Biology Commons^™

Temperature Changes Resulting From A Gaalas Laser In The Decontamination Of A Failing Dental Implant, Adam B. Oppenheimer

Journal of the South Carolina Academy of Science

No abstract provided.

Where Do Mouse Embryos Thrive Best? Comparison Of Mammalian Embryo Development Under Varying Laboratory Environments, Yvonne K. Kao, H. Lee Higdon Iii, Ph.D, Jennifer E. Graves-Herring , M.S., William R. Boone Ph.D

Journal of the South Carolina Academy of Science

No abstract provided.

Contributions Of Gut Bacteria To Bacillus Thuringiensis-Induced Mortality Vary Across A Range Of Lepidoptera, Nichole Broderick, Courtney Robinson, Matthew Mcmahon, Kenneth Raffa

Department of Biology Faculty Publications

Gut microbiota contribute to the health of their hosts, and alterations in the composition of this microbiota can lead to disease. Previously, we demonstrated that indigenous gut bacteria were required for the insecticidal toxin of Bacillus thuringiensis to kill the gypsy moth, Lymantria dispar. B. thuringiensis and its associated insecticidal toxins are commonly used for the control of lepidopteran pests. A variety of factors associated with the insect host, B. thuringiensis strain, and environment affect the wide range of susceptibilities among Lepidoptera, but the interaction of gut bacteria with these factors is not understood. To assess the contribution of gut …

Inheritance Of Shoulder Spotting In The Tetra, Hyphessobrycon Bentosi Characidae, Jack Frankel

Department of Biology Faculty Publications

The tetra (Hyphessobrycon bentosi) exhibits two phenotypes associated with shoulder spotting. Fish possess ei-ther a prominent black vertical spot located directly behind the operculum (H. b. bentosi,  bentosi  white  tip  tetra) or  lack  this spot (H. b. rosaceus, rosy tetra). Segregation patterns observed from the progenies of ten different crosses suggest that the  inheritance  of  these  phenotypes  is  controlled  by  two  autosomal  loci  acting  in  a complementary  fashion,  with  domi-nance at both loci required for the expression of the spotted phenotype. 

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. A. Long, Jianjun Hu

Faculty Publications

Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), …

Rex1p Deficiency Leads To Accumulation Of Precursor Initiator TrnaMet And Polyadenylation Of Substrate Rnas In Saccharomyces Cerevisiae, Sarah G. Ozanick, Xuying Wang, Michael Costanzo, Renee L. Brost, Charles Boone, James T. Anderson

Biological Sciences Faculty Research and Publications

A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of any non-essential gene in Saccharomyces cerevisiae. We found that deletion of the REX1 gene resulted in a slow-growth phenotype in the trm6-504 strain. Previously, REX1 was shown to be involved in processing the 3′ ends of 5S rRNA and the dimeric tRNA^Arg-tRNA^Asp. In this study, we have discovered a requirement for Rex1p in processing the 3′ end of tRNA_i^Met precursors and …

Dna Before Proteins? Recent Discoveries In Nucleic Acid Catalysis Strengthen The Case, Aaron Steven Burton, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes— a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5’-glyceryl- and 3’- glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template …

Crosslinking Of Cell-Derived 3d Scaffolds Up-Regulates The Stretching And Unfolding Of New Extracellular Matrix Assembled By Reseeded Cells, Kristopher Kubow

Selected Works

No abstract provided.

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 …

Coiled-Coil-Mediated Dimerization Is Not Required For Myosin Vi To Stabilize Actin During Spermatid Individualization In Drosophila Melanogaster, Tatsuhiko Nogushi, Deborah J. Frank, Mamiko Isaji, Kathryn G. Miller

Biology Faculty Research

Myosin VI is a pointed-end-directed actin motor that is thought to function as both a transporter of cargoes and an anchor, capable of binding cellular components to actin for long periods. Dimerization via a predicted coiled coil was hypothesized to regulate activity and motor properties. However, the importance of the coiled-coil sequence has not been tested in vivo. We used myosin VI's well-defined role in actin stabilization during Drosophila spermatid individualization to test the importance in vivo of the predicted coiled coil. If myosin VI functions as a dimer, a forced dimer should fully rescue myosin VI loss of function …

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 …

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%) …

Homeotic Mutants And The Assimilation Of Developmental Genetics Into The Evolutionary Synthesis, Michael Dietrich, Gregory K. Davis, David K. Jacobs

Dartmouth Scholarship

No abstract provided.

Numerical Modeling Of Hemodynamics In The Thoracic Aorta And Alterations By Dacron Patch Treatment Of Aortic Coarctation, Ronak Jashwant Dholakia

Master's Theses (2009 -)

Coarctation of the aorta (CoA) is a major congenital heart disease, characterized by a severe stenosis of the proximal descending thoracic aorta. Traditionally, surgery has been the treatment of choice for CoA. Dacron patch aortoplasty gained increased popularity after its introduction in the mid-twentieth century due to its advantages over other surgical treatment methods available at the time. A major complication with Dacron patch aortoplasty has been the formation of late aneurysm with as much as 51% incidence reported in follow up studies. The change in aortic morphology and formation of aneurysms after Dacron patch surgery could lead to local …

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 Effect Of Caffeine On The Bacterial Populations In A Freshwater Aquarium System, Adrienne M. Gibson, Roderick M. Morgan, Alexey G. Nikitin

Student Summer Scholars Manuscripts

Caffeine is becoming a common chemical found in the environment but, little research has been done to understand the environmental effects of caffeine, including dissolved caffeine in aquatic systems. The goal of this research study was to begin to understand how caffeine may interact with aquatic environment, using the bacteria of the genus Pseudomonas, commonly found in the aquatic habitat. We found that Pseudomonas shows an increase in growth when exposed to caffeine, which results in a change in spectrophotometric absorbance, increase in bacterial colony count in the presence of caffeine, and in bio-film like sheen appearing on the glass …

An Examination Of Speciation, Extinction, And Evolutionary Relationships In Plants From Two Continents, Corey Davis, Timothy Evans

Student Summer Scholars Manuscripts

No abstract provided.

Sex Differences In Innate Immunity In Tree Swallows, Bradley J. Houdek, Michael P. Lombardo, Patrick A. Thorpe

Student Summer Scholars Manuscripts

Evolutionary theory predicts that exposure to more diverse pathogens will lead to the evolution of more effective immune responses. The innate immune system defends the host from pathogens in a non-specific manner and is an important first-line of defense. We predicted that female Tree Swallows have more robust innate immunocompetence than males because females are exposed to more microbes during the breeding season than are males. This is because (a) females participate in extra-pair copulations with multiple males exposing them to sexually transmitted microbes (STMs) (e.g., bacteria, fungi, viruses), (b) the transmission of STMs during copulation is asymmetrical because ejaculates …

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.

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 …