Molecular Genetics Commons^™

Separation Of Blood Mixtures Using Fluorescently Labeled Antibodies, Christopher Ehrhardt, Dani Jabado, Emily Brocato

Undergraduate Research Posters

Identifying and analyzing biological mixture samples at a crime scene are of paramount concern for forensic scientists, especially if that type of evidence contains only one cell type. The presence of multiple contributors in a biological evidence sample reduces the probative value of DNA evidence and can sometimes lead to its eventual loss of value. As such, this study was performed in an attempt to examine and evaluate flow cytometry analysis as a means to separate blood mixture samples labeled with fluorescent antibodies. Fluorescein Isothiocyanate (FITC) antibodies were specifically targeted and bound to HLA (Human Leukocyte Antigens) markers present on …

An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh

Biology Faculty Publications

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel …

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

Role Of Mitochondrial Beta-Oxidation In Ethanol Response: A Candidate Gene Study Using Caenorhabditis Elegans, Harini Pallikarana Tirumala

Theses and Dissertations

Alcohol use disorder (AUD) is the fourth leading cause of preventable death in the United States, and the fifth leading risk factor for premature death and disability, globally. There are currently very few treatment options for AUD and there is a need for effective preventive and treatment strategies for this condition. AUD risk has a significant hereditary component, with the contribution of genetic factors being estimated to be about 50%. The Davies-Bettinger laboratory uses C. elegans as a model organism to study the contribution of genetic factors in modulating neuronal responses to ethanol. In this project, we examined the role …

Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders, Robin F. Chan

Theses and Dissertations

DNA methylation is necessary for learning, memory consolidation and has been implicated in a number of neuropsychiatric disorders. Obtaining high quality and comprehensive data for the three common forms of methylation in brain is challenging for methylome-wide association studies (MWAS). To address this we optimized a panel of enrichment methods for screening the brain methylome. Results show that these enrichment techniques approach the coverage and fidelity of the current gold standard bisulfite based techniques. Our MBD-based method can also be used with low amounts of genomic material from limited human biomaterials. Psychiatric disorders have high prevalence and are often chronic …

Pnpase In C. Elegans: Mutagenic Analysis To Complement Knockdown Studies, Danielle K. Seibert

Theses and Dissertations

PNPase is a gene implicated as a potential target for cancer therapy; human mutations also present with deafness, myopathies, and neuropathies. In this study, C. elegans was used to investigate the effect of knocking out PNPase in a whole animal. C. elegans knockdown studies have reported an extended lifespan via an increase in ROS production. Further noted are larger mitochondria and an increase in fzo-1 expression. Knockout animals previously constructed using CRISPR/Cas9 were used for this study. We aimed to confirm these findings validating previous studies. It was discovered that PNPase knockout animals demonstrated a similar lifespan extension that was …

Taf2: A Potential Oncogene For Hepatocellular Carcinoma, Saranya Chidambaranathan Reghupaty

Theses and Dissertations

Astrocyte Elevated Gene 1 (AEG1) is an oncogene for hepatocellular carcinoma (HCC). Its role in HCC pathogenesis has been well studied. A pan cancer analysis of gene expression in multiple databases identified TATA-box binding protein associated factor 2 (TAF2) as the gene that is most frequently co-expressed with AEG1. TAF2 is a protein that is involved in transcription of genes by RNA polymerase II. It is a factor that is dispensable for basal transcription but, required for activated transcription. It has also been shown to be involved in regulating cyclin levels and hence cell cycle progression. Bioinformatic analysis on data …

Investigating Mirna Functions In Arabidopsis By Short Tandem Target Mimic (Sttm), Yiyou Gu

Dissertations, Master's Theses and Master's Reports

MicroRNA (miRNAs) and other endogenous small RNAs play important role in regulating gene expression in eukaryotes. Till now, several techniques have been developed for miRNA function analysis. Because of the characteristic of miRNAs, the most applicable method for miRNA function research is blocking the whole miRNA family specifically. Here, we report an artificial non-coding transcript termed Short Tandem Target Mimic (STTM) for blocking miRNA activity in Arabidopsis thaliana. The STTM composed of two miRNA target sites with three nucleotides bulge in the miRNA cleavage site, the two-miRNA targets separated by spacer linker. We used this technique blocking several important endogenous …

Characterization Of Staphylococcal Nuclease And Tudor Domain Containing Protein 1 (Snd1) As A Molecular Target In Hepatocellular Carcinoma And Non-Alcoholic Steatohepatitis, Nidhi H. Jariwala

Theses and Dissertations

CHARACTERIZATION OF STAPHYLOCOCCAL NUCLEASE AND TUDOR DOMAIN CONTAINING PROTEIN 1 (SND1) AS A MOLECULAR TARGET IN HEPATOCELLULAR CARCINOMA AND NON-ALCOHOLIC STEATOHEPATITIS

Nidhi Jariwala, PhD

A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Integrative Life Sciences

Virginia Commonwealth University, 2017

Devanand Sarkar, M.B.B.S., PhD.

Associate Professor, Department of Human and Molecular Genetics

Virginia Commonwealth University

Richmond, Virginia

SND1, a subunit of the miRNA regulatory complex RISC, has been implicated as an oncogene in hepatocellular carcinoma (HCC). Oncoprotein SND1 regulates gene expression at a post-transcriptional level in multiple cancers including hepatocellular carcinoma (HCC). …

Mitochondrial And Nuclear Patterns Of Conflict And Concordance At The Gene, Genome, And Behavioral Scales In Desmognathus Salamanders, Justin D. Kratovil

Theses and Dissertations--Biology

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns …

Transcriptomic Analyses Of Cathatranthus Roseus Hairy Roots Overexpressing Crmyc2 And Orca3 And Roles Of Cross-Family Transcription Factor Interaction In Terpenoid Indole Alkaloid Biosynthesis, Xueyi Sui

Theses and Dissertations--Plant and Soil Sciences

Catharanthus roseus (Madagascar periwinkle), is a well-known medicinal plant that produces a vast array of terpenoid indole alkaloids (TIAs), including two anticancer compounds vinblastine and vincristine. Industrial scale production of TIAs is hampered by the difficulties of total chemical synthesis of these compounds and the fragmented knowledge on TIA pathway. Transcriptional regulation of the TIA biosynthetic pathway has not been thoroughly investigated in Catharanthus and only a few structural genes have been identified as the targets of two master regulators: the basic helix-loop-helix (bHLH) transcription factor (TF) CrMYC2 and APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF), ORCA3. Next generation sequencing (NGS) has been …

Detection Of Antibiotic Resistance Loci In Wastewater And Fresh Water Samples, Mohammed Hamed Almalki

Masters Theses

Proper treatment of municipal wastewater is important not only for prevention of eutrophication but also for public health concerns. One consideration for wastewater treatment is the presence of organisms carrying antibiotic resistance genes. If these organisms survive the wastewater treatment process and are released into the streams, they can pose significant risks to public health. In addition, their presence also raises concerns for lateral gene transfer events at the wastewater plant. The spread of antibiotic loci has a major impact in public health and clinical therapy because resistant organisms render conventional treatments of important illnesses difficult. Beta-lactam drugs are known …

Characterization Of Genic Microsatellite Markers (Est-Ssrs) In The Endangered Oak Species Quercus Georgiana M.A.Curtis, Priyanka Dipak Kadav

Dissertations, Master's Theses and Master's Reports

Quercus is important ecologically and economically because it provides food and habitat for wildlife, wood and paper products for humans. Oaks are endangered due to various factors like shifting climates, habitat loss, drought, pathogens and genetic swamping. Quercus georgiana (M.A. Curtis) is an endangered and restricted oak species which is remaining only in the southeastern part of the US. Efforts are required to conserve this endangered species from extinction. Conservation of this species can be done through these methods: ex-situ conservation (arboretum and botanical garden) and in-situ conservation strategies which protect the species in its natural habitat. For this conservation …

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

Feasibility & Discovery Using Fox System To Generate Gain-Of-Function Mutations With Hybrid Poplars, James Rauschendorfer

Dissertations, Master's Theses and Master's Reports

The Full-length complementary DNA OvereXpression (FOX) system is an approach to generating gain-of-function (GF) plants predominantly used for studying Arabidopsis. This approach inserts T-DNAs containing random full-length complementary DNA (fl-cDNA) with upstream promoter and downstream terminator into the host plant genome. Studies using this method report the success generating overexpression populations with high mutation rates. We choose to investigate the feasibility and effectiveness of this method using poplars. We suspected using a succulent xylem specific fl-cDNAs library would enrich the transformant poplars with mutants affected in traits specific to woody tissue development. We observed a characteristically high mutation rate …