Life Sciences Commons^™

Genetic And Genomic Analysis Of Hyperlipidemia, Obesity And Diabetes Using (C57bl/6j × Tallyho/Jngj) F2 Mice, Taryn P. Stewart, Hyoung Y. Kim, Arnold M. Saxton, Jung H. Kim

Nutrition Publications and Other Works

Background

Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.

Results

In order to determine the genetic factors that contribute to these T2D related characteristics in TH mice, we interbred TH mice with C57BL/6J (B6) mice. The parental, F1, and …

Sp569 Parenting Apart: Effective Co-Parenting, Denise Brandon

Family

Version 2.0

Third Thursday 11-2010, Institute Of Agriculture

Third Thursday

No abstract provided.

Climate Change Alters Seedling Emergence And Establishment In An Old-Field Ecosystem, Aimée T. Classen, Richard J. Norby, Courtney E. Campany, Katherine E. Sides, Jake F. Weltzin

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future.

Methodology/Principal Findings

We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and …

T-Rfpred: A Nucleotide Sequence Size Prediction Tool For Microbial Community Description Based On Terminal-Restriction Fragment Length Polymorphism Chromatograms, Antonio Fernandez-Guerra, Alison Buchan, Xiaozhen Mou, Emilio O. Casamayor, Jose M. Gonzalez

Microbiology Publications and Other Works

Background

Terminal-Restriction Fragment Length Polymorphism (T-RFLP) is a technique used to analyze complex microbial communities. It allows for the quantification of unique or numerically dominant phylotypes in amplicon pools and it has been used primarily for comparisons between different communities. T-RFPred, Terminal-Restriction Fragment Prediction, was developed to identify and assign taxonomic information to chromatogram peaks of a T-RFLP fingerprint for a more comprehensive description of microbial communities. The program estimates the expected fragment size of representative 16S rRNA gene sequences (either from a complementary clone library or from public databases) for a given primer and restriction enzyme(s) and provides candidate …

Discovering Gene Functional Relationships Using Faun (Feature Annotation Using Nonnegative Matrix Factorization), Elina Tjioe, Michael W. Berry, Ramin Homayouni

Faculty Publications and Other Works -- EECS

Background

Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics. While numerous (software) tools have been developed to extract and identify gene relationships from biological databases, few effectively deal with extracting new (or implied) gene relationships, a process which is useful in interpretation of discovery-oriented genome-wide experiments.

Results

In this study, we develop a Web-based bioinformatics software environment called FAUN or Feature Annotation Using Nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity …

Explorations Volume 1 Fall 2010, Department Of Ecology & Evolutionary Biology

EEB Newsletter

No abstract provided.

Discovery Fall 2010, Misty Bailey

Discovery Research Newsletter

Discovery is a quarterly research newsletter published by the College of Veterinary Medicine Office of Research and Graduate Studies. It is intended to highlight research and sponsored programs in the college and provide information about research opportunities.

Third Thursday 10-2010, Institute Of Agriculture

Third Thursday

No abstract provided.

Selected Hormonal And Neurotransmitter Mechanisms Regulating, James L. Sartin, Joseph A. Daniel, Brian K. Whitlock, Robyn R. Wilborn

Faculty Publications and Other Works -- Large Animal Clinical Sciences

Appetite control is a major issue in normal growth and in suboptimal growth performance settings. A number of hormones, in particular leptin, activate or inhibit orexigenic or anorexigenic neurotransmitters within the arcuate nucleus of the hypothalamus, where feed intake regulation is integrated. Examples of appetite regulatory neurotransmitters are the stimulatory neurotransmitters neuropeptide Y (NPY), agouti-related protein (AgRP), orexin and melanin-concentrating hormone and the inhibitory neurotransmitter, melanocyte-stimulating hormone (MSH). Examination of messenger RNA (using in situ hybridization and realtime PCR) and proteins (using immunohistochemistry) for these neurotransmitters in ruminants has indicated that physiological regulation occurs in response to fasting for several …

Effect Of Social Status On Behavioral And Neural Response To Stress, Daniel W. Curry, Kathleen E. Morrison, Matthew A. Cooper

Senior Thesis Projects, 2009

Individuals respond differently to traumatic stress. Social status, which plays a key role in how animals experience and interact with their social environment, may influence how individuals respond to stressors. In this study, we used a conditioned defeat model to investigate whether social status alters susceptibility to the behavioral and neural consequences of traumatic stress. Conditioned defeat is a model in Syrian hamsters in which an acute social defeat encounter results in a long term increase in submissive behavior and a loss of normal territorial aggression. To establish social status, we weight matched and paired Syrian hamsters in daily aggressive …

Temporal Diversification Of Central American Cichlids, C Darrin Hulsey, Phillip R. Hollingsworth, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Cichlid fishes are classic examples of adaptive radiation because of their putative tendency to explosively diversify after invading novel environments. To examine whether ecological opportunity increased diversification (speciation minus extinction) early in a species-rich cichlid radiation, we determined if Heroine cichlids experienced a burst of diversification following their invasion of Central America.

Results

We first reconstructed the Heroine phylogeny and determined the basal node to use as the root of Central American Heroine diversification. We then examined the influence of incomplete taxon sampling on this group's diversification patterns. First, we added missing species randomly to the phylogeny and assessed …

Effect Of Correlated Tran Abundances On Translation Errors And Evolution Of Codon Usage Bias, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find …

Third Thursday 9-2010, Institute Of Agriculture

Third Thursday

No abstract provided.

Translation Reinitiation And Development Are Compromised In Similar Ways By Mutations In Translation Initiation Factor Eif3h And The Ribosomal Protein Rpl24, Fujun Zhou, Bijoyita Roy, Albrecht G. Von Arnim

Plant Sciences Publications and Other Works

Background

Within the scanning model of translation initiation, reinitiation is a non-canonical mechanism that operates on mRNAs harboring upstream open reading frames. The h subunit of eukaryotic initiation factor 3 (eIF3) boosts translation reinitiation on the uORF-containing mRNA coding for the Arabidopsis bZip transcription factor, AtbZip11, among others. The RPL24B protein of the large ribosomal subunit, which is encoded by SHORT VALVE1, likewise fosters translation of uORF-containing mRNAs, for example mRNAs for auxin response transcription factors (ARFs).

Results

Here we tested the hypothesis that RPL24B and eIF3h affect translation reinitiation in a similar fashion. First, like eif3h mutants, rpl24b …

Translation Reinitiation And Development Are Compromised In Similar Ways By Mutations In Translation Initiation Factor Eif3h And The Ribosomal Protein Rpl24, Fujun Zhou, Bijoyita Roy, Albrecht G. Von Arnim

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

Background

Within the scanning model of translation initiation, reinitiation is a non-canonical mechanism that operates on mRNAs harboring upstream open reading frames. The h subunit of eukaryotic initiation factor 3 (eIF3) boosts translation reinitiation on the uORF-containing mRNA coding for the Arabidopsis bZip transcription factor, AtbZip11, among others. The RPL24B protein of the large ribosomal subunit, which is encoded by SHORT VALVE1, likewise fosters translation of uORF-containing mRNAs, for example mRNAs for auxin response transcription factors (ARFs).

Results

Here we tested the hypothesis that RPL24B and eIF3h affect translation reinitiation in a similar fashion. First, like eif3h mutants, rpl24b …

Third Thursday 8-2010, Institute Of Agriculture

Third Thursday

No abstract provided.

Comparative Functional Genomic Study Of Substrate Specificity Evolution Of The Sabath Family Of Methyltransferases In Plants, Nan Zhao, Jean-Luc Ferrer, Xiaofeng Zhuang, Feng Chen

Plant Sciences Publications and Other Works

Background

The plant SABATH protein family is composed of a group of related small molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine dependent methylation of a variety of plant small molecular weight metabolites encompassing widely divergent structures. Some of these substrates are important plant hormones and signaling molecules, such as indole-3-acetic acid (IAA), jasmonic acid (JA) and salicylic acid (SA). Methylating these compounds may have important impacts on plant growth and development. In the previous paper, we presented Indole-3-acetic acid (IAA) methyltransferase (IAMT) as an evolutionarily ancient member of the SABATH family in higher plants. Whether the IAMT exists in less …

Graph Algorithms For Machine Learning: A Case-Control Study Based On Prostate Cancer Populations And High Throughput Transcriptomic Data, Gary L. Rogers, Pablo Moscato, Michael A. Langston

Faculty Publications and Other Works -- EECS

Background

The continuing proliferation of high-throughput biological data promises to revolutionize personalized medicine. Confirming the presence or absence of disease is an important goal. In this study, we seek to identify genes, gene products and biological pathways that are crucial to human health, with prostate cancer chosen as the target disease.

Materials and methods

Using case-control transcriptomic data, we devise a graph theoretical toolkit for this task. It employs both innovative algorithms and novel two-way correlations to pinpoint putative biomarkers that classify unknown samples as cancerous or normal.

Results and conclusion

Observed accuracy on real data suggests that we are …

Serendipitous Discoveries In Microarray Analysis, Sally R. Ellingson, Charles A. Phillips, Randy Glenn, Douglas Swanson, Thomas Ha, Daniel Goldowitz, Michael A. Langston

Faculty Publications and Other Works -- EECS

Background

Scientists are capable of performing very large scale gene expression experiments with current microarray technologies. In order to find significance in the expression data, it is common to use clustering algorithms to group genes with similar expression patterns. Clusters will often contain related genes, such as co-regulated genes or genes in the same biological pathway. It is too expensive and time consuming to test all of the relationships found in large scale microarray experiments. There are many bioinformatics tools that can be used to infer the significance of microarray experiments and cluster analysis.

Materials and methods

In this project …

Interpreting The Γ Statistic In Phylogenetic Diversification Rate Studies: A Rate Decrease Does Not Necessarily Indicate An Early Burst, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the γ statistic.

Methodology

Using simulations under varying conditions, I examine the sensitivity of γ to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a …

Changes In Plasma Concentrations Of Leptin In Ewes During Pregnancy, Joseph A. Daniel, A B. Milam, M E. Gafnea, Brian K. Whitlock, D H. Keisler

Animal Science Publications and Other Works

Previous research has demonstrated circulating concentrations of leptin increase in ewes during mid pregnancy then decline in late pregnancy and early lactation. The objective of this study was to more narrowly define the timing of changes in circulating concentrations of leptin with pregnancy in ewes. Katahdin ewes (n= 19) located at latitude 34.275 and longitude -85.183 (Mount Berry, GA) were utilized. Blood samples were collected weekly via jugular veinpuncture beginning immediately before ram exposure on September 23 and continuing until 4 weeks post-lambing. Ewes were exposed to a ram fitted with a marking harness for a 63 day breeding season. …

Effect Of Leukemia Inhibitory Factor On Feed Intake And Body Temperature In Sheep, James L. Sartin, D L. Marks, Brian K. Whitlock, Joseph A. Daniel, Barbara P. Steele

Animal Science Publications and Other Works

Leukemia inhibitory factor (LIF) has been suggested to function as a potent inhibitor of feed intake in rodents. These studies were designed to determine whether LIF was found in the ovine hypothalamus and whether LIF inhibited feed intake in sheep. Sheep hypothalami were used to clone LIF to indicate presence of the gene in the hypothalamus. The sequence was similar to published data. Another group of sheep were provided intraventricular (ICV) cannulas and injected with doses of LIF at 250, 500, 1000 and 2500 ng per sheep, ICV. Feed intake was inhibited by the 1000 and 2500 ng dose (trt, …

Changes In Plasma Concentrations Of Growth Hormone And Luteinizing Hormone In Ewes Following Central And Peripheral Treatment With Kisspeptin, Brian K. Whitlock, Joseph A. Daniel, Barbara P. Steele, James L. Sartin

Animal Science Publications and Other Works

Kisspeptin (KP), a neuroendocrine regulator of gonadotropin releasing hormone, has been hypothesized as an integrator of nutrition and hormones critical to metabolism and regulation of reproduction. Recent evidence suggests growth hormone (GH) secretion may be influenced by KP. The objective of this study was to determine if the GH stimulatory effect of KP is due to actions on the hypothalamus or anterior pituitary gland in ewes. Adult ovariectomized ewes (n=8) were fitted with intracerebroventricular (ICV) cannula to facilitate central administration of experimental treatments. Ewes received one of eight treatments [four intravenously (IV) and four ICV]. Peripheral treatments [0 (Veh), 100, …

Volume 7, Number 2 (Spring/Summer 2010), Ut Institute Of Agriculture

Tennessee Land, Life and Science Magazine

Issue Highlights:

• Celebrating UT Extension and 4-H's Centennial
• A Veterinarian Alum Blogs on His Life, Work
• Workshops and Tours Promote Direct Farm Marketing

Third Thursday 7-2010, Institute Of Agriculture

Third Thursday

No abstract provided.

Is Thermosensing Property Of Rna Thermometers Unique?, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at …

Naïve T Cells Re-Distribute To The Lungs Of Selectin Ligand Deficient Mice, Thandi M. Onami, John R. Harp

Microbiology Publications and Other Works

BACKGROUND: Selectin mediated tethering represents one of the earliest steps in T cell extravasation into lymph nodes via high endothelial venules and is dependent on the biosynthesis of sialyl Lewis X (sLe(x)) ligands by several glycosyltransferases, including two fucosyltransferases, fucosyltransferase-IV and -VII. Selectin mediated binding also plays a key role in T cell entry to inflamed organs.

METHODOLOGY/PRINCIPAL FINDINGS: To understand how loss of selectin ligands (sLe(x)) influences T cell migration to the lung, we examined fucosyltransferase-IV and -VII double knockout (FtDKO) mice. We discovered that FtDKO mice showed significant increases (approximately 5-fold) in numbers of naïve T cells in …

Coupling Metabolism And Chemotaxis-Dependent Behaviours By Energy Taxis Receptors, Gladys Alexandre

Microbiology Publications and Other Works

Bacteria have evolved the ability to monitor changes in various physico-chemical parameters and to adapt their physiology and metabolism by implementing appropriate cellular responses to these changes. Energy taxis is a metabolism-dependent form of taxis and is the directed movement of motile bacteria in gradients of physico-chemical parameters that affect metabolism. Energy taxis has been described in diverse bacterial species and several dedicated energy sensors have been identified. The molecular mechanism of energy taxis has not been studied in as much detail as chemotaxis, but experimental evidence indicates that this behaviour differs from metabolism-independent taxis only by the presence of …

Retention Of Low-Fitness Genotypes Over Six Decades Of Admixture Between Native And Introduced Tiger Salamanders, Jarrett R. Johnson, Benjamin M. Fitzpatrick, Bradley H. Shaffer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary …