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Articles 1 - 14 of 14

Full-Text Articles in Molecular Biology

Reprogramming The Retina: Next Generation Strategies Of Retinal Neuroprotection And Gene Therapy Vector Potency Assessment, Devin Scott Mcdougald Jan 2018

Reprogramming The Retina: Next Generation Strategies Of Retinal Neuroprotection And Gene Therapy Vector Potency Assessment, Devin Scott Mcdougald

Publicly Accessible Penn Dissertations

Mutations within over 250 known genes are associated with inherited retinal degeneration. Clinical success following gene replacement therapy for Leber’s congenital amaurosis type 2 establishes a platform for the development of downstream treatments targeting other forms of inherited and acquired ocular disease. Unfortunately, several challenges relevant to complex disease pathology and limitations of current gene transfer technologies impede the development of gene replacement for each specific form of retinal degeneration. Here we describe gene augmentation strategies mediated by recombinant AAV vectors that impede retinal degeneration in pre-clinical models of acquired and inherited vision loss. We demonstrate distinct neuroprotective effects ...


All The Right Noises: Causes And Consequences Of Stochastic Trimethylamine Oxide Reductase Expression In Escherichia Coli, Jeffrey Carey Jan 2018

All The Right Noises: Causes And Consequences Of Stochastic Trimethylamine Oxide Reductase Expression In Escherichia Coli, Jeffrey Carey

Publicly Accessible Penn Dissertations

Microbial populations can maximize fitness in dynamic environments through bet hedging, a process wherein a subpopulation assumes a phenotype not optimally adapted to the present environment but well adapted to an environment likely to be encountered. Here we show that oxygen induces fluctuating expression of the trimethylamine oxide (TMAO) respiratory system of Escherichia coli, diversifying the cell population and enabling a bet-hedging strategy that permits growth following oxygen loss. This regulation by oxygen affects the variance in gene expression but leaves the mean unchanged. We show that the oxygen-sensitive transcription factor IscR is the key regulator of variability. Oxygen causes ...


Novel Cell Surface Anchoring Mechanism Of Prokaryotic Secreted Protein, Mohd Farid Abdul Halim Jan 2017

Novel Cell Surface Anchoring Mechanism Of Prokaryotic Secreted Protein, Mohd Farid Abdul Halim

Publicly Accessible Penn Dissertations

The microbial cell surface is decorated with a variety of protein structures that play important roles in key cellular processes such as providing cell stability, facilitating interactions between cells, and interacting with the environment. One important feature of the biosynthesis of these structures is the proper anchoring of proteins to the cell surface. In silico work recently predicted a novel protein anchoring mechanism for a subset of surface proteins that contain a conserved C-terminal tripartite architecture, which consists of a conserved motif, followed by a hydrophobic (H) domain, and positively charged amino acids. Using the well-studied model archaeon Haloferax volcanii ...


Haloferax Volcanii Strategies To Regulate Type Iv Pilus Dependent Adhesion And Microcolony Formation, Rianne Nicole Esquivel Jan 2016

Haloferax Volcanii Strategies To Regulate Type Iv Pilus Dependent Adhesion And Microcolony Formation, Rianne Nicole Esquivel

Publicly Accessible Penn Dissertations

Microorganisms can utilize type IV pili to initiate and maintain biofilms - microbial communities that provide protection against stressful conditions. Because environmental conditions change suddenly, microorganisms have evolved multiple mechanisms to rapidly transition from a planktonic to sessile cell state. Despite the presence of archaea alongside bacteria throughout the environment, including the human microbiome, little is known about how these organisms form and maintain biofilms. Here we use genetic, microscopic and biochemical techniques to investigate multiple strategies the model archaeon Haloferax volcanii employs to permit effective adhesion and microcolony formation, early steps in biofilm formation and maturation, as well as eventual ...


Siv Infected Chimpanzees: Consequences Of Long-Term Infection And Potential Intervention Strategies, Hannah J. Barbian Jan 2016

Siv Infected Chimpanzees: Consequences Of Long-Term Infection And Potential Intervention Strategies, Hannah J. Barbian

Publicly Accessible Penn Dissertations

Simian immunodeficiency virus of chimpanzees (SIVcpz) is widespread in wild-living chimpanzees and can cause mortality and AIDS-like immunopathology. However, due to limited access to naturally infected chimpanzees, little is known about SIVcpz pathogenesis and potential intervention strategies that might be effective in captivity or in the wild. Given the central role of the intestinal microbiome in mammalian health, I asked whether gut microbial constituents could reveal any insights into SIVcpz-associated pathogenicity. I characterized the gut microbiome and virome of SIVcpz infected and uninfected chimpanzees in Gombe National Park, Tanzania. I found that SIVcpz infected chimpanzees retain a stable gut microbiome ...


Insight Into Tetherin-Mediated Signaling Via The Discovery Of A Novel Isoform With Biologically Distinct Properties, Luis Jose Cocka Jan 2015

Insight Into Tetherin-Mediated Signaling Via The Discovery Of A Novel Isoform With Biologically Distinct Properties, Luis Jose Cocka

Publicly Accessible Penn Dissertations

Viruses are obligate, intracellular pathogens that hijack host cell machinery to replicate. Innate immunity is the first line of defense against such perceived threats through recognition of broadly conserved pathogen signatures. Tetherin (also known as BST2/CD317/HM1.24) is an innate immune factor that senses and restricts egress, the final step of viral replication. Tetherin potently reduces cell-free virus spread by indiscriminately “tethering” particles at the cell surface via direct anchoring to the host membrane. The majority of previous studies on Tetherin focused on elucidating the minimal structural features necessary for tethering viral particles and understanding how viruses counter ...


The Cellular Mirna, Mir-190, Is Upregulated In Type I Ebv Latency By Ebers And Modulates Cellular Mrnas Involved In Cell Survival And Viral Reactivation, Elizabeth Mary Cramer Jan 2015

The Cellular Mirna, Mir-190, Is Upregulated In Type I Ebv Latency By Ebers And Modulates Cellular Mrnas Involved In Cell Survival And Viral Reactivation, Elizabeth Mary Cramer

Publicly Accessible Penn Dissertations

Epstein-Barr Virus (EBV) is a highly prevalent human pathogen infecting over 90% of the population. Much of the success of the virus is attributed to its ability to maintain latency through different programs in host cells. MicroRNAs (miRNA) are small, non-coding RNAs capable of post-transcriptionally regulating mRNA expression. A microarray comparison of EBV type I latency and type III latency infected cells yielded evidence of differential cellular microRNA expression. I hypothesized that one of these differentially upregulated type I latency miRNAs, miR-190, is important in maintenance of latency I, and miR-190 upregulation is due to viral gene expression. Lentiviral overexpression ...


Molecular Characterization Of The Transmission And Early Diversification Of Hepatitis C Virus, Mark Bevan Stoddard Jan 2015

Molecular Characterization Of The Transmission And Early Diversification Of Hepatitis C Virus, Mark Bevan Stoddard

Publicly Accessible Penn Dissertations

Hepatitis C virus (HCV) is a medically important RNA virus in the Flaviviridae family. It persists in chronically infected individuals by replicating in hepatocytes and by evolving as a genetically diverse "quasispecies" that evades host immune pressures. However, transmission, with its attendant population bottlenecking, represents a period of relative vulnerability and is of particular importance with respect to viral natural history, immunopathogenesis, treatment intervention, and vaccine development. A precise molecular characterization of HCV transmission and early diversification has not previously been possible. In this dissertation work, it was hypothesized that HCV genomes that are transmitted from one individual to the ...


Role Of The Ebolavirus Glycoprotein In Countering Tetherin During Viral Budding, Nathan Henry Vande Burgt Jan 2015

Role Of The Ebolavirus Glycoprotein In Countering Tetherin During Viral Budding, Nathan Henry Vande Burgt

Publicly Accessible Penn Dissertations

Ebola virus (EBOV) is the causative agent of Ebola virus hemorrhagic fever and initiates sporadic outbreaks with very high mortality rates of up to 90%. The only viral surface protein on EBOV virions, the EBOV Glycoprotein (GP1,2), is a known antagonist of the intrinsic innate immune effector Tetherin, which prevents release of budded virions by “tethering” them to the cell. Unlike other Tetherin antagonists, GP1,2 does not degrade Tetherin, remove Tetherin from the cell surface, or sequester Tetherin in intracellular compartments. Thus, the mechanism of how GP1,2 counters Tetherin is not well understood. This study utilizes methods ...


Tegument Protein Bnrf1 Regulation Of Epstein-Barr Virus Genome Chromatinization During Early Infection, Kevin Tsai Jan 2014

Tegument Protein Bnrf1 Regulation Of Epstein-Barr Virus Genome Chromatinization During Early Infection, Kevin Tsai

Publicly Accessible Penn Dissertations

Epstein-Barr virus (EBV) is a ubiquitously prevalent human herpesvirus whose persistent latent infection is associated with many lymphomas. The prevalence of this virus can be attributed to its ability to establish a persistent latent infection in host cells, during which only a small number of viral genes are expressed from a highly regulated viral genome. However, it is not completely understood how EBV evades cellular antiviral defenses and regulates chromatin assembly to establish latent infections. The EBV major tegument protein BNRF1 was found to be required for the establishment of latent infections, and contains sequence homology to cellular purine biosynthesis ...


Multiple Roles Of Brd4 In The Human Papillomavirus Life Cycle, Christine M. Helfer Jan 2014

Multiple Roles Of Brd4 In The Human Papillomavirus Life Cycle, Christine M. Helfer

Publicly Accessible Penn Dissertations

ABSTRACT

MULTIPLE ROLES OF BRD4 IN THE HUMAN

PAPILLOMAVIRUS LIFE CYCLE

Christine M. Helfer

Jianxin You

While human papillomavirus (HPV) vaccines protect against acquiring new infections, there is currently no antiviral treatment for eradicating persistent HPV infections. In this study, I demonstrated that the cellular chromatin binding protein, Brd4, in association with HPV E2 protein, is important for multiple HPV functions including replication, maintenance of viral genomes, and regulation of viral gene transcription. These studies suggest that the E2–Brd4 complex could be an effective target to disrupt the HPV life cycle. Using bimolecular fluorescence complementation, we demonstrate that E2 ...


Distinct Patterns Of Ccr5 Versus Alternative Coreceptor Dependence In Non-Natural Host Versus Natural Host Simmian Immunodeficiency Virus Infection, Sarah Tc Elliott Jan 2014

Distinct Patterns Of Ccr5 Versus Alternative Coreceptor Dependence In Non-Natural Host Versus Natural Host Simmian Immunodeficiency Virus Infection, Sarah Tc Elliott

Publicly Accessible Penn Dissertations

Natural host sooty mangabeys infected with simian immunodeficiency viruses (SIV) exhibit high plasma viral loads without widespread CD4+ T cell loss. By contrast, non-natural host rhesus macaques experimentally infected with related SIV exhibit high viral loads but display subsequent CD4+ T cell loss and progression to AIDS, analogous to the effects of HIV-1 infection in humans. Several mechanisms have been proposed to explain these discrepant outcomes, including infection of distinct target cells in vivo. Cell targeting is substantially determined at the level of viral entry. Prior work demonstrated that sooty mangabey infection occurs in the absence of functional coreceptor CCR5 ...


Phenotypic Characteristics Of Mucosally Transmitted Hiv-1, Nicholas F. Parrish Jan 2013

Phenotypic Characteristics Of Mucosally Transmitted Hiv-1, Nicholas F. Parrish

Publicly Accessible Penn Dissertations

Mucosal transmission accounts for the majority of new human immunodeficiency virus type 1 (HIV-1) infections and results in a genetically and phenotypically homogenous founder virus population in 60-80 percent of cases. Biological properties common to these transmitted and founder (T/F) viruses but not chronic control (CC) viruses would define key targets for microbicides and vaccines. To identify such properties, we tested 45 T/F and 52 CC envelope glycoproteins (Envs) from the best studied and most prevalent HIV-1 subtypes (B and C, respectively) in various pseudotype assays to determine their receptor and coreceptor interaction, tropism for primary CD4+ T ...


A Novel Ccr5 Mutation In Sooty Mangabeys Reveals Sivsmm Infection Of Ccr5-Null Natural Hosts: Examining The Potential Roles Of Alternative Entry Pathways In Hiv And Siv Infection, Nadeene E. Riddick Jan 2012

A Novel Ccr5 Mutation In Sooty Mangabeys Reveals Sivsmm Infection Of Ccr5-Null Natural Hosts: Examining The Potential Roles Of Alternative Entry Pathways In Hiv And Siv Infection, Nadeene E. Riddick

Publicly Accessible Penn Dissertations

Natural hosts of SIV, such as sooty mangabeys (SM), maintain high levels of virus replication, but do not typically develop CD4+ T cell loss and immunodeficiency. Understanding the virus/host relationship in natural hosts will enable better understanding of pathogenic HIV infection of humans. Host cell targeting in vivo is an important determinant of pathogenesis, and is defined mainly by expression of coreceptors used by the virus for entry, in conjunction with CD4. Established dogma holds that, with rare exceptions, SIV uses CCR5 for entry. However, SM and other natural hosts express extremely low CCR5 levels on CD4+ T cells ...