Systems Biology Commons^™

Evidence For Use Of Alliaria Petiolata In North America By The European Cabbage White Butterfly, Pieris Rapae, Sam L. Davis, Don Cipollini

Biological Sciences Faculty Publications

Pieris rapae L., an invasive crop pest, may have recently begun using Alliaria petiolata Bieb. (Cavara & Grande), a European invasive biennial. We investigated how P. rapae uses forest habitats for nectar and oviposition and examined larval performance on A. petiolata in the field and laboratory. Being known primarily to occupy open habitats, we found that P. rapae regularly uses forest edge habitats, most surveyed A. petiolata plants had P. rapae damage, and P. rapae successfully used both stages of A. petiolata for larval development.

Home-Field Advantage? Evidence Of Local Adaptation Among Plants, Soil, And Arbuscular Mycorrhizal Fungi Through Meta-Analysis, Megan A. Rúa, Anita Antoninka, Pedro M. Antunes, V. Bala Chaudhary, Catherine Gehring, Louis J. Lamit, Bridget J. Piculell, James D. Bever, Cathy Zabinski, James F. Meadow, Marc J. Lajeunesse, Brook G. Milligan, Justine Karst, Jason D. Hoeksema

Biological Sciences Faculty Publications

Background: Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactions may be particularly important for plants, as they associate with microbial symbionts that can significantly affect their fitness and may enable rapid evolution. The arbuscular mycorrhizal (AM) symbiosis is ideal for investigations of local adaptation because it is globally widespread among most plant taxa and can significantly affect plant growth and fitness. Using meta-analysis on 1170 studies …

Twenty-Five Year Response Of The Herbaceous Layer Of A Temperate Hardwood Forest To Elevated Nitrogen Deposition, Frank S. Gilliam, Nicole Turrill Welch, Anne Hockenberry Phillips, Jake H. Billmyer, William T. Peterjohn, Zachariah K. Fowler, Christopher A. Walter, Mark B. Burnham, Jeffrey D. May, Mary Beth Adams

Biological Sciences Faculty Research

Increasing rates of atmospheric deposition of nitrogen (N) present a novel threat to the biodiversity of terrestrial ecosystems. Many forests are particularly susceptible to excess N given their proximity to sources of anthropogenic N emissions. This study summarizes results of a 25-yr treatment of an entire central Appalachian hardwood forest watershed via aerial applications of N with a focus on effects of added N on the cover, species richness, and composition of the herbaceous layer. Research was carried out on two watersheds of the Fernow Experimental Forest (FEF), West Virginia. The long-term reference watershed at FEF (WS4) was used as …

Epigenetics And Shared Molecular Processes In The Regeneration Of Complex Structures, Labib Rouhana, Junichi Tasaki

Biological Sciences Faculty Publications

The ability to regenerate complex structures is broadly represented in both plant and animal kingdoms. Although regenerative abilities vary significantly amongst metazoans, cumulative studies have identified cellular events that are broadly observed during regenerative events. For example, structural damage is recognized and wound healing initiated upon injury, which is followed by programmed cell death in the vicinity of damaged tissue and a burst in proliferation of progenitor cells. Sustained proliferation and localization of progenitor cells to site of injury give rise to an assembly of differentiating cells known as the regeneration blastema, which fosters the development of new tissue. Finally, …

Tachinid Collecting In Temperate South America. Expeditions Of The Phylogeny Of World Tachinide Project. Part Iii. Chile, John O. Stireman Iii, James E. O'Hara, Pierfilippo Cerretti, Diego J. Inclán

Biological Sciences Faculty Publications

As readers of this newsletter are likely familiar, we and our collaborators have been working for the past several years on a family-wide phylogeny of the Tachinidae of the world (see Stireman et al. 2013, Winkler et al. 2014). We have already published a morphological analysis of tachinid phylogenetics (Cerretti et al. 2014), as well as an initial molecular phylogenetic framework for the family (Winkler et al. 2015). An in-depth molecular phylogenetic analysis of the Phasiinae led by Jeremy Blaschke (originally at University of Tennessee and now at Union University, TN) and Kevin Moulton (U. of Tenn.) is currently being …

Transcriptome Analysis Of Vaccine Responses To Francisella Tularensis Or Venezuelan Equine Encephalitis Virus, Rebecca Ann Erwin-Cohen

Walden Dissertations and Doctoral Studies

The lack of vaccines for emerging and re-emerging diseases highlights technical gaps and indicates a need for innovative approaches to produce new vaccines. Vaccines may be improved by knowledge of host responses to vaccination, disease pathogenesis, and the effect of age and genetics on vaccine outcome. This study's purpose was to quantitatively assess the molecular epidemiology of Francisella tularensis (Ft) and Venezuelan Equine Encephalitis Virus (VEEV). Study results support the Epidemiology Nexus model which holds that association of changes in gene expression to vaccination facilitate understanding the mechanisms of immune development and link public health and disease epidemiology. My research …

A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris

Theses and Dissertations

The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …

Synthesis Of Satellite Microwave Observations For Monitoring Global Land-Atmosphere Co2 Exchange, Lucas Alan Jones

Graduate Student Theses, Dissertations, & Professional Papers

This dissertation describes the estimation, error quantification, and incorporation of land surface information from microwave satellite remote sensing for modeling global ecosystem land-atmosphere net CO₂ exchange. Retrieval algorithms were developed for estimating soil moisture, surface water, surface temperature, and vegetation phenology from microwave imagery timeseries. Soil moisture retrievals were merged with model-based soil moisture estimates and incorporated into a light-use efficiency model for vegetation productivity coupled to a soil decomposition model. Results, including state and uncertainty estimates, were evaluated with a global eddy covariance flux tower network and other independent global model- and remote-sensing based products.

Mitochondrial Function Assessed By 31p Mrs And Bold Mri In Non-Obese Type 2 Diabetic Rats, Yuchi Liu, Xunbai Mei, Jielei Li, Nicola Lai, Xin Yu

Electrical & Computer Engineering Faculty Publications

The study aims to characterize age-associated changes in skeletal muscle bioenergetics by evaluating the response to ischemia-reperfusion in the skeletal muscle of the Goto-Kakizaki (GK) rats, a rat model of non-obese type 2 diabetes (T2D). ³¹P magnetic resonance spectroscopy (MRS) and blood oxygen level-dependent (BOLD) MRI was performed on the hindlimb of young (12 weeks) and adult (20 weeks) GK and Wistar (control) rats. ³¹P-MRS and BOLD-MRI data were acquired continuously during an ischemia and reperfusion protocol to quantify changes in phosphate metabolites and muscle oxygenation. The time constant of phosphocreatine recovery, an index of mitochondrial oxidative capacity, …

Suppression Of F1 Male-Specific Lethality In Caenorhabditis Hybrids By Cbr-Him-8, Vaishnavi Ragavapuram, Emily Elaine King, Scott Everet Baird

Biological Sciences Faculty Publications

Haldane's Rule and Darwin's Corollary to Haldane's Rule are the observations that heterogametic F1 hybrids frequently are less fit than their homogametic siblings and that asymmetric results often are obtained from reciprocal hybrid crosses. In Caenorhabditis, Haldane's Rule and Darwin's Corollary have been observed in several hybrid crosses, including crosses of Caenorhabditis briggsae and Caenorhabditis nigoni. Fertile F1 females are obtained from reciprocal crosses. However, F1 males obtained from C. nigoni mothers are sterile and F1 males obtained from C. briggsae die during embryogenesis. We have identified cbr-him-8 as a recessive maternal-effect suppressor of F1 hybrid male-specific lethality …

Classification Of Breast Cancer Patients Using Somatic Mutation Profiles And Machine Learning Approaches, Suleyman Vural

Theses & Dissertations

The high degree of heterogeneity observed in breast cancers makes it very difficult to classify cancer patients into distinct clinical subgroups and consequently limits the ability to devise effective therapeutic strategies. In this study, we explore the use of gene mutation profiles to classify, characterize and predict the subgroups of breast cancers. We analyzed the whole exome sequencing data from 358 ethnically similar breast cancer patients in The Cancer Genome Atlas (TCGA) project. Identified somatic and non-synonymous single nucleotide variants were assigned a quantitative score (C-score) that represents the extent of negative impact on the function of the gene. Using …

Are Immune Modulating Single Nucleotide Polymorphisms Associated With Necrotizing Enterocolitis?, Ashanti L Franklin, Mariam Said, Clint D Cappiello, Heather Gordish-Dressman, Zohreh Tatari-Calderone, Stanislav Vukmanovic, Khodayar Rais-Bahrami, Naomi L C Luban, Joseph M Devaney, Anthony D Sandler

Genomics and Precision Medicine Faculty Publications

Necrotizing enterocolitis (NEC) is a devastating gastrointestinal emergency. The purpose of this study is to determine if functional single nucleotide polymorphisms (SNPs) in immune-modulating genes pre-dispose infants to NEC. After Institutional Review Board approval and parental consent, buccal swabs were collected for DNA extraction. TaqMan allelic discrimination assays and BglII endonuclease digestion were used to genotype specific inflammatory cytokines and TRIM21. Statistical analysis was completed using logistic regression. 184 neonates were analyzed in the study. Caucasian neonates with IL-6 (rs1800795) were over 6 times more likely to have NEC (p = 0.013; OR = 6.61, 95% CI 1.48-29.39), and over …

Book Reviews: Bumble Bees Of North America. Paul H. Williams, Robbin W. Thorp, Leif L. Richardson, And Sheila R. Colla., Samuel O’Dell

The Prairie Naturalist

Bumblebee identification is generally considered straight- forward, yet mistakes often are made due to the degree of similarity between the color patterns of different species. Bumble Bees of North America aims to improve the accuracy of identifications by both casual observers and professionals through the use of intuitive diagrams, descriptions, and the more technical dichotomous keys. In addition to providing the first complete field guide to North American bumblebees, the authors make efficient use of the reader’s attention by summarizing taxonomic history, favored food plants, and environmental issues concerning bumblebees.

Bumble Bees of North America is organized into three distinct …

Sage-Grouse Nests In An Active Conifer Mastication Site, Charles P. Sandford, David K. Dahlgren, Terry A. Messmer

The Prairie Naturalist

Greater sage-grouse (Centrocercus urophasianus; sage-grouse) have experienced long-term range-wide population declines and now may occupy less than 50% of their historic range (Schroeder et al. 2004). Conifer encroachment into sagebrush (Artemisia spp.) habitat was identified as a major conservation threat by the United States Fish and Wildlife Service (USFWS) as the agency reviewed the listing status of the species for possible protection under the Endangered Species Act of 1973 (USFWS 2013).

Conifer encroachment into sagebrush habitats negatively impacts sage-grouse at landscape scales (Doherty et al. 2008, Casazza et al. 2011, Baruch-Mordo et al. 2013). Sage-grouse will utilize …

North Shore: A Natural History Of Minnesota’S Superior Coast, Janet R. Keough

The Prairie Naturalist

Many readers of The Prairie Naturalist have lived along or visited Lake Superior’s coast. Like me, you have probably wondered about the geology and history of this beautiful and dramatic feature of northeastern Minnesota. Chel Anderson and Adelheid Fischer have written an accessible book that comprehensively describes the history and geology of the coast, surrounding highlands, and Lake Superior itself. In addition, the authors have provided fascinating subchapters on some of the most interesting species that are key elements of the region.

This rather large but beautiful book is arranged in five major chapters that cover the dominant geological units …

Notes: Woodpecker Forage Availability In Habi- Tat Disturbances Of The Black Hills, Brian E. Dickerson, Angie K. Ambourn, Mark A. Rumble, Kurt K. Allen, Chad P. Lehman

The Prairie Naturalist

Habitat disturbance events are critical to ecological systems in which some bird species have become specialized. The vegetation community, reduced competition, ability to avoid predators, nest-site characteristics, and forage opportunities within a disturbed ecosystem are all aspects that make it desirable for selection by particular species (Svärdson 1949, Cody 1981, Martin 1998). Specifically, avian species rely on the forest conditions created by fire, insects, and disease (Brawn et al. 2001, Hunter et al. 2001, Devictor et al. 2008). In the Black Hills National Forest (BHNF) of South Dakota,two major types of natural disturbances include wildfires and mountain pine beetle (Dendroctonus …

Estimating Herbaceous Biomass Of Grassland Vegetation Using The Reference Unit Method, Eric D. Boyda, Jack L. Bulter, Lan Xu

The Prairie Naturalist

Aboveground net primary production provides valuable information on wildlife habitat, fire fuel loads, and forage availability. Aboveground net primary production in herbaceous plant communities is typically measured by clipping aboveground biomass. However, the high costs associated with physically harvesting plant biomass may prevent collecting sufficient data to account for natural spatial and temporal variability of vegetation at a landscape scale. Various double-sampling techniques have been developed to increase sample size while reducing cost. We applied a biomass estimation technique previously developed for estimating shrub biomass using representative samples or “reference units” to estimate herbaceous grassland biomass. Our reference units consisted …

Sampling Terrestrial Arthropod Biodiversity: A Case Study In Arkansas, Michael Joseph Skvarla

Graduate Theses and Dissertations

The Interior Highlands is a biodiversity hotspot, with at least 200 known endemic species, but is understudied compared to hotspots, such as the Southern Appalachians. In order to begin to rectify this issue, a nine month study was conducted from mid-March through early December at a 4 ha site at Steel Creek, Buffalo National River, in Newton County, Arkansas. Thirteen collecting methods were employed, including three colors of Lindgren funnel trap, five colors of pan trap, Malaise traps, canopy traps with upper and lower collectors, pitfall traps, and Berlese-Tullgren extraction of leaf litter, which resulted in the collection of 1311 …

Systematics Of Testudacarine Torrent Mites (Parasitengona: Torrenticolidae), Joseph Charles O'Neill

Graduate Theses and Dissertations

Thirteen new species of Testudacarus (Torrenticolidae: Testudacarinae) are described, four species are redescribed, and the status of previously problematic species are addressed. For Testudacarinae this represents the first published: 1) descriptions from multiple specimens (therefore providing ranges); 2) colored photographs; 3) explicit illustrations and discussion of sexual dimorphism within the subfamily; 4) genetic data. A comprehensive literature review is also included.

Effects Of Short-Term Soil Conditioning By Cheatgrass And Western Wheatgrass, James J. O'Connor, Janet S. Prevey

The Prairie Naturalist

The exotic grass Bromus tectorum (cheatgrass) is a ubiquitous invader in the western USA. Cheatgrass is a proficient competitor, frequently displacing native plants, forming monotypic stands and reducing biodiversity in ecosystems it invades. Our experiment tested whether short-term soil modification by cheatgrass and a predominant native grass, Pascopyrum smithii (western wheatgrass), affected subsequent growth of both species. We compared productivity of cheatgrass and western wheatgrass by harvesting aboveground biomass of plants grown in either cheatgrass- or western wheatgrass-conditioned soils over two simulated growing seasons. Results indicated that cheatgrass soils do not inhibit the productivity of the native grass, but do …