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Full-Text Articles in Molecular Biology

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 ...


The Molecular Basis Of Substrate Recognition By The Family Of Pellino E3 Ubiquitin Ligases, Yu-San Huoh Jan 2013

The Molecular Basis Of Substrate Recognition By The Family Of Pellino E3 Ubiquitin Ligases, Yu-San Huoh

Publicly Accessible Penn Dissertations

The four mammalian Pellinos (Pellinos 1, 2, 3a, and 3b) are E3 ubiquitin ligases that have emerging roles in the regulation of Toll-like receptors, interleukin-1 receptor, T-cell receptor, Nod2, and TNF receptor signaling pathways. While each Pellino has a distinct role in facilitating various cellular processes, the underlying mechanisms by which these highly homologous proteins act selectively in these signaling pathways are not clear. In this dissertation, we elucidate the molecular basis of Pellino substrate specificity in order to gain a better understanding of the roles that individual Pellinos play in orchestrating inflammation and cell death. Pellino substrate recognition is ...


Regulators Of Mouse And Human Beta Cell Proliferation, Yang Jiao Jan 2013

Regulators Of Mouse And Human Beta Cell Proliferation, Yang Jiao

Publicly Accessible Penn Dissertations

Diabetes mellitus is an increasingly prevalent metabolic disorder that is estimated to affect over 300 million people by 2025. Common to either type 1 or type 2 diabetes is a progressive inadequacy of functional beta-cell mass. Recent studies have shown that during times of prolonged metabolic demand for insulin, the endocrine pancreas can respond by increasing beta-cell mass by beta-cell proliferation. Advances that further our knowledge of the molecular factors that control beta-cell proliferation will be crucial for understanding the homeostasis of beta-cell mass during adulthood, and are pivotal for any attempt to use instructive cues to induce the proliferation ...


Genome-Wide Analysis Of Rna Secondary Structure In Eukaryotes, Fan Li Jan 2013

Genome-Wide Analysis Of Rna Secondary Structure In Eukaryotes, Fan Li

Publicly Accessible Penn Dissertations

The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. Over the past decades, myriad studies have revealed specific examples of structural elements that direct the expression and function of both protein-coding messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In this work, we develop and apply a novel high-throughput, sequencing-based, structure mapping approach to study RNA secondary structure in three eukaryotic organisms.

First, we assess global patterns of secondary structure across protein-coding transcripts and identify a conserved mark of strongly reduced base pairing at transcription start and stop sites, which we hypothesize helps ...


Nucleic Acid Determinants Of Cytosine Deamination By Aid/Apobec Enzymes In Immunity And Epigenetics, Christopher Nabel Jan 2013

Nucleic Acid Determinants Of Cytosine Deamination By Aid/Apobec Enzymes In Immunity And Epigenetics, Christopher Nabel

Publicly Accessible Penn Dissertations

A multitude of functions have evolved around cytosine within DNA, endowing the base with physiological significance beyond simple information storage. This versatility arises from enzymes that chemically modify cytosine to expand the potential of the genome. Cytosine can be methylated, oxidized, and deaminated to modulate transcription and immunologic diversity. At the crossroads of these modifications sit the AID/APOBEC family deaminases, which accomplish diverse functions ranging from antibody diversification and innate immunity to mRNA editing. In addition, novel roles have been proposed in oncogenesis and DNA demethylation. Behind these established and emerging physiologic activities remain important questions about the substrate ...


Novel Roles For The Tumor Suppressor Apc Through Regulation Of Gsk-3, Alexander James Valvezan Jan 2013

Novel Roles For The Tumor Suppressor Apc Through Regulation Of Gsk-3, Alexander James Valvezan

Publicly Accessible Penn Dissertations

Adenomatous Polyposis Coli (APC) is a tumor suppressor and essential negative regulator of the Wnt signaling pathway. Wnt signaling is crucial for proper patterning and cell fate specification during development and regulates stem cell homeostasis throughout adulthood. Mutations in Apc are strongly linked to human colorectal cancers and these mutations aberrantly activate Wnt signaling. How APC regulates the Wnt pathway and how oncogenic Apc mutations activate Wnt signaling and promote tumorigenesis are not fully understood. To address these questions, we utilized in vitro reconstitution assays, as well as Apc knockdown or mutation in human cells, zebrafish, and mice. We find ...


Change And Impact Of Microrna Modification With Age In Drosophila Melanogaster, Masashi Abe Jan 2013

Change And Impact Of Microrna Modification With Age In Drosophila Melanogaster, Masashi Abe

Publicly Accessible Penn Dissertations

microRNAs (miRNAs) are 20~24nt small RNAs that are critical for many biological aspects, from development to age-associated processes. Starting from the identification of the first miRNA, lin-4, hundreds of miRNAs have been discovered across species. To reveal the role of miRNAs in aging, studies have profiled changes in miRNA levels with age. However, increasing evidence suggests that miRNAs show heterogeneity in length and sequence in different biological contexts. Despite the observation of such heterogeneity, it is largely unknown how such heterogeneity is generated, and whether it is biologically regulated or important. Here we report the characterization of a novel ...


Genomic Imprinting: Establishment, Maintenance And Stability Of Dna Methylation Imprints, Lara Kimberly Abramowitz Jan 2013

Genomic Imprinting: Establishment, Maintenance And Stability Of Dna Methylation Imprints, Lara Kimberly Abramowitz

Publicly Accessible Penn Dissertations

Genomic imprinting is an epigenetic phenomenon in which genes are monoallelicaly expressed according to their parent-of-origin. Imprinted expression entails marking parental chromosomes so that a specific parental allele is stably repressed or expressed. Differential DNA methylation is essential for marking and regulating imprinted genes and is often found at imprinting control regions (ICRs). These DNA methylation imprints must be maintained throughout early development despite genome-wide epigenetic reprogramming to allow for stable allelic expression in differentiated tissues. Moreover, marking of the alleles must be erased in the germline so that establishment of sex-specific marks can occur during gametogenesis. These processes are ...


Dissecting Molecular Pathways That Underlie Disease-Causing Gata1 Mutations, Amy Erin Campbell Jan 2013

Dissecting Molecular Pathways That Underlie Disease-Causing Gata1 Mutations, Amy Erin Campbell

Publicly Accessible Penn Dissertations

Each mammalian cell type has a unique gene expression pattern that supports its specialized function. Mutations in factors that regulate gene expression can disrupt normal function and cause human disease, though the mechanistic consequences of these defects are often unknown. Here, we address how alterations in the transcription factor GATA1 lead to distinct hematologic disorders by combining structural, biochemical, and genomic approaches with gene complementation systems that examine GATA1 function in biologically relevant cellular contexts. We first investigated missense mutations in the GATA1 N-terminal zinc finger (NF) and found that NF mutations impair association with essential GATA1 cofactors. Several NF ...


Molecular Mechanisms Of Alternative Splicing Regulation: An Investigation Of The Spliceosome Repressed By Hnrnp L On Cd45 Exon 4, Ni-Ting Chiou Jan 2013

Molecular Mechanisms Of Alternative Splicing Regulation: An Investigation Of The Spliceosome Repressed By Hnrnp L On Cd45 Exon 4, Ni-Ting Chiou

Publicly Accessible Penn Dissertations

Alternative splicing is a key step in gene regulation and involves the differential selection of splice sites to generate different pre-mRNA transcripts. It has been shown that 90-95% of pre-mRNAs are alternatively spliced in human cells. Pre-mRNA splicing is catalyzed the spliceosome, which consists mainly of the U1, U2, U4, U5 and U6 snRNP, and about a hundred of non-snRNP proteins. Splicing regulators that bind to enhancer or silencer elements on the pre-mRNA can alter assembly of these spliceosome components. Understanding how splicing regulators control spliceosome assembly will bring insights to the prediction of splice site choices. In our lab ...


Developmental Regulation Of Strongyloides Stercoralis Infectious Third-Stage Larvae By Canonical Dauer Pathways, Jonathan David Chaffee Stoltzfus Jan 2013

Developmental Regulation Of Strongyloides Stercoralis Infectious Third-Stage Larvae By Canonical Dauer Pathways, Jonathan David Chaffee Stoltzfus

Publicly Accessible Penn Dissertations

Parasitic nematodes inflict a vast global disease burden in humans as well as animals and plants of agricultural importance; understanding how these worms infect their hosts has significant health and economic implications. In humans, soil-transmitted parasitic nematodes cause hookworm disease and strongyloidiasis, and vector-transmitted parasitic nematodes cause filariasis. The infectious form of the species causing these diseases is a developmentally arrested third-stage larva (L3i). Molecular mechanisms governing L3i developmental arrest and activation within a host have been poorly understood. An analogous developmentally arrested third-stage larva--the dauer larva--forms during stressful environmental conditions in the free-living nematode Caenorhabditis elegans and is controlled ...


Control Of The Tumor Suppressor P53 By Regulating Mdm2 Activity And Stability, Ruchira S. Ranaweera Jan 2013

Control Of The Tumor Suppressor P53 By Regulating Mdm2 Activity And Stability, Ruchira S. Ranaweera

Publicly Accessible Penn Dissertations

p53 is a tumor suppressor that is widely mutated or deleted in cancer cells. Mdm2, an E3 ubiquitin ligase, is the master regulator of p53. It targets p53 for proteasomal degradation, restraining the potent activity of p53 and enabling cell survival and proliferation. There are complex regulatory mechanisms balancing the activity and stability of Mdm2 in a cell. Mdm2 has an extremely short half-life in the unstressed cell and its regulation is not well understood. Like most E3 ligases, Mdm2 can autoubiquitinate. Previously, the sole function of autoubiquitination was thought to be to signal Mdm2 degradation. Here I show that ...


Methods In And Applications Of The Sequencing Of Short Non-Coding Rnas, Paul Ryvkin Jan 2013

Methods In And Applications Of The Sequencing Of Short Non-Coding Rnas, Paul Ryvkin

Publicly Accessible Penn Dissertations

Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields ranging from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non-coding RNAs, as well as a study in which they are applied to Alzheimer ...


Multiple Conserved Enhancers Of The Osteoblast Master Transcription Factor, Runx2, Integrate Diverse Signaling Pathways To Direct Expression To Developing Bone, Christopher Weber Jan 2013

Multiple Conserved Enhancers Of The Osteoblast Master Transcription Factor, Runx2, Integrate Diverse Signaling Pathways To Direct Expression To Developing Bone, Christopher Weber

Publicly Accessible Penn Dissertations

The vertebrate skeleton forms via two distinct modes of ossification, membranous and endochondral. Osteoblasts are also heterogeneous in embryonic origin; bone formed by either mode can be derived from neural crest cells or mesoderm. In contrast, all bone develops via a common genetic pathway regulated by the transcription factor Runx2. Runx2 is required for bone formation, and haploinsufficiency in humans causes the skeletal syndrome cleidocranial dysplasia, demonstrating the importance of gene dosage. Despite the central role of Runx2 in directing bone formation, little is understood about how its expression is regulated in development. We took an unbiased approach to identify ...


Cellular Mechanisms Of Mammalian Liver Regeneration, Kilangsungla Yanger Jan 2013

Cellular Mechanisms Of Mammalian Liver Regeneration, Kilangsungla Yanger

Publicly Accessible Penn Dissertations

ABSTRACT

CELLULAR MECHANISMS OF MAMMALIAN LIVER REGENERATION

Kilangsungla Yanger

Ben Z. Stanger

The liver is an essential organ that aids in metabolic processes, protein synthesis and detoxification of harmful substances. As the centre for detoxification, the liver is able to compensate for this routine damage with its robust regenerative ability. All vertebrate livers, for example, can make up for tissue mass loss (via surgical excision of a portion of the liver) by replication of their differentiated cells within the remnant lobes. These differentiated cells include parenchymal cells such as the hepatocytes and biliary epithelial cells (BECs) and also non-parenchymal cells ...


Regulation Of Egf Receptor Dynamics By Protein Tyrosine Phosphatases, Calixte Monast Jan 2013

Regulation Of Egf Receptor Dynamics By Protein Tyrosine Phosphatases, Calixte Monast

Publicly Accessible Penn Dissertations

The phosphorylated epidermal growth factor receptor (EGFR) initiates intracellular signaling processes that regulate cell growth, survival, and migration, and disregulated EGFR-mediated signaling occurs in many cancers. While the processes that lead to EGFR activation and phosphorylation have been studied in detail, quantitative aspects of the spatiotemporal regulation of EGFR by protein tyrosines phosphatases (PTPs) are not well understood. To begin to address this, we developed a new compartmentalized mechanistic model of EGFR phosphorylation dynamics and used it to interpret quantitative biochemical measurements to show that EGFR is dephosphorylated at the plasma membrane and in the cell interior with a time ...


Regulation And Dynamic Behavior Of The Heat Shock Transcription Factor Hsf-1 In C. Elegans, Elizabeth A. Morton Jan 2013

Regulation And Dynamic Behavior Of The Heat Shock Transcription Factor Hsf-1 In C. Elegans, Elizabeth A. Morton

Publicly Accessible Penn Dissertations

Eukaryotic cells respond to heat stress by activating the transcription factor HSF1. In addition to its role in stress response, HSF1 also functions in protein homeostasis, aging, innate immunity, and cancer. Despite prominent HSF1 involvement in processes pertinent to human health and disease, there are still gaps in our understanding of HSF1. For example, controversy exists regarding the localization of HSF1, the identity of HSF1 regulators, and the function and conservation of heat-induced HSF1 stress granules. Many of the physiological roles for HSF1 have been defined using the model organism Caenorhabditis elegans, yet little is known about how the molecular ...


Abnormal Smooth Muscle Contraction Alters Gut Motility And Propagates Epithelial Invasion In The Larval Zebrafish Intestine, Joshua Abrams Jan 2013

Abnormal Smooth Muscle Contraction Alters Gut Motility And Propagates Epithelial Invasion In The Larval Zebrafish Intestine, Joshua Abrams

Publicly Accessible Penn Dissertations

Coordinated smooth muscle contraction is critical for force production and proper functioning of numerous organ systems. Activation at the myosin motor domain via phosphorylated myosin light chain (phospho-MLC) remains the primary signal to initiate contraction, but it is now appreciated that there are additional force modulators also present in smooth muscle. One particularly well studied modulatory protein is Caldesmon (CaD), which has been implicated in controlling contractile force in vascular smooth muscle, however little is known of CaD's physiological role in vivo. Studies in vitro have shown that CaD inhibits actomyosin interactions and that this effect is reversed after ...


The Multifunctional Protein Daxx: Studies Of Its Biology And Regulation, And Discovery Of A Novel Function, Trisha Agrawal Jan 2013

The Multifunctional Protein Daxx: Studies Of Its Biology And Regulation, And Discovery Of A Novel Function, Trisha Agrawal

Publicly Accessible Penn Dissertations

Daxx, a multifunctional protein with a diverse set of proposed functions, is ubiquitously expressed and highly conserved through evolution. A primarily nuclear protein, Daxx is able to regulate apoptosis, transcription, and cellular proliferation. Despite many studies into the function of Daxx, its precise role in the cell remains enigmatic. Herein, evidence is presented to expand upon the known anti-apoptotic function of Daxx, to establish Daxx as a novel molecular chaperone, and to further its repertoire of transcriptional targets. As an apoptotic inhibitor, Daxx is known to regulate p53 by stabilizing its main negative regulator, Mdm2, via formation of a ternary ...


Epigenomic And Transcriptional Regulation Of Hepatic Metabolism By Rev-Erb And Hdac3, Dan Feng Jan 2013

Epigenomic And Transcriptional Regulation Of Hepatic Metabolism By Rev-Erb And Hdac3, Dan Feng

Publicly Accessible Penn Dissertations

Metabolic activities are regulated by the circadian clock, and disruption of the clock exacerbates metabolic diseases including obesity and diabetes. Transcriptomic studies in metabolic organs suggested that the circadian clock drives the circadian expression of important metabolic genes. Here we show that histone deacetylase 3 (HDAC3) is recruited to the mouse liver genome in a circadian manner. Histone acetylation is inversely related to HDAC3 binding, and this rhythm is lost when HDAC3 is absent. Diurnal recruitment of HDAC3 corresponds to the expression pattern of REV-ERBĪ±, an important component of the circadian clock. REV-ERBĪ± colocalizes with HDAC3 near genes regulating lipid ...


The Role Of Tipe2 In The Regulation Of Inflammation And Tumorigenesis, Derek Johnson Jan 2013

The Role Of Tipe2 In The Regulation Of Inflammation And Tumorigenesis, Derek Johnson

Publicly Accessible Penn Dissertations

TIPE2 is a recently discovered regulator of immunity and inflammation. Here we describe a new function of TIPE2 in the regulation of Ras signaling and Tumorigenesis. By using various stimuli and inhibitors in T Cells and macrophages we discovered that TIPE2 is regulated at both the message and protein level by inflammatory stimuli. TIPE2 mRNA is regulated in the short to intermediate term by an NF-Kappa B induced micro RNA, and TIPE2 is also ubiquitylated and degraded, possibly by SCF-Beta TRCP. Mechanistically TIPE2 interacts with and inhibits the Ras-interacting domain of the RalGDS family of Ras effectors, leading to a ...


Host-Apicomplexan Parasite Interactions: Leveraging Biological Discovery Into Antiparasitic Drug Development, Melanie Grace Millholland Jan 2013

Host-Apicomplexan Parasite Interactions: Leveraging Biological Discovery Into Antiparasitic Drug Development, Melanie Grace Millholland

Publicly Accessible Penn Dissertations

The obligate intracellular pathogens Plasmodium falciparum and Toxoplasma gondii remodel their host cell to facilitate their intracellular development and progress through their asexual life cycle, a virulent lytic cycle responsible for parasite-mediated pathogenesis. While several studies have highlighted parasite proteins that interact with the host cell during this cycle, host proteins exploited by the parasite for successful growth and conversely, host molecules evolutionarily tuned to control parasite infection remain unclear. We addressed this question from both sides of the host-parasite interaction in the hope to leverage biological discovery of host molecules involved in infection into the validation of novel drug ...