Systems Biology Commons^™

Mathematical Modeling Of Clostridium Thermocellum’S Metabolic Responses To Environmental Perturbation, Bless Adotey

Theses and Dissertations--Biosystems and Agricultural Engineering

Clostridium thermocellum is a thermophilic anaerobe that is capable of producing ethanol directly from lignocellulosic compounds, however this organism suffers from low ethanol tolerance and low ethanol yields. In vivo mathematical modeling studies based on steady state traditional metabolic flux analysis, metabolic control analysis, transient and steady states’ flux spectrum analysis (FSA) were conducted on C. thermocellum’s central metabolism. The models were developed in Matrix Laboratory software ( MATLAB^® (The Language of Technical Computing), R2008b, Version 7.7.0.471)) based on known stoichiometry from C. thermocellum pathway and known physical constraints. Growth on cellobiose from Metabolic flux analysis (MFA) and Metabolic …

The Proteomic Response Of Sea Squirts (Genus Ciona Congeners) To Heat Stress: Evidence For Differential Thermal Sensitivities, Loredana Serafini

Master's Theses

The sea squirts Ciona intestinalis and C. savignyi have disparate distribution patterns, which may result from differences in their thermal tolerance limits. Because C. intestinalis, an almost cosmopolitan species, has a more widespread distribution, it is thought that it is better adapted to endure a wide range of temperatures. In order to compare the heat stress response between these two congeners, we studied global changes in protein expression, using a proteomics approach. To characterize the response to extreme heat stress, animals of both species were exposed to temperatures of 22°C, 25°C, and 28°C for 6 h, and then were …

Computer Simulation Of A Hollow-Fiber Bioreactor: Heparan Regulated Growth Factors-Receptors Binding And Dissociation Analysis, Changjiang Zhang

University of Kentucky Doctoral Dissertations

This thesis demonstrates the use of numerical simulation in predicting the behavior of proteins in a flow environment.

A novel convection-diffusion-reaction computational model is first introduced to simulate fibroblast growth factor (FGF-2) binding to its receptor (FGFR) on cell surfaces and regulated by heparan sulfate proteoglycan (HSPG) under flow in a bioreactor. The model includes three parts: (1) the flow of medium using incompressible Navier-Stokes equations; (2) the mass transport of FGF-2 using convection-diffusion equations; and (3) the cell surface binding using chemical kinetics. The model consists of a set of coupled nonlinear partial differential equations (PDEs) for flow and …

Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer

Mark R Segal

Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …

Chloroplast Phenomics: Systematic Phenotypic Screening Of Chloroplast Protein Mutants In Arabidopsis, Yan Lu, Linda Savage, Robert Last

Yan Lu

No abstract provided.

Revegetating Burned Arid Lands: Identifying Successful Native Species Using Trait And Competition Analysis: Final Report, Scott R. Abella

Fire Science

Species selection can make the difference between successful revegetation projects and costly failures. Candidate native species for revegetating burned arid lands in the southwestern United States must meet at least two criteria. These species must: (1) be competitive in postfire environments typically dominated by exotic grasses, and (2) be able to become established reliably by seeding or planting. In response to Manager’s Request Task 3 (reestablishment of native vegetation after fires on arid lands) in the 2006 JFS announcement for proposals, this research tackled the problem of selecting native species with the greatest chance of revegetation success by conducting synergistic …

Current Distribution Of Rare Fishes In Eastern Wyoming Prairie Streams, Christina E. Barrineau, Elizabeth A. Bear, Anna C. Senecal

The Prairie Naturalist

Distributions of native fishes have declined throughout the Great Plains region. Over 50% of native fishes within the Missouri River drainage in Wyoming have experienced declines in distributions. Thus, the primary goal of our study was to assess current distribution of rare native fishes in eastern Wyoming prairie streams. Of the 10 rare fishes sampled, goldeye (Hiodon alosoides), western silvery minnow (Hybognathus argyritis), plains minnow (H. hankinsoni), and Iowa darter (Etheostoma exile) have experienced declines in distribution over the last decade. Plains topminnow (Fundulus sciadicus) appears to be expanding to areas outside …

Population And Diet Assessment Of White Bass In Lake Sharpe, South Dakota, Andrew E. Ahrens, Travis W. Schaeffer, Melissa R. Wuellner, David W. Willis

The Prairie Naturalist

White bass (Morone chrysops) have been introduced into all 4 South Dakota Missouri River reservoirs and compose a substantial proportion of the annual recreational harvest. To date, limited studies have examined white bass population dynamics and food habits in South Dakota Missouri River reservoirs. Our objective was to examine population dynamics and food habits of white bass in Lake Sharpe, a South Dakota mainstem Missouri River reservoir. White bass consistently consumed invertebrates during May but switched to a more piscivorous diet later in the growing season; most of the fish consumed were gizzard shad (Dorosoma cepedianum). …

Cropland Nesting By Long-Billed Curlews In Southern Alberta, James H. Devries, Steven O. Rimer, Elizabeth M. Walsh

The Prairie Naturalist

Long-billed curlews (Numenius americanus) are described primarily as a grassland nesting species. However, no studies to date have quantified nest habitat selection among available habitats. During a study of waterfowl nest habitat selection and success in landscapes ranging from cropland to grassland-dominated, we found 9 curlew nests of which 8 were located in active cropland within cropland-dominated landscapes. Cropland nests occurred in fall-seeded winter wheat and spring-seeded barley and nests were clumped in distribution. Four cropland nests and 1 nest in native grass pasture hatched young. Further research is needed to characterize nesting habitat selection and reproductive success …

Population Characteristics Of Central Stonerollers In Iowa Streams, Scott M. Bisping, Jesse R. Fischer, Michael C. Quist, Andrew J. Schaefer

The Prairie Naturalist

The central stoneroller (Campostoma anomalum) is a herbivore that can have substantial effects on algal communities, nutrient dynamics, and energy flow in streams. Despite its importance in lotic ecosystems, little is known about its population dynamics in streams of the Great Plains. Our objective was to describe age structure, age-specific mortality, and growth rates of central stonerollers in three Iowa streams. We sampled fish from 41 reaches during June-August 2007. We sampled 466 central stonerollers, of which we aged 192. Fish varied in length from 32 to 130 mm and in age from age 0 to 4 years. …

Examination Of Owl Pellets For Northern Pocket Gophers At Crescent Lake National Wildlife Refuge, Nebraska, Stacey L. Bonner, Keith Geluso

The Prairie Naturalist

Analysis of regurgitated pellets from owls is a well-known and nondestructive method that provides useful information regarding diet (Errington 1930). This technique also is used to examine composition of small mammal communities and distribution of prey species (e.g. Kamler et al. 2003, Torre et al. 2004, Poole and Matlack 2007). In western Nebraska, two species of owls that regularly breed in the region are the common barn owl (Tyto alba) and great horned owl (Bubo virginianus). In the early 1970s, Rickart (1972) studied the diet of both species at Crescent Lake National Wildlife Refuge (CLNWR), Garden …

Reporting Results Of Data Analysis, Preparing Scientific Manuscripts, And Website Development Efforts, Christopher N. Jacques

The Prairie Naturalist

Preparation of scientific manuscripts and use and presentation of statistics have been topics of several commentaries from previous journal Editors-in-Chief, and have been submitted as invited papers, so I would like to share my perspective as the current Editor-in-Chief (Editor) of The Prairie Naturalist (Journal). Because there is not complete consensus among the experts about when hypothesis testing versus information theoretic methods, or Bayesian versus frequentist methods are suitable, previous Editors have avoided presenting their perspectives (Thompson 2010). I also will avoid presenting my perspective as Editor. I will, however, present my perspective on several of these approaches and then …

The Prairie Naturalist, Vol. 42, Issue 3/4, December 2010, The Great Plains Natural Science Society

The Prairie Naturalist

EDITOR'S NOTE: REPORTING RESULTS OF DATA ANALYSIS, PREPARING SCIENTIFIC MANUSCRIPTS, AND WEBSITE DEVELOPMENT EFFORTS • Christopher N. Jacques

Current Distribution of Rare Fishes in Eastern Wyoming Prairie Streams • Christina E. Barrineau, Elizabeth A. Bear, and Anna C. Senecal

Diets of Nesting Swainson's Hawks in Relation to Land Cover in Northwestern North Dakota • Robert K. Murphy

Resource Selection of Greater Prairie-Chicken and and Sharp-Tailed Grouse Broods in Central South Dakota • Mark A. Norton, Kent C. Jensen, Anthony P. Leif, Thomas R. Kirschenmann, and Gregory A. Wolbrink

Population Characteristics of Central Stonerollers in Iowa Streams • Scott M Bisping, …

Summer Activity Pattern And Home Range Of Northern Pocket Gophers In An Alfalfa Field, Jon C. Pigage, Helen K. Pigage

The Prairie Naturalist

AIlocation of time for feeding, resting and reproduction in subterranean animals is difficult to determine. Although pocket gophers (Thomomys spp.) are among the most widely studied subterranean rodents, there are conflicting reports on activity measurement in these animals. Activity studies have included opening gopher burrows (Tryon 1947), laboratory studies of activity (Vaughan and Hansen 1961), telemetry studies (Anderson and McMahon 1981, Bandoli 1987, and Cameron et al. 1988), and subcutaneously implanted radioactive gold wires (Gettinger 1984). The diversity of techniques reflects the difficulty of generalizing results from different species of pocket gophers in natural and artificial environments. Patton and …

Seasonal Yellow Perch Harvest In Two Dissimilar South Dakota Fisheries, Casey W. Schoenebeck, Michael L. Brown, David O. Lucchesi

The Prairie Naturalist

Angler effort and fish harvest in South Dakota have historically been quantified through summer and winter creel surveys. However, the late-summer, pulsed recruitment of yellow perch (Perea flavescens) into a fishery combined with an increase in fall movement and feeding activity suggested September and October could be significant periods of perch harvest in South Dakota lakes. Seasonal trends in angler effort and yellow perch harvest during 2005-2007 were compared for high- and low-quality yellow perch fishery types commonly found in eastern South Dakota glacial lakes. High-quality yellow perch fisheries are characterized by fast growth (mean total length at age-3 greater …

Resource Selection Of Greater Prairie-Chicken And Sharp-Tailed Grouse Broods In Central South Dakota, Mark A. Norton, Kent C. Jensen, Anthony P. Leif, Thomas R. Kirschenmann, Gregaory A. Wolbrink

The Prairie Naturalist

Habitat use of sympatric greater prairie-chicken (Tympanuchus cupido) and sharp-tailed grouse (T. phasianellus) broods during the brood-rearing season has not been quantified for stable prairie grouse populations in large contiguous grassland landscapes in the Northern Great Plains. Characteristics of habitats used by prairie grouse broods were described based on data collected from 35 broods (18 greater prairie-chicken and 17 sharp-tailed grottse) during the breeding seasons of 2004 and 2005. Greater prairie-chicken and sharp-tailed grouse broods used vegetation with visual obstruction heights 2:26 cm and 37 cm, respectively. Greater prairie-chicken broods selected western wheatgrass (Pascopyrum smithii …

Characterization Of The Extracellular Proteome Of A Natural Microbial Community With An Integrated Mass Spectrometric / Bioinformatic Approach, Brian Keith Erickson

Doctoral Dissertations

Proteomics comprises the identification and characterization of the complete suite of expressed proteins in a given cell, organism or community. The coupling of high performance liquid chromatography (LC) with high throughput mass spectrometry (MS) has provided the foundation for current proteomic progression. The transition from proteomic analysis of a single cultivated microbe to that of natural microbial assemblages has required significant advancement in technology and has provided greater biological understanding of microbial community diversity and function.

To enhance the capabilities of a mass spectrometric based proteomic analysis, an integrated approach combining bioinformatics with analytical preparations and experimental data collection was …

Review Of Grouse Of The Plains And Mountains - The South Dakota Story, By Lester D. Flake, John W. Connelly, Thomas R. Kirschenmann, And Andrew J. Lindbloom., Brent E. Jamison

The Prairie Naturalist

Grouse are a fascinating group of birds that offer elaborate breeding displays for birders in the spring, provide sporting opportunities for hunters in the fall, and serve as indicators of grassland health. Though the authors claim that the book targets those who enjoy the outdoors, bird watching, and upland game bird hunting, there is ample reason for ecologists, ornithologists, and grouse researchers to reference this book as well. The book contains general information of interest to a broad audience, but often moves beyond the introductory information to greater detail. Many details are supported by peer-reviewed literature. This book strikes a …

Correlation Of Mature Walleye Relative Abundance To Egg Density, Jordan D. Katt, Casey W. Schoenebeck, Keith D. Koupal, Brian C. Peterson, W. Wyatt Hoback

The Prairie Naturalist

Knowledge of spawning areas can benefit fisheries management (Marsden et al. 1991). Identification of spawning areas allows managers to protect, enhance, and/or restore critical habitat (Gunn et al. 1996, Thompson 2009), examine important biotic and abiotic conditions necessary for reproduction (Quist et al. 2003), and to efficiently collect broodstock for production (Satterfield and Flickinger 1996). The most effective method to directly identify spawning areas of fish with demersal eggs is to sample the substrate for eggs (Marsden et al. 1991). This method has been used to locate spawning areas of several species (Michaletz 1984, Zorn et al. 1998, Martin 2008). …

Review Of Weeds Of The Midwestern United States & Central Canada, Edited By Charles T. Bryson And Michael S. Defelice, James Stubbendieck

The Prairie Naturalist

This volume is the culmination of work by more than 40 weed scientists and botanists. Its stated purpose is to help identifY the great diversity of weedy and invasive plants that interface with agriculture, industry, and natural ecosystems in central North America. The geographic range covered by this book extends from southeastern Saskatchewan to eastern Kansas, northern Kentucky, northwestern Pennsylvania, and southwestern Quebec. This is a welcome edition because a current book on unwanted plants has not been available for the eastern two-thirds of this region. The book is arranged taxonomically by family and alphabetically by species within each family. …