Systems Biology Commons^™

Grass And Canada Goldenrod (Solidago Canadensis) Competition And Implications For Management In The Northern Tallgrass Prairie, Alexander J. Smart, Gary E. Larson, Peter J. Bauman

The Prairie Naturalist

Canada goldenrod (Solidago canadensis L.) is a native perennial forb that can form dense clonal patches and become weedy in pastures of the Northern Tallgrass Prairie Ecoregion. Our objectives were to determine 1) the competitive effects between Canada goldenrod and grass, 2) the relationship between Canada goldenrod stem density and grass biomass, and 3) the distribution of Canada goldenrod stem density at the pasture scale. We used regression analysis to develop a relationship between Canada goldenrod stem density and grass biomass. Additionally, we estimated the frequency distribution of Canada goldenrod stem density categories using three evenly distributed 100 × 100-m …

Sickleweed On The Fort Pierre National Grassland: An Emerging Threat, Jack L. Bulter, Stefanie D. Wacker

The Prairie Naturalist

We report the first detailed field survey of sickleweed (Falcaria vulgaris L.) in the United States. Sickleweed is native to Europe, the Mediterranean, Asia Minor, and Iran and was first reported in the United States in 1922. It is listed by the Nebraska Invasive Species Council as a Category II invasive plant species. In recent years, abundance and distribution of sickle- weed has increased dramatically in and around the Fort Pierre National Grassland (FPNG), South Dakota. Management of such a rapidly expanding population is hampered by a general lack of baseline information on the biology and ecology of sickleweed. We …

Energy-Saving Hypothermia Reduces Flight Ability In Mourning Doves, Jennie M. Carr, Steven L. Lima

Symposium 2012

Overwintering birds are frequently exposed to thermal challenges that can quickly decrease energy reserves, thus leading to an increase in the risk of starvation. During these periods of energetic hardship, many avian species use nocturnal hypothermia to conserve energy that would otherwise be lost remaining warm throughout the night (McKechnie & Lovegrove 2002). However, a cool body temperature (Tb) may limit a bird’s ability to monitor the environment and may slow their response to a potential threat. Thus, birds likely trade-off between the benefits of energy-saving hypothermia and the potential costs of reduced behavioral responsiveness to predators (Welton et al. …

Sphingosine-1-Phosphate Enhances Satellite Cell Activation In Dystrophic Muscles Through A S1pr2/Stat3 Signaling Pathway, Kenneth C. Loh, Weng-In Leong, Morgan E. Carlson, Babak Oskouian, Ashok Kumar, Henrik Fyrst, Meng Zhang, Richard L. Proia, Eric P. Hoffman, Julie D. Saba

Genomics and Precision Medicine Faculty Publications

No abstract provided.

San Antonio High School Food Justice Program: A Handbook And Evaluation Of Edible Education, Katherine B. Tenneson

Pitzer Senior Theses

This senior environmental studies thesis explains and analyzes edible education through a food and gardening program at a continuation high school in Claremont, California. The first chapter situates the program-specific analysis by providing background information of the edible education movement, a history of the Edible Schoolyard in Berkeley, California, and an explanation of why food is a powerful teaching tool. The second chapter delineates the program by describing all of its components and compiling essential resources and teaching documents. The third chapter is based on interviews with 9 of 12 involved students and 7 teachers, and thoroughly explains the outcomes …

Analysis Of Large Phenotypic Variability Of Eec And Shfm4 Syndromes Caused By K193e Mutation Of The Tp63 Gene, Jianhua Wei, Yang Xue, Lian Wu, Jie Ma, Xiuli Yi, Junrui Zhang, Bin Lu, Chunying Li, Dashuang Shi, Songtao Shi, Xinghua Feng, Tao Cai

Genomics and Precision Medicine Faculty Publications

No abstract provided.

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.

Determining The Genotype-Phenotype Connection In Synthetic Inducible Gene Expression Systems, Rhys M. Adams

Dissertations and Theses (Open Access)

Introduction Gene expression is an important process whereby the genotype controls an individual cell’s phenotype. However, even genetically identical cells display a variety of phenotypes, which may be attributed to differences in their environment. Yet, even after controlling for these two factors, individual phenotypes still diverge due to noisy gene expression. Synthetic gene expression systems allow investigators to isolate, control, and measure the effects of noise on cell phenotypes. I used mathematical and computational methods to design, study, and predict the behavior of synthetic gene expression systems in S. cerevisiae, which were affected by noise.

Methods I created probabilistic …

Investigating Three Decades Of Vegetation Change In A Mojave Desert Mountain Range, Chris Lee Roberts

UNLV Theses, Dissertations, Professional Papers, and Capstones

This project is a vegetation change study spanning 29 years in the Newberry Mountains of Southern Nevada. Long term monitoring data are crucial for understanding the effects of climate change on vegetation dynamics. Successful management intervention in vegetation change will require identification of early indicator plant species and their responses to climatic cues. This project is one of the oldest comparisons of resurveyed Mojave vegetation community plots with repeatable methodology and the longest survey interval reported for the southeastern Mojave Desert. 103 plots were relocated and resurveyed based on data methods in Jim Holland's thesis titled "A Vegetative Analysis of …

Role Of Non-Immune Mechanisms Of Muscle Damage In Idiopathic Inflammatory Myopathies, William Coley, Sree Rayavarapu, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

No abstract provided.

Glucocorticoid-Treated Mice Are An Inappropriate Positive Control For Long-Term Preclinical Studies In The Mdx Mouse, Arpana Sali, Alfredo D. Guerron, Heather Gordish-Dressman, Christopher F. Spurney, Micaela Iantorno, Eric P. Hoffman, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

No abstract provided.

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

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 …

Family History Of Autoimmune Disease In Patients With Aicardi-Goutières Syndrome, Johanna L. Schmidt, Ivana Olivieri, Jodie M. Vento, Elisa Fazzi, Heather A. Gordish-Dressman, Simona Orcesi, Adeline Vanderver

Genomics and Precision Medicine Faculty Publications

PURPOSE: The purpose of this study was to explore anecdotal evidence for an increase in the prevalence of autoimmune diseases in family members of patients with Aicardi-Goutières syndrome (AGS).

METHODS: Pedigrees of patients and controls were analyzed using chi-square and logistic regression to assess differences in reports of autoimmune disease among family members of cases and controls. Data was collected at Children's National Medical Center in Washington, DC, USA and at the International Aicardi-Goutières Syndrome Association Scientific Headquarters, C. Mondino National Institute of Neurology in Pavia, Italy.

RESULTS: The number of individuals with reported autoimmune disease is significantly related to …

Phylogenetic Search Through Partial Tree Mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith Crandall

Computational Biology Institute

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

CONCLUSIONS: The use of Partial Tree Mixing …

Eps Homology Domain Endosomal Transport Proteins Differentially Localize To The Neuromuscular Junction, Suzanne E. Mate, Jack H. Van Der Meulen, Priyanka Arya, Sohinee Bhattacharyya, Hamid Band, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

No abstract provided.

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 …

The Sign And Strength Of Plant-Soil Feedback For The Invasive Shrub, Lonicera Maackii, Varies In Different Soils, Kelly Schradin, Don Cipollini

Biological Sciences Faculty Publications

Plants alter soil characteristics causing changes in their subsequent growth resulting in positive or negative feedback on both their own fitness and that of other plants. In a greenhouse study, we investigated whether the sign and strength of feedback changed across two distinct soil types, and whether effects were due to shifts in biotic or abiotic soil traits. Using soils from two different locations, we examined growth of the exotic invasive shrub, Lonicera maackii and the related native shrub, Diervilla lonicera, in unconditioned soils and in soils conditioned by previous growth of L. maackii, D. lonicera, and …

Gene Duplication And The Evolution Of The Higher Diptera, Riyue Bao

Wayne State University Dissertations

Gene duplication is an important source of evolutionary innovation. Using the publicly available genomic information, I studied lineage-specific gene duplications in Drosophila melanogaster (fruit fly), Anopheles gambiae (mosquito), Tribolium castaneum (red flour beetle), and Apis mellifera (honey bee) at three scales: eye-specific genes, developmental genes, and genome-wide. All three studies consistently show that the Drosophila genome contains an exceptionally high number of lineage-specific yet ancient gene duplicates, the majority of which must have originated during the early diversification of the higher Diptera (Brachycera) at least 100 million years ago. Genetic data suggest that gene duplication played an important role in …

An Investigation Of Reflective Mulches For Use Over Capillary Mat Systems For Winter-Time Greenhouse Strawberry Production, George E. Meyer, Ellen T. Paparozzi, Elizabeth Walter-Shea, Erin E. Blankenship, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

Photosynthethically active radiation (PAR) is a principle environmental variable used by horticultural specialists, agronomists and ecosystem modelers to characterize the quantity and quality of light conducive to plant growth and development. Spatial distribution of PAR in a greenhouse can be quite variable and diffuse throughout the day time photoperiod, especially at low sun angles in northern regions of the United States. Four colors of reflective plastic mulches (white, red, olive, and black) were evaluated for winter-time strawberry (Fragaria × ananassa Duch.) production based on their reflectance and transmittance properties in a double-polyethylene, plastic-glazed Quonset greenhouse inNebraska. The spectral properties …

Multivariate Models And Algorithms For Systems Biology, Lipi Rani Acharya

LSU New Orleans Theses and Dissertations

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete …

Genetic Structure Of Grass Carp Populations In The Missouri And Mississippi River Basins, Usa, Bobbi M. Adams, Katie N. Bertrand, Michael L. Brown, Donald Auger

The Prairie Naturalist

We provided an early characterization of the genetic structure of the grass carp (Ctenopharyngodon idella) population as it expands its distribution in both the Missouri and Mississippi River basins. Further, we provided initial comparisons of allelic richness at 17 polymorphic microsatellite markers between 56 grass carp from the USA, and six from the Yangtze River in China. The number of alleles per locus ranged from two to eight and size ranges of alleles for fish collected from the invaded and native ranges were similar (P ≤ 0.001; 107–226 bp) to those previously reported in the literature. Distance-based clustering …

Notes On The Distribution Of Eastern Woodrats And Hispid Cotton Rats In South-Central Nebraska, Heather D. Wills, Keith Geluso, Eric J. Smits, Joseph T. Springer, Wesley E. Newton

The Prairie Naturalist

The eastern woodrat (Neotoma floridana) and hispid cotton rat (Sigmodon hispidus) reach distributional limits in southern Nebraska (Jones 1964, Farney 1975). In the last half-century, both species have expanded their distributional ranges in the region (Kugler and Geluso 2009, Wright et al. 2010). Herein, we report new localities of occurrence for both species that extend known distributional boundaries in south-central Nebraska beyond those reported by Kugler and Geluso (2009) and Wright et al. (2010).

Associated with other studies, we captured small mammals in Sherman live-traps in south-central Nebraska. Voucher specimens were deposited in collections at the …

Comparison Of Fish Communities In Recently Constructed Side-Channel Chutes With The Main Stem Missouri River, Kasey Whiteman, Vincent H. Travnichek, Darrick L. Garner, Brandon Eder, Kirk Steffensen

The Prairie Naturalist

Two United States Army Corp of Engineers- (USACE) funded projects were conducted from 2006 to 2008 along the Missouri River to monitor fish communities in recently constructed side-channel chutes and to monitor pallid sturgeon (Scaphirhynchus albus) and the associated fish assemblage in the main stem Missouri River. Data from both monitoring projects were compared to evaluate fish assemblages among four mitigated habitats (e.g., constructed side-channel chutes) and the main-stem Missouri River. Chutes had a greater overall number of species (n = 59) and higher species richness (Margalef’s index = 5.81), but richness was not different (F1, 4 = …

Patterns Of Age-0 Gizzard Shad Abundance And Food Habits In A Nebraska Irrigation Reservoir, Christopher L. Sullivan, Casey W. Schoenebeck, Keith D. Koupal, W. Wyatt Hoback, Brian C. Peterson

The Prairie Naturalist

Gizzard shad (Dorosoma cepedianum) are prolific spawners that can influence reservoir communities. Larval gizzard shad may compete with larval recreational fish for zooplankton resources. Therefore, it is necessary to determine larval gizzard shad dynamics and food habits to better understand their potential for competition with larval recreational fish. Our study examined age-0 gizzard shad abundance in Harlan County Reservoir during late spring/summer from 2002–2010 and food habits and prey electivity of age-0 gizzard shad during late spring/summer 2008 and 2009. The annual peak age-0 gizzard shad density 3 from 2002–2010 ranged from 50 to 380/100 m , which …

Northern Harrier Hatches Mallard Nest, Jeffery W. Stackhouse, Benjamin A. Geaumont

The Prairie Naturalist

The northern harrier (Circus cyaneus) is a widespread raptor commonly found nesting throughout the Northern Great Plains. Northern harriers forage primarily on small mammals and passerines with the males providing the majority of prey to nestlings until 14–28 days of age (Redpath et al. 2006, Vukovich and Ritchison 2006). Although the genus Circus is known to predate eggs from nest of many nesting birds (Hiraldo et al. 1975, Donaszar et al. 1996, Opermanis et al. 2000), few have been recorded commandeering nests of different species (Laine 1928, Fleskes 1992). In June 2010, we observed a northern harrier that …