Open Access. Powered by Scholars. Published by Universities.®

Biochemistry, Biophysics, and Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 30 of 163

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Induction Of Antibodies To Hiv-1 Envelope Using Simian Adenovirus Vaccines, Kristel Lucie Emmer Jan 2018

Induction Of Antibodies To Hiv-1 Envelope Using Simian Adenovirus Vaccines, Kristel Lucie Emmer

Publicly Accessible Penn Dissertations

Human immunodeficiency virus type 1 (HIV-1) has infected 76 million people since the beginning of the epidemic. The first evidence that an HIV-1 vaccine could prevent infection in humans was provided in the RV144 vaccine efficacy trial. RV144 demonstrated 31.2% efficacy and immune correlate analyses indicated that antibodies targeting the variable 2 (V2) region of HIV-1 envelope (Env) correlated with decreased risk of infection. However, significant improvements are needed to develop a globally effective vaccine against HIV-1.

Several approaches can be employed to improve upon vaccination strategies: heterologous prime-boost regimens, immunogen design, and alternative adjuvants. To enhance Env-specific antibodies ...


Use Of Induced Pluripotent Stem Cell Models To Elucidate Retinal Disease Pathogenesis And To Develop Gene-Based Therapies, Thu Thi Duong Jan 2018

Use Of Induced Pluripotent Stem Cell Models To Elucidate Retinal Disease Pathogenesis And To Develop Gene-Based Therapies, Thu Thi Duong

Publicly Accessible Penn Dissertations

Choroideremia (CHM) is a rare monogenic, X-linked recessive inherited retinal degenerative disease caused by mutations in the Rab Escort Protein-1 (REP1) encoding CHM gene. CHM is characterized by childhood-onset night blindness (nyctalopia), progressive peripheral vision loss due to the degeneration of neural retina, RPE and choroid in a peripheral-to-central fashion. Most of CHM mutations are loss-of-function mutations leading to the complete lacking of REP1 protein. However, the primary retinal cell type leading to CHM and molecular mechanism remains unknown in addition to the fact of lacking proper disease models. In this study, we explored the utility of induced pluripotent stem ...


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 ...


Chromatin Remodeling Dynamics During Brown Adipogenesis, Suzanne Natalie Shapira Jan 2018

Chromatin Remodeling Dynamics During Brown Adipogenesis, Suzanne Natalie Shapira

Publicly Accessible Penn Dissertations

Brown adipose tissue (BAT) is specialized to expend energy through the action of the mitochondrial uncoupling protein UCP1. Increasing brown fat mass or activity through genetic or chemical manipulation in mice suppresses obesity and its comorbidities; as such, there is great interest in developing approaches to increase the amount and/or function of brown fat to combat metabolic disorders. My thesis work aimed to dissect the molecular mechanisms by which the helix- loop-helix transcription factor Early B-Cell Factor 2 (EBF2) regulates brown adipocyte commitment and terminal differentiation. Through analysis of tissue-specific knockout mouse models, we found that EBF2 is required ...


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 ...


Wnt5a Signaling Induced Phosphorylation Increases Acyl Protein Thioesterase Activity And Promotes Melanoma Metastatic Behavior, Rochelle Shirin Sadeghi Jan 2018

Wnt5a Signaling Induced Phosphorylation Increases Acyl Protein Thioesterase Activity And Promotes Melanoma Metastatic Behavior, Rochelle Shirin Sadeghi

Publicly Accessible Penn Dissertations

Wnt5a has been implicated in melanoma progression and metastasis, although the exact downstream signaling events that contribute to melanoma metastasis are poorly understood. Wnt5a signaling results in acyl protein thioesterase 1 (APT1) mediated depalmitoylation of pro-metastatic cell adhesion molecules CD44 and MCAM, resulting in increased melanoma invasion. The mechanistic details that underlie Wnt5a-mediated regulation of APT1 activity and cellular function remains unknown. Here, we show Wnt5a signaling regulates APT1 activity through induction of APT1 phosphorylation and we further investigate the functional role of APT1 phosphorylation on its depalmitoylating activity. We found phosphorylation increased APT1 depalmitoylating activity and reduced APT1 dimerization ...


Exploring The Role Of Tet1 In Genomic Imprinting, Jennifer Myers Sanmiguel Jan 2018

Exploring The Role Of Tet1 In Genomic Imprinting, Jennifer Myers Sanmiguel

Publicly Accessible Penn Dissertations

DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified ...


Gene Therapy Approaches To Immune Tolerance Induction In Canine Hemophilia, Robert French Jan 2018

Gene Therapy Approaches To Immune Tolerance Induction In Canine Hemophilia, Robert French

Publicly Accessible Penn Dissertations

A key issue in gene therapy is the immune response to the therapeutic transgene. This is especially important in applications where current treatments often elicit an antibody response, like hemophilia, where protein replacement therapy results in neutralizing

antibodies (“inhibitors”) in ~25% of severe hemophilia A and 1-3% of severe hemophilia B patients. To test the ability of skeletal muscle-directed gene therapy to prevent an immune response, we used an inhibitor-prone dog model of severe hemophilia B to express a hyperactive factor IX (FIX) variant from skeletal muscle via adeno-associated viral (AAV) vector and observed curative levels of expression that lasted ...


Β Cell Replacement Therapy: A Novel Application For Targeted Epigenetic Editing, Kristy Ou Jan 2018

Β Cell Replacement Therapy: A Novel Application For Targeted Epigenetic Editing, Kristy Ou

Publicly Accessible Penn Dissertations

Pancreatic β cells are the exclusive source of insulin, which normalizes blood glucose levels under hyperglycemic conditions. In 2015, over 252,000 deaths in the United States were contributed by diabetes, a family of disorders directly linked to defects in the pancreatic β cells. β cell deficiency or dysfunction leads to insufficient insulin secretion, resulting in chronic hyperglycemia and increased risk for severe health complications. Although severely diabetic patients can clinically manage their glucose levels with mealtime delivery of insulin analogues, many still experience potentially life-threatening hypoglycemic episodes due to erroneous insulin administration. Only β cell replacement therapy, through the ...


The Role Of Molecular Motors In Peripheral Nerve Regeneration, Melissa D. Priest Jan 2018

The Role Of Molecular Motors In Peripheral Nerve Regeneration, Melissa D. Priest

Publicly Accessible Penn Dissertations

Following injury, axons of the peripheral nervous system have retained the capacity for regeneration. While it is well established that injury signals require molecular motors for their transport from the injury site to the nucleus, whether kinesin and dynein motors play additional roles in peripheral nerve regeneration is not well understood. Here we use genetic mutants of motor proteins in a zebrafish peripheral nerve regeneration model to visualize and define in vivo roles for kinesin and dynein. We find that both kinesin-1 and dynein are required for zebrafish peripheral nerve regeneration. While loss of kinesin-1 reduced the overall robustness of ...


Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function, Alex Martin Rohacek Jan 2018

Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function, Alex Martin Rohacek

Publicly Accessible Penn Dissertations

Hearing loss is the most common form of congenital birth defect, affecting an estimated

35 million children worldwide. To date, nearly 100 genes have been identified which

contribute to a deafness phenotype in humans, however, many cases remain in which a

causative mutation has yet to be found. In addition, the exact mechanism by which

hearing loss occurs in the presence of many of these mutations is still not understood.

This is due, in part, to the complex nature of the development and function of the

cochlear duct, the organ of hearing. The cochlea undergoes an intricate morphogenetic

development and ...


Nonclassical Sex Hormone Signaling In Melanocytes And Melanoma, Christopher Anthony Natale Jan 2018

Nonclassical Sex Hormone Signaling In Melanocytes And Melanoma, Christopher Anthony Natale

Publicly Accessible Penn Dissertations

The primary pigment in mammalian skin and hair is melanin, which is synthesized locally by differentiated melanocytes and transferred into surrounding epidermal keratinocytes and hair shafts. Because pigmentation differences are often readily visible clinically, melanocyte function is known to correlate with changes in environment, as well as physiologic and pathologic changes in other organ systems. We utilized these clinical associations to inspire the hypothesis that sex hormones influence melanocyte biology. For over 2,000 years, it has been appreciated that pregnancy is associated with changes in skin pigmentation, but the specific processes, hormones, receptors, and downstream signaling cascades responsible have ...


Investigating Molecular Mechanisms Underlying Mild Phenotype In Friedreich Ataxia Patients With G130v Missense Mutation, Elisia Clark Jan 2018

Investigating Molecular Mechanisms Underlying Mild Phenotype In Friedreich Ataxia Patients With G130v Missense Mutation, Elisia Clark

Publicly Accessible Penn Dissertations

Friedreich’s Ataxia (FRDA) is an incurable neurodegenerative disease caused by mutations in the frataxin (FXN) gene, resulting in decreased expression of the mitochondrial protein FXN. 2-3% of FRDA patients carry a GAA expansion on one FXN allele, and a missense mutation on the other. The mechanism behind the disease‐causing features remains elusive. The phenotype associated with patients carrying point mutations cannot be predicted with certainty; these patients can have a mild or severe clinical outcome, creating a unique platform to understand clinical heterogeneity. FXN is important for proper mitochondrial function, and is involved in Fe-S cluster biogenesis, metabolism ...


Epigenetic Mechanisms Governing Behavioral Reprogramming In The Ant Camponotus Floridanus, Riley John Graham Jan 2018

Epigenetic Mechanisms Governing Behavioral Reprogramming In The Ant Camponotus Floridanus, Riley John Graham

Publicly Accessible Penn Dissertations

Eusocial insect colonies divide behaviors among specialist groups called castes. In some species, caste identity is determined by the interaction of endogenous (e.g. genomic) and exogenous (e.g. juvenile hormone from nurses) signals during larval development, suggesting epigenetic mechanisms underlie plastic traits tied to caste identity. Previous work demonstrated a link between patterns of histone H3 lysine 27 acetylation (H3K27ac) and caste-specific gene expression in Major and Minor workers of the ant Camponotus floridanus, and we hypothesized caste-specific behaviors such as foraging may be similarly regulated by histone acetylation. To test this hypothesis, we fed mature (~30d old) Majors ...


Decoding Calcium Encoding Through Bi-Directional Optogenetic Control Over Gq-Protein Signaling, Pimkhuan Hannanta-Anan Jan 2018

Decoding Calcium Encoding Through Bi-Directional Optogenetic Control Over Gq-Protein Signaling, Pimkhuan Hannanta-Anan

Publicly Accessible Penn Dissertations

Calcium is a fundamental secondary messenger responsible for relaying information from the extracellular space to the cell interior. Extracellular cues are temporally encoded through calcium signals, which often arise in the form of oscillations. These oscillations are then decoded to inform cellular decisions and regulate cellular functions. Despite its crucial role in cell signaling, the encoding and decoding of calcium oscillations is poorly understood. The current biological tools and methods used to study calcium signaling lack the temporal precision and specificity necessary to precisely manipulate, perturb, and dissect calcium signaling circuits. To address this need, we developed a new set ...


Dissecting The Functions Of Atr In Replication Fork Stability, Theonie Anastassiadis Jan 2017

Dissecting The Functions Of Atr In Replication Fork Stability, Theonie Anastassiadis

Publicly Accessible Penn Dissertations

Genome maintenance is required for cellular viability, and failure to preserve genomic integrity is associated with an increased risk of diseases, such as cancer. To ensure genomic stability, cells have checkpoints that control cell cycle progression in the event of DNA damage or incomplete DNA replication. The DNA replication checkpoint is regulated by the ATR-CHK1 pathway that stabilizes stalled replication forks and prevents their collapse into DNA double-strand breaks (DSBs). Two distinct models have been proposed to explain how ATR stabilizes stalled forks: 1) through local modulation of fork remodelers, such as SMARCAL1 inhibition, and 2) through inhibition of CDK-dependent ...


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 ...


The Human Heterochromatin Landscape: Genomic Subtypes, Bound Proteins, And Contributions To Cell Identity, Justin S. Becker Jan 2017

The Human Heterochromatin Landscape: Genomic Subtypes, Bound Proteins, And Contributions To Cell Identity, Justin S. Becker

Publicly Accessible Penn Dissertations

Large portions of mammalian genomes are packaged into structurally compact heterochromatin, which protects genome integrity and suppresses transcription of lineage-inappropriate genes. Characterization of heterochromatic regions has relied on genomic mapping of associated histone modifications, such as H3K9me3 and H3K27me3, and purification of proteins interacting with these modifications. Heterochromatic regions marked by H3K9me3 have been shown to impede gene activation during reprogramming to pluripotency, and I find that H3K9me3 domains can similarly impede conversion of fibroblasts to hepatocytes. However, both H3K9me3 and H3K27me3 can be found in transcriptionally active chromatin, limiting the accuracy of histone marks alone for identifying heterochromatin domains ...


Tumor Interferon Signaling Initiates And Sustains A Multigenic Resistance Program To Immune Checkpoint Blockade, Joseph Lawrence Benci Jan 2017

Tumor Interferon Signaling Initiates And Sustains A Multigenic Resistance Program To Immune Checkpoint Blockade, Joseph Lawrence Benci

Publicly Accessible Penn Dissertations

Therapeutic blockade of the CTLA4 and/or PD1 immune checkpoint pathways has resulted in significant anti-tumor responses in broad variety of cancer types, but resistance is common. Using mouse models of metastatic melanoma and breast cancer in combination with CRISPR/Cas9 to selectively delete genes in our tumor cells, we demonstrate that prolonged interferon signaling orchestrates PDL1-dependent and PDL1-independent resistance to immune checkpoint blockade (ICB), and to combinations such as radiation plus anti-CTLA4. Furthermore, we show that this interferon driven resistance mechanism primarily occurs in ICB resistant tumors and not in ICB responsive tumors. Persistent type II interferon signaling allows ...


Transcriptome-Wide Analysis Of Hypoxic Cancer Cells Identify Alternative Splicing As A Mechanism To Inhibit Translation, Lauren Kathleen Brady Jan 2017

Transcriptome-Wide Analysis Of Hypoxic Cancer Cells Identify Alternative Splicing As A Mechanism To Inhibit Translation, Lauren Kathleen Brady

Publicly Accessible Penn Dissertations

Cellular adaptation to hypoxia involves downregulation of energy-consuming processes such as macromolecular synthesis, and leads to tumor aggressiveness and resistance to therapies for many solid cancers. To delineate mechanisms underlying this process, I carried out a transcriptome-wide study to measure hypoxia-mediated changes in gene expression and alternative splicing in in vivo and in vitro models of hypoxic head and neck carcinoma (HNC) cells. These data represent the first nucleotide-resolution study of the hypoxic transcriptome of HNC cells in vivo and in vitro. This investigation uncovered a global downregulation of genes known to regulate RNA processing, including a significant number of ...


Histone Variant Macroh2a In The Gut And Beyond: A Study Of Intestinal Fortitude, Ryan James Cedeno Jan 2017

Histone Variant Macroh2a In The Gut And Beyond: A Study Of Intestinal Fortitude, Ryan James Cedeno

Publicly Accessible Penn Dissertations

Epigenetic factors guide chromatin remodeling during cell state transitions and confer resistance to genotoxic stressors that could induce deleterious transformations. A particularly peculiar component of the epigenome with emerging roles in fine-tuning cell identity and upholding genomic stability is the structural histone variant macroH2A. Relatively little is currently known about macroH2A’s influence on overall cell developmental potency and less still is known about macroH2A’s contributions to adult stem cell identity and function in vivo. In this work, we use induced pluripotent stem cell (iPSC) reprogramming and the murine intestinal stem cell (ISC) system to model macroH2A’s overall ...


Modulation Of Transcription In The Murine Gut Epithelium In Development, Differentiation, And Disease, Julia Elise Kieckhaefer Jan 2017

Modulation Of Transcription In The Murine Gut Epithelium In Development, Differentiation, And Disease, Julia Elise Kieckhaefer

Publicly Accessible Penn Dissertations

The intestinal epithelium is a continuously self-renewing tissue that must balance its function as the site of nutrient absorption with its role as a barrier between the body and the external environment. With its high cellular turnover and continual exposure to lumenal antigens, the intestinal epithelium is highly susceptible to developing diseases, such as inflammatory bowel disease (IBD) and cancer. Understanding the factors that control intestinal epithelial development are key to discovering disease etiology and to engineering new treatments. In mammals, studies have pointed to dysregulation of RNA Polymerase III as playing a role in oncogenic transformation. A deletion in ...


Genomics-Based Studies Identify Cis And Trans Acting Post-Transcriptional Regulators, Shawn W. Foley Jan 2017

Genomics-Based Studies Identify Cis And Trans Acting Post-Transcriptional Regulators, Shawn W. Foley

Publicly Accessible Penn Dissertations

The identity of every organism is stored in its genetic material. Each gene is transcribed into an intermediate RNA molecule, which undergoes complex processing before translation into a functional protein. RNA processing is controlled by RNA binding proteins (RBPs). Each RBP binds to and regulates the processing, stability, and translation of hundreds to thousands of RNA targets, thereby making these proteins essential for organismal development. RBPs bind to their targets by recognizing both the RNA sequence and secondary structure, which is the interaction between complementary RNA sequences within a single molecule. These interactions can be regulated by changing the chemical ...


Pre-Clinical Development Of Aav Mediated Gene Therapy For Familial Lecithin Cholesterol Acyltransferase Deficiency, Devin Mae Christopher Jan 2017

Pre-Clinical Development Of Aav Mediated Gene Therapy For Familial Lecithin Cholesterol Acyltransferase Deficiency, Devin Mae Christopher

Publicly Accessible Penn Dissertations

Familial lecithin cholesterol acyltransferase (LCAT) deficiency (FLD), is a rare monogenic disease, characterized by abnormal lipid profile, corneal opacities, anemia and renal disease which progresses to renal failure. There is currently no approved treatment for patients with this disease. FLD is a good candidate for AAV mediated gene therapy but this therapeutic avenue has not been pursued until now. Here, we completed dose response studies in LCAT KO and LCAT KO/ human ApoA-I transgenic mice using AAV8 expressing human LCAT. AAV8-TBG-hLCAT induces significant increases in plasma % cholesterol esterified at a dose as low as 3e9 GC per mouse, which is ...


The Cellular And Molecular Underpinnings Of Intestinal Epithelial Regeneration, Maryam Yousefi Jan 2017

The Cellular And Molecular Underpinnings Of Intestinal Epithelial Regeneration, Maryam Yousefi

Publicly Accessible Penn Dissertations

Injury to the intestinal epithelium is a hallmark of numerous common clinical disorders, including radiation enteropathy, ischemia-reperfusion, and inflammatory bowel diseases. Disruption of the epithelial barrier in these conditions must be quickly restored to avoid dehydration and translocation of gut microbiota to the bloodstream. Short-term calorie restriction can enhance regenerative response of the intestinal epithelium following DNA damaging injury. However, the specific cell type responsible for this enhanced regenerative capacity and as a result the molecular determinants of this process remain unknown.

Regeneration of the intestinal epithelium is driven by multiple intestinal stem cell (ISC) types, including an active, radiosensitive ...


Shedding Light On General Anesthesia: Uncovering The Molecular Mechanisms For Propofol And Volatile Anesthetics, Kellie Ann Woll Jan 2017

Shedding Light On General Anesthesia: Uncovering The Molecular Mechanisms For Propofol And Volatile Anesthetics, Kellie Ann Woll

Publicly Accessible Penn Dissertations

General anesthetics have played a pivotal role in the history of medicine. Despite accounts of their use within the earliest of human records, our understanding of anesthetic mechanisms remains unclear. Understanding these molecular mechanisms would be a significant advance toward enhanced drug design and optimal the clinical use of these potentially hazardous agents. Recent advances in chemical and molecular biology, including photoaffinity labeling, have allowed enhanced appreciation of the complex interactions anesthetic’s have with their macromolecular substrates. This work is dedicated to further define the protein interactions of the frequently administered volatile anesthetics sevoflurane and isoflurane, as well as ...


Intrathecal Aav9.Trastuzumab Tumor Prophylaxis And Treatment In A Murine Xenograft Model Of Her2+ Breast Cancer Brain Metastases, William Thomas Rothwell Jan 2017

Intrathecal Aav9.Trastuzumab Tumor Prophylaxis And Treatment In A Murine Xenograft Model Of Her2+ Breast Cancer Brain Metastases, William Thomas Rothwell

Publicly Accessible Penn Dissertations

Breast cancer brain metastases (BCBM) are a deadly sequela of breast tumors that overexpress human epidermal growth factor receptor 2 (HER2). HER2+ BCBM affects approximately 17,000 women in the US every year. Median survival is 10-13 months from the time of diagnosis of central nervous system (CNS) disease. Current therapeutic interventions are invasive, toxic, and largely ineffective, leaving a clear, unmet need for targeted HER2+ BCBM treatments. Trastuzumab(Herceptin®) is a monoclonal antibody used to treat HER2+ breast cancer successfully, but systemic trastuzumab cannot bypass the blood-brain barrier (BBB). To solve this problem, we have developed an adeno-associated virus ...


Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology, Matthew Joseph Emmett Jan 2017

Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology, Matthew Joseph Emmett

Publicly Accessible Penn Dissertations

Brown adipose tissue (BAT) is a thermogenic organ, which helps to protect body temperature against cold and can counteract metabolic disease. Numerous pathways modulate the activity of BAT in a highly regulated and coordinated manner to exert tight control over its immense calorie burning capacity. However, less is known regarding the transcriptional and epigenomic mechanisms controlling the thermogenic gene program of brown adipocytes. Here, we show that histone deacetylase 3 (HDAC3) is required for the activation of BAT enhancers to ensure thermogenic aptitude, thus enabling survival of dangerously cold environmental temperature. Loss of HDAC3 leads to deficient expression of uncoupling ...


Defining Sites Of Replication Fork Collapse Caused By Atr Inhibition, Nishita Kalpendu Shastri Jan 2017

Defining Sites Of Replication Fork Collapse Caused By Atr Inhibition, Nishita Kalpendu Shastri

Publicly Accessible Penn Dissertations

DEFINING SITES OF REPLICATION FORK COLLAPSE CAUSED BY ATR INHIBITION

Nishita K. Shastri

Eric J. Brown

Replication stress, characterized by stalling of DNA replication and the accumulation of abnormal replication intermediates, has been linked to the genomic instability observed in cancer. Previous studies have defined specific genomic sequences that are difficult to replicate to be more vulnerable to replication-associated breaks and rearrangements. However, many of these sequences have been identified through indirect and potentially biased approaches. To identify DNA sequences that contribute to replication-associated genomic instability, I will describe genome-wide screens I have performed to determine the location, sequence, and ...


Biochemical And Functional Studies Of Histone Deacetylase 3 In Metabolic Tissues, Jarrett Renn Remsberg Jan 2017

Biochemical And Functional Studies Of Histone Deacetylase 3 In Metabolic Tissues, Jarrett Renn Remsberg

Publicly Accessible Penn Dissertations

Organismal physiology is built upon the foundation of molecular processes. A central axis to maintaining homeostasis in vivo is at the level of gene regulation. Tissue specific gene expression is created at the level of epigenetics, where proteins guided by tissue specific DNA binding proteins create a chromatin landscape for precise gene programs. Understanding these molecular processes is of vital importance to understand the underpinning pathologies, such as metabolic syndrome, which are a growing medical concern and require greater research efforts in order to tackle its challenges. A major epigenetic regulator is histone deacetylase 3 (HDAC3), which is a core ...