Systems Biology Commons^™

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.

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 …

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 …

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 …

Manuscript Content: Where Does It Belong?, Christopher N. Jacques

The Prairie Naturalist

One of the most common issues we address during content editing of papers for The Prairie Naturalist (journal) is the appropriate placement of content in the text body. Based on my experience with the editorial process, content placement also is one of the issues that authors are most resistant to suggestions or do not fully understand why we are so persistent about it (Thompson 2010). One of the primary objectives of scientific writing is to concisely and accurately disseminate information. Scientific papers are structured to help both the author and reader accomplish this objective. The material that belongs in each …

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 = …

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 …

Book Review Of Encyclopedia Of Biological Invasions, Edited By Daniel Simberloff And Marcel Rejmanek, Qinfeng Guo

The Prairie Naturalist

Book review of Encyclopedia of Biological Invasions, edited by Daniel Simberloff and Marcel Rejmanek.

Species introductions and consequent biotic invasions and homogenization are major components of global change that are drawing increasing concern and various levels of actions and reactions around the world. Invasion ecology has advanced rapidly during the last few decades, and the discipline is now increasingly integrated with the social and economic sciences. A better understanding of the invasion process and its effects is thus clearly needed. For basic research, invasion biology offers fascinating and sometimes unique opportunities for testing certain ecological or evolutionary theories and …

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 …

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 …

Late Seasonal Captures Of The Plains Pocket Mouse (Perognathus Flavescens) In Iowa, Hans W. Otto, Jeremy A. White

The Prairie Naturalist

The plains pocket mouse, Perognathus flavescens, is a nocturnal granivore that inhabits friable soils in sparsely vegetated areas (Monk and Jones 1996). In the United States, the distribution of the plains pocket mouse extends from Arizona, New Mexico, and Texas through the Great Plains to North Dakota and Minnesota (Hall 1981). This species reaches its easternmost limits in Iowa, where it has been documented from a limited number of grassland sites in eastern, central, and western parts of the state (Bowles 1975, Wilson et al. 1996). Due to loss of grassland habitat, the plains pocket mouse is currently listed …