Systems Biology Commons^™

Book Review: Effects Of Climate Change On Birds, Edited By Anders Pape Meller, Wolfgang Fiedler, And Peter Berthold, Brian J. Olsen

The Prairie Naturalist

Book review of Effects of Climate Change on Birds, edited by Anders Pape Meller, Wolfgang Fiedler, and Peter Berthold.

Climate scientists from across the globe predict vast changes during the next century in the planet's temperatures, precipitation, storm intensities, fire regimes, hydrologic cycles, and atmospheric, water, and soil chemistries. The changes will be global, but their effects will be felt locally everywhere. To find a scientifically and socially engaging bellwether of these events, we need to look only through the lens of avian biology. Birds are found from pole to pole; their movements connect continents. They are loud, colorful …

State Space Model With Hidden Variables For Reconstruction Of Gene Regulatory Networks, Xi Wu, Peng Li, Nan Wang, Ping Gong, Edward J. Perkins, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: State Space Model (SSM) is a relatively new approach to inferring gene regulatory networks. It requires less computational time than Dynamic Bayesian Networks (DBN). There are two types of variables in the linear SSM, observed variables and hidden variables. SSM uses an iterative method, namely Expectation-Maximization, to infer regulatory relationships from microarray datasets. The hidden variables cannot be directly observed from experiments. How to determine the number of hidden variables has a significant impact on the accuracy of network inference. In this study, we used SSM to infer Gene regulatory networks (GRNs) from synthetic time series datasets, investigated …

Living With Emerging Contaminants: Proteomics Of 4-Nonylphenol Exposed Arrow Goby (Clevelandia Ios), Sarah Emily Johnson

Master's Theses

Alkylphenol ethoxylates (APEs) are widely used in industrial and household products as surfactants. APEs degrade into more toxic ethoxylates, such as 4-nonylphenol (NP), which has been shown to be an endocrine disruptor and enhance the growth of tumor cells. Nonylphenol is wider spread in Pacific estuaries than originally thought. Organisms in Morro Bay, California contain some of the highest concentrations of NP reported, while containing few other contaminants. As a benthic mud-dwelling fish, the arrow goby (Clevelandia ios) may be exposed to high levels of NP due to high contaminant sequestration rates in anaerobic mud. While ecotoxicology suggests …

Review Of Teaching Children Science: Hands-On Nature Study In North America, 1890-1930 By Sally Kohlstedt, Meena M. Balgopal

The Prairie Naturalist

Many scientists and educators agree that the goal of science education is to prepare students "to know, use and interpret scientific explanations of the natural world," as cited in the National Research Council publication, Taking Science to School: Learning and Teaching Science in Grades K-8 (DuschI et al. 2007). Yet, many science instructors of K-12 and post-secondary students often rely on teacher-telling modes of pedagogy and neglect to engage their students in natural inquiry and scientific study that model the research methods used by scientists. As a result, many young people are not aware of how scientists make discoveries about …

Review Of Sandhill And Whooping Cranes: Ancient Voices Over America's Wetlands\ By Paul Johnsgard, Jane Austin

The Prairie Naturalist

Paul Johnsgard has long been captivated by wild cranes and their unique vocalizations, courtship dances, and wide-ranging migrations. As a scientist and an admirer, Johnsgard has watched their migrations and behaviors for decades as hundreds of thousands of cranes staged each spring by the central Platte River, not far from his home in Lincoln, Nebraska. As an artist, he has skillfully captured their courtship dances and other behaviors in his exceptional line drawings. And, as an author, he has written extensively on their ecology in three earlier books: Cranes of the World (1983), Those of the Gray Wind: The Sandhill …

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 …

Massasauga Repatriation On A Restored Wet Prairie, Francis E. Durbian, Brian N. Lomas, Jeff Briggler, Paul Mckenzie, Tom Nagel

The Prairie Naturalist

The massasauga (Sistrurus catenatus) is a small rattlesnake that occurs from Texas to New York (Schmidt and Davis 1941, Conant and Collins 1991, Szymanski 1998). In Missouri, the Eastern massasauga rattlesnake (EMR; S. c. catenatus), a subspecies of the massasauga, occurs north and east of the Missouri River, is a former candidate for listing under the United States Endangered Species Act (Code of Federal Regulations 64 FR 57534; Szymanski 1998), and is listed as a state endangered species (Missouri Natural Heritage Program 2011). Missouri currently harbors five extant EMR populations (Johnson 2000, Durbian et al., unpublished report, …

Depth And Littoral Habitat Association Of Age-0 Yellow Perch In Two South Dakota Glacial Lakes, Daniel J. Dembkowski, Melissa R. Wuellner, David W. Willis

The Prairie Naturalist

Yellow perch (Perca flavescens) are a recreationally important species and represent a key ecological component of glacial lake littoral fish assemblages (Stone 1996, Blackwell et al. 1999). Research has shown a generalized pattern of juvenile (age-0) yellow perch spatial distribution wherein larvae hatch in near-shore areas, migrate to limnetic areas where they remain for approximately 40 d, and then return to demersal behaviors and within near-shore littoral habitats (Noble 1975, Whiteside et al. 1985). However, anomalous distribution and habitat use by age-0 yellow perch has been observed in South Dakota glacial lakes (Fisher and Willis 1997) and the …

Modeling Parental Provisioning By Red-Winged Blackbirds In North Dakota, George M. Linz, Richard S. Sawin, Mark W. Lutman, William J. Bleier

The Prairie Naturalist

Male red-winged blackbirds (Agelaius phoeniceus) exhibit a difference in nest provisioning rates along an east-west gradient in North America. North Dakota is located in the center of North America and harbors a large population of breeding red-winged blackbirds (RWBL). This location provided an opportunity to compare provisioning rates in the central U.S. with those reported for the eastern and western populations. We placed video cameras at RWBL nests to record male and female feeding trips. Thirty-four nests were located on territories with original males and 30 were on territories where a replacement (floater) male had taken over a …

Modelling Β2ar Regulation, Sharat J. Vayttaden

Dissertations and Theses (Open Access)

The β2 adrenergic receptor (β2AR) regulates smooth muscle relaxation in the vasculature and airways. Long- and Short-acting β-agonists (LABAs/SABAs) are widely used in treatment of chronic obstructive pulmonary disorder (COPD) and asthma. Despite their widespread clinical use we do not understand well the dominant β2AR regulatory pathways that are stimulated during therapy and bring about tachyphylaxis, which is the loss of drug effects. Thus, an understanding of how the β2AR responds to various β-agonists is crucial to their rational use. Towards that end we have developed deterministic models that explore the mechanism of drug- induced β2AR regulation. These mathematical models …

Global And Specific Controls Of Protein Synthesis In Hibernators, Peipei Pan

UNLV Theses, Dissertations, Professional Papers, and Capstones

Mammalian hibernation is a highly dynamic physiological process that is composed of a series of torpor bouts, wherein hibernators oscillate between periods of torpor and interbout arousal. Although normally vital to homeostasis, many energetically consumptive processes such as translation or protein synthesis are virtually ceased during hibernation. Earlier studies indicated that protein synthesis had fallen to almost negligible levels. Cap-dependent initiation of translation is well regulated by eukaryotic translation initiation factor 4E (eIF4E) and its binding partner eIF4E-binding protein 1 (4E-BP1) when hibernators cycle in and out the torpor state. Herein, I investigated well-characterized regulatory mechanisms of global and specific …

Msh1 Influence On Plant Mitochondrial Genome Recombination And Phenotype In Tobacco, Peibei Sun

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are composed of unusually complex structures, due to active recombination at numerous repeated sequences in the genome. The maintenance of mitochondrial genome stability is under the control of identifiable nuclear genes. In plants, three nuclear genes (MSH1, RECA3 and OSB1) have been shown to participate in recombination surveillance and the suppression of illegitimate recombination in mitochondria. Disruption of these loci in Arabidopsis results in reproducible mitochondrial genome rearrangements. We demonstrated that repeat-mediated de novo recombination was also enhanced in both Arabidopsis and tobacco during passage through in vitro culture. Furthermore, in vitro conditions led …

Caenorhabditis Briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility And The Evolution Of Recombination, Joseph A. Ross, Daniel C. Koboldt, Julia E. Staisch, Helen M. Chamberlin, Bhagwati P. Gupta, Raymond D. Miller, Scott Everet Baird, Eric S. Haag

Biological Sciences Faculty Publications

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by …

Loss Of Expression Of Neutrophil Proteinase-3: A Factor Contributing To Thrombotic Risk In Paroxysmal Nocturnal Hemoglobinuria, Anna M. Jankowska, Hadrian Szpurka, Mark Calabro, Sanjay Mohan, Andrew E. Schade, Michael Clemente, Roy L. Silverstein, Jaroslaw P. Maciejewski

Biological Sciences Faculty Publications

Background: A deficiency of specific glycosylphosphatidyl inositol-anchored proteins in paroxysmal nocturnal hemoglobinuria may be responsible for most of the clinical features of this disease, but some functional consequences may be indirect. For example, the absence of certain glycosylphosphatidyl inositol-anchored proteins in paroxysmal nocturnal hemoglobinuria cells may influence expression of other membrane proteins. Membrane-bound proteinase 3 co-localizes with glycosylphosphatidyl inositol-linked neutrophil antigen 2a, which is absent in patients with paroxysmal nocturnal hemoglobinuria. Design and Methods: We compared expression of proteinase 3 and neutrophil antigen 2a by flow cytometry and western blotting in normal and paroxysmal nocturnal hemoglobinuria cells and measured cytoplasmic …

The Effects Of Arbuscular Mycorrhizal (Am) Fungal And Garlic Mustard Introductions On Native Am Fungal Diversity, Alexander M. Koch, Pedro M. Antunes, Kathryn Barto, Don Cipollini, Daniel L. Mummey, John N. Klironomos

Biological Sciences Faculty Publications

Introduced, non-native organisms are of global concern, because biological invasions can negatively affect local communities. Arbuscular mycorrhizal (AM) fungal communities have not been well studied in this context. AM fungi are abundant in most soils, forming symbiotic root-associations with many plant species. Commercial AM fungal inocula are increasingly spread worldwide, because of potentially beneficial effects on plant growth. In contrast, some invasive plant species, such as the non-mycorrhizal Alliaria petiolata, can negatively influence AM fungi. In a greenhouse study we examined changes in the structure of a local Canadian AM fungal community in response to inoculation by foreign AM fungi …

Herbicide-Resistant Risk Assessment: Response Of Common Nebraska Weeds To Dicamba Dose, Roberto J. Crespo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Dicamba-resistant soybeans are being developed to provide an additional herbicide mechanism of action that can be used in soybean, and to provide a tool to help manage or mitigate the evolution of other herbicide-resistant weed populations. The objectives of this thesis were to assess the risk of common Nebraska weeds developing resistance to dicamba, quantify baseline dose-response to dicamba of high-risk weed species, and survey the variability in dicamba dose-response among populations of those species. Twenty-five weed scientists were asked to estimate the risk likelihood of ten weed species evolving resistance to dicamba following the commercialization of dicamba-resistant soybean. Palmer …

Prairie Restoration And Species Diversity: A Comparison Of Propagation Success Between Seeded And Planted Forbs, Julie A. Widinski

All Student Theses and Dissertations

Prairie ecosystems used to dominate Illinois’ landscapes, providing some of the most organically rich soils in the world, supplying homes to hundreds of native species, and conserving soil and water. The deep rooted forbs prevent water runoff and soil erosion. Economically the prairies have provided medicines, commercial forbs, and aesthetically pleasing landscapes for humans. Society is dependent on the rich soils these prairies have provided for agriculture and for prevention of erosion and water runoff. With less than one tenth of one percent of Illinois prairies still remaining, successful prairie restoration is of the utmost importance. In order to achieve …

Effects Of Species, Water, And Nitrogen On Competition Among Three Prairie Grasses, Jerry L. Weatherford, Randall W. Myster

The Prairie Naturalist

We conducted an experiment to investigate effects of species, water (W), and nitrogen (N) on competition among little bluestem (Schizachyrium scoparium), sideoats grama (Bouteloua curtipendula), and indiangrass (Sorghastrum nutans). All biomass parameters and the root:shoot ratio of little bluestem were reduced by the presence off 1 of 2 other species, and its shoot biomass and total biomass were both increased by addition of N. Root and shoot biomass of sideoats grama were reduced by the presence of indiangrass and its total biomass was reduced by the presence of itself, whereas its shoot biomass was increased by addition of W at …

Crustaceous Zooplankton Transfer Between A Floodplain Wetland And The Missouri River, Shannon J. Fisher

The Prairie Naturalist

Floodplain interactions are a critical riverine ecosystem function, including zooplankton transfer. Floodplain alternations have had an assumed impact on zooplankton productivity. I assessed floodplain wetland and main channel densities of crustaceous zooplankton, alluding to organism transfer in the Missouri River, North Dakota. Significant t-test differences (P < 0.05) were present between backwater and channel habitat zooplankton densities in 83, 75, 83, and 50% of the sample periods for cyclopoid copepods, copepod nauplii, Daphnia spp., and Bosmina spp. respectively, suggesting the presence of uncoupled zooplankton dynamics during portions of each annual cycle. Two relationships with increased flows were found, including a biologically significant decrease (P = 0.09) of backwater copepod nauplii numbers and a significant increase (P = 0.02) in the channel density of Daphnia spp. During the highest flow periods, fewer significant differences in zooplankton densities were present between the backwater and channel habitats, indicating moderate homogenization.

Notes: River Otters Use Agricultural Field Along The Turtle Riveri In Eastern North Dakota As Crossover And Latrine Area, Maggie D. Triska, Steven C. Loughry, Thomas L. Sergass

The Prairie Naturalist

Recently, the Nearctic river otter (Lontra canadensis) has been re-colonizing portions of eastern North Dakota. The landscape in eastern North Dakota is dominated by agricultural fields and pastures, habitats which have received little research attention related to otter habitat use. During 2008, we searched shorelines to detect otter latrines, which is a common method for determining otter presence. Generally, latrines are locations along bodies of water where otters deposit scats, urine, and glandular secretions for olfactory communication, and groom, wrestle, and play, which may mat vegetation. In the northeastern United States, inland riverine system studies have shown latrines …