Systems Biology Commons^™

Field Discrimination Of Prairie Deer Mice And White-Footed Mice Using Morphological Characteristics, Jacob L. Berl, Kelton M. Verble, Elizabeth A. Flaherty, Robert K.S. Swihart

The Prairie Naturalist

Field discrimination of prairie deer mice (Peromyscus maniculatus bairdii) and white-footed mice (P. leucopus noveboracensis) can be difficult throughout much of the central United States where they co-occur. We live-trapped prairie deer mice and white-footed mice within forested and row-crop habitats in central Indiana and used multiplex PCR with species-specific primers to positively determine species identification. We collected a suite of commonly measured external morphological traits (body weight and lengths of ear, hindfoot, tail, and body) from each captured animal. Individuals were assigned to species based on analysis of DNA; discriminant function analysis was used to …

Cytoplasmic Cyclin E Mediates Resistance To Aromatase Inhibitors In Breast Cancer, Iman Doostan

Dissertations and Theses (Open Access)

Almost seventy percent of patients with breast cancer have tumors that express hormone receptors and need hormonal therapy. Aromatase inhibitors (AIs) block estrogen biosynthesis and are considered as the first line hormonal therapy for ER⁺ post-menopausal patients. However, resistance to these drugs remains a major challenge in clinic and the biology of such resistance is not completely understood. Cyclin E is deregulated in breast cancer through generation of low molecular weight isoforms that renders patients to a poor survival. Herein, we show that HR+ patients with LMW-E expressing tumors show diminished early response to neo-adjuvant AIs as well as …

Hydrology And Macroinvertebrates As Biological Indicators- An Integrated Study Of The Río Zamora Watershed, Loja, Ecuador, Isabel Ryde

Independent Study Project (ISP) Collection

Water quality and access is under grave threat in Ecuador, yet remains poorly studied. Macroinvertebrates were used as biological indicators to study water quality around Reserva Natural Madrigal del Podocarpus, Loja Province, Ecuador. Data on macroinvertebrates was combined with hydrologic measurements of stream functions. Macroinvertebrate sampling was conducted from 6 sites within the Upper Río Zamora watershed. Geologic outcrops were observed along several roadcuts and stream banks. Hydrologic data was collected by measuring discharge, elevation change, and finding the highest permanent spring. The EPT index (number of EPT individuals and percentage of EPT individuals) and the BMWP/Colombia Index for macroinvertebrates …

Modeling Virus Coinfection To Inform Management Of Maize Lethal Necrosis In Kenya, Frank H. Hilker, Linda S. J. Allen, Vrushali A. Bokil, Cheryl J. Briggs, Zhilan Feng, Karen A. Garrett, Louis J. Gross, Frédéric M. Hamelin, Michael J. Jeger, Carrie A. Manore, Alison G. Power, Margaret G. Redinbaugh, Megan A. Rúa, Nik J. Cunniffee

Biological Sciences Faculty Publications

Maize lethal necrosis (MLN) has emerged as a serious threat to food security in sub-Saharan Africa. MLN is caused by coinfection with two viruses, Maize chlorotic mottle virus and a potyvirus, often Sugarcane mosaic virus. To better understand the dynamics of MLN and to provide insight into disease management, we modeled the spread of the viruses causing MLN within and between growing seasons. The model allows for transmission via vectors, soil, and seed, as well as exogenous sources of infection. Following model parameterization, we predict how management affects disease prevalence and crop performance over multiple seasons. Resource-rich farmers with …

Systems Biology Approach To Late-Onset Alzheimer's Disease Genome-Wide Association Study Identifies Novel Candidate Genes Validated Using Brain Expression Data And Caenorhabditis Elegans Experiments, Shubhabrata Mukherjee, Joshua C. Russell, Daniel T. Carr, Jeremy D. Burgess, Mariet Allen, Daniel J. Serie, Kevin L. Boehme, John S. K. Kauwe, Adam C. Naj, David W. Fardo, Dennis W. Dickson, Thomas J. Montine, Nilufer Ertekin-Taner, Matt R. Kaeberlein, Paul K. Crane

Biostatistics Faculty Publications

Introduction—We sought to determine whether a systems biology approach may identify novel late-onset Alzheimer's disease (LOAD) loci.

Methods—We performed gene-wide association analyses and integrated results with human protein-protein interaction data using network analyses. We performed functional validation on novel genes using a transgenic Caenorhabditis elegans Aβ proteotoxicity model and evaluated novel genes using brain expression data from people with LOAD and other neurodegenerative conditions.

Results—We identified 13 novel candidate LOAD genes outside chromosome 19. Of those, RNA interference knockdowns of the C. elegans orthologs of UBC, NDUFS3, EGR1, and ATP5H were associated with Aβ …

Exploring Biological Heterogeneity And Its Consequences At Tissue And Cellular Scales Through Mathematical And Computational Modeling, Romica Kerketta

Biomedical Sciences ETDs

This dissertation explores the effects of heterogeneity across different biological scales in cancer as well as normal cells. At the tissue scale, we investigated the variability present in the tumor microenvironment and its effect on patient chemotherapeutic outcomes using a mathematical model of drug transport. We found that parameters such as tumor blood perfusion and radius of blood vessel had an impact on the tumor cytotoxicity. This indicated that the physical microenvironment of the tumor is an important regulator of the tumor response to chemotherapy. At the cellular scale, we investigated the heterogeneity present on the membrane landscape of ErbB2 …

The Angiotensin-Converting Enzyme Insertion/Deletion Polymorphism Rs4340 Associates With Habitual Physical Activity Among European American Adults., Michael Bruneau, Theodore J Angelopoulos, Paul Gordon, Niall Moyna, Paul Visich, Robert Zoeller, Rick Seip, Stephen Bilbie, Paul Thompson, Joseph Devaney, Heather Gordish-Dressman, Eric Hoffman, Linda S Pescatello

Genomics and Precision Medicine Faculty Publications

BACKGROUND: The angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism (rs4340) (ACE DIP) accounts for half of the variability in plasma ACE concentrations. ACE has been widely studied for its influence on sports performance; however, research on its influence in physical activity is limited and inconsistent. We examined the influence of the ACE DIP on physical activity among 461 European Americans.

METHODS: Subjects completed the Paffenbarger Physical Activity Questionnaire for weekly walking distance. Multivariate analysis of covariance (MANCOVA) tested log-transformed differences in weekly walking distance among ACE DIP genotypes (II, ID, DD) with gender as a fixed factor, and age and body …

Itraq-Based Proteomics Analysis And Network Integration For Kernel Tissue Development In Maize, Long Zhang, Yongbin Dong, Qilei Wang, Chunguang Du, Wenwei Xiong, Xinyu Li, Sailan Zhu, Yuling Li

Department of Biology Faculty Scholarship and Creative Works

Grain weight is one of the most important yield components and a developmentally complex structure comprised of two major compartments (endosperm and pericarp) in maize (Zea mays L.), however, very little is known concerning the coordinated accumulation of the numerous proteins involved. Herein, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic method to analyze the characteristics of dynamic proteomics for endosperm and pericarp during grain development. Totally, 9539 proteins were identified for both components at four development stages, among which 1401 proteins were non-redundant, 232 proteins were specific in pericarp and 153 proteins were specific in …

Allergen Homologs In The Euroglyphus Maynei Draft Genome, S. Dean Rider, Majorie S. Morgan, Larry G. Arlian

Biological Sciences Faculty Publications

Euroglyphus maynei is a house dust mite commonly found in homes worldwide and is the source of allergens that sensitize and induce allergic reactions in humans. It is the source of species-specific allergens as well as allergens that are cross-reactive with the allergens from house dust mites Dermatophagoides farinae and D. pteronyssinus, and the ectoparasitic scabies mite Sarcoptes scabiei. The genomics, proteomics and molecular biology of E. maynei and its allergens have not been as extensively investigated as those of D. farinae, D. pteronyssinus, and S. scabiei where natural and recombinant allergens from these species have been characterized. Until now, …

The Mayfly Newsletter, Donna J. Giberson

The Mayfly Newsletter

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

African-American Esophageal Squamous Cell Carcinoma Expression Profile Reveals Dysregulation Of Stress Response And Detox Networks., Hayriye Verda Erkizan, Kory Johnson, Svetlana Ghimbovschi, Deepa Karkera, Gregory Trachiotis, Houtan Adib, Eric P Hoffman, Robert G Wadleigh

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC), the subtype that shows marked variation in geographic frequency. The molecular architecture of African-American ESCC is still poorly understood. It is unclear why African-American ESCC is more aggressive and the survival rate in these patients is worse than those of other ethnic groups.

METHODS: To begin to define genetic alterations that occur in African-American ESCC we conducted microarray expression profiling in pairs of esophageal squamous cell tumors and matched control tissues.

RESULTS: …

Identification Of Antigenic Sarcoptes Scabiei Proteins For Use In A Diagnostic Test And Of Non-Antigenic Proteins That May Be Immunomodulatory, Majorie S. Morgan, S. Dean Rider, Larry G. Arlian

Biological Sciences Faculty Publications

Background

Scabies, caused by the mite, Sarcoptes scabiei, infects millions of humans, and many wild and domestic mammals. Scabies mites burrow in the lower stratum corneum of the epidermis of the skin and are the source of substances that are antigenic or modulate aspects of the protective response of the host. Ordinary scabies is a difficult disease to diagnose.

Objective

The goal of this project was to identify S. scabiei proteins that may be candidate antigens for use in a diagnostic test or may be used by the mite to modulate the host’s protective response.

Methods

An aqueous …

Exploring The Biogeography Of South American Rainforest Understory Birds Using Morphological Variation In The Wedge-Billed Woodcreeper ( Glyphorynchus Spirurus ), Gregory Tito

Theses and Dissertations

Tropical rainforests in the Amazon Basin show an extraordinarily high degree of biodiversity, the reasons for which are poorly understood. A number of biogeographical models have been proposed to account for the variation present within and among species, including birds. This study tests the predictive ability of six major historical vicariant biogeographical models (Andean uplift, marine incursion, Amazonian lake, river barrier, refuge, and river refuge) using a large data set of morphological characters in the Wedge-billed Woodcreeper (Glyphorynchus spirurus), a small understory songbird found mostly in terra firme tropical rain forest. It also characterizes variation in key morphological characters and …

Book Reviews: American Serengeti: The Last Big Animals Of The Great Plains. Dan Flores., Daniel S. Licht

The Prairie Naturalist

Before describing what Flores’ book is, I must state what it is not. It is not a technical book designed for scholarly readers. Sources are not fully cited, and the bibliography is of limited scope. Nor is it a comprehensive book of all the megafauna of the Great Plains. Although chapters are devoted to extant species such as American bison (Bison bison), pronghorn (Antilocapra americana), and coyote (Canis latrans), there are only passing references to mule and white-tailed deer (Odocoileus hemionus and O. virginianus, respectively), elk (Cervus canadensis), and bighorn sheep (Ovis canadensis). Rather, Flores devotes chapters to grizzly bears …

Pheasant Response To Lead Ingestion, Travis J. Runia, Alex J. Solem

The Prairie Naturalist

Lead is toxic to all vertebrate species and ingestion of spent lead pellets from hunting is the primary method of exposure in birds. Both acute and chronic effects occur in response to lead ingestion including death, weight loss, and reduced body function, but the effect is highly variable among species. Most research has focused on lead ingestion impacts on waterfowl, but less is known about the effects of lead ingestion by upland game such as ring-necked pheasants (Phasianus colchicus). We gavage- fed zero, one, or three lead pellets to 90 (n = 30/group) captive-raised adult hen pheasants and monitored survival …

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 49 No. 1

The Prairie Naturalist

TABLE OF CONTENTS

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Diel and Monthly Movement Rates by Migratory and Resident Female Pronghorn Paul F. Jones, T. Andrew Hurley, Chelsea Jensen, Karl Zimmer, and Andrew Jakes

13 Pheasant Response to Lead Ingestion Travis J. Runia and Alex J. Solem

NOTES

19 Examining the Potential Competitive Effects of Ventenata dubia on Annual and Perennial Grasses Shawn McKay, Lesley R. Morris, Christopher E. Morris, and Elizabeth A. Leger

23 Adult Red-Headed Woodpecker Interaction with Bullsnake After Arboreal Nest Depradation Brittany J. Yohannes and James L. Howitz

26 Breeding Trumpeter Swans in Northeastern North Dakota Mark …

Notes: Examining The Potential Competitive Effects Of Ventenata Dubia On Annual And Perennial Grasses, Shawn Mckay, Lesley R. Morris, Christopher E. Morris, Elizabeth A. Leger

The Prairie Naturalist

Portions of the United States are becoming increasingly dominated by annual species, with cheatgrass (Bromus tectorum L.) and medusahead (Taeniatherum caput-medusae [L.] Nevski) as the most common and well-known invaders (Bansal et al. 2014). Other invasive annual species also are present and increasing in abundance, including ventenata (Ventenata dubia [Leers] Coss.), an invasive annual grass that has been expanding within the Pacific Northwest, Great Basin, and Great Plains regions of the United States. Ventenata was first reported in North America in 1952 in Washington (Old and Callihan 1987) and has since spread to 7 western states in the USA (CA, …

Adult Red-Headed Woodpecker Interaction With Bullsnake After Arboreal Nest Depredation, Brittney J. Yohannes, James L. Howitz

The Prairie Naturalist

Nest success rates often are higher among cavity-nesting birds than those that nest in open cups or on the ground. Among cavity-nesting birds, woodpeckers have some of the highest rates of nest success. A review of woodpecker nesting ecology across species documented nest success ranging from 0.42 to 1.00 with a median of 0.80 (n = 84 populations), and that predation was low, ranging from 0.00 to 0.35 with a median of 0.13 (n = 33 populations). The constrained opening to a cavity nest limits predation to relatively small animals or those able to break open cavity walls. …

Diel And Monthly Movement Rates By Migratory And Resident Female Pronghorn, Paul F. Jones, T. Andrew Hurly, Chelsea Jensen, Karl Zimmer, Andrew Jakes

The Prairie Naturalist

Animal movement patterns are variable, with certain species primarily being diurnal and others nocturnal. Pronghorn (Antilocapra americana) are regarded as diurnal animals moving predominately during daylight hours. Anecdotal accounts, however, suggest that pronghorn move during the night but the extent, frequency, and importance of these nocturnal movement behaviors are unknown. To evaluate movements, we combined global positioning system relocation data from collared female pronghorn in the Northern Sagebrush Steppe between 2003 and 2007 with sunrise/sunset data within a geographical information system platform. We assessed whether mean and maximum movement rates were influenced by diel period (dawn, day, dusk, and night), …

Use Of Satellite Trap Transmitters In Capturing Mountain Lions, Randy D. Johnson, Jonathan A. Jenks, Stephanie A. Tucker

The Prairie Naturalist

The use of safe and humane methods for the capture of wild animals is imperative in wildlife research, wildlife damage management, and feral animal control. When capturing animals successfully and humanely, several items must be addressed, including animal safety, personnel safety, non-target captures, and cost (Sikes et al. 2016). Additionally, public pressures against the use of traps have led to significant changes in trapping regulations across North America and beyond (Andelt et al. 1999, Darrow and Shivik 2008) and can place research projects at risk to loss of Institutional Animal Care and Use Committee (IACUC) approval (Larkin et al. 2003). …