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Optimization Strategies For Electrospun Silk Fibroin Tissue Engineering Scaffolds, Kristopher Kubow

Selected Works

No abstract provided.

Patterning Defects In Silkworm Embryos Analysed Through Cuticle Preparations, Amit Singh, Madhuri Kango-Singh, K. P. Gopinathan

Biology Faculty Publications

The mulberry silkworm, Bombyx mori, a holometabolous lepidopteran insect, has a metameric body plan. Due to its functional adaptation, B. mori presents some unique deviations in its pal/ern from the evolutionarily advanced dipteran insect, Drosophila melanogaster. Previous studies on mutant phenotype analysis in B. mori have been carried out in late stages of larval development. Here we employ, the cuticle preparation approach during embryonic development to study morphological landmarks associated with B. mori, Eri, another race a/silkworm, and pattern defects associated with Ekp mutant of B.mori. The homeotic mutant Ekp, generates ectopic abdominallegs, a feature …

Biology In Mathematics At The University Of Richmond, Lester Caudill

Department of Math & Statistics Faculty Publications

In an effort to meet the needs of science students for modeling skills, three new courses have been created at the University of Richmond: Scientific Calculus I and II, and Mathematical Models in Biology and Medicine. The courses are described, and lessons learned and future directions are discussed.

Management And Social Indicators Of Soil Carbon Storage In A Residential Ecosystem, Midlothian, Va, Christopher M. Gough, Eliza A. Fritz

Virginia Journal of Science

Soil carbon storage- defined here as carbon mass per unit ground area- is an important ecosystem service, sequestering carbon that might otherwise exist in atmospheric CO₂ . Significant attention has focused on the effects that humans have on carbon cycling, but little is known about how human behaviors and attitudes relate to lawn carbon storage. The objectives of this study were to conduct household surveys in concert with soil carbon sampling in a 10-year-old exurban neighborhood near Richmond, Virginia to quantify differences in soil carbon storage between residential lawns and mixed pine-hardwood forest fragments, and to determine how lawn …

Production And Characterization Of Multifunctional Endoxylanase By Bacillus Sp. X13, Ashabil Aygan, Burhan Arikan

Turkish Journal of Biology

A multifunctional endoxylanase producing Bacillus sp. was isolated from soil. Enzyme synthesis occurred at temperatures between 20 °C and 60 °C with an optimum 37 °C. Analysis of the enzyme by SDS-PAGE revealed 4 active enzyme bands, which were estimated to be 66.5 kDa, 80.6 kDa, 95.5 kDa, and 108.4 kDa. The enzyme has a broad temperature range, between 20 and 90 °C, with an optimum at 40 °C; and maximum activity was at pH 6.0. The enzyme showed a gradual decrease in the remaining activity as the pre-incubation temperature increase. Thermostability was not also increased in the presence of …

Adrenergic Receptor Expression On Raw264.7 Macrophages, Lindsay Ward

Honors Theses

In this study, AR surface expression patterns and regulation via AR-catecholamine interactions were characterized. Macrophage function was shown to be regulated by catecholamines through both Alpha- and Beta-ARs, as evidenced by corresponding alterations in cytokine production. Treatment of activated macrophages with NE, a general catecholamine, or fomoterol, a P-AR agonist, produced significant decreases in TNF and IL-6 secretion. The effecis of clonidine, an Alpha-AR agonist, produced less consistent results, but clonidine-mediated enhancement of cytokine secretion appears to be mediated by Alpha-AR signaling. LPS was shown to noticeably change the surface expression ofboth types of ARs in RAW264.7 macrophages. However, NE …

Sequences Of Tibetan Macaque (Macaca Thibetana) And Tourist Behaviors At Mt. Huangshan, China, Maureen S. Mccarthy, Megan D. Matheson, Jack D. Lester, Lori K. Sheeran, Jin-Hua Li

Biology Faculty Scholarship

Previous research on Tibetan macaques (Macaca thibetana) at Mt. Huangshan, China, suggested that ecotourism can have detrimental consequences. This study identified sequences of behaviors that typically occur in macaque-tourist interactions to examine whether particular tourist behaviors precipitate monkey responses. Focal sampling was used to record relevant behaviors from tourists and 10 macaques over 28 data collection sessions in August 2006. Data collectors recorded whether each behavior occurred as part of a sequence. Sequences were defined as two or more behaviors in which each behavior occurred within five seconds of the previous behavior. Of 3,129 total behaviors, 2,539 (81.1%) …

Optimization Of Ethanol Production By Yeasts From Lignocellulosic Feedstocks, Stephanie Lee Groves

Dissertations, Master's Theses and Master's Reports - Open

Ethanol from lignocellulosic feedstocks is not currently competitive with corn-based ethanol in terms of yields and commercial feasibility. Through optimization of the pretreatment and fermentation steps this could change. The overall goal of this study was to evaluate, characterize, and optimize ethanol production from lignocellulosic feedstocks by the yeasts Saccharomyces cerevisiae (strain Ethanol Red, ER) and Pichia stipitis CBS 6054.

Through a series of fermentations and growth studies, P. stipitis CBS 6054 and S. cerevisiae (ER) were evaluated on their ability to produce ethanol from both single substrate (xylose and glucose) and mixed substrate (five sugars present in hemicellulose) fermentations. …

Arrangement Of Gene Pairs, Retrotransposon Insertions, And Regulation Of Gene Expression In Plants, Nicholas D. Krom

Dissertations, Master's Theses and Master's Reports - Open

Plant genomes are extremely complex. Myriad factors contribute to their evolution and organization, as well as to the expression and regulation of individual genes. Here we present investigations into several such factors and their influence on genome structure and gene expression: the arrangement of pairs of physically adjacent genes, retrotransposons closely associated with genes, and the effect of retrotransposons on gene pair evolution.

All sequenced plant genomes contain a significant fraction of retrotransposons, including that of rice. We investigated the effects of retrotransposons within rice genes and within a 1 kb putative promoter region upstream of each gene. We found …

Biology Department To Honor Larry Hinck, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Demographics And Habitat Selection For The Western Meadowlark (Sturnella Neglecta) In The Nebraska Sandhills, Matthew D. Giovanni

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

The prairie ecosystems of the Great Plains region in North America have largely been replaced and fragmented with industrial agriculture and invasive herbaceous and woody plant species. The concurrent and large-scale suppression of wildfire and elimination of grazing by native ungulates may have further decreased the availability and quality of habitat for wildlife. Indeed, 2004 estimates indicate only 30% of historic grasslands in the Great Plains still exist, while the trends of decreased land area enrolled in the Conservation Reserve Program and increased land area in commercial agriculture indicate continued loss of habitat. This decrease in habitat availability continues to …

The Development Of Preservice Elementary Teachers' Pedagogical Content Knowledge For Scientific Modeling, Michelle Elizabeth Cotterman

Browse all Theses and Dissertations

For teachers to effectively engage students in scientific modeling, they require pedagogical content knowledge (PCK) for this practice. This study examines how preservice elementary teachers develop PCK for scientific modeling when given modeling centered instruction in a science methods course. Our findings indicate preservice teachers made significant pedagogical gains in this practice, shifting from using models as static products to using them as thinking tools for students to develop science content knowledge. However, few viewed learning the practice of scientific modeling as an important learning goal. Preservice teachers also had difficulty translating the depth of their understandings into lesson designs, …

Protein-Protein Docking Using Region-Based 3d Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur.

Results

We present a novel protein docking algorithm based …

Application Of 3d Zernike Descriptors To Shape-Based Ligand Similarity Searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed.

Results

In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, …

G-Trace: Rapid Gal4-Based Cell Lineage Analysis In Drosophila, Cory J. Evans, John M. Olson, Kathy T. Ngo, Eunha Kim, Noemi E. Lee, Edward Kuoy, Alexander N. Patananan, Daniel Sitz, Phuong Thao Tran, Minh Tu Do, Kevin Yackle, Albert Cespedes, Volker Hartenstein, Gerald B. Call, Utpal Banerjee, Miriam Beyder, Kush V. Bhatt, Chinmay Bhoot, Aaron W. Bradshaw, Tierney G. Brannigan, Boyu Cao, Yancey Y. Cashell, Timothy Chai, Alex W. Chan, Carissa Chan, Inho Chang, Jonathan Chang, Michael T. Chang, Patrick W. Chang, Stephen Chang, Neel Chari

Biology Faculty Works

We combined Gal4-UAS and the FLP recombinase–FRT and fluorescent reporters to generate cell clones that provide spatial, temporal and genetic information about the origins of individual cells in Drosophila melanogaster. We named this combination the Gal4 technique for real-time and clonal expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale.

Arbuscular Mycorrhizal Fungi: Factors Affecting Soil Organic Matter Storage, Carl Lee Rosier

Graduate Student Theses, Dissertations, & Professional Papers

Arbuscular mycorrhizal fungi (AMF) are soil fungi forming symbiotic associations with majority of land plants. AMF alter soil organic matter (SOM) directly through stabilization of soil aggregates and indirectly providing a path in which plant fixed C02 is transferred below-ground. Understanding contributions of AMF to SOM via protein production and stabilization of soil aggregates will greatly aid our understanding of soil carbon sequestration, nutrient cycling and mitigation of soil erosion. The work presented in chapter 2 challenges the glomalin extraction process and assesses the accuracy of the Bradford and monoclonal-antibody ELISA detection methods. My results clarify the contribution of glomalin …

Mckillop Library Electricity Use, Impacts And Solutions, Nellie Tarini, Marisa Volo, Carly Ouellette, Other Students

BIO140 Carbon Footprint Project

A few weeks ago, our class went on a guided tour of the library, which taught us about what goes on in the library, how resources are used, and basically how the library operates. From our tour, we saw many problem areas that could use improvements. One of these areas is the library’s use of electricity. Our group focused on the computers, printers, copiers, lights, and elevators in the library and how the library could use their electricity more efficiently. We have found that the library is not always using electricity effectively and efficiently. There are lights on when nobody …

Ecological Determinants Of Survival And Reproduction In The Spotted Hyena, Heather E. Watts

Biology Faculty Works

Large carnivores play a key role in the structuring and dynamics of many ecosystems, yet the factors influencing dynamics of carnivore populations themselves are often poorly understood. Spotted hyenas (Crocuta crocuta) are the most abundant large carnivores in many African ecosystems. We describe demographic patterns in a population of spotted hyenas observed continuously for 15.5 years, and assess the effects of per capita prey availability, interspecific competition, rainfall, anthropogenic disturbance, and disease on 2 key determinants of population dynamics: reproduction and survival. Annual reproduction, survival of juveniles (i.e., recruitment to adulthood), and mortality of adults varied among years of the …

The Effects Of Coaching Strategies For Primary Prevention Of Coronary Heart Disease Involving Asymptomatic Hospital Employees, Gabriel Mario Moreno

Browse all Theses and Dissertations

Introduction: An effective coronary heart disease (CHD) prevention program is needed. Currently, prevention of CHD is being sought through pre-CHD risk stratification of patients using office-based screening tools such as the Framingham risk model (Greenland, Smith, and Grundy, 2001). However, patients who are given recommendations for lifestyle behavior modification find difficulty employing and sustaining the changes. The recent popularity of coaching for health behavior change has prompted the question of whether coaching is an effective method to produce a higher success rate for lowering cardiovascular disease following risk stratification.

The main purpose of this study was to investigate the effectiveness …

Risk-Sensitive Foraging Facilitates Species-Level Trophic Cascades Among Terrestrial Mammals: A Meta-Analysis, Bryan David Murray

Browse all Theses and Dissertations

The widespread removal of large carnivores from terrestrial ecosystems may be contributing to plant species loss and biotic homogenization through trophic cascades. A few plants not preferred by ungulates are increasing in abundance while the majority of preferred plants are in decline. A meta-analysis of recruitment gaps in browse-sensitive tree species demonstrated that failed recruitment coincided in time with carnivore loss. In all studies recruitment continued in nearby browsing refugia. A second meta-analysis revealed that the mechanism of mammalian herbivore-mediated trophic cascades contains a behavioral component. Foraging mammals exhibited higher giving-up densities (GUDs) when under higher predation risk. GUDs were …

A Potential Strategy To Maintain Hsv-1 In A Latent State: Use Of Immunoregulatory Peptide Mimetics, Nasrin Majidi

Browse all Theses and Dissertations

This study reviews the role of interferon-gamma (IFN-gamma) in HSV-1 latency. CD8+ T cells inhibit the reactivation of HSV-1 in trigeminal ganglia (TG) by production of IFN-gamma. Although CD8+ T cells include all the cytotoxic apparatus for cytotoxicity, latently infected neuronal cells are not killed by CD8+ T cells. The CD94-NKG2a molecule on CD8+ T cells, binds to Qa-1b (a MHC class I like molecule) present on neuronal cell to inhibit CD8+ T cells cytotoxicity. Other studies have also determined that the IFN-gamma peptide mimetic 95-132 inhibits HSV-1 replication in the same way as IFN-gamma in infected cells. IFN-gamma mimetic …

Finding The Trophic Trickle: Using Herbaceous Indicator Species To Investigate Plant Recovery From Intense Browsing By White-Tailed Deer (Odocoileus Virginianus) After The Re-Colonization Of A Top Predator (Canis Lupus), Krystle A. Bouchard

Browse all Theses and Dissertations

High densities of white-tailed deer (Odocoileus virginianus) have been implicated in changing forest community structure and composition. Top predators, including gray wolf (Canis lupus), were extirpated from much of their range by the mid 1900s, but have since returned to Northern Wisconsin. To determine whether the re-colonization of wolves could initiate a trophic cascade resulting in the recovery of understory plants from deer browsing, I surveyed four herbaceous species in areas without wolves and areas with 4-6 year old wolf packs and 12-13 year old wolf packs. Plant size and reproduction were greater in areas where wolves had been for …

Influence Of Diet On Population Growth And Allergen Production In Cultured House Dust Mites - Dermatophagoides Farinae And Dermatophagoides Pteronyssinus, Swetha Avula Poola

Browse all Theses and Dissertations

Dermatophagoides farinae and Dermatophagoides pteronyssinus culture extracts are used for skin testing, immunotherapy and research studies. There is a need to develop an effective culture method so that standardized extracts and allergens can be produced. The purpose of this study was to examine if different diets effect mite population growth and the amount of allergen produced in cultures. Dermatophagoides farinae and Dermatophagoides pteronyssinus were cultured on diets A and B. The density of mites, life stage composition and allergen concentration was determined at two week intervals. Enzyme-linked immune sorbent assays (ELISA) were used to assess group 1 and group 2 …

Characterization Of Microtubule Depolymerization By The Hiv Protein Rev, Shimpi Bedi

Browse all Theses and Dissertations

The HIV-1 Rev protein enables the nucleocytoplasmic export of unspliced or partially spliced mRNAs that is required for the synthesis of structural proteins. By doing so, it regulates the switch to the late phase of the viral replication cycle (Cullen, 1992). This regulatory control over viral replication makes Rev an attractive target for anti-viral intervention. The development of anti-viral remedies is hindered because the three-dimensional structure of Rev has not yet been solved by X-ray crystallography and NMR. Rev, which polymerizes into regular hollow filaments at high concentrations, forms side-to-side and end-to-side interactions making it prone to aggregation and precipitation …

Immunolocalization And Changes In Expression Levels Of Glyceroporin Hc-3 In Several Tissues Of Gray Tree Frogs, Hyla Chrysoscelis Under Different Physiological Conditions, Sushmita Yaganti

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Previous studies show that aquaporin HC-3 in gray tree frogs, Hyla chrysoscelis, a homolog of mammalian AQP3 is an aqua glyceroporin also responsible for freeze tolerance. Our study tried to localize and compare the protein expression levels of aquaporin HC-3 in seven different organs of gray tree frogs under five different physiological conditions using immuno histofluorescence and western blot. HC-3 was immunolocalized in the epidermis and dermis of the skin, basolateral portion of the collecting ducts in the kidney, red blood cells in the liver and other tissues, muscle Schwann cells and the basolateral portion of the large intestine epithelial …

Probing A Role For Trap150 In Gene Regulation, Divya Potabathula

Browse all Theses and Dissertations

The mammalian cell nucleus is a highly organized cellular compartment. The nucleus is surrounded by the nuclear envelope and contains distinct domains such as nucleoli, nuclear speckles and Cajal bodies that may reflect nuclear functions such as transcription and RNA processing. Nuclear speckles are regions in the nucleus that are enriched in splicing factors and other RNA processing factors, as well as some transcription factors and the large subunit of RNA polymerase II. Mass spectrometry analysis of purified nuclear speckles revealed 146 nuclear speckle proteins of which 33 are novel nuclear speckle components. One such novel nuclear speckle protein is …

Inflammatory Cytokines In Jet Propulsion Fuel-8 Induced Irritant Contact Dermatitis In Male Fischer Rats, Thomas Joseph Kannanayakal

Browse all Theses and Dissertations

Contact dermatitis is one of the most common occupational diseases. Absenteeism of the affected workers and associated health care costs makes this disease an economically important issue. Irritant contact dermatitis (ICD) is a common contact dermatitis observed among workers. As each category of irritants triggers the inflammatory process by different method, studying the mechanism of ICD is difficult. Information on the mechanism of action of an irritant is indispensable for the development of effective prophylactic and therapeutic measures. In this study, we have investigated the early changes in rat skin induced by jet fuel-8 (JP-8). Although previous studies have described …

Physiological Effects On The Expression Of Aquaporin 1-Like Hc-1 In Cope's Gray Tree Frog, Hyla Chrysoscelis, Ram Naresh Pandey

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Aquaporin 1 is a cell membrane integral protein, which functions for water transport through the hydrophobic cell membrane to the cytoplasm. HC-1 is an aquaporin 1-like protein expressed in Hyla chrysoscelis and amphibian that survives at sub-freezing temperatures in its natural habitat. The goal of the current study was to investigate the expression of HC-1 during changing physiological conditions. The expression level of HC-1 was determined in skin, muscle, liver, kidney, and intestines of warm, cold, frozen, and dehydrated frogs using Western blot and immunohistofluorescence. Although HC-1 was widely distributed, the expression level varied among tissues and physiological conditions. In …

The Influence Of Temperature On Population Growth And Allergen Production In Cultured House Dust Mites - Dermatophagoides Pteronyssinus And Dermatophagoides Farinae, Lakshmi Yella

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Dermatophagoides pteronyssinus and Dermatophagoides farinae are commercially cultured to produce materials to make extracts for diagnostic tests and immunotherapy. There is some speculation as to how the culture conditions such as time of culture, temperature, relative humidity and food might influence the mite populations and subsequent production of allergens. The purpose of our investigation was to see how temperature influenced the population growth and allergen production of cultured house dust mites. D. pteronyssinus and D. farinae were cultured at 20°C and 25°C. Samples were collected at two week intervals for live mite count, life stage composition and to determine Group …

Pollen-Based Biome Reconstructions For Latin America At 0, 6000 And 18 000 Radiocarbon Years Ago, Rob A. Marchant, Antoine M. Cleef, Sandy P. Harrison, Henry Hooghiemstra, Vera Markgraf, John H. Van Boxel, Thomas A. Ager, Lucia Almeida, R. Anderson, C. Baied, H. Behling, J. C. Berrio, R. Burbridge, S. Bjorck, R. Byrne, Mark B. Bush, J. Duivenvoorden, J. Flenley, P. De Oliveira, B. Van Geel, K. Graf, W. D. Gosling, S. Harbele, T. Van Der Hammen, B. Hansen, S. Horn, P. Kuhry, M.-.P Ledru, F. Mayle, B. Leyden, S. Lozano-Garcia, A. M. Melief, P. Moreno, N. T. Moar, A. Prieto, G. Van Reenen, M. Salgado-Labouriau, F. Schabitz, E. J. Schreve-Brinkman, M. Wille

Ocean Engineering and Marine Sciences Faculty Publications

The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human …