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Comprehensive Computational Assessment And Evaluation Of Epstein Barr Virus (Ebv) Variations, Mirnas, And Ebers In Ebl, Aml And Across Cancers, Mercedeh J. Movassagh Apr 2019

Comprehensive Computational Assessment And Evaluation Of Epstein Barr Virus (Ebv) Variations, Mirnas, And Ebers In Ebl, Aml And Across Cancers, Mercedeh J. Movassagh

GSBS Dissertations and Theses

Viruses are known to be associated with 20% of human cancers. Epstein Barr virus (EBV) in particular is the first virus associated with human cancers. Here, we computationally detect EBV and explore the effects of this virus across cancers by taking advantage of the fact that EBV microRNAs (miRNAs) and Epstein Barr virus small RNAs (EBERs) are expressed at all viral latencies. We identify and characterize two sub-populations of EBV positive tumors: those with high levels of EBV miRNA and EBERS expression and those with medium levels of expression.

Based on principal component analysis (PCA) and hierarchical clustering of viral ...


A Suite Of Computational Tools To Interrogate Sequence Data With Local Haplotype Analysis Within Complex ​Plasmodium​ Infections And Other Microbial Mixtures, Nicholas J. Hathaway Mar 2018

A Suite Of Computational Tools To Interrogate Sequence Data With Local Haplotype Analysis Within Complex ​Plasmodium​ Infections And Other Microbial Mixtures, Nicholas J. Hathaway

GSBS Dissertations and Theses

The rapid development of DNA sequencing technologies has opened up new avenues of research, including the investigation of population structure within infectious diseases (both within patient and between populations). In order to take advantage of these advances in technologies and the generation of new types of data, novel bioinformatics tools are needed that won’t succumb to artifacts introduced by the data generation, and thus provide accurate and precise results. To achieve this goal I have create several tools.

First, SeekDeep, a pipeline for analyzing targeted amplicon sequencing datasets from various technologies, is able to achieve 1-base resolution even at ...


Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu Feb 2018

Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu

GSBS Dissertations and Theses

A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we are able to sequence exome and ...


Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli Dec 2017

Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli

GSBS Dissertations and Theses

The translation of mRNA into functional proteins is essential for all life. In eukaryotes, aberrant RNAs containing sequence features that stall or severely slow down ribosomes are subject to translation-dependent quality control. Targets include mRNAs encoding a strong secondary structure (No-Go Decay; NGD) or stretches of positively-charged amino acids (Peptide-dependent Translation Arrest/Ribosome Quality Control; PDTA/RQC), mRNAs lacking an in-frame stop codon (Non-Stop Decay; NSD), or defective 18S rRNAs (18S Nonfunctional rRNA Decay; 18S NRD). Previous work from our lab showed that the S. cerevisiae NGD factors DOM34 and HBS1, and PDTA/RQC factor ASC1, all participate in the ...


Dosage Compensation Of Trisomy 21 And Its Implications For Hematopoietic Pathogenesis In Down Syndrome, Jen-Chieh Chiang Nov 2017

Dosage Compensation Of Trisomy 21 And Its Implications For Hematopoietic Pathogenesis In Down Syndrome, Jen-Chieh Chiang

GSBS Dissertations and Theses

Down Syndrome (DS), the most common aneuploidy seen in live-borns, is caused by trisomy for chromosome 21. DS imposes high risks for multiple health issues involving various systems of the body. The genetic complexity of trisomy 21 and natural variation between all individuals has impeded understanding of the specific cell pathologies and pathways involved. In addition, chromosomal disorders have been considered outside the hopeful progress in gene therapies for single-gene disorders. Here we test the feasibility of correcting imbalanced expression of genes across an extra chromosome by expression of a single gene, XIST, the key player in X chromosome inactivation ...


Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster Aug 2017

Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster

GSBS Dissertations and Theses

Environmental conditions imposed onto organisms during certain phases of their life cycles such as embryogenesis or puberty can not only impact the organisms’ own health, but also affect subsequent generations. The underlying mechanisms causing intergenerational phenotypes are not encoded in the genome, but the result of reversible epigenetic modifications. This work investigates in a mouse model the impact of paternal nicotine exposure on the next generation regarding addictive behavior modulation, metabolic changes, and molecular mechanisms. It provides evidence that male offspring from nicotine-exposed fathers (NIC offspring) is more resistant to lethal doses of nicotine. This phenotype is gender-specific and depends ...


Genomic And Transcriptomic Investigation Of Endemic Burkitt Lymphoma And Epstein Barr Virus, Yasin Kaymaz Jul 2017

Genomic And Transcriptomic Investigation Of Endemic Burkitt Lymphoma And Epstein Barr Virus, Yasin Kaymaz

GSBS Dissertations and Theses

Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt Lymphoma (sBL) that occurs with a lower incidence in developed countries. Despite this increased burden the study of eBL has lagged. Additionally, while EBV was isolated from an African Burkitt lymphoma tumor 50 years ago, however, the impact of viral variation in oncogenesis is just beginning to be fully explored. In my thesis research, I focused on investigating molecular genetics of the endemic form of this lymphoma with a particular emphasis on the role of the ...


A Two-Pronged Approach To Preeclampsia: Understanding Gene Expression And Targeting Sflt1 Using Rnai, Ami Ashar-Patel Jul 2017

A Two-Pronged Approach To Preeclampsia: Understanding Gene Expression And Targeting Sflt1 Using Rnai, Ami Ashar-Patel

GSBS Dissertations and Theses

Preeclampsia (PE) is a disorder affecting 2-10% of pregnancies worldwide. Clinical signs include high blood pressure (HBP) and proteinuria in the mother after the 20th week of pregnancy. Currently, the only cure for PE is delivery of the fetus, which is often necessary preterm and thus dangerous for both mother and fetus. Maternal symptoms of PE are caused by excess anti-angiogenic proteins of placental origin called soluble Flt1s (sFlt1s). sFlt1 mRNA isoforms are produced by alternative polyadenylation (APA) of full-length Flt1 (fl-Flt1) pre- mRNA. While fl-Flt1 encodes a transmembrane protein, sFlt1s encode truncated proteins that are soluble. Multiple sFlt1 isoforms ...


Histone Deacetylase 3 Coordinates Heart Development Through Stage-Specific Roles In Cardiac Progenitor Cells, Sara L. Lewandowski Dec 2016

Histone Deacetylase 3 Coordinates Heart Development Through Stage-Specific Roles In Cardiac Progenitor Cells, Sara L. Lewandowski

GSBS Dissertations and Theses

Disruptions in cardiac development cause congenital heart disease, the most prevalent and deadly congenital malformation. Genetic and environmental factors are thought to contribute to these defects, however molecular mechanisms remain largely undefined. Recent work highlighted potential roles of chromatin- modifying enzymes in congenital heart disease pathogenesis. Histone deacetylases, a class of chromatin-modifying enzymes, have developmental importance and recognized roles in the mature heart. This thesis aimed to characterize functions of Hdac3 in cardiac development. We found loss of Hdac3 in the primary heart field causes precocious progenitor cell differentiation, resulting in hypoplastic ventricular walls, ventricular septal defect, and mid- gestational ...


Investigation Of Rna Binding Protein Pumilio As A Genetic Modifier Of Mutant Chmp2b In Frontotemporal Dementia (Ftd): A Masters Thesis, Xing Du Aug 2016

Investigation Of Rna Binding Protein Pumilio As A Genetic Modifier Of Mutant Chmp2b In Frontotemporal Dementia (Ftd): A Masters Thesis, Xing Du

GSBS Dissertations and Theses

Frontotemporal dementia (FTD) is the second most common early-onset dementia. A rare mutation in CHMP2B gene was found to be associated with FTD linked to chromosome 3. Previous studies have shown that mutant CHMP2B could lead to impaired autophagy pathway and altered RNA metabolism. However, it is still unknown what genes mediate the crosstalk between different pathways affected by mutant CHMP2B. Genetic screens designed to identify genes interacting with mutant CHMP2B represents a key approach in solving the puzzle. Expression of mutant CHMP2B (CHMP2Bintron5) in Drosophila eyes leads to a neurodegenerative phenotype including melanin deposition and disrupted internal structure of ...


Plague And The Defeat Of Mammalian Innate Immunity: Systematic Genetic Analysis Of Yersinia Pestis Virulence Factors: A Dissertation, Samantha G. Palace Jul 2016

Plague And The Defeat Of Mammalian Innate Immunity: Systematic Genetic Analysis Of Yersinia Pestis Virulence Factors: A Dissertation, Samantha G. Palace

GSBS Dissertations and Theses

Yersinia pestis, the causative agent of plague, specializes in causing dense bacteremia following intradermal deposition of a small number of bacteria by the bite of an infected flea. This robust invasiveness requires the ability to evade containment by the innate immune system. Of the various mechanisms employed by Y. pestis to subvert the innate immune response and to proliferate rapidly in mammalian tissue, only a few are well-characterized. Here, I present two complementary genetic analyses of Y. pestis adaptations to the mammalian environment. In the first, genome-wide fitness profiling for Y. pestis by Tn-seq demonstrates that the bacterium has adapted ...


A Walk On The Fine Line Between Reward And Risk: Aav-Ifnβ Gene Therapy For Glioblastoma: A Dissertation, Dwijit Guhasarkar Jul 2016

A Walk On The Fine Line Between Reward And Risk: Aav-Ifnβ Gene Therapy For Glioblastoma: A Dissertation, Dwijit Guhasarkar

GSBS Dissertations and Theses

Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor. The current standard-of-care treatment including surgery, radiation and temozolomide (TMZ) chemotherapy does not prolong the survival satisfactorily. Here we have tested the feasibility, efficacy and safety of a potential gene therapy approach using AAV as gene delivery vehicle for treatment of GBM.

Interferon-beta (IFNβ) is a cytokine molecule also having pleiotropic anticancerous properties. Previously it has been shown by our group that AAV mediated local (intracranial) gene delivery of human IFNβ (hIFNβ) could be an effective treatment for non-invasive human glioblastoma (U87) in orthotopic xenograft mouse model.But ...


Characterization Of Higher-Order Chromatin Structure In Bone Differentiation And Breast Cancer: A Dissertation, Ahmet Rasim Barutcu Feb 2016

Characterization Of Higher-Order Chromatin Structure In Bone Differentiation And Breast Cancer: A Dissertation, Ahmet Rasim Barutcu

GSBS Dissertations and Theses

Higher-order genome organization is important for the regulation of gene expression by bringing different cis-regulatory elements and promoters in proximity. The establishment and maintenance of long-range chromatin interactions occur in response to cellular and environmental cues with the binding of transcription factors and chromatin modifiers. Understanding the organization of the nucleus in differentiation and cancer has been a long standing challenge and is still not well-understood. In this thesis, I explore the dynamic changes in the higher-order chromatin structure in bone differentiation and breast cancer. First, we show dynamic chromatin contact between a distal regulatory element and the promoter of ...


Developing An Adeno-Associated Viral Vector (Aav) Toolbox For Cns Gene Therapy: A Dissertation, Sourav Roy Choudhury Jan 2016

Developing An Adeno-Associated Viral Vector (Aav) Toolbox For Cns Gene Therapy: A Dissertation, Sourav Roy Choudhury

GSBS Dissertations and Theses

Neurological disorders – disorders of the brain, spine and associated nerves – are a leading contributor to global disease burden with a sizable economic cost. Adeno-associated viral (AAV) vectors have emerged as an effective platform for CNS gene therapy and have shown early promise in clinical trials. These trials involve direct infusion into brain parenchyma, an approach that may be suboptimal for treatment of neurodegenerative disorders, which often involve more than a single structure in the CNS. However, overall neuronal transduction efficiency of vectors derived from naturally occurring AAV capsids after systemic administration is relatively low. We have developed novel capsids AAV-AS ...


Functional Characterization Of Novel Pfn1 Mutations Causative For Familial Amyotrophic Lateral Sclerosis: A Dissertation, Chi-Hong Wu Dec 2015

Functional Characterization Of Novel Pfn1 Mutations Causative For Familial Amyotrophic Lateral Sclerosis: A Dissertation, Chi-Hong Wu

GSBS Dissertations and Theses

Amyotrophic lateral sclerosis (ALS) is a progressive adult neurodegenerative disease that causes death of both upper and lower motor neurons. Approximately 90 percent of ALS cases are sporadic (SALS), and 10 percent are inherited (FALS). Mutations in the PFN1 gene have been identified as causative for one percent of FALS. PFN1 is a small actin-binding protein that promotes actin polymerization, but how ALS-linked PFN1 mutations affect its cognate functions or acquire gain-of-function toxicity remains largely unknown.

To elucidate the contribution of ALS-linked PFN1 mutations to neurodegeneration, we have characterized these mutants in both mammalian cultured cells and Drosophila models. In ...


Gene Therapy For Amyotrophic Lateral Sclerosis: An Aav Delivered Artifical Microrna Against Human Sod1 Increases Survival And Delays Disease Progression Of The Sod1G93a Mouse Model: A Dissertation, Lorelei I. Stoica Dec 2015

Gene Therapy For Amyotrophic Lateral Sclerosis: An Aav Delivered Artifical Microrna Against Human Sod1 Increases Survival And Delays Disease Progression Of The Sod1G93a Mouse Model: A Dissertation, Lorelei I. Stoica

GSBS Dissertations and Theses

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by loss of motor neurons, resulting in progressive muscle weakness, atrophy, paralysis and death within five years of diagnosis. About ten percent of cases are inherited, of which twenty percent are due to mutations in the superoxide dismutase 1 (SOD1) gene. Since the only FDA approved ALS drug prolongs survival by just a few months, new therapies for this disease are needed. Experiments in transgenic ALS mouse models have shown that decreasing levels of mutant SOD1 protein alters and in some cases entirely prevents disease progression. We explored this potential ...


Identifying, Targeting, And Exploiting A Common Misfolded, Toxic Conformation Of Sod1 In Als: A Dissertation, Melissa S. Rotunno Jun 2015

Identifying, Targeting, And Exploiting A Common Misfolded, Toxic Conformation Of Sod1 In Als: A Dissertation, Melissa S. Rotunno

GSBS Dissertations and Theses

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a loss of voluntary movement over time, leading to paralysis and death. While 10% of ALS cases are inherited or familial (FALS), the majority of cases (90%) are sporadic (SALS) with unknown etiology. Approximately 20% of FALS cases are genetically linked to a mutation in the anti-oxidizing enzyme, superoxide dismutase (SOD1). SALS and FALS are clinically indistinguishable, suggesting a common pathogenic mechanism exists for both types. Since such a large number of genetic mutations in SOD1 result in FALS (>170), it is reasonable to suspect that non-genetic modifications to SOD1 ...


Yeast Upf1 Associates With Ribosomestranslating Mrna Coding Sequences Upstream Of Normal Termination Codons: A Dissertation, Ei Ei Min Apr 2015

Yeast Upf1 Associates With Ribosomestranslating Mrna Coding Sequences Upstream Of Normal Termination Codons: A Dissertation, Ei Ei Min

GSBS Dissertations and Theses

Nonsense-mediated mRNA decay (NMD) specifically targets mRNAs with premature translation termination codons for rapid degradation. NMD is a highly conserved translation-dependent mRNA decay pathway, and its core Upf factors are thought to be recruited to prematurely terminating mRNP complexes, possibly through the release factors that orchestrate translation termination. Upf1 is the central regulator of NMD and recent studies have challenged the notion that this protein is specifically targeted to aberrant, nonsense-containing mRNAs. Rather, it has been proposed that Upf1 binds to most mRNAs in a translation-independent manner. In this thesis, I investigated the nature of Upf1 association with its substrates ...


Dissecting The Role Of A Lncrna And Involvement Of Plasmodium Infections In The Innate Immune Response: A Dissertation, Jennie Chan Apr 2015

Dissecting The Role Of A Lncrna And Involvement Of Plasmodium Infections In The Innate Immune Response: A Dissertation, Jennie Chan

GSBS Dissertations and Theses

The innate immune system is a multicomponent response governed by intricate mechanisms of induction, regulation and resolution to elicit antimicrobial defenses. In recent years, the complexity of eukaryotic transcriptomes has become the subject of intense scrutiny and curiosity. It has been established, that RNA polymerase II (RNAPII) transcribes hundreds to thousands of long noncoding RNAs (lncRNAs), often in a stimulus and cell-type specific manner. However, the functional significance of these transcripts has been particularly controversial. While the number of identified lncRNAs is growing, our understanding of how lncRNAs themselves regulate other genes is quite limited. In chapter 2, a novel ...


Subtle Controllers: Micrornas Drive Pancreatic Tumorigenesis And Progression: A Dissertation, Brian J. Quattrochi Apr 2015

Subtle Controllers: Micrornas Drive Pancreatic Tumorigenesis And Progression: A Dissertation, Brian J. Quattrochi

GSBS Dissertations and Theses

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies in the United States, with an average five-year survival rate of just 6.7%. One unifying aspect of PDAC is mutational activation of the KRAS oncogene, which occurs in over 90% of PDAC. Therefore, inhibiting KRAS function is likely an effective therapeutic strategy for this disease, and current research in our lab and others is focused on identifying downstream effectors of KRAS signaling that may be therapeutic targets. miRNAs are powerful regulators of gene expression that can behave as oncogenes or tumor suppressors. Dysregulation of miRNA expression is commonly observed ...


Endothelial Driven Inflammation In Metabolic Disease: A Dissertation, Anouch Matevossian Feb 2015

Endothelial Driven Inflammation In Metabolic Disease: A Dissertation, Anouch Matevossian

GSBS Dissertations and Theses

Obesity has been on the rise over the last 30 years, reaching worldwide epidemic proportions. Obesity has been linked to multiple metabolic disorders and co-morbidities such as Type 2 Diabetes Mellitus (T2DM), cardiovascular disease, non-alcoholic steatohepatitis and various cancers. Furthermore, obesity is associated with a chronic state of low-grade inflammation in adipose tissue (AT), and it is thought that insulin resistance (IR) and T2DM is associated with the inflammatory state of AT.

Endothelial cells (ECs) mediate the migration of immune cells into underlying tissues during times of inflammation, including obesity- and cardiovascular disease-associated inflammation. Cytokines and chemoattractants released from inflamed ...


Raav-Mediated Gene Transfer For Study Of Pathological Mechanisms And Therapeutic Intervention In Canavan's Disease: A Dissertation, Seemin Seher Ahmed Dec 2014

Raav-Mediated Gene Transfer For Study Of Pathological Mechanisms And Therapeutic Intervention In Canavan's Disease: A Dissertation, Seemin Seher Ahmed

GSBS Dissertations and Theses

Canavan’s Disease is a fatal Central Nervous System disorder caused by genetic defects in the enzyme – aspartoacylase and currently has no effective treatment options. We report additional phenotypes in a stringent preclinical aspartoacylase knockout mouse model. Using this model, we developed a gene therapy strategy with intravenous injections of the aspartoacylase gene packaged in recombinant adeno associated viruses (rAAVs). We first investigated the CNS gene transfer abilities of rAAV vectors that can cross the blood-brain-barrier in neonatal and adult mice and subsequently used different rAAV serotypes such as rAAV9, rAAVrh.8 and rAAVrh.10 for gene replacement therapy. A ...


The Three-Dimensional Structure Of The Cystic Fibrosis Locus: A Dissertation, Emily M. Smith Nov 2014

The Three-Dimensional Structure Of The Cystic Fibrosis Locus: A Dissertation, Emily M. Smith

GSBS Dissertations and Theses

The three dimensional structure of the human genome is known to play a critical role in gene function and expression. I used chromosome conformation capture (3C) and 3C-carbon copy (5C) techniques to investigate the three-dimensional structure of the cystic fibrosis transmembrane conductance regulator (CFTR) locus. This is an important disease gene that, when mutated, causes cystic fibrosis. 3C experiments identified four distinct looping elements that contact the CFTR gene promoter only in CFTR-expressing cells. Using 5C, I expanded the region of study to a 2.8 Mb region surrounding the CFTR gene. The 5C study shows 7 clear topologically associating ...


Approaches And Considerations Towards A Safe And Effective Adeno-Associated Virus Mediated Therapeutic Intervention For Gm1-Gangliosidosis: A Dissertation, Cara M. Weismann Aug 2014

Approaches And Considerations Towards A Safe And Effective Adeno-Associated Virus Mediated Therapeutic Intervention For Gm1-Gangliosidosis: A Dissertation, Cara M. Weismann

GSBS Dissertations and Theses

GM1 gangliosidosis is a lysosomal storage disorder caused by a deficiency in the catabolizing enzyme β-galactosidase (βgal). This leads to accumulation of GM1-ganglioside (GM1) in the lysosome inducing ER stress and cell death. GM1 gangliosidosis is primarily a disorder of the central nervous system (CNS) with peripheral organ involvement. In this work we report two major findings, 1) systemic treatment of GM1 gangliosidosis with an adenoassociated virus (AAV9) encoding mouse-βgal (mβgal) in a GM1 gangliosidosis mouse model (βGal-/-), and 2) an investigation into an intracranial injection of a therapeutic AAVrh8 encoding mβgal. Systemic treatment of GM1 gangliosidosis with AAV9 resulted ...


Fus/Tls In Stress Response - Implications For Amyotrophic Lateral Sclerosis: A Dissertation, Reddy Ranjith Kumar Sama Mar 2014

Fus/Tls In Stress Response - Implications For Amyotrophic Lateral Sclerosis: A Dissertation, Reddy Ranjith Kumar Sama

GSBS Dissertations and Theses

Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig’s disease is a fatal neurodegenerative disease. ALS is typically adult onset and is characterized by rapidly progressive loss of both upper and lower motor neurons that leads to death usually within 3-5 years. About 90% of all the cases are sporadic with no family history while the remaining 10% are familial cases with mutations in several genes including SOD1, FUS/TLS, TDP43 and C9ORF72.

FUS/TLS (Fused in Sarcoma/Translocated in Liposarcoma or FUS) is an RNA/DNA binding protein that is involved in multiple cellular functions including DNA damage ...


Identification And Characteristics Of Factors Regulating Hepatocellular Carcinoma Progression And Metastasis: A Dissertation, Leanne G. Ahronian Mar 2014

Identification And Characteristics Of Factors Regulating Hepatocellular Carcinoma Progression And Metastasis: A Dissertation, Leanne G. Ahronian

GSBS Dissertations and Theses

Hepatocellular carcinoma (HCC) is a common malignancy of the liver that is one of the most frequent causes of cancer-related death in the world. Surgical resection and liver transplantation are the only curative options for HCC, and tumor invasion and metastasis render many patients ineligible for these treatments. Identification of the mechanisms that contribute to invasive and metastatic disease may enlighten therapeutic strategies for those not eligible for surgical treatments. In this dissertation, I describe two sets of experiments to elucidate mechanisms underlying HCC dissemination, involving the activities of Krüppel-like factor 6 and a particular p53 point mutation, R172H.

Gene ...


Rna Interference By The Numbers: Explaining Biology Through Enzymology: A Dissertation, Liang Meng Wee Jun 2013

Rna Interference By The Numbers: Explaining Biology Through Enzymology: A Dissertation, Liang Meng Wee

GSBS Dissertations and Theses

Small silencing RNAs function in almost every aspect of cellular biology. Argonaute proteins bind small RNA and execute gene silencing. The number of Argonaute paralogs range from 5 in Drosophila melanogaster , 8 in Homo sapiens to an astounding 27 in Caenorhabditis elegans. This begs several questions: Do Argonaute proteins have different small RNA repertoires? Do Argonaute proteins behave differently? And if so, how are they functionally and mechanistically distinct?

To address these questions, we examined the thermodynamic, kinetic and functional properties of fly Argonaute1 (dAgo1), fly Argonaute2 (dAgo2) and mouse Argonaute2 (mAGO2). Our studies reveal that in fly, small RNA ...


The Study Of Two Strategies For Decreasing Mutant Huntingtin: Degradation By Puromycin Sensitive Aminopeptidase And Rna Interference: A Dissertation, Joanna Chaurette May 2013

The Study Of Two Strategies For Decreasing Mutant Huntingtin: Degradation By Puromycin Sensitive Aminopeptidase And Rna Interference: A Dissertation, Joanna Chaurette

GSBS Dissertations and Theses

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by a CAG repeat expansion in exon 1 of the huntingtin gene, resulting in an expanded polyglutamine (polyQ) repeat in the huntingtin protein. Patients receive symptomatic treatment for motor, emotional, and cognitive impairments; however, there is no treatment to slow the progression of the disease, with death occurring 15-20 years after diagnosis. Mutant huntingtin protein interferes with multiple cellular processes leading to cellular dysfunction and neuronal loss. Due to the complexity of mutant huntingtin toxicity, many approaches to treating each effect are being investigated. Unfortunately, addressing one cause of toxicity ...


Gene Expression And Profiling Of Human Islet Cell Subtypes: A Master’S Thesis, David M. Blodgett Jul 2012

Gene Expression And Profiling Of Human Islet Cell Subtypes: A Master’S Thesis, David M. Blodgett

GSBS Dissertations and Theses

Background: The endocrine pancreas contains multiple cell types co-localized into clusters called the Islets of Langerhans. The predominant cell types include alpha and beta cells, which produce glucagon and insulin, respectively. The regulated release of these hormones maintains whole body glucose homeostasis, essential for normal metabolism and to prevent diabetes and complications from the disease. Given the heterogeneous nature of islet composition and absence of unique surface markers, many previous studies have focused on the whole islet. Sorting islet cells by intracellular hormone expression overcomes this limitation and provides pure populations of individual islet cell subsets, specifically alpha and beta ...


Therapeutic Silencing Of Mutant Huntingtin By Targeting Single Nucleotide Polymorphisms: A Dissertation, Edith L. Pfister Jul 2012

Therapeutic Silencing Of Mutant Huntingtin By Targeting Single Nucleotide Polymorphisms: A Dissertation, Edith L. Pfister

GSBS Dissertations and Theses

Huntington’s disease (HD) is an autosomal dominant, progressive neurodegenerative disorder. Invariably fatal, HD is caused by expansion of the CAG repeat region in exon 1 of the Huntingtin gene which creates a toxic protein with an extended polyglutamine tract 1. Silencing mutant Huntingtin messenger RNA (mRNA) is a promising therapeutic approach 2-6. The ideal silencing strategy would reduce mutant Huntingtin while leaving the wild-type mRNA intact. Unfortunately, targeting the disease causing CAG repeat expansion is difficult and risks targeting other CAG repeat containing genes.

We examined an alternative strategy, targeting single nucleotide polymorphisms (SNPs) in the Huntingtin mRNA. The ...