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Articles 1 - 13 of 13

Full-Text Articles in Molecular Biology

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 ...


Centromere Identity And The Nature Of The Cenp-A-Containing Nucleosome, Samantha Jane Falk Jan 2016

Centromere Identity And The Nature Of The Cenp-A-Containing Nucleosome, Samantha Jane Falk

Publicly Accessible Penn Dissertations

The centromere is an essential chromosomal locus that serves as the site of kinetochore formation, ensuring accurate chromosome segregation during mitosis and meiosis. While most centromeres form on repetitive DNA, the underlying DNA sequence is neither necessary nor sufficient to support centromere function, suggesting that this locus is epigenetically defined. The histone H3 variant centromere protein A (CENP-A) replaces H3 in nucleosomes at the centromere and is the best candidate to provide this epigenetic mark. This thesis aims to understand the features of the CENP-A nucleosome that impart its ability to mark and stabilize functional centromeres. In the first part ...


The Regulation Of Psf Activity In T Cells By Trap150 And Gsk3, Christopher Yarosh Jan 2016

The Regulation Of Psf Activity In T Cells By Trap150 And Gsk3, Christopher Yarosh

Publicly Accessible Penn Dissertations

PSF is a ubiquitously expressed and essential nuclear protein that influences many aspects of the genome maintenance and gene expression pathways. Although previous studies have identified numerous protein cofactors and nucleic acid targets of PSF, insufficient work has been done to understand how it is regulated to accomplish its various functions in a coordinated manner. Previous research in the Lynch laboratory demonstrated that, in T cells, PSF is a downstream target of the serine/threonine kinase GSK3. Phosphorylation of PSF T687 by GSK3 promotes interaction of PSF with another multifunctional nuclear factor, TRAP150. This interaction prevents PSF from binding RNA ...


Deciphering The Tetrad Of Epigenetic Cytosine Modifications, Monica Yun Liu Jan 2016

Deciphering The Tetrad Of Epigenetic Cytosine Modifications, Monica Yun Liu

Publicly Accessible Penn Dissertations

A tetrad of epigenetic cytosine modifications imbues the DNA code with complex, dynamic meaning. DNA methyltransferase enzymes deposit methyl marks on the 5-carbon of cytosine, forming 5-methylcytosine (mC), which generally mediates long-term, locus-specific transcriptional repression during development and reprogramming. Ten-eleven translocation (TET) family enzymes oxidize the methyl group in three steps, forming predominantly 5-hydroxymethylcytosine (hmC) but also low levels of 5-formylcytosine (fC) and 5-carboxylcytosine (caC). These additional bases likely provide pathways for erasing methylation, but they may also harbor epigenetic functions in their own right. Questions regarding how each base forms and functions drive at the fundamental biology of the ...


Mechanisms Of Non-Canonical Nf-Kappab Regulation, Carolyn Margaret Gray Jan 2014

Mechanisms Of Non-Canonical Nf-Kappab Regulation, Carolyn Margaret Gray

Publicly Accessible Penn Dissertations

NF-kappaB is activated through two signaling cascades: the classical and non-canonical pathways, which are distinguished based on the Inhibitor of kappaB Kinase (IKK) components required to activate each pathway. Whereas classical NF-kappaB requires NF-kappaB Essential Modulator (NEMO) and IKKbeta, non-canonical NF-kappaB requires IKKalpha and upstream stabilization of NF-kappaB Inducing Kinase (NIK), but not NEMO. However, we have previously shown that IKKalpha contains a functional NEMO binding domain and associates with NEMO and IKKbeta as part of the heterotrimeric IKK complex. The overarching goal of the work described in this thesis was to determine whether the interaction between NEMO and IKKalpha ...


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 ...


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 ...


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 ...


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 ...


Phoq: Structural And Mechanistic Investigations Into An Important Bacterial Sensor Kinase, Graham David Clinthorne Jan 2012

Phoq: Structural And Mechanistic Investigations Into An Important Bacterial Sensor Kinase, Graham David Clinthorne

Publicly Accessible Penn Dissertations

Two-component systems represent the dominant mechanism for cellular signal transduction in prokaryotes. One particular system, PhoQ, has been the focus of our interest because it is the switch that controls virulence in Salmonella and other pathogenic gram negative bacteria. Certain domains of PhoQ and other two-component systems have been studied extensively and this research has yielded several structures with atomic level resolution. However, no complete structure or experimentally-based model has been forthcoming and the precise mechanism by which these diverse systems transmit signals from the exterior of the cell to the interior has remained elusive. We have undertaken a study ...


The Role Of Fibrin Clot Properties And Fibrinogen Nitration In The Pathology Of Venous Thromboembolism., Marissa Rose Martinez Jan 2012

The Role Of Fibrin Clot Properties And Fibrinogen Nitration In The Pathology Of Venous Thromboembolism., Marissa Rose Martinez

Publicly Accessible Penn Dissertations

Deep vein thrombosis (DVT) and pulmonary embolism (PE) together comprise the disease state of venous thromboembolism (VTE). Thrombi in the veins of the lower extremities (DVT) can embolize, resulting in complete or partial occlusion of circulation through the pulmonary vasculature (PE). Despite a common etiology between DVT and PE, the cause of embolization remains mostly unknown. Research indicates that fibrin clot structure and functional properties are altered in VTE compared to healthy controls. Whether these properties differ between DVT and PE subjects remains to be determined, and may underscore possible mechanisms of embolization. Inflammation and oxidant production are involved in ...


Lysine Post-Translational Modifications Of Saccharomyces Cerevisiae Chromatin Proteins, Christopher Richard Edwards Jan 2012

Lysine Post-Translational Modifications Of Saccharomyces Cerevisiae Chromatin Proteins, Christopher Richard Edwards

Publicly Accessible Penn Dissertations

DNA exists within the cell as part of a complex structure called chromatin which is comprised of many proteins, including histones, and participates in and influences every DNA-related process. Chromatin's proteins are modified post-translationally and this impacts their functions and in turn, the DNA processes in which they participate. However, the repertoire of post-translational modifications (PTMs), the enzymes that create and remove them, and their roles in chromosome biology are not fully understood. We have used the budding yeast Saccharomyces cerevisiae to investigate chromatin PTMs, specifically lysine modifications, through three avenues: the enzymes that regulate lysine PTMs, the histone ...


Investigating Trna Release From The Bacterial Ribosome, Ian S. Farrell Aug 2011

Investigating Trna Release From The Bacterial Ribosome, Ian S. Farrell

Publicly Accessible Penn Dissertations

Translation of mRNA into proteins is integral in all living organisms, and takes place on the ribosome. In recent years, the X-ray crystal structures of biologically relevant ribosome complexes came into light, and the advance of kinetic studies was soon to follow, leading to a better understanding of the general ribosomal mechanism. However, there still remains some ambiguity in certain ribosome functions.

Ribosomal protein L1 initially became relevant in the early 1980s when it was determined that ribosomes lacking L1 showed a decreased capacity for in vitro protein synthesis. Later, it was shown that the L1-stalk is a highly mobile ...