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 96

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

The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang Aug 2018

The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA and protein interact with each other in the cell nucleus to form RNP (ribonucleoprotein) complexes. These RNPs play key roles in various steps of gene expression. This thesis focuses on two nuclear RNA-binding proteins: Fused in Sarcoma (FUS) and Polycomb Repressive Complex 2 (PRC2).

The normal functions of FUS are not fully understood, but RNA binding has been suggested to be crucial for FUS function and many RNA targets have been identified. Yet the features of RNAs necessary for FUS binding had not been systematically characterized. FUS bound all five published RNA motifs and other RNAs tightly, including fragments ...


Multimodal Recognition Of Diverse Peptides By The Sh2 Domains Of Plcγ1 And Sh2b1, Marissa A. Mckercher Feb 2018

Multimodal Recognition Of Diverse Peptides By The Sh2 Domains Of Plcγ1 And Sh2b1, Marissa A. Mckercher

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

SH2 domains recognize phosphotyrosine (pY)-containing peptide ligands and regulate a wide array of signaling events within receptor tyrosine kinase pathways. SH2 domains have individualized specificity for peptides, encoded in the amino acids neighboring the pY of the ligand. In contrast to this simple view of signaling specificity, high-throughput array studies have identified several SH2 domains capable of recognizing peptides containing chemically distinct amino acids at the positions neighboring the pY. For example, the C-terminal SH2 domain (PLCC) of phospholipase C-γ1 (PLCγ1) typically binds peptides containing small and hydrophobic amino acids adjacent to the pY, but can also recognize unexpected ...


Development And Characterization Of Improved Red Fluorescent Protein Variants, Premashis Manna Jan 2018

Development And Characterization Of Improved Red Fluorescent Protein Variants, Premashis Manna

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Aequorea victoria-based green fluorescent proteins and their blue, cyan and red counterparts offer unprecedented advantage as biological markers owing to their genetic encodability and straightforward expression in different organisms. Fluorescent proteins are characterized with complex photo-kinetics due to the presence of light-induced non-fluorescent or dark states which are responsible for their fluorescence intermittency or 'blinking'. We developed time- and frequency-domain techniques for probing the kinetics involving dark state conversion (DSC) and ground state recovery (GSR) in red fluorescent proteins (RFPs). Ensemble-level DSC and GSR kinetics in FPs were presented in the context of their single molecule fluorescence behaviors. Although ...


High Precision Afm-Based Smfs Of Mechanically Labile Type Iii Secretion System Effectors, Marc-Andre Leblanc Jan 2018

High Precision Afm-Based Smfs Of Mechanically Labile Type Iii Secretion System Effectors, Marc-Andre Leblanc

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Pathogenic bacteria have developed a wide range of tools for circumventing or overcoming the host’s defenses. Over time, these tools have become increasingly complex, allowing bacteria to live and thrive within a wide variety of host environments. One such tool is the Type III Secretion System (T3SS), a needle-like complex that allows bacteria to directly inject proteins, known as effectors, from their cytoplasm into host cells. Once inside host cells, effector proteins have a wide range of effects, from shutting down the host immune response to rearranging the host cytoskeleton to accommodate invading bacteria.

Because the T3SS needle presents ...


Design And Synthesis Of Potential Tlr7 And Tlr8 Inhibitors, Patrick Nordeen Jan 2018

Design And Synthesis Of Potential Tlr7 And Tlr8 Inhibitors, Patrick Nordeen

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Toll-like receptors (TLRs) detect invading viral and bacterial pathogens and play a critical role in the initiation and regulation of the innate immune system. Over-active TLR signaling has been indicated in the disease pathology of numerous crippling inflammatory autoimmune disorders and inhibition of these receptors is of considerable interest for therapeutic intervention. TLR7 and TLR8 are the two TLRs that share the most similarity in both sequence and structure. Despite their similarity, selective inhibition represents a promising therapy for diseases such as systemic lupus erythematosus (lupus) and rheumatoid arthritis (RA). The goal of this master’s thesis is to identify ...


The Role Of Dynamics Within Bama, The Central Component Of The Bam Complex, Pamela Arden Doerner Barbour Jan 2018

The Role Of Dynamics Within Bama, The Central Component Of The Bam Complex, Pamela Arden Doerner Barbour

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

BamA is an essential component of the β-­‐barrel assembly machine that folds and inserts outer membrane proteins (OMPs) into the outer membrane of Gram-­‐negative bacteria. BamA is an OMP itself comprised of two domains, a soluble periplasmic N-­‐terminal domain consisting of five polypeptide transport associated (POTRA) repeats and a C-­‐terminal 16-­‐stranded β-­‐barrel domain. The mechanism of BamA is poorly understood but structural data suggests BamA is a dynamic protein with respect to the POTRA domains and barrel. The POTRA domains, numbered 1-5 from the N- to C- termini, can be divided into two sub-domains ...


Investigations Into Higher Order Assemblies Of Rna And Protein In Health And Disease, Joshua Riley Wheeler Jan 2018

Investigations Into Higher Order Assemblies Of Rna And Protein In Health And Disease, Joshua Riley Wheeler

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA and proteins (RNPs) can form highly ordered aggregates in living organisms with functional or toxic properties. Clumps of toxic, cytoplasmic RNP aggregates are steeped in an association with neuronal (e.g. amyotrophic lateral sclerosis) and skeletal muscle (e.g. inclusion body myositis) degenerative diseases. The role of these aggregates in disease pathology is unknown; however, these aggregates may arise from molecularly similar RNP aggregates, called stress granules, which form naturally in all cells. Stress granules are conserved higher order RNP assemblies that form during physiologic stress when RNA translation is decreased. Clarifying the properties of higher order RNP assemblies ...


Discrimination Of Ssrna By Pot1 And Identification Of A Novel Cype Aptamer Through An Optimized Rna Selex Protocol, Neil Ryan Lloyd Jan 2018

Discrimination Of Ssrna By Pot1 And Identification Of A Novel Cype Aptamer Through An Optimized Rna Selex Protocol, Neil Ryan Lloyd

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Protein-ligand specificity forms the fundamental basis for many biological mechanisms with properly tuned binding being required for most biological processes. Aberrant interactions can result in consequences ranging from wasted cellular resources to disease pathologies and death. As such, characterizing interaction specificities is a critical step in understanding biological systems. In this thesis I have characterized the RNA-binding properties of the telomere protection protein Pot1, developed an optimized SELEX protocol to characterize RNA-binding by newly identified RNA-binding proteins, and expanded on the RNA-binding specificity of one of those proteins, the epigenetic regulator CypE.

High fidelity binding to ssDNA, but not ssRNA ...


Rna-Rna Interactions In Rnp Granule Assembly, Briana Nicole Van Treeck Jan 2018

Rna-Rna Interactions In Rnp Granule Assembly, Briana Nicole Van Treeck

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Ribonucleoprotein (RNP) granules, which are composed of numerous RNAs and proteins, are ubiquitous features of eukaryotic cells. This thesis investigates the assembly mechanisms of P-bodies and stress granules, two cytoplasmic granules that rely on RNAs unengaged in translation to form. Previous studies in the field have focused on the roles of proteins, and specifically their intrinsically disordered regions (IDRs), in targeting components and driving granule assembly. However, domain analysis of four proteins illustrates that having an IDR is neither sufficient nor necessary for targeting to P-bodies. Although IDRs have been shown to be important in some contexts, these results suggest ...


Composition And Dynamics Of Stress Granules, Tyler Matheny Jan 2018

Composition And Dynamics Of Stress Granules, Tyler Matheny

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Stress granules are non-membranous assemblies of RNA and protein that form during conditions in which translation initiation is limited. Stress granules are of interest due to their potential role in the regulation of gene expression and their relation to other cytoplasmic RNP granules, such as p-bodies, germ granules, and neuronal granules. Additionally, stress granules are related to pathological aggregates observed in neurodegenerative diseases since (1) they share many protein components with these aggregates and (2) mutations that promote stress granule assembly or inhibit their clearance are causative in neurodegenerative disease.

The goals of this thesis are (1) to understand the ...


Remodeling Of Zinc Homeostasis In Differentiated Mammary Epithelial Cells, Yu Han Jan 2018

Remodeling Of Zinc Homeostasis In Differentiated Mammary Epithelial Cells, Yu Han

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Zinc is the second most abundant transition metal in mammals and an essential nutrient required for growth. Coupled with the biological significance of zinc, zinc homeostasis needs to be tightly controlled because too little zinc leads to zinc deficiency and too much zinc is toxic. Unfortunately, most of our understanding of zinc homeostasis regulation to date was obtained using non-physiological manipulation via external supplementation or depletion of zinc, which can cause non-specific side effects. A systematic study of zinc homeostasis regulation under physiological condition is needed for a better understanding of how mammalian cells balance zinc distribution to fulfill biological ...


Synthesis And Biochemical Evaluation Of Aminoboranephosphonate Phosphoramidimidate And Phosphoramidate Dna, Ayman Ghalib Alawneh Jan 2018

Synthesis And Biochemical Evaluation Of Aminoboranephosphonate Phosphoramidimidate And Phosphoramidate Dna, Ayman Ghalib Alawneh

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Antisense oligonucleotides are synthetic DNAs that bind to RNA and alter or reduce the biological activity of the target RNA. Studies performed in recent years have demonstrated that an antisense strategy can be utilized to address various issues in fundamental biomedical research and have additionally shown that this approach can be used to create novel therapeutic drugs. For example, IONIS Pharmaceuticals has so far commercialized three drugs using antisense oligonucleotides. These drugs target spinal muscular atrophy, homozygous familial hypercholesterolemia, and pouchitis. Antisense oligonucleotides targeting several other diseases are in various stages of clinical study at IONIS and elsewhere.

My research ...


Synthesis Of The Key Fragments Of Micrococcin P1 And Thiocillin I, Aaron Bret Hinds Jan 2018

Synthesis Of The Key Fragments Of Micrococcin P1 And Thiocillin I, Aaron Bret Hinds

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Thiopeptide antibiotics are members of the ribosomally synthesized and post-translationally modified peptide class of natural products. They contain a unique trisubstituted six-membered nitrogen ring decorated with azol(in)e heterocycles, dehydroamino acids, and a macrocyclic structure. Thiopeptides act by inhibiting the bacterial ribosome and have demonstrated potent activities against a wide range of Gram-positive pathogens.

This work describes the synthesis of the two key fragments used in our total syntheses of micrococcin P1 and thiocillin I. The “bottom” fragments were assembled through modification and coupling of amino acids as well as the use of a molybdenum catalyzed cyclodehydration of cysteine ...


Characterization Of Chemical Probes For Therapeutic Intervention Of Innate Immune Signaling, Christina Elizabeth Boville Jan 2017

Characterization Of Chemical Probes For Therapeutic Intervention Of Innate Immune Signaling, Christina Elizabeth Boville

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The innate immune system protects us from incessant attacks by microorganisms. However, immunity is a double-edged sword, and inflammation must be carefully regulated. Chemical biology offers a means to maintain healthy homeostasis by influencing the immune response. We have used small molecule and peptide chemistries to exploit Toll-like receptor, caspase, and antimicrobial peptide signaling for therapeutic purposes. These compounds may find applications treating sepsis and autoimmune disease, and can influence the design of next-generation antibiotics and vaccines.

Toll-like receptors are pattern recognition receptors that sense bacteria and viruses, and then induce inflammation to stave off infection. We have designed saccharin-derived ...


Live Cell Methods To Visualize Translocated Salmonella Effectors And Monitor Ca2+ Transients During Infection, Alexandra Marie Young Jan 2017

Live Cell Methods To Visualize Translocated Salmonella Effectors And Monitor Ca2+ Transients During Infection, Alexandra Marie Young

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Salmonella species invade and survive within eukaryotic host cells by using a Type Three Secretion System (T3SS) to translocate bacterial effector proteins into the host cell and commandeer host-cell signaling processes, including Ca2+ regulation. T3SS effector activity is tightly regulated, in part by their different spatial distribution within the host cell, to coordinate each stage of the infection process. To date, more than 40 T3SS effector proteins have been identified, but their biochemical functions and role in the infection process are often poorly understood. Complexity of effector regulation coupled with growing evidence for cell-to-cell heterogeneity of infection underscores the ...


Biophysical Characterization Of Map Kinase Activation And Regulation, Jennifer C. Liddle Jan 2017

Biophysical Characterization Of Map Kinase Activation And Regulation, Jennifer C. Liddle

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The mitogen-activated protein kinase signaling pathways play a central role in the majority of cellular behaviors. The RAF/MKK/ERK pathway in particular is responsible for cellular proliferation and differentiation, and mutations that divorce downstream signaling from upstream regulation not only underlie the majority of melanoma cases, but play a significant role in a wide variety of other cancers as well. However, many questions about ERK still remain open in the field, including the differences between its two isoforms in humans, the precise nature of the activated state and the enzyme’s potential for autoactivation, and the effects of newly-developed ...


Novel Insights Into Tace Regulation Of Autocrine And Paracrine Signaling In Epithelial Cells, Eric Newman Bunker Jan 2017

Novel Insights Into Tace Regulation Of Autocrine And Paracrine Signaling In Epithelial Cells, Eric Newman Bunker

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

A multitude of cellular functions are controlled by the activity of the membrane-bound

protease TACE, including immune response and development. Through cleavage of its

membrane anchored substrates, TACE can activate a myriad of signaling pathways in

an auto- or paracrine manner, transferring signals across a tissues and systems.

Despite its importance, it is highly debated how TACE is regulated. I helped generate

TSen, a fluorescence-based sensor of TACE activity, a critical tool that proved

necessary to interrogate the underlying signaling that leads to TACE activation. TSen

enabled us to uncover a wide variation between cell lines and their underlying signaling ...


The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang Jan 2017

The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA and protein interact with each other in the cell nucleus to form RNP (ribonucleoprotein) complexes. These RNPs play key roles in various steps of gene expression. This thesis focuses on two nuclear RNA-binding proteins: Fused in Sarcoma (FUS) and Polycomb Repressive Complex 2 (PRC2).

The normal functions of FUS are not fully understood, but RNA binding has been suggested to be crucial for FUS function and many RNA targets have been identified. Yet the features of RNAs necessary for FUS binding had not been systematically characterized. FUS bound all five published RNA motifs and other RNAs tightly, including fragments ...


Toward A Mechanistic Understanding Of Outer Membrane Protein Biogenesis, Alex Hunt Hopkins Jan 2017

Toward A Mechanistic Understanding Of Outer Membrane Protein Biogenesis, Alex Hunt Hopkins

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The outer membranes of Gram-negative bacteria are essential to their survival and have a unique asymmetric structure that features an outer leaflet of lipopolysaccharide. Bacterial outer membranes are populated by integral membrane proteins with amphipathic transmembrane β-barrel domains called outer membrane proteins (OMPs). OMPs are translated in the cytoplasm and translocated across the inner membrane and periplasm before being inserted into the outer membrane. The β-barrel Assembly Machine (BAM), a hetero-pentameric protein complex at the outer membrane, recognizes, folds, and releases OMPs into the membrane. However, the functional contributions of individual BAM subunits, the architecture of the BAM, and the ...


Engineering And Evaluating Fluorescent Tools For Endoplasmic Reticulum Zinc, Kyle Pierce Carter Jan 2017

Engineering And Evaluating Fluorescent Tools For Endoplasmic Reticulum Zinc, Kyle Pierce Carter

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Zinc (Zn2+) is an essential micronutrient for human health. However, excess Zn2+ is toxic and Zn2+ deficiency can be fatal, so the concentration of this ion must be carefully controlled within cells. Highlighting the importance of Zn2+ is the observation that approximately 10 % of the genes in the human genome potentially code for a Zn2+-binding protein. The Palmer lab has developed a suite of genetically-encoded biosensors for Zn2+ that use Förster Resonance Energy Transfer (FRET) to provide a readout of Zn2+ concentration within human cells. Measurements with these sensors have revealed heterogeneous ...


Multimodal Recognition Of Diverse Peptides By The Sh2 Domains Of Plcγ1 And Sh2b1, Marissa A. Mckercher Jan 2017

Multimodal Recognition Of Diverse Peptides By The Sh2 Domains Of Plcγ1 And Sh2b1, Marissa A. Mckercher

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

SH2 domains recognize phosphotyrosine (pY)-containing peptide ligands and regulate a wide array of signaling events within receptor tyrosine kinase pathways. SH2 domains have individualized specificity for peptides, encoded in the amino acids neighboring the pY of the ligand. In contrast to this simple view of signaling specificity, high-throughput array studies have identified several SH2 domains capable of recognizing peptides containing chemically distinct amino acids at the positions neighboring the pY. For example, the C-terminal SH2 domain (PLCC) of phospholipase C-γ1 (PLCγ1) typically binds peptides containing small and hydrophobic amino acids adjacent to the pY, but can also recognize unexpected ...


Structure Determination Of Vascular Endothelial Growth Factor Heparin-Binding Domain In Complex With A Dna Aptamer, Sabrina Robin Hunt Jan 2017

Structure Determination Of Vascular Endothelial Growth Factor Heparin-Binding Domain In Complex With A Dna Aptamer, Sabrina Robin Hunt

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Vascular endothelial growth factor is a cytokine that is required for the maintenance of healthy vasculature, and it is responsible for a variety of pathogenic conditions, such as age-related macular degeneration and tumor growth in numerous cancers. As an important therapeutic target, vascular endothelial growth factor has been the focus of many in vitro selection strategies to identify aptamers that bind the protein with high affinity and specificity. One of these is a 25-nucleotide DNA aptamer that targets the heparin-binding domain (HBD) of vascular endothelial growth factor. The work presented here focuses on determining the solution structure of the HBD-aptamer ...


Discovery And Characterization Of An Anti-Inflammatory Lipid Derived From Mycobacterium Vaccae, David Gregory Smith Jan 2017

Discovery And Characterization Of An Anti-Inflammatory Lipid Derived From Mycobacterium Vaccae, David Gregory Smith

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

In modern urban environments there is an increased prevalence of allergies, asthma, inflammatory bowel diseases (IBD), and anxiety disorders. The underlying cause for these disorders, as postulated by the Hygiene Hypothesis, is chronic inflammation, and the imbalance in the immune system is caused by a lack of interaction with microbes that have been removed from the urban space and lifestyle. One such microbe is the environmental saprophyte, Mycobacterium vaccae. In animal models, immunization with M. vaccae protects against the development of these prevalent inflammatory disorders. This immunoregulatory effect has been shown to occur due to the expansion of regulatory ...


Automated Analysis Pipeline For Inferring Phenotypic Changes In Cell Granules, Van Tra Jan 2017

Automated Analysis Pipeline For Inferring Phenotypic Changes In Cell Granules, Van Tra

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

In Saccharomyces cerevisiae, P-bodies play critical roles in the control of gene expression in localized cellular domains. Many P-bodies components contain intrinsically disordered regions (IDR). This thesis explores the hypothesis that the IDR of one P-body component Dhh1 plays a role in P-body assembly. To answer this question, an automated analysis pipeline was created to compare changes in the phenotypes of P-bodies in the full length Dhh1 protein and the Dhh1 protein without the IDR (d_IDR). I found that the IDR of Dhh1, though not necessary for Dhh1 recruitment to P-bodies, increases the number of P-bodies in each cell and ...


Interplay Between The Helicase-Primase And The Dna Polymerase-Processivity Factor During Herpes Dna Replication, Sarah Michelle Dickerson Jan 2017

Interplay Between The Helicase-Primase And The Dna Polymerase-Processivity Factor During Herpes Dna Replication, Sarah Michelle Dickerson

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

There are seven proteins essential for Herpes Simplex Virus Type 1 (HSV-1) DNA replication. While some of their roles are known, many of their mechanisms remain unclear. Understanding the mechanism by which herpes replicates its viral genome may provide insight into targeting critical pathways to more effectively treat infection.

This work identifies new roles and mechanisms of the essential enzymes at the herpes replication fork: the helicase-primase (UL5-UL8-UL52) and polymerase-processivity factor (UL30-UL42). I determined that as with other helicases, herpes helicase-primase displays varied ability to displace different bound proteins. Though the polymerase-processivity factor enhances helicase activity considerably, bound proteins still ...


Contributions Of Intrinsically Disordered Regions Of Proteins To The Assembly Of Ribonucleoprotein Granules, David Stephen Warren Protter Jan 2017

Contributions Of Intrinsically Disordered Regions Of Proteins To The Assembly Of Ribonucleoprotein Granules, David Stephen Warren Protter

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Cells assemble large, non-membrane bound granules of protein and RNA, termed Ri- bonucleoprotein granules (RNP granules), often in response to a wide variety of cellular stresses. This behavior is conserved from yeast to mammals. Some RNP granules ap- pear important in the stress response, while others are important for proper organismal development, and still others for control of RNA degradation and transport. Curiously, proteins found within granules are disproportionately likey to contain Intrinsically Dis- ordered Regions. Here, I show that those disordered regions can often drive higher order assembly in vitro and contribute to granule assembly in vivo. I found ...


Chemical Biology Of Protein O-Glycosylation, Patrick Chaffey Jan 2016

Chemical Biology Of Protein O-Glycosylation, Patrick Chaffey

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Protein glycosylation, the covalent attachment of carbohydrates to amino acid side chains of proteins, is a ubiquitous post-translational modification across all branches of life. Due to many factors including the vast structural complexity of glycans and the convoluted processes regulating their construction, protein glycosylation is a significantly understudied phenomenon. In particular, the study of protein O-glycosylation, where the carbohydrate moieties are attached via the oxygen of a serine or threonine residue, is lacking because there exists no well-defined consensus sequence for its occurrence and the enzymatic construction of O-glycosylated proteins in a controlled manner is very difficult. We ...


Structural And Mechanistic Aspects Of Ligand Selectivity And Gene Regulation By Cobalamin Riboswitches, Jacob Tyler Polaski Jan 2016

Structural And Mechanistic Aspects Of Ligand Selectivity And Gene Regulation By Cobalamin Riboswitches, Jacob Tyler Polaski

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA-based genetic regulatory mechanisms in bacteria are critical for maintaining normal cellular homeostasis and response to a broad spectrum of environmental and intracellular signals. Riboswitches are structured elements typically found in the 5' leader regions of mRNAs that often control the expression of genes involved in the transport or biosynthesis of small-molecule metabolites. These regulatory elements are comprised of two domains, a highly conserved receptor (aptamer domain) that directly binds a small-molecule and a regulatory domain (expression platform) that controls the gene expression machinery.

Atomic level structures of riboswitch receptor domains bound to their effector have revealed how mRNAs recognize ...


Noncoding Mrp Rna Function Investigated By Genetic Manipulation And Biochemical Analysis, Katherine Coperine Goldfarb Jan 2016

Noncoding Mrp Rna Function Investigated By Genetic Manipulation And Biochemical Analysis, Katherine Coperine Goldfarb

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia. MRP RNA folds into a structure similar to that of RNase P RNA and assembles with at least seven human proteins, all of which also assemble with RNase P. The thesis presents detailed investigations into the 3’ terminal profile of human MRP RNA and establishes its specific role in human pre-ribosomal RNA processing.

Post-transcriptional 3’ end processing is a key component of RNA ...


Dose-Dependent Inhibition Of Histone Deacetylases Reprograms Gene Expression Through Global Remodeling Of The Enhancer Landscape, Gilson John Sanchez Jan 2016

Dose-Dependent Inhibition Of Histone Deacetylases Reprograms Gene Expression Through Global Remodeling Of The Enhancer Landscape, Gilson John Sanchez

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Histone deacetylases (HDACs) regulate gene expression through deacetylation of histones and non-histone proteins. Histone deacetylase inhibitors (HDACIs) are known to alter gene expression by both up- and down-regulation of protein coding genes in normal and cancer cells. However, the mechanisms that are responsible for activation and repression of gene expression remain obscure. To understand the underlying mode of action of HDACIs, I used genome wide chromatin immunoprecipitation sequencing (CHIP-seq) to determine dose-dependent changes in histone acetylation and methylation marks in HCT116 cells treated with increasing concentrations of the natural product largazole, a class I and class IIb selective HDAC inhibitor ...