Biology Commons^™

Integration Mechanism Of The Site Specific Non-Ltr Retrotransposon, R2bm, Christi Lynn Hull

Biology Theses - Archive

The focus of this thesis is the mechanistic study of non-LTR retrotransposon replication using the site specific transposon R2Bm. Non-LTR retrotransposons integrate into new chromosomal sites by copying their RNA back into DNA at the site of insertion using an exposed chromosomal 3' OH to prime cDNA synthesis.1 Although some of the early steps of an integration event have been detailed, how the element completes integration remains unknown.¹ ² ³ ⁴ ⁵ ⁶ Clarifying the last integration step, known as second strand synthesis, is a major goal of this research. In order to accomplish this, R2 RNA and protein substrates …

Insights Into The Transmission Of Helitrons And Their Impact On The Genome Architecture Of Myotis Lucifugus, The Little Brown Bat, Jainy Thomas

Biology Dissertations - Archive

Probably the most dynamic proportion of multicellular eukaryotic genomes is composed of teeming populations of parasitic mobile DNA, called transposable elements (TEs). Helitrons are rolling circle TEs that have a limited distribution among mammals, having been identified only in the genome of the little brown bat, Myotis lucifugus, and a few closely related species. One family of Helitrons, called Helibat, was estimated to make up as much as 3% of the M. lucifugus genome. In addition, Helibat was shown to have captured and amplified the promoter and 5' UTR of a highly conserved single copy gene to >1000 copies. Together …

Reproductive Isolation In Drosophila: From Behavior To Genome, Daina Ma

Biology Dissertations - Archive

In this study, I investigate factors underlying reproductive isolation in Drosophila. I begin (Part I) by measuring behavioral isolation between Zimbabwe and cosmopolitan D. melanogaster, and asking the following questions: What is the pattern? What are the sensory cues leading to isolation? In Part II, I present results of a genomic screen for candidate genes underlying behavioral isolation between Zimbabwe and cosmopolitan D. melanogaster. Then I turn to the genomic causes of postzygotic reproductive isolation (Parts III and IV): What are the possible genes associated with hybrid sterility? What are the relationships between fertility/sterility and genotypes and allelic expression? What …

Comparison Of The Dna Methylation Patterns Between Interspecific Xenopus F1 Hybrids And Their Parental Species, Alie Patrick Koroma

Biology Dissertations - Archive

In this study the main focus is to compare the methylation patterns of interspecific Xenopus F1 hybrids to the parental species using Methyl-Sensitive Amplification Polymorphisms (MSAPs). Genomic DNA was extracted from the liver and muscle tissues from a representative sample of F1 hybrids and the parental species (Xenopus laevis and X. muelleri). First, the MSAP markers were very effective in comparing the methylation patterns of hybrids and the parental species. Genetic analysis of 504 liver and 364 muscle MSAP markers revealed that these markers were highly polymorphic. Principal coordinate analysis showed four distinct clusters with the two parental species separate …

Effects Of The Exotic Invader, Tamarix Spp., On Aspects Of The Aquatic Ecosystem At Mccomb Creek, Presidio County, Texas, Jane Blaisdell Nellan Moore

Biology Dissertations - Archive

The effects of saltcedar, Tamarix spp., invasion in riparian zones of the western United States have been well documented. These include, but are not limited to soil salinization, and shifts in hydrology and water use. Comparatively unknown are the effects on the associated aquatic systems and if a significant increase in water salinity accompanies these invasions. Shifts in stream metabolism have been reported, but the impacts of saltcedar invasion on the algal species, which are the dominant primary producers in desert aquatic ecosystems, are unknown. A two year study was conducted in an oligotrophic desert stream, currently experiencing an invasion, …

Role Of Repetitive Dna In Apicomplexan Genome Evolution, Assiatu B. Barrie

Biology Theses - Archive

The Apicomplexa represent a phylum of obligate intracellular parasites that impart significant medical, veterinary, and socioeconomic burdens worldwide. The opportunistic, AIDS-associated, pathogen Toxoplasma gondii for instance, infects about one-third of the human population causing serious, life-threatening illness and birth defects in some. The genomes of fifteen apicomplexan species ranging in size from 8.3Mb to 64.0Mb have been sequenced and reveal a significant amount of plasticity in terms of size, AT-richness, introns and gene density. In many instances, genome size variation can be explained by differential expansion of repetitive DNA acquired through varying processes: intracellular organellar DNA transfer events, and proliferation …

Patterns Of Subnet Usage Reveal Distinct Scales Of Regulation In The Transcriptional Regulatory Network Of Escherichia Coli, Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hutt

Publications and Research

The set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer …

Building Better Scientists Through Cross-Disciplinary Collaboration In Synthetic Biology: A Report From The Genome Consortium For Active Teaching Workshop 2010, Michael J. Wolyniak, Consuelo J. Alvarez, Vidya Chandrasekaran, Theresa M. Grana, Andrea Holgado, Christopher J. Jones, Robert W. Morris, Anil L. Pereira, Joyce Stamm, Talitha M. Washington, Yixin Yang

Biological Sciences Research

A common problem faced by primarily undergraduate institutions is the lack of funding and material support needed to adequately expose students to modern biology, including synthetic biology. To help alleviate this problem, the Genome Consortium for Active Teaching (GCAT) was founded in 2000 by Malcolm Campbell at Davidson College to bring genomics into the undergraduate curriculum. GCAT’s first tangible activity was to serve as a central clearinghouse both for the purchase and reading of DNA microarrays and for information on how to execute genomics experiments at undergraduate institutions. In response to the evolution of molecular biology in the last decade, …

First Report Of The Developmental Changes Inside The Eggs Of The Chinese Freshwater Crab , J Xue, Y Liu, Neil Cumberlidge, H X. Wu

Journal Articles

No abstract provided.

Integrating Spatial And Temporal Approaches To Understanding Species Richness, Ethan P. White, S. K. Morgan Ernest, Peter B. Adler, Allen H. Hurlbert, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Understanding species richness patterns represents one of the most fundamental problems in ecology. Most research in this area has focused on spatial gradients of species richness, with a smaller area of emphasis dedicated to understanding the temporal dynamics of richness. However, few attempts have been made to understand the linkages between the spatial and temporal patterns related to richness. Here, we argue that spatial and temporal richness patterns and the processes that drive them are inherently linked, and that our understanding of richness will be substantially improved by considering them simultaneously. The species–time–area relationship provides a case in point: successful …

Analysis Of Bacterial Diversity In Arctic Soil And Sediment Samples From Ny-Alesund, Norway Using Denaturing Gradient Gel Electrophoresis., Yew Wen Chyin

Student Works (2010-2019)

Bacterial diversity in soil and sediment samples from eighteen sites in and around Dasan Station, Ny-Ålesund, Norway was analyzed using Denaturing Gradient Gel Electrophoresis (DGGE), and was correlated with the environmental variables. Samples analysed included terrestrial soils, beach soil, periglacier soils, inland lake bank sediments, melt lake sediments, and marine sediments. Spearman rank order correlation showed significant correlations (P = 0.001) between conductivity (r = 0.470) and pH (r = 0.294) with the bacterial diversity. Soil from the tundra site (sample 17) appeared to have the most diverse bacterial community while inland lake bank sediment from the …

Fabrication Of Miniature Drug Screening Platform Using Low Cost Bioprinting Technology, Jorge Ivan Rodriguez

Open Access Theses & Dissertations

In the pharmaceutical industry, new chemicals and substances are being tested to find appropriate compounds or mix for treating a specific disease. The demand for screening large compound collections against and increasing number of therapeutic targets has stimulated technology development in the areas of assay automation and miniaturization. Current methods for evaluating the reactions of cells use a volume in the range of microliters. We have developed a new and low-cost deposition method to fabricate miniature drug screening platform that can realistically and inexpensively evaluate biochemical reactions up to 4 substances per trial in a picoliter-scale volume. This paper describes …

Phylogeographic Patterns And Intervarietal Relationships Within Lupinus Lepidus: Morphological Differences, Genetic Similarities, Kevin Allen Weitemier

Dissertations and Theses

Lupinus lepidus (Fabaceae) contains many morphologically divergent varieties and was restricted in its range during the last period of glaciation. A combination of phylogenetic (with the trnDT and LEGCYC1A loci) and population genetics approaches (with microsatellites and LEGCYC1A are used here to characterize intervarietal relationships and examine hypotheses of recolonization of areas in the Pacific Northwest affected by glaciation. Sequenced loci are not found to form a clade exclusive to L. lepidus, nor are any of the varieties found to form clades. Population genetics analyses reveal only negligible genetic structure within L. lepidus, with the majority of variation …

Spatial Segregation Of The Sexes In A Salt Marsh Grass Distichlis Spicata (Poaceae), Charlene Ashley Mercer

Dissertations and Theses

Understanding the maintenance of sexual systems is of great interest to evolutionary and ecological biologists because plant systems are extremely varied. Plant sexual systems have evolved to include not only complete plants with both male and female reproduction occurring on one plant (i.e., monoecious and hermaphroditic) but also plants with male and female function on separate plants (dioecious). The dioecious reproductive system can be used to test theories on niche differentiation given that having separate plants potentially allows for the exploitation of a broader niche. This increase in the realized niche is due to the ability for separate sexes to …

The Combined Influence Of The Local Environment Andregional Enrichment On Bird Species Richness, Ethan P. White, A. H. Hurlbert

Biology Faculty Publications

It is generally accepted that local species richness at a site reflects the combined influence of local and regional processes. However, most empirical studies evaluate the influence of either local environmental variables or regional enrichment but not both simultaneously. Here we demonstrate the importance of combining these processes to understand continental scale richness patterns in breeding birds. We show that neither regional enrichment nor the local environment in isolation is sufficient to characterize observed patterns of species richness. Combining both sets of variables into a single model results in improved model fit and the removal of residual spatial autocorrelation. At …

Loss Of Foundation Species Increases Population Growth Of Exotic Forbs In Sagebrush Steppe, J S. Prevey, M J. Germino, Nancy J. Huntly

Biology Faculty Publications

The invasion and spread of exotic plants following land disturbance threatens semiarid ecosystems. In sagebrush steppe, soil water is scarce and is partitioned between deeprooted perennial shrubs and shallower-rooted native forbs and grasses. Disturbances commonly remove shrubs, leaving grass-dominated communities, and may allow for the exploitation of water resources by the many species of invasive, tap-rooted forbs that are increasingly successful in this habitat. We hypothesized that exotic forb populations would benefit from increased soil water made available by removal of sagebrush, a foundation species capable of deep-rooting, in semiarid shrub-steppe ecosystems. To test this hypothesis, we used periodic matrix …

Seasonal Patterns Of Arthropod Diversity And Abundance On Big Sagebrush, Artemisia Trientata, M P. Stanford, Nancy J. Huntly

Biology Faculty Publications

The sagebrush biotype is the largest in the western United States. This vast sagebrush community is thought to harbor equally vast and diverse arthropod communities, but these remain little explored. Our objective was to examine the diversity, abundance, and seasonal phenology of arthropod taxa found on the dominant shrub of the sagebrush ecosystem, big sagebrush (Artemisia tridentata). We wanted to improve understanding of this little-studied arthropod assemblage that may play significant roles in the dynamics of sagebrush populations and the sagebrush ecosystem. We sampled free-living and gall-forming arthropods from a stratified random sample of sagebrush plants at the Barton Road …

The Herpetofauna Of The Virunga Mountains With Emphasis On Two Species Of Albertine Rift Endemic Treefrogs Of The Genus Leptopelis., Corey Edward Roelke

Biology Dissertations - Archive

I present a short description of the biodiversity crisis, the Albertine Rift as a biodiversity hotspot, and a literature review of the taxonomy of the genus Leptopelis. I then present a list of the reptiles and anurans from the Parc National des Volcans (PNV)(01°43'S, 29°52'W), an area in the west and north provinces of the Republic of Rwanda in the Albertine Rift region of Africa. Fieldwork was conducted for two to six days per week from June through August of 2007 and 2008. I also conducted literature searches of all historical expeditions within the park for species records. Seventeen species …

Leptodactylus Savagei, W. R. Heyer, Miriam M. Heyer, Rafael O. De Sá

Biology Faculty Publications

Adult Leptodactylus savagei are large, the head is as wide as long or usually wider than long, and the hind limbs are moderate in length (Table 1; Heyer and Thompson (2000) provided definitions of adult size and leg length categories for Leptodactylus). Male vocal sacs are not visible externally. Sexually active males have hypertrophied forearms, usually 1 large black spine on each thumb, rarely with 1 large spine and a prepollical bump, and a pair of black chest spines. A pair of entire dorsolateral folds extend anteriorly from at least one_half to full distance from eye to groin, the …

Description Of The Tadpole Of Proceratophrys Renalis (Miranda-Ribeiro, 1920) (Anura: Cycloramphidae), Filipe Augusto C. Do Nascimento, Barnagleison S. Lisboa, Gabriel O. Skuk, Rafael O. De Sá

Biology Faculty Publications

The tadpole of Proceratophrys renalis is described based on specimens from Maceió, State of Alagoas, northeastern Brazil. At stage 35 the body is slightly dorso-ventrally depressed, ovoid in lateral, dorsal, and ventral views. Oral disc is ventral with lateral emarginations, surrounded by a single row of marginal papillae with a large gap on the upper labium. Labial tooth row formula is 2(2)/3(1). The analysis of internal oral anatomy revealed two possible characters that readily distinguish P. renalis from P. boiei, supporting the recent ressurection of P. renalis. Comparisons with available descriptions of the larvae for other species in the …

Mechanisms Of Apoptosis In Crustacea : What Conditions Induce Versus Suppress Cell Death?, Michael Menze, Grady Fortner, Suman Nag, Steven Hand

Faculty and Staff Scholarship

Arthropoda is the largest of all animal phyla and includes about 90% of extant species. Our knowledge about regulation of apoptosis in this phylum is largely based on findings for the fruit fly Drosophila melanogaster. Recent work with crustaceans shows that apoptotic proteins, and presumably mechanisms of cell death regulation, are more diverse in arthropods than appreciated based solely on the excellent work with fruit flies. Crustacean homologs exist for many major proteins in the apoptotic networks of mammals and D. melanogaster, but integration of these proteins into the physiology and pathophysiology of crustaceans is far from complete. Whether apoptosis …

Substrate And Cover Object Choice By The Red-Backed Salamander (Plethodon Cinereus), J. P. Iverson, Geoffrey R. Smith

Faculty Publications

No abstract provided.

The Role Of Taabf1 In Abscisic Acid-Mediated Suppression Of 𝒶-Amylase Gene Expression In Cereal Grains, Lauren J. Harris

Honors Theses

The phytohormones gibberellin (GA) and abscisic acid (ABA) regulate important developments events in germinating seeds. Specifically, GA induces the expression of hyrolase genes, like the α-amylase gene Amy32b, which mobilizes starch reserves to be used by the embryo, and ABA suppresses this induction. Recent advancements identified ABA and GA receptors and key components in the signaling pathways, however, the mechanism of crosstalk between the hormones remains largely unknown. To further elucidate the mechanism of ABA suppression of GA-induced genes, we focused on the transcription factor TaABF1, a member of the ABA response element binding factor family. TaABF1 has been shown …

The Seasonality Of Parasites In Illinois House Sparrows (Passer Domesticus): Effect Of Stress On Infection Parameters, Tiffany C.M. Gibson

Masters Theses

Parasitism often shows seasonal variation in their hosts and has been associated with host densities, host stress levels or transmission strategies (Moller et al 2003, Andersen and May 1982 ). This study was designed to evaluate the role of direct versus indirect life cycle transmission strategies, using Isospora and haemosporidians; and the impact of proposed ecological (winter) and physiological (breeding) stresses on parasitism levels. Coccidia have direct life cycles and infect gut tissues and are passed by fecal-oral transmission. Haemosporidians are blood parasites with an indirect life cycle that requires blood-feeding insects for transmission. If parasitemias are influenced by host …

Multiple Endpoints Of Endocrine Disruption In Gravid Watersnakes (Colubridae:Nerodia) As A Function Of Ingestion Of A Common Herbicide, Lorin Anne Neuman-Lee

Masters Theses

Ecotoxicological studies that focus on a single endpoint might not accurately represent the true ecological effects of a contaminant. Exposure to atrazine, a widelyused herbicide, disrupts endocrine function and sexual development in amphibians, but studies involving reptilian species are lacking. This study examines several effects of atrazine ingestion on gravid females and neonates exposed in utero of the Northern Watersnake (Nerodia sipedon). Twenty-five gravid N. sipedon were collected and kept in the lab for the entirety of their gestation period. Each snake received one of four doses of atrazine: control, 2, 20, or 200 ppb. Blood samples were drawn each …

A Spatially Explicit Model To Predict Radiocesium Body Burdens In White-Tailed Deer On The Department Of Energy's Savannah River Site, Christopher W. Bobryk

Masters Theses

A spatially explicit exposure model was developed to interpolate and predict radiocesium (137Cs) body burdens found in white-tailed deer (Odocoileus virginianus) on the U.S. Department of Energy's Savannah River Site (SRS) in west-central South Carolina. Since 1965 hunting has been allowed from permanent stands as a mechanism to manage the herd and all animals have been monitored in the field for gross beta/gamma activity levels providing a long-term spatially explicit dataset. Until now no study has attempted to model deer 137Cs at the hunt-stand level, but rather at the compartment level (1,000 - 5,200 ha). The models described here use …

The Spatial Distribution Of Japanese Beetles, Popillia Japonica, In Soybean Fields, Stacey A. Sara

Masters Theses

The Japanese beetle, Popilliajaponica Newman, is a serious pest of many agricultural and horticultural plants. Little is known about the distributions of Japanese beetles in agricultural fields which makes pest managyment more difficult. We studied the spatial distribution of Japanese be~tles in soybean fields. In particular, we examined how distance from an edge, edge direction, and edge type affected the distribution and abundance of beetles. Twenty-five soybean fields were transected parallel with the field edges at varying distances from the field edges and sampled for beetles. An edge effect for density was discovered; beetle numbers decreased significantly with increasing distance …

Prey Preference As A Function Of Feeding Experience And Prey Type In Neonate Gartersnakes (Colubridae: Thamnophis), Kathryn B. Hale

Masters Theses

Several species of potential prey have been introduced into the geographic range of the Two-striped Gartersnake, Thamnophis hammondii. Some of these prey species possess defenses that present novel challenges to the snake predator. Despite novel predator defense mechanisms (including secretions from skin glands), adult T. hammondii ingest several of these prey species without adverse effects. Although ~dult T hammondii are dietary generalists, almost nothing is known about prey preferences in newborn individuals that lack feeding experience. My study determined whether or not T. hammondii innately exhibits a preference among native and introduced prey types. Furthermore, I compared the degree of …

A Model Cost Analysis Comparing Solar, Wind And Geothermal Energies, Including Alternatives To Changing Energy Sources, Using Texas Households And Weather, Kimberly Speed

Masters Theses

The Emergency Economic Stabilization Act of2008 (P.L. 110-343) provides several incentives and tax credits for Americans interested in investing in alternative energy resources. Solar, wind, and. geothermal systems receive the most tax credits due to their low carbon output, but a determination must be made as to which resource is the most accessible and economically feasible. The State of Texas was used as a model for comparing the three renewable energy resources through analysis of weather variables, geological features, resource availability, amount of energy harvested in relation to equipment, and installation and maintenance costs.

All three energy systems have positive …

Introduction: Protistan Biology, Horizontal Gene Transfer, And Common Descent Uncover Faulty Logic In Intelligent Design, Avelina Espinosa

Arts & Sciences Faculty Publications

THE International Society of Protistologists (ISOP) organized a pre-meeting workshop entitled ‘‘Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design,’’ as part of the 1st North American Section meeting held June 11–13, 2009, at Roger Williams University, Bristol, RI, USA. This workshop focused on the acceptance of Darwinian evolution in the United States and the role of intelligent design (ID) in the ongoing controversy between scientific knowledge and popular belief. Intelligent design, a doctrine born in the 1980s, proposes that a ‘‘Designer’’ is responsible for the complexity in biological systems and that Darwinism cannot explain holistically the origin and evolution …