Systems Biology Commons^™

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 …

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 …

Remembering Paul B. Kannowski, Robert Seabloom

The Prairie Naturalist

I am saddened to report that Dr. Paul Kannowski passed away 3 September 2015, succumbing to cancer. He was 88. A native of Grand Forks, Paul attended the University of North Dakota for his B.S. and M.S. degrees, and the University of Michigan for his Ph.D. He joined the University of North Dakota Biology Department in 1957, retiring in 1990 after 33 years of service

Paul chaired UND’s Biology Department twice, totaling 13 years, considered to be a remarkable achievement by many of us who have been exposed to that task! His leadership was instrumental in the nearly exponential growth …

Variability In The Selection Patterns Of Pronghorn: Are They Really Native Prairie Obligates?, Paul F. Jones, Mike Grue, Mike Suitor, Darren J. Bender, Cormack Gates, Dale Eslinger, Julie Landry-Deboer

The Prairie Naturalist

In Canada, pronghorn (Antilocapra americana) are primarily considered a native prairie obligate because of their reliance on open grassland vegetation communities, although an assessment of local ecological knowledge suggests that pronghorn in Alberta select a variety of habitat from native prairie to cultivated lands. The primary objective of our study was to assess whether pronghorn in Alberta and Saskatchewan are native prairie obligates. Specifically, we addressed the following questions: 1) do individual pronghorn show similar selection patterns for native prairie and, therefore, support the notion that they are prairie obligates; 2) do pronghorn show consistent resource selection patterns …

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 …

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 …

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 …

Distribution And Occurrence Of Bat Species In North Dakota, Josiah J. Nelson, Paul R. Barnhart, Erin H. Gillam

The Prairie Naturalist

Prior to 2009, a detailed survey of occurrence and distribution of bats in North Dakota had not been conducted. Localized surveys, occurrence reports, and museum specimens provided the only records of bats in the state. Ongoing habitat loss, exploitation of natural resources, and the impending spread of white-nose syndrome to the western United States are major threats to bat populations of the region. The objective of this study was to document presence and distributions of bat species resident in North Dakota. From 2009 to 2012, multiple mist-netting and acoustic surveys were conducted to document species presence across North Dakota. A …

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

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 …

Remembering The Days Of Old: Data Exploration And Simple Statistics, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! By the time you read this editorial, most of you will probably be enjoying spectacular seasonal changes in the outdoors this autumn and a hint of winter in the air (for those of us in the northern Great Plains region). I write this editorial during my favorite time of year, deer hunting in the Midwest. Temperatures are finally start- ing to resemble the fall and the Christmas Holiday season is just around the corner. Much like my children have images of Santa dancing in their heads on Christmas Eve, each fall I replay images of a trophy …

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.

Effect Of Genetic Background On The Dystrophic Phenotype In Mdx Mice., William D Coley, Laurent Bogdanik, Maria Candida Vila, Qing Yu, Terence A Partridge, Kanneboyina Nagaraju, +12 Additional Authors

Genomics and Precision Medicine Faculty Publications

Genetic background significantly affects phenotype in multiple mouse models of human diseases, including muscular dystrophy. This phenotypic variability is partly attributed to genetic modifiers that regulate the disease process. Studies have demonstrated that introduction of the γ-sarcoglycan null allele onto the DBA/2J background confers a more severe muscular dystrophy phenotype than the original strain, demonstrating the presence of genetic modifier loci in the DBA/2J background. To characterize the phenotype of dystrophin deficiency on the DBA/2J background, we created and phenotyped DBA/2J-congenic Dmdmdx mice (D2-mdx) and compared them to the original, C57BL/10ScSn-Dmdmdx (B10-mdx) model. These strains were compared to their respective …

Sidestream Smoke Exposure Increases The Susceptibility Of Airway Epithelia To Adenoviral Infection, Priyanka Sharma, Abimbola O. Kolawole, Susan B. Core, Adriana E. Kajon, Katherine J.D.A. Excoffon

Biological Sciences Faculty Publications

Background: Although significant epidemiological evidence indicates that cigarette smoke exposure increases the incidence and severity of viral infection, the molecular mechanisms behind the increased susceptibility of the respiratory tract to viral pathogens are unclear. Adenoviruses are non-enveloped DNA viruses and important causative agents of acute respiratory disease. The Coxsackievirus and adenovirus receptor (CAR) is the primary receptor for many adenoviruses. We hypothesized that cigarette smoke exposure increases epithelial susceptibility to adenovirus infection by increasing the abundance of apical CAR. Methodology and Findings: Cultured human airway epithelial cells (CaLu-3) were used as a model to investigate the effect of sidestream cigarette …

Age-Associated Methylation Suppresses Spry1, Leading To A Failure Of Re-Quiescence And Loss Of The Reserve Stem Cell Pool In Elderly Muscle., Anne Bigot, William J Duddy, Zamalou G Ouandaogo, Elisa Negroni, Virginie Mariot, Svetlana Ghimbovschi, Brennan Harmon, Aurore Wielgosik, Camille Loiseau, Joseph Devaney, Julie Dumonceaux, Gillian Butler-Browne, Vincent Mouly, Stéphanie Duguez

Genomics and Precision Medicine Faculty Publications

The molecular mechanisms by which aging affects stem cell number and function are poorly understood. Murine data have implicated cellular senescence in the loss of muscle stem cells with aging. Here, using human cells and by carrying out experiments within a strictly pre-senescent division count, we demonstrate an impaired capacity for stem cell self-renewal in elderly muscle. We link aging to an increased methylation of the SPRY1 gene, a known regulator of muscle stem cell quiescence. Replenishment of the reserve cell pool was modulated experimentally by demethylation or siRNA knockdown of SPRY1. We propose that suppression of SPRY1 by age-associated …

Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20151027 - Please Download "75" Instead, George Mcnamara

George McNamara

McNamara 201412 NIH SCAP InnoCentive Challenge Solution - T-Bow Rainbow T-cells and Tumor Cells Spatial Multiplexing Gene Expression Reporter System – plus supplement plus posters - 20151027.

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Please download the current 20151027 (October 27, 2015) Tattletales and T-Bow update from

http://works.bepress.com/gmcnamara/75/

The bepress web site is not letting me replace the old pdf here at "65" with the additional 10 pages update.

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The download is my/Cooper lab solution (submission) to the 2014 NIH Single Cell Analysis Program (SCAP) InnoCentive Challenge, "Follow That Cell". I submitted the Solution on 20141215Mon (with 20 minutes to spare). The Challenge web page …

The Potential For A Blood Test For Scabies, Larry G. Arlian, Hermann Feldmeier, Majorie S. Morgan

Biological Sciences Faculty Publications

Scabies, caused by the mite S. scabiei that burrows in the skin of humans, is a contagious skin disease that affects millions of people worldwide. It is a significant public health burden in economically disadvantaged populations, and outbreaks are common in nursing homes, daycare facilities, schools and workplaces in developed countries. It causes significant morbidity, and in chronic cases, associated bacterial infections can lead to renal and cardiac diseases. Scabies is very difficult to diagnose by the usual skin scrape test, and a presumptive diagnosis is often made based on clinical signs such as rash and itch that can …

Immunopurification Of Ago1 Mirnps Selects For A Distinct Class Of Microrna Targets, Xin Hong, Molly Hammell, Victor Ambros, Stephen Cohen

Victor R. Ambros

microRNAs comprise a few percent of animal genes and have been recognized as important regulators of a diverse range of biological processes. Understanding the biological functions of miRNAs requires effective means to identify their targets. Combined efforts from computational prediction, miRNA over-expression or depletion, and biochemical purification have identified thousands of potential miRNA-target pairs in cells and organisms. Complementarity to the miRNA seed sequence appears to be a common principle in target recognition. Other features, including miRNA-target duplex stability, binding site accessibility, and local UTR structure might affect target recognition. Yet computational approaches using such contextual features have yielded largely …

Tnf-Α-Induced Micrornas Control Dystrophin Expression In Becker Muscular Dystrophy., Alyson A. Fiorillo, Christopher R. Heier, James S. Novak, Christopher B. Tully, Kristy J. Brown, Kitipong Uaesoontrachoon, Maria C. Vila, Peter P. Ngheim, Luca Bello, Joe N. Kornegay, Corrado Angelini, Terence A. Partridge, Kanneboyina Nagaraju, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

The amount and distribution of dystrophin protein in myofibers and muscle is highly variable in Becker muscular dystrophy and in exon-skipping trials for Duchenne muscular dystrophy. Here, we investigate a molecular basis for this variability. In muscle from Becker patients sharing the same exon 45–47 in-frame deletion, dystrophin levels negatively correlate with microRNAs predicted to target dystrophin. Seven microRNAs inhibit dystrophin expression in vitro, and three are validated in vivo (miR-146b/miR-374a/miR-31). microRNAs are expressed in dystrophic myofibers and increase with age and disease severity. In exon-skipping-treated mdx mice, microRNAs are significantly higher in muscles with low …

Gene Diversification Of An Emerging Pathogen: A Decade Of Mutation In A Novel Fish Viral Hemorrhagic Septicemia (Vhs) Substrain Since Its First Appearance In The Laurentian Great Lakes, Carol A. Stepien, Lindsey R. Pierce, Douglas W. Leaman, Megan D. Niner, Brian S. Shepherd

Biological Sciences Faculty Publications

Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus, which causes one of the world's most serious fish diseases, infecting >80 freshwater and marine species across the Northern Hemisphere. A new, novel, and especially virulent substrain—VHSv-IVb—first appeared in the Laurentian Great Lakes about a decade ago, resulting in massive fish kills. It rapidly spread and has genetically diversified. This study analyzes temporal and spatial mutational patterns of VHSv-IVb across the Great Lakes for the novel non-virion (Nv) gene that is unique to this group of novirhabdoviruses, in relation to its glycoprotein (G), phosphoprotein (P), …

Macroecology Of North American Suckers (Catostomidae): Tests Of Bergmann's And Rapoport's Rules, Stephen J. Jacquemin, Jason C. Doll

Biological Sciences Faculty Publications

Discerning spatial macroecological patterns in freshwater fishes has broad implications for community assembly, ecosystem dynamics, management, and conservation. This study explores the potential interspecific covariation of geographic range (Rapoport's rule) and body size (Bergmann's rule) with latitude in North American sucker fishes (Cypriniformes: Catostomidae). While numerous tests of Rapoport's and Bergmann's rules are documented in the literature, comparatively few of these studies have specifically tested for these patterns, and none have incorporated information reflecting shared ancestry into analyses of North American freshwater fish through a hierarchical model. This study utilized a hierarchical modeling approach with Bayesian inference to evaluate the …

Ichthyoplankton Distribution And Assemblage Within And Around The Saco River Plume, Tracey Bauer

All Theses And Dissertations

A majority of research has focused on the importance of large river plumes for ichthyoplankton survival and recruitment. However, the impacts of smaller, more ephemeral river plumes, such as those commonly found in the Gulf of Maine, on ichthyoplankton are far less understood. The purpose of the current study was to use a small river plume located in the southern Gulf of Maine as a model system to increase our understanding of their effects on ichthyoplankton distribution and diversity, and determine what biotic and abiotic factors may be influencing any differences observed. Plankton tow sampling revealed that although ichthyoplankton abundance …

Bioregulatory Systems Medicine: An Innovative Approach To Integrating The Science Of Molecular Networks, Inflammation, And Systems Biology With The Patient's Autoregulatory Capacity?, Alyssa W Goldman, Yvonne Burmeister, Konstantin Cesnulevicius, Martha Herbert, Mary Kane, David Lescheid, Timothy Mccaffrey, Myron Schultz, Bernd Seilheimer, Alta Smit, Georges St Laurent, Brian Berman

Medicine Faculty Publications

Bioregulatory systems medicine (BrSM) is a paradigm that aims to advance current medical practices. The basic scientific and clinical tenets of this approach embrace an interconnected picture of human health, supported largely by recent advances in systems biology and genomics, and focus on the implications of multi-scale interconnectivity for improving therapeutic approaches to disease. This article introduces the formal incorporation of these scientific and clinical elements into a cohesive theoretical model of the BrSM approach. The authors review this integrated body of knowledge and discuss how the emergent conceptual model offers the medical field a new avenue for extending the …

Functional Analysis Of Synthetic Gene Circuits Controlling A Protein Pump In Yeast, Junchen Diao

Dissertations & Theses (Open Access)

Synthetic biology aims to build biological devices to understand living systems and explore new applications. Synthetic gene circuits such as genetic switches, oscillators and logic gates are at the core of many synthetic biology applications. These gene circuits often include a sensor/regulator protein capable to detect small molecules and then transduce them into a regulatory signal to generate measurable output. Similar signal transduction networks are also abundant in nature. However, in many natural and engineered scenarios, the output also affects the regulator/sensor protein. How such interactions between the regulator/sensor and the output affect synthetic gene circuit function has not been …

The Greenhouse Effect: Decomposition Rates In Human Remains Wrapped In Plastic, Barbara R. Forman

Masters Theses

Determining an accurate estimation of the postmortem interval (PMI) of human remains is important for several reasons. First, it is used to determine whether the individual is recently deceased, and therefore of medicolegal concern. If so, the estimated PMI is used in narrowing the possible identities of the deceased. PMI can also be used in excluding, or convicting, a murder suspect.

Though deviations may occur, it has been found that PMI can be calculated from the decomposition stages with reasonable accuracy (Galloway 1989, Megyesi 2001, Megyesi et al. 2005, Schiel 2008, Simmons et al. 2010). Some factors, such as low …

Century-Long Warming Trends In The Upper Water Column Of Lake Tanganyika, Benjamin Kraemer, Simon Hook, Timo Huttula, Pekka Kotilainen, Catherine M. O'Reilly, Anu Peltonen, Pierre-Denis Plisnier, Jouko Sarvala, Rashid Tamatamah, Yvonne Vadeboncoeur, Bernhard Wehrli, Peter B. Mcintyre

Biological Sciences Faculty Publications

Lake Tanganyika, the deepest and most voluminous lake in Africa, has warmed over the last century in response to climate change. Separate analyses of surface warming rates estimated from in situ instruments, satellites, and a paleolimnological temperature proxy (TEX86) disagree, leaving uncertainty about the thermal sensitivity of Lake Tanganyika to climate change. Here, we use a comprehensive database of in situ temperature data from the top 100 meters of the water column that span the lake’s seasonal range and lateral extent to demonstrate that long-term temperature trends in Lake Tanganyika depend strongly on depth, season, and latitude. The observed spatiotemporal …