Life Sciences Commons^™

Statistical Tools For Transgene Copy Number Estimation Based On Real-Time Pcr, Joshua S. Yuan, Jason N Burris, Nathan R. Stewart, Ayalew Mentewab, C. Neal Stewart

Faculty Publications and Other Works -- General Biology

Background

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination.

Results

Three experimental designs and four data quality control integrated statistical models are …

Third Thursday 11-2007, Institute Of Agriculture

Third Thursday

No abstract provided.

Modeling Sage Tag Formation And Its Effects On Data Interpretation Within A Bayesian Framework, Michael A. Gilchrist, Hong Qin, Russell Zaretzki

Faculty Publications and Other Works -- General Biology

Abstract

Background

Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore the fact that the probability of generating an observable tag varies across genes and between experiments. As a consequence, these analyses result in biased estimators and posterior probability intervals for gene expression levels in the transcriptome.

Results

Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation …

The Beasts In Our Brain, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

In the neuropsychology of art, we must remember that the Brain of Man has not abandoned its ancient animal foundations, it has built upon them . . . . But it has also reconstructed them as the shifting earth beneath dictates . . . . We have done the best possible in the landscape in which we have found ourselves with the raw materials we have inherited." --(Greenberg, Prolegomena to a Study of Mind, 1973, ch. 42)

Third Thursday 10-2007, Institute Of Agriculture

Third Thursday

No abstract provided.

Liver Lipid Molecules Induce Pepck-C Gene Transcription And Attenuate Insulin Action., Guoxun Chen

Nutrition Publications and Other Works

Cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) plays key roles in gluconeogenesis, glyceroneogenesis, and cataplerosis. Experiments were designed to examine the effects of endogenous lipid molecules from rat livers on the expression of PEPCK-C gene in primary rat hepatocytes. The lipid extracts prepared from livers of Zucker fatty, lean, and Wistar rats induced the expression levels of PEPCK-C transcripts. Insulin-mediated reduction of PEPCK-C gene expression was attenuated by the same treatment. The lipid extracts induced the relative luciferase activity of reporter gene constructs that contain a 2.2-kb 5' promoter fragment of PEPCK-C gene, but not the construct that contains only the 3' untranslated …

Pb1594-Insect And Mite Management In Greenhouses, The University Of Tennessee Agricultural Extension Service

Commercial Horticulture

Pest Management (PM) is a term that refers to the use of various strategies to manage greenhouse insect and mite pests. The focus of PM is to use a variety of management strategies to deal with existing pest problems, rather than relying solely on pest control materials such as insecticides and/or miticides. PM involves the use of cultural, physical, biological and/or chemical management strategies.

PM programs typically require growers to be proactive rather than reactive. An effective PM program begins by regularly scouting the greenhouse for insect and mite pests. A PM program may include establishing action thresholds for specific …

Pb1741-Horse Welfare, The University Of Tennessee Agricultural Extension Service

Animals/Livestock

In Tennessee, horses are commonly owned throughout the state. Tennessee law requires that all animals have necessary water, feed, shelter and care. This publication defines what are considered the minimum requirements for horses in these areas. It is important to remember that these represent only the minimums, and horse owners should strive to provide care above these levels.

Third Thursday 9-2007, Institute Of Agriculture

Third Thursday

No abstract provided.

Past Fire Regimes Of Table Mountain Pine (Pinus Pungens L.) Stands In The Central Appalachian Mountains, Virginia, U.S.A., Georgina Deweese

Doctoral Dissertations

Table Mountain pine is an Appalachian endemic that occurs in a patchy distribution from Georgia to Pennsylvania and is prolific at sites with a history of fire disturbance. The purpose of this dissertation was to reconstruct the fire regimes of Table Mountain pine stands in the Jefferson National Forest, Virginia. Sections from firescarred Table Mountain pines were collected at four sites to analyze fire history, while increment cores and stand composition information were collected from macroplots within each fire history site to investigate the possible influence of fires that were more ecologically severe. Results show that fire was frequent before …

Characterization Of The Role Of Mouse Nell1 Gene In Osteogenesis And Chondrogenesis During Mammalian Fetal Development, Jayashree Basavaraj Desai

Doctoral Dissertations

The mammalian Nell1 gene encodes a PKC-β1 binding protein that belongs to a new class of cell-signaling molecules controlling cell growth and differentiation. Overexpression of NELL1/Nell1 in the developing cranial sutures in both human and mouse induces craniosynostosis, the premature fusion of cranial sutures. This study describes the characterization of Nell1^6R (102DSJ), a recessive, neonatal-lethal point mutation in the mouse Nell1 gene, induced by N-ethyl-N-nitrosourea (ENU). The generation and sequencing of the mouse full-length cDNA (2862 bp) revealed that the Nell1 gene has an open reading frame of 2433 bp and encodes an 810 amino acid protein …

Bat Population Dynamics: An Individual-Based Model Approach, Paula Federico

Doctoral Dissertations

Temperate zone bats are subject to serious energetic constraints due to their high surface area to volume relations, the cost of temperature regulation, the high metabolic cost of flight, and the seasonality of their resources. To my knowledge, there are no individual-based mathematical models for any bat species. The model developed here for a female bat is primarily based on life history and energetics. It describes the growth of an individual female bat using a system of differential equations modeling the dynamics of two main compartments: storage (lipids) and structure (proteins and carbohydrates). The model is parameterized for the little …

The Influence Of Atmospherics On Consumer Perceptions Of Service Quality, Merchandise Price, And Merchandise Quality Influencing Behavioral Intentions: A Retailing Study Of Outlet Malls, Alycia Fogle Holmes

Doctoral Dissertations

This study examines the influence of atmospherics on consumer perceptions of service quality, merchandise price, and merchandise quality influencing behavioral intentions in an outlet mall environment. The research design was a survey method and data were collected through a mall intercept questionnaire. A pilot test of the instrument was conducted with 43 subjects. The final questionnaire contained 30 items and a demographic section. A total of 586 questionnaires were collected from three different outlet malls. The results indicated that the atmospheric variables and the human variable of crowding are related to consumer’s perceptions of the service quality, merchandise price, and …

Establishment, Growth, Spread, And Ecological Impacts Of Microstegium Vimineum In Central Hardwood Forests, Jordan M. Marshall

Doctoral Dissertations

Microstegium vimineum is an annual exotic grass common through the Southeastern United States. Adding M. vimineum to native plant communities may alter future forest composition through inhibiting the growth and influencing recruitment of seedlings into larger size classes, as well as significantly altering vertical structure and community richness, which may influence the distribution of insects.

The main objectives of these studies were to 1) establish how different mineral soil and litter disturbances, in combination with various forest canopy coverage, influence the establishment, growth, and spread of M. vimineum, 2) quantify effects of competition between M. vimineum and native hardwood …

An Experimental Release Of Elk Into Great Smoky Mountains National Park, Jennifer Lynn Murrow

Doctoral Dissertations

I conducted 6 years of field work to evaluate the habitat use and population dynamics of an experimental release of elk (Cervus elaphus) into Great Smoky Mountains National Park (Park). Elk exhibited relatively small home ranges (female: 10.4 km² and males: 22.4 km²) and movement distances decreased over time. I calculated survival rates (x = 0.73–0.93) and litter production rates (x = 0.73) for the population. To assess the potential for a long-term elk population, I incorporated those vital rates into the population modeling software Riskman and tested its sensitivity to any given …

Identification And Characterization Of Phenotypically Distinct Aggregates Within Huntingtin-Inducible Pc12 Cell Models, Erica Leann Rowe

Doctoral Dissertations

The role of various polyglutamine (polyGln) aggregated states in the disease mechanism of expanded CAG repeat disorders continues to be a perplexing subject. We are interested in learning more about these species and the relationship between the aggregation pathways. We have developed an innovative staining technique that allows, for the first time, the visualization of small polyGln aggregates, which we refer to as aggregation foci (AF), that are functionally distinguished by their ability to serve as seeds for amyloid growth. The aggregation foci stain should prove useful in the Huntington’s disease research as a tool for the identification of a …

Program, Classroom, And Teachers Characteristics: Their Associations With Classroom Quality In State-Funded Pre-K Classrooms, Mi-Hyang Ryu

Doctoral Dissertations

With data from the NCEDL Multi-State Pre-Kindergarten Study, the relationship between the characteristics of program, classroom, and teachers and classroom quality was examined in this study. Classroom quality was measured by the Classroom Assessment Scoring System and the Emerging Academics Snapshot. The sample consisted of 227 pre-k teachers in state-funded programs from six states. The percentage of children from low-income families in the classroom and the number of children with limited English proficiency (the only two predictive variables that described children’s characteristics) were found to be statistically significant predictors of classroom process quality. These findings were discussed with regard …

A Systematic Study Of Trillium Subgenus Delostylis, Susan B. Farmer

Doctoral Dissertations

This study focused on the systematics of Trillium subg. Delostylis, an enigmatic group endemic to the southeastern United States. Phylogenetic analysis of DNA sequence data was used to examine the circumscription and phylogenetic placement of Delostylis. The results of the phylogenetic analysis of data from the ITS, matK, and psbA-trnH sequence data suggested that the circumscription of Delostylis be narrowed to consist of T. persistens, T. catesbaei, and T. pusillum sensu lato. A revised Delostylis was characterized by the presence of a style with three slender stigmatic branches in those plants whose flowers are either white-fading-to-pink …

Construction Of Bacteriophage-Based Bioluminescent Bioreporters For Staphylococcus Aureus And Salmonella Monitoring, Aysu Ozen

Doctoral Dissertations

Construction of two recombinant luxI bacteriophage-based bioluminescent bioreporters was undertaken to develop detection and monitoring systems for Staphylococcus aureus and Salmonella spp. These systems take advantage of the high specificity of bacteriophage for their hosts and the Vibrio fischeri lux operon responsible for quorum sensing bioluminescence. The detection system is composed of two elements, a recombinant phage with luxI which is specific for the target pathogen, and an acylhomoserine lactone (AHL)-inducible bioreporter cell line carrying the reporter lux genes. The goal of this study was to construct Salmonella- and S. aureus-specific recombinant phages which contain luxI.

The …

W166 Accent™ Herbicide For Weed Control In Sweet Corn, The University Of Tennessee Agricultural Extension Service

Field & Commercial Crops

The convenient control of perennial and annual grass weeds in fresh market sweet corn has been difficult for a number of years due to the lack of available postemergence herbicide options. Accent™ herbicide has been labeled for use in processing sweet corn for a number of years but was not cleared for fresh market use until fall 2006. One concern with Accent™ use is that a small number of sweet corn hybrids could have low tolerance to nicosulfuron, the active ingredient (Figure 1). Additionally, delayed applications of the herbicide or applications with improperly calibrated spray equipment could result in ear …

W168 Controlling Volunteer Cotton In Soybeans, The University Of Tennessee Agricultural Extension Service

Field & Commercial Crops

No abstract provided.

W166-Accent™ Herbicide For Weed Control In Sweet Corn, The University Of Tennessee Agricultural Extension Service

Commercial Horticulture

The convenient control of perennial and annual grass weeds in fresh market sweet corn has been difficult for a number of years due to the lack of available postemergence herbicide options. Accent™ herbicide has been labeled for use in processing sweet corn for a number of years but was not cleared for fresh market use until fall 2006. One concern with Accent™ use is that a small number of sweet corn hybrids could have low tolerance to nicosulfuron, the active ingredient (Figure 1). Additionally, delayed applications of the herbicide or applications with improperly calibrated spray equipment could result in ear …

Pb1624-Managing Nuisance Animals And Associated Damage Around The Home, The University Of Tennessee Agricultural Extension Service

Insects, Pests, Plant Diseases and Weeds

Managing wildlife damage is the opposite of traditional wildlife management where practices are implemented to attract wildlife. To attract wildlife, food, water and cover are made available for animals throughout the year. If unwanted wild animals are frequenting your home or garden, there is at least one source of food, water and/or cover that is attracting them. The solution is to remove or alter these resources so that the area is no longer attractive. Most wildlife, like humans, are creatures of habit; thus, steps should be taken immediately upon observing damage.

Third Thursday 8-2007, Institute Of Agriculture

Third Thursday

No abstract provided.

Application Of Solid Phase Micro-Extraction With Gas Chromatography-Mass Spectrometry For The Determination Of Geosmin And 2-Methylisoborneol In Processed Navy Beans (Phaseolus Vulgaris), Coesha Ancoinette Fairley

Doctoral Dissertations

This investigation was conducted to address the issue of musty bean products. The main objectives of this study were to: (1) identify the source of the musty, off-flavor in processed navy beans, (2) determine and identify the associated off-flavor compounds (geosmin and 2-methylisoborneol (2-MIB)), and (3) isolate the microorganism(s) responsible for production of the compounds.

To confirm the presence of geosmin and 2-MIB in processed baked beans, an automated gas chromatographic method employing solid phase micro-extraction (SPME-GC-MS) was used. Artificially musty baked beans, known musty beans, and raw ingredients (bacon, navy beans, and water) were analyzed. Results of this investigation …

Analysis Of Tourists Attending A Culinary Event: Motivations, Satisfaction, And Behavioral Outcomes, Sylvia Smith

Doctoral Dissertations

The study constructs a causal model of culinary tourist behavior from the theoretical framework of push and pull motivations and related concepts with regard to satisfaction and behavioral intentions. Respondents were distinguished with regards to socio-demographic characteristics, travel behavior, and importance of event attributes. Further, importance-performance hypothetical framework was utilized to measure pull motivations. The study proposed that culinary event attendees’ expenditures, word-of-mouth behavior, and repeat patronage intentions would be related to their overall event satisfaction. Culinary event attendees were segmented on the basis of push motivations. Using factor, cluster, and multiple regression analyses with data collected from an international …

Adiposity Related Protection Of Intestinal Tumorigenesis: Interaction With Dietary Calcium, Shengli Ding

Doctoral Dissertations

Excess adipose tissue is a risk factor for developing colorectal cancer. However, the present studies demonstrate that lack of adipose-derived factor(s), such as adiponectin, due to the substantial loss of body fat on high dairy calcium diet could increase susceptibility to intestinal tumorigenesis. These studies suggest that a minimum amount or threshold level of adipose tissue may be required to significantly attenuate tumorigenesis.

In Apc^Min/+ mice, consumption of high dairy calcium diet exhibited markedly reduced adipose tissue and increased tumor number. Our results showed that the high calcium diet reduced fat pad mass by 65%-82% in Apc^Min/+ (p …

The Role Of Soluble Fibrin In Lymphocyte And Lak Cell Adherence To And Migration Across Vascular Endothelial Cells: Implications For Immunotherapy And Cancer, Brandy Lee Weidow

Masters Theses

Although conventional therapies for metastatic cancers have made significant progress in recent years, they are relatively nonspecific and have many deleterious side-effects. Recently, novel therapies, including adoptive cellular immune therapies have had sporadic, but spectacular success in cancers such as malignant melanoma and renal cell carcinoma: tumors in which an immune response has been demonstrated. However, other physiological mechanisms, such as blood coagulation inhibit the immune response against cancers. Our previous work has shown that one of these coagulation proteins, soluble fibrin (sFn), inhibits unstimulated and activated lymphocyte adherence to tumor cells by blocking leukocyte integrin (CD11a/CD18) binding to tumor …

An Evaluation Of Field Management Practices To Improve Bobwhite Habitat, John P. Gruchy

Masters Theses

Conversion of tall fescue (Festuca arundinacea) to managed native warm-season grasses (nwsg) and associated forbs benefits many wildlife species that depend on early successional habitat. Planting nwsg, however, may not be necessary depending on the composition of the seedbank. Treatments were implemented in a randomized complete block design with replication during 2003 and 2004 at three study sites across Tennessee to determine the effects of seasonal herbicide applications and disking on tall fescue eradication and resulting vegetation composition and structure. Treatments included: fall glyphosate (2.2 kg ai/ha; Gly-4 2qt/ac); fall glyphosate followed by winter disking; fall imazapic (0.2 …

Influences Of Cattle On Community Structure And Pathogen Prevalence In Larval Amphibians On The Cumberland Plateau, Tennessee, Anne Chandler Schmutzer

Masters Theses

There is considerable evidence that amphibians are declining globally due to various anthropogenic stressors. Cattle grazing in wetlands is a stressor that may have negative impacts on amphibians and has not been investigated intensively. Cattle could have a negative effect on larval amphibians by decreasing water quality through deposition of nitrogenous waste. Reduction in water quality also may compromise immune function by inducing stress thus making larvae more susceptible to pathogens. My objective was to quantify differences in amphibian larvae community metrics, water quality, and pathogen prevalence between cattle-access and non-access wetlands. I also measured fish abundance and biomass of …