shown to have a coordinated diurnal regulation of mRNA and protein throughout mouse brain, and an age-dependent decline in protein expression within synaptoneurosomal fractions. Mechanisms that control time-of-day changes in expression and trafficking Fabp7 to the perisynaptic process are not known. In this study, we confirmed an enrichment of Fabp7 mRNA and protein in the astrocytic perisynaptic compartment, and observed a diurnal change in the intracellular distribution of Fabp7 mRNA in molecular layers of hippocampus. Northern blotting revealed a coordinated time-of-day-dependent oscillation for the Fabp7 mRNA poly(A) tail throughout …

Correlation Of Air Displacement Plethysmography With Alternative Body Fat Measurement Techniques In Men And Women, Brittany L. Reinert, Roberta L. Pohlman, Lynn K. Hartzler

Biological Sciences Faculty Publications

Obesity has reached epidemic proportions with serious health consequences. Techniques used to measure body fat (BF) yield variable BF estimates, and this variability may lead to underestimation or overestimation of BF and subsequent treatment options. The measurements that are most accurate (Dual-Energy X-ray Absorptiometry (DEXA) and Air Displacement Plethysmography (ADP)) are expensive and often unavailable. The purpose of this study is to find the commonly available BF measurement that is the most accurate and practical for individual body types in the general population and compare these measurements to ADP (BOD POD^®) as the standard. Field measurements include skinfolds …

Prmt5 And The Role Of Symmetrical Dimethylarginine In Chromatoid Bodies Of Planarian Stem Cells, Labib Rouhana, Ana P. Vieira, Rachel H. Roberts-Galbraith, Phillip A. Newmark

Biological Sciences Faculty Publications

Planarian flatworms contain a population of adult stem cells (neoblasts) that proliferate and generate cells of all tissues during growth, regeneration and tissue homeostasis. A characteristic feature of neoblasts is the presence of chromatoid bodies, large cytoplasmic ribonucleoprotein (RNP) granules morphologically similar to structures present in the germline of many organisms. This study aims to reveal the function, and identify additional components, of planarian chromatoid bodies. We uncover the presence of symmetrical dimethylarginine (sDMA) on chromatoid body components and identify the ortholog of protein arginine methyltransferase PRMT5 as the enzyme responsible for sDMA modification in these proteins. RNA interference-mediated depletion …

Morphological Variation Of Rusty Crayfish Orconectes Rusticus (Cambaridae) With Gender And Local Scale Spatial Gradients, Luke Etchison, Stephen J. Jacquemin, Michael Allen, Mark Pyron

Biological Sciences Faculty Publications

We tested for the influence of gender, stream, and urbanization on morphological variation in rusty crayfish (Orconectes rusticus) in an east-central Indiana, US watershed. We used geometric morphometrics to characterize shape and tested for differences among and within sites. Males had shallower rostrum, increased head width and length, decreased abdomen and cephalothorax width and length, and increased telson length compared to females. Morphology of males did not vary with stream or along an urban gradient. The morphology of females varied with stream and along an urban gradient. Female shapes from small creek sites were stouter and less fusiform …

Modelling Β2ar Regulation, Sharat J. Vayttaden

Dissertations and Theses (Open Access)

The β2 adrenergic receptor (β2AR) regulates smooth muscle relaxation in the vasculature and airways. Long- and Short-acting β-agonists (LABAs/SABAs) are widely used in treatment of chronic obstructive pulmonary disorder (COPD) and asthma. Despite their widespread clinical use we do not understand well the dominant β2AR regulatory pathways that are stimulated during therapy and bring about tachyphylaxis, which is the loss of drug effects. Thus, an understanding of how the β2AR responds to various β-agonists is crucial to their rational use. Towards that end we have developed deterministic models that explore the mechanism of drug- induced β2AR regulation. These mathematical models …