Medicine and Health Sciences Commons^™

Leveraging Global Gene Expression Patterns To Predict Expression Of Unmeasured Genes, James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene S. Greene, Jennifer A. Doherty

Dartmouth Scholarship

BackgroundLarge collections of paraffin-embedded tissue represent a rich resource to test hypotheses based on gene expression patterns; however, measurement of genome-wide expression is cost-prohibitive on a large scale. Using the known expression correlation structure within a given disease type (in this case, high grade serous ovarian cancer; HGSC), we sought to identify reduced sets of directly measured (DM) genes which could accurately predict the expression of a maximized number of unmeasured genes.

The Conserved G-Protein Coupled Receptor Fshr-1 Regulates Protective Host Responses To Infection And Oxidative Stress, Elizabeth V. Miller, Leah N. Grandi, Jennifer A. Giannini, Joseph D. Robinson, Jennifer R. Powell

Biology Faculty Publications

The innate immune system’s ability to sense an infection is critical so that it can rapidly respond if pathogenic microorganisms threaten the host, but otherwise maintain a quiescent baseline state to avoid causing damage to the host or to commensal microorganisms. One important mechanism for discriminating between pathogenic and non-pathogenic bacteria is the recognition of cellular damage caused by a pathogen during the course of infection. InCaenorhabditis elegans, the conserved G-protein coupled receptor FSHR-1 is an important constituent of the innate immune response. FSHR-1 activates the expression of antimicrobial infection response genes in infected worms and delays accumulation …

Plasticity Of Boldness In Rainbow Trout, Oncorhynchus Mykiss: Do Hunger And Predation Influence Risk-Taking Behaviour?, Jack S. Thomson, Phillip C. Watts, Tom G. Pottinger, Lynne U. Sneddon

Lynne U. Sneddon, Ph.D.

Boldness, a measure of an individual's propensity for taking risks, is an important determinant of fitness but is not necessarily a fixed trait. Dependent upon an individual's state, and given certain contexts or challenges, individuals may be able to alter their inclination to be bold or shy in response. Furthermore, the degree to which individuals can modulate their behaviour has been linked with physiological responses to stress. Here we attempted to determine whether bold and shy rainbow trout, Oncorhynchus mykiss, can exhibit behavioural plasticity in response to changes in state (nutritional availability) and context (predation threat). Individual trout were initially …

Molecular Correlates Of Social Dominance: A Novel Role For Ependymin In Aggression, Lynne U. Sneddon, Rupert Schmidt, Yongxiang Fang, Andrew R. Cossins

Lynne Sneddon, PhD

Theoretical and empirical studies have sought to explain the formation and maintenance of social relationships within groups. The resulting dominance hierarchies have significant fitness and survival consequences dependent upon social status. We hypothesised that each position or rank within a group has a distinctive brain gene expression profile that correlates with behavioural phenotype. Furthermore, transitions in rank position should determine which genes shift in expression concurrent with the new dominance status. We used a custom cDNA microarray to profile brain transcript expression in a model species, the rainbow trout, which forms tractable linear hierarchies. Dominant, subdominant and submissive individuals had …

Co-Ingestion Of Carbohydrate With Branched-Chain Amino Acids Or L-Leucine Does Not Preferentially Increase Serum Igf-1 And Expression Of Myogenic-Related Genes In Response To A Single Bout Of Resistance Exercise, Rui Li, Maria Pontes Ferreira, Matthew B. Cooke, Paul La Bounty, Bill Campbell, Mike Greenwood, Darren S. Willoughby, Richard B. Kreider

Nutrition and Food Science Faculty Research Publications

This study determined if the co-ingestion of carbohydrate (CHO) with branched-chain amino acids (BCAA) or L-leucine (LEU) preferentially affected serum IGF-1 and the expression of myogenic-related genes in response to resistance exercise (RE). Forty one, college-age males were randomly assigned to 1 of 4 groups: CHO, CHO-BCAA, CHO-LEU, or placebo (PLC). Resistance exercise consisted of 4 sets of leg press and leg extension at 80% 1RM. Supplements were ingested peri-exercise, and venous blood and muscle biopsies were obtained pre-exercise (PRE), and at 30, 120, and 360 min post-exercise. Serum IGF-1 was determined with ELISA, and skeletal muscle mRNA expression of …

Coexpression Network Analysis Of Mirna-142 Overexpression In Neuronal Cells, Ishwor Thapa, Howard S. Fox, Dhundy Raj Bastola

Interdisciplinary Informatics Faculty Publications

MicroRNAs are small noncoding RNA molecules, which are differentially expressed in diverse biological processes and are also involved in the regulation of multiple genes. A number of sites in the 3′ untranslated regions (UTRs) of different mRNAs allow complimentary binding for a microRNA, leading to their posttranscriptional regulation. The miRNA-142 is one of the microRNAs overexpressed in neurons that is found to regulate SIRT1 and MAOA genes. Differential analysis of gene expression data, which is focused on identifying up- or downregulated genes, ignores many relationships between genes affected by miRNA-142 overexpression in a cell. Thus, we applied a correlation network …

Increased Tissue Temperature Improves Electro-Transfer Mediated Gene Delivery To Skin, Anna Bulysheva, Amy Donate, Chelsea Edelblute, Derrick Jung, Karl Schoenbach, Richard Heller

Bioelectrics Publications

[Introduction] Developing an optimal gene electro-transfer system for delivery of plasmid DNA to the skin in vivo has been challenging with expression often confined in the epithelium requiring high voltage electric fields, which can cause cellular and tissue damage. Minimizing such damage, while optimizing gene expression profiles, are highly desirable for therapeutic applications of gene delivery to the skin. Cell membrane fluidity is temperature dependent, thus moderate temperature elevation can increase membrane fluidity. Utilizing this concept, we developed a novel gene electro-transfer electrode for in vivo applications with ability to heat tissue with a laser integrated into a four pin …

High-Throughput Data Analysis: Application To Micronuclei Frequency And T-Cell Receptor Sequencing, Mateusz Makowski

Theses and Dissertations

The advent of high-throughput sequencing has brought about the creation of an unprecedented amount of research data. Analytical methodology has not been able to keep pace with the plethora of data being produced. Two assays, ImmunoSEQ and the cytokinesisblock micronucleus (CBMN), that both produce count data and have few methods available to analyze them are considered.

ImmunoSEQ is a sequencing assay that measures the beta T-cell receptor (TCR) repertoire. The ImmunoSEQ assay was used to describe the TCR repertoires of patients that have undergone hematopoietic stem cell transplantation (HSCT). Several different methods for spectratype analysis were extended to the TCR …

A Genetic Epidemiologic Investigation Of Breast Cancer Susceptibility, Cristy Ellen Stagnar

Legacy Theses & Dissertations (2009 - 2024)

Introduction

Gene Expression And Alzheimer's Disease: Evaluation Of Gene Expression Patterns In Brain And Blood For An Alzheimer's Disease Mouse Model, Amanda Hazy

Senior Honors Theses

Previous studies have established a causative role for altered gene expression in development of Alzheimer’s disease (AD). These changes can be affected by methylation and miRNA regulation. In this study, expression of miRNA known to change methylation status in AD was assessed by qPCR. Genome-wide expression changes were determined by RNA-sequencing of mRNA from hippocampus and blood of control and AD mice. The qPCR data showed significantly increased expression of Mir 17 in AD, and sequencing data revealed 230 genes in hippocampus, 58 genes in blood, and 8 overlapping genes showing significant differential expression (p value ≤ 0.05). Expression data …

Sulforaphane Reverses The Expression Of Various Tumor Suppressor Genes By Targeting Dnmt3b And Hdac1 In Human Cervical Cancer Cells, Munawwar Ali Khan, Madhumitha Kedhari Sundaram, Amina Hamza, Uzma Quraishi, Dian Gunasekera, Laveena Ramesh, Payal Goala, Usama Al Alami, Mohammad Zeeshan Ansari, Tahir A. Rizvi, Chhavi Sharma, Arif Hussain

All Works

© 2015 Munawwar Ali Khan et al. Sulforaphane (SFN) may hinder carcinogenesis by altering epigenetic events in the cells; however, its molecular mechanisms are unclear. The present study investigates the role of SFN in modifying epigenetic events in human cervical cancer cells, HeLa. HeLa cells were treated with SFN (2.5 μM) for a period of 0, 24, 48, and 72 hours for all experiments. After treatment, expressions of DNMT3B, HDAC1, RARβ, CDH1, DAPK1, and GSTP1 were studied using RT-PCR while promoter DNA methylation of tumor suppressor genes (TSGs) was studied using MS-PCR. Inhibition assays of DNA methyl transferases (DNMTs) and …

Effect Of Diet Type And Added Copper On Growth Performance, Carcass Characteristics, Energy Digestibility, Gut Morphology, And Mucosal Mrna Expression Of Finishing Pigs, K. F. Coble, D. D. Burnett, R. D. Goodband, J. M. Gonzales, J. Usry, M. D. Tokach, J. R. Pluske, J. M. Derouchey, J. C. Woodworth, S. S. Dritz, J. R. Flohr, M. A. Vaughn

Kansas Agricultural Experiment Station Research Reports

A total of 757 pigs (PIC 337 × 1050, initially 60.8 lb) were used to determine the effects of added Cu (TBCC, tribasic copper chloride, IntelliBond C; Micronutrients, Inc., Indianapolis, IN) and diet type on growth performance, carcass characteristics, energy digestibility, gut morphology, and mucosal mRNA expression of finishing pigs. Pens of pigs were allotted to 1 of 4 dietary treatments, balanced on average pen weight in a randomized complete-block design with 26 to 28 pigs per pen and 7 replications per treatment. Treatments were arranged as a 2 × 2 factorial with main effects of diet type, a corn-soybean …