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

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese May 2019

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

MSU Graduate Theses

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered ...


Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk Jan 2019

Student Understanding Of Dna Structure–Function Relationships Improves From Using 3d Learning Modules With Dynamic 3d Printed Models, Michelle E. Howell, Christine S. Booth, Sharmin M. Sikich, Tomáš Helikar, Rebecca Roston, Brain A. Couch, Karin Van Dijk

Biochemistry -- Faculty Publications

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure–function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure–function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA ...


Estimating The Age Of A Bloodstain Using Droplet Digital Pcr, Kalee Rae Crampton Jan 2019

Estimating The Age Of A Bloodstain Using Droplet Digital Pcr, Kalee Rae Crampton

Graduate Theses, Dissertations, and Problem Reports

Biological evidence is extremely valuable in the investigation of a crime due to the presence of DNA. DNA evidence is considered the gold standard in court cases due to its ability to link a suspect to a piece of evidence. In addition to DNA evidence, biological stains have the potential to provide a temporal link between an individual and a crime scene. Previous studies have shown that relative rates of RNA degradation can be used in order to estimate the age of bloodstains. Here, we examined the ability of droplet digital PCR to be used in place of quantitative PCR ...


Synergistic Assembly Of Human Pre-Spliceosomes Across Introns And Exons, Joerg E. Braun, Larry J. Friedman, Jeff Gelles, Melissa J. Moore Jun 2018

Synergistic Assembly Of Human Pre-Spliceosomes Across Introns And Exons, Joerg E. Braun, Larry J. Friedman, Jeff Gelles, Melissa J. Moore

RNA Therapeutics Institute Publications

Most human genes contain multiple introns, necessitating mechanisms to effectively define exons and ensure their proper connection by spliceosomes. Human spliceosome assembly involves both cross-intron and cross-exon interactions, but how these work together is unclear. We examined in human nuclear extracts dynamic interactions of single pre-mRNA molecules with individual fluorescently tagged spliceosomal subcomplexes to investigate how cross-intron and cross-exon processes jointly promote pre-spliceosome assembly. U1 subcomplex bound to the 5' splice site of an intron acts jointly with U1 bound to the 5' splice site of the next intron to dramatically increase the rate and efficiency by which U2 subcomplex ...


All-In-One Adeno-Associated Virus Delivery And Genome Editing By Neisseria Meningitidis Cas9 In Vivo, Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue, Erik J. Sontheimer May 2018

All-In-One Adeno-Associated Virus Delivery And Genome Editing By Neisseria Meningitidis Cas9 In Vivo, Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) has been extensively used for genome editing. Currently, three Cas9 orthologs have been adapted forin vivo genome engineering applications: SpyCas9, SauCas9 and CjeCas9. However, additional in vivo editing platforms are needed, in part to enable a greater range of sequences to be accessed via viral vectors, especially those in which Cas9 and sgRNA are combined into a single vector genome. Here, we present an additional in vivo editing platform using Neisseria ...


Small Rnas Gained During Epididymal Transit Of Sperm Are Essential For Embryonic Development In Mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, Oliver J. Rando Apr 2018

Small Rnas Gained During Epididymal Transit Of Sperm Are Essential For Embryonic Development In Mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, Oliver J. Rando

University of Massachusetts Medical School Faculty Publications

The small RNA payload of mammalian sperm undergoes dramatic remodeling during development, as several waves of microRNAs and tRNA fragments are shipped to sperm during post-testicular maturation in the epididymis. Here, we take advantage of this developmental process to probe the function of the sperm RNA payload in preimplantation development. We generated zygotes via intracytoplasmic sperm injection (ICSI) using sperm obtained from the proximal (caput) vs. distal (cauda) epididymis, then characterized development of the resulting embryos. Embryos generated using caput sperm significantly overexpress multiple regulatory factors throughout preimplantation development, and subsequently implant inefficiently and fail soon after implantation. Remarkably, microinjection ...


Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban Apr 2018

Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban

Program in Molecular Medicine Publications and Presentations

HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, these individuals have chronic inflammation associated with heightened risk of cardiovascular pathology. HIV-1 establishes proviruses in long-lived CD4+ memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Though the majority of proviruses that persist during antiviral therapy are defective for production of infectious virions, many are expressed, raising the possibility that the HIV-1 provirus or its transcripts contribute to ongoing inflammation. Here we found that the HIV-1 provirus activated innate immune ...


Heavily And Fully Modified Rnas Guide Efficient Spycas9-Mediated Genome Editing, Aamir Mir, Julia F. Alterman, Matthew R. Hassler, Alexandre J. Debacker, Edward Hudgens, Dimas Echeverria, Michael H. Brodsky, Anastasia Khvorova, Jonathan K. Watts, Erik J. Sontheimer Mar 2018

Heavily And Fully Modified Rnas Guide Efficient Spycas9-Mediated Genome Editing, Aamir Mir, Julia F. Alterman, Matthew R. Hassler, Alexandre J. Debacker, Edward Hudgens, Dimas Echeverria, Michael H. Brodsky, Anastasia Khvorova, Jonathan K. Watts, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

RNA-based drugs depend on chemical modifications to increase potency and nuclease stability, and to decrease immunogenicity in vivo. Chemical modification will likely improve the guide RNAs involved in CRISPR-Cas9-based therapeutics as well. Cas9 orthologs are RNA-guided microbial effectors that cleave DNA. No studies have yet explored chemical modification at all positions of the crRNA guide and tracrRNA cofactor. Here, we have identified several heavily-modified versions of crRNA and tracrRNA that are more potent than their unmodified counterparts. In addition, we describe fully chemically modified crRNAs and tracrRNAs (containing no 2'-OH groups) that are functional in human cells. These designs ...


Liquid Crystal Phases Of Rna Mononucleosides, Emily Hayden Jan 2018

Liquid Crystal Phases Of Rna Mononucleosides, Emily Hayden

Undergraduate Honors Theses

Deoxyribonucleic Acid (DNA) can form columnar liquid crystal phases in solutions of both short strand, base-pair oligomer solutions, and in solutions of single DNA Nucleoside Tri-Phosphates (dNTP), the molecular constituents that make up helical DNA. The spontaneous phase transition to columnar liquid crystals by the dNTPs occurs without the necessity of the sugar-phosphate backbone of helical DNA, and exhibits key structural elements of biologic nucleic acids including long-range columnar stacking of base-pairs and Watson-Crick selectivity. This spontaneous increase in structural complexity is useful when discussing liquid crystal formation as relevant to the increasingly complexity of prebiotic life.

Ribonucleic acid (RNA ...


Effect Of Variation In An Essential Folding Element On The Cobalamin Riboswitch, Marcus Urquijo Jan 2018

Effect Of Variation In An Essential Folding Element On The Cobalamin Riboswitch, Marcus Urquijo

Undergraduate Honors Theses

Riboswitches are RNA-based genetic regulatory elements that control gene expression without the need for protein cofactors. These RNA motifs are found within the 5’ untranslated regions of mRNA and promote genetic regulation by altering the structure of RNA through binding small molecule effector ligands that cause conformational changes that repress or activate translation/transcription. The env8 cobalamin riboswitch binds cyanocobalamin (CNCbl) to repress gene expression of the downstream mRNA. It accomplishes this through an interplay of two separate domains; an aptamer domain which binds the effector ligand and a regulatory domain which contains the genetic switch. Within the aptamer domain ...


Split Deoxyribozyme Probe For Efficient Detection Of Highly Structured Rna Targets, Sheila Raquel Solarez Jan 2018

Split Deoxyribozyme Probe For Efficient Detection Of Highly Structured Rna Targets, Sheila Raquel Solarez

Honors Undergraduate Theses

Transfer RNAs (tRNAs) are known for their role as adaptors during translation of the genetic information and as regulators for gene expression; uncharged tRNAs regulate global gene expression in response to changes in amino acid pools in the cell. Aminoacylated tRNAs play a role in non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosynthesis. [1] tRNAs have a highly stable structure that can present a challenge for their detection using conventional techniques. [2] To enable signal amplification and lower detection limits, a split probe - split deoxyribozyme (sDz or BiDz) probe, which uses ...


Structure Of The Picornavirus Replication Platform: A Potential Drug Target For Inhibiting Virus Replication, Meghan Suzanne Warden Jan 2018

Structure Of The Picornavirus Replication Platform: A Potential Drug Target For Inhibiting Virus Replication, Meghan Suzanne Warden

Chemistry & Biochemistry Theses & Dissertations

Picornaviruses are small, positive-stranded RNA viruses, divided into twelve different genera. Members of the Picornaviridae family cause a wide range of human and animal diseases including the common cold, poliomyelitis, foot and mouth disease, and dilated cardiomyopathy. The picornavirus genome is replicated via a highly conserved mechanism involving a presumed cloverleaf structure located at the 5’ noncoding region of the virus genome. The 5’ cloverleaf consists of three stem loops (B, C, and D) and one stem (A), which interact with a variety of virus and host cell proteins during replication. In this dissertation, human rhinovirus serotype 14 (HRV-14) SLB ...


Uncovering The Identity And Metabolism Of Bacterial Coa-Rna, Joseph R. Spangler May 2017

Uncovering The Identity And Metabolism Of Bacterial Coa-Rna, Joseph R. Spangler

Dissertations

Coenzyme A is an indispensable molecule in all known life with roles in metabolism, gene regulation, and macromolecule synthesis. As CoA is derived from RNA itself, it’s incorporation into RNA by in vitro methods has proven useful in research probing the origin of life based on the RNA World theory. The discovery in contemporary bacteria of RNA modified with CoA, however, provided an unexpected twist to previously well-characterized bacterial systems. The identity of sequences associated with CoA-RNA has been elusive since their discovery in 2009 based on the difficulties in isolation while maintaining RNA quality. The aim of this ...


Liquid Crystal Phase Behavior Of A Dna Dodecamer And Sunset Yellow, Joseph Theis Jan 2017

Liquid Crystal Phase Behavior Of A Dna Dodecamer And Sunset Yellow, Joseph Theis

Undergraduate Honors Theses

The organic molecule Sunset Yellow, a chromonic dye, and reverse Dickerson dodecamer DNA, a self-complementary, 12 base pair strand of nucleic acids, both self-assemble into rod shaped aggregates that exhibit liquid crystal phases in solution. The sunset yellow molecules and the nano-DNA duplexes have similar structure with hydrophobic cores and peripheral hydrophilic ions. The focus of this research is on mixtures of these two aggregates in miscible liquid crystal states and the phase separation that occurs at higher concentrations in the columnar phase. The structure and phase space of this mixture was determined using polarized optical microscopy and x-ray diffraction ...


Elucidating Nucleic Acid Binding Properties Of Polycomb Repressive Complex 2, Richard D. Paucek Jan 2017

Elucidating Nucleic Acid Binding Properties Of Polycomb Repressive Complex 2, Richard D. Paucek

Undergraduate Honors Theses

Polycomb Repressive Complex 2 (PRC2) is a histone methyltransferase that specifically deposits mono-, di-, and tri-methylation marks onto chromatin. This activity triggers epigenetic silencing, a process critical for cell differentiation and maintenance of cellular identity. In mammalian cells, how PRC2 is recruited to target sites is unknown, but it is speculated that RNA, histone modifications, nucleosome architecture, and DNA elements all possess direct or indirect recruitment and regulatory roles. However, the relative binding affinity of PRC2 for these diverse biological substrates remains poorly understood. In the present study, the binding affinity of PRC2 for various RNAs and nucleosomes were tested ...


The Association Of Dcc Mrna Alternative Splicing With Colorectal Cancer, Natalie Graham Jan 2017

The Association Of Dcc Mrna Alternative Splicing With Colorectal Cancer, Natalie Graham

Undergraduate Honors Theses

In as many as 70% of colorectal cancer cell (CRC) lines, there is a deletion of a chromosomal region, 18q21, which contains the Deleted in Colorectal Carcinoma (DCC) gene (Mehlen & Fearon, 2004). In adult cells, this single transmembrane receptor plays a role in both cell proliferation and cell death, thereby making it a promising candidate gene for the pathogenesis of colorectal cancer. It has been observed that alternative splicing of the DCC can affect its activity and that alternative splicing of DCC can be disrupted in cancer (Leggere et al., 2016; Reale et al., 1994). In this experiment, we sought to determine the association of alternative splicing of the DCC with colorectal cancer in cells without the deletion of the 18q21 region. By extracting RNA from 35 CRC cell lines and performing RT-PCR, we observed levels of the two DCC isoforms compared to normal adult colon cells. In this way, we determined that 29 of 35 CRC cell lines had altered ...


Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman Sep 2016

Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman

Chemistry Faculty Publications and Presentations

Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (KD) between the 3-nucleotide internal guide sequence (IGS) of ...


Rsq: A Statistical Method For Quantification Of Isoform-Specific Structurome Using Transcriptome-Wide Structural Profiling Data, Yunfei Wang, University Of Texas At Dallas, Xiaopeng Zhu, Ming Sun, Yong Chen, Michael Q. Zhang, Yiwen Chen, Shikui Tu, Qi Dai, Haozhe Wang, Boyang Bai Jun 2016

Rsq: A Statistical Method For Quantification Of Isoform-Specific Structurome Using Transcriptome-Wide Structural Profiling Data, Yunfei Wang, University Of Texas At Dallas, Xiaopeng Zhu, Ming Sun, Yong Chen, Michael Q. Zhang, Yiwen Chen, Shikui Tu, Qi Dai, Haozhe Wang, Boyang Bai

University of Massachusetts Medical School Faculty Publications

The structure of RNA, which is considered to be a second layer of information alongside the genetic code, provides fundamental insights into the cellular function of both coding and non-coding RNAs. Several high-throughput technologies have been developed to profile transcriptome-wide RNA structures, i.e., the structurome. However, it is challenging to interpret the profiling data because the observed data represent an average over different RNA conformations and isoforms with different abundance. To address this challenge, we developed an RNA structurome quantification method (RSQ) to statistically model the distribution of reads over both isoforms and RNA conformations, and thus provide accurate ...


Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas Jun 2016

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

All Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is ...


Single Molecule Analysis Reveals Reversible And Irreversible Steps During Spliceosome Activation, Aaron A. Hoskins, Margaret L. Rodgers, Larry J. Friedman, Jeff Gelles, Melissa J. Moore May 2016

Single Molecule Analysis Reveals Reversible And Irreversible Steps During Spliceosome Activation, Aaron A. Hoskins, Margaret L. Rodgers, Larry J. Friedman, Jeff Gelles, Melissa J. Moore

Open Access Articles

The spliceosome is a complex machine composed of small nuclear ribonucleoproteins (snRNPs) and accessory proteins that excises introns from pre-mRNAs. After assembly the spliceosome is activated for catalysis by rearrangement of subunits to form an active site. How this rearrangement is coordinated is not well-understood. During activation, U4 must be released to allow U6 conformational change, while Prp19 complex (NTC) recruitment is essential for stabilizing the active site. We used multi-wavelength colocalization single molecule spectroscopy to directly observe the key events in Saccharomyces cerevisiae spliceosome activation. Following binding of the U4/U6.U5 tri-snRNP, the spliceosome either reverses assembly by ...


Elucidation Of The Effects Of The Cellular Environment On The Uncg Hairpin Motif, Michelle Whittum May 2016

Elucidation Of The Effects Of The Cellular Environment On The Uncg Hairpin Motif, Michelle Whittum

Senior Honors Theses

The effects of osmolytes on nucleic acid chemistry are generally not as well understood as for their protein counterparts. Recent studies have shown that these effects are rather complex and show significant dependencies on the chemical and structural properties of both the nucleic acid and the cosolute. Osmolytes have the potential to affect the stability of secondary structure motifs and alter preferences for conserved stable nucleic acid sequences. The goal of this research is to contribute to the understanding of the in vivo function of nucleic acids by studying the effects of different classes of osmolytes on the UNCG tetraloop ...


The Foundations Of Network Dynamics In An Rna Recombinase System, Jessica Anne Mellor Yeates May 2016

The Foundations Of Network Dynamics In An Rna Recombinase System, Jessica Anne Mellor Yeates

Dissertations and Theses

How life originated from physical and chemical processes is one of the great questions still unanswered today. Studies towards this effort have transitioned from the notion of a single self-replicating entity to the idea that a network of interacting molecules made this initial biological leap. In order to understand the chemical kinetic and thermodynamic mechanisms that could engender pre-life type networks we present an empirical characterization of a network of RNA recombinase molecules. We begin with 1-, 2-, and 3-molecular ensembles and provide a game theoretic analysis to describe the frequency dependent dynamics of competing and cooperating RNA genotypes. This ...


Stabilin-Mediated Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos), Colton M. Miller, Aaron J. Donner, Emma K. Blank, Andrew W. Egger, Brianna M. Kellar, Punit P. Seth, Edward N. Harris Apr 2016

Stabilin-Mediated Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos), Colton M. Miller, Aaron J. Donner, Emma K. Blank, Andrew W. Egger, Brianna M. Kellar, Punit P. Seth, Edward N. Harris

UCARE Research Products

Introduction: Antisense oligonucleotides (ASOs) are short chemically modified oligonucleotides (5-7.4 kDa) that can produce a pharmacological effect by binding to RNA and affecting intermediary metabolism. Over 35 phosphorothioate (PS) ASOs are at various stages of clinical development for use as therapeutic agents and pharmacological tools. Antisense therapy is a progressing area of research, as these small strands of nucleotide oligomers can be produced to silence genes that aggravate chronic disorders or infections. An important distinction for ASOs compared to DNA is the substitution of the phosphodiester (PO) backbone with the PS modification. This sulfur substitution allows for these polar ...


Messenger Rna Transport And Translation Regulated By The 3' Utrs Of Dendritic Mrnas And Abnormal Alternative Splicing Of Neuroligin1 In The Fmr1 Ko Mouse Hippocampus, Tianhui Zhu Feb 2016

Messenger Rna Transport And Translation Regulated By The 3' Utrs Of Dendritic Mrnas And Abnormal Alternative Splicing Of Neuroligin1 In The Fmr1 Ko Mouse Hippocampus, Tianhui Zhu

All Dissertations, Theses, and Capstone Projects

Fragile X Syndrome (FXS) is one of the most commonly inherited mental retardations. It is caused by the loss of functional fragile X mental retardation protein (FMRP). Loss of functional FMRP is the most widespread single-gene cause of autism. The most prominent phenotype of FXS patients is an IQ ranging from 20 to 70. FMRP is an RNA binding protein, widely expressed in almost all tissues and highly expressed in brain. As a RNA binding protein, 85-90 % of FMRP in the brain is associated with polyribosomes. Approximately 4 % of total mRNA is associated with FMRP, which functions in the stability ...


The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann Jan 2016

The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann

Wayne State University Dissertations

ABSTRACT

THE DEVELOPMENT OF PEPTIDE LIGANDS TO TARGET H69

by

DANIELLE NICOLE DREMANN

December 2015

Advisor: Prof. Christine S. Chow

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

In the development of peptide ligands to target H69, SPPS and ESI MS was used to determine if 1) peptides could bind to modified H69 and 2) if increased affinity for the target RNA could be enhanced with modification. An alanine and arginine scan was synthesized and tested for this determination. Selected peptides were then tested using biophysical techniques such as circular dichroism and isothermal titration calorimetry. An assay was also designed to ...


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 ...


Genome-Wide Approaches To Study Rna Secondary Structure, Nathan Daniel Berkowitz Jan 2016

Genome-Wide Approaches To Study Rna Secondary Structure, Nathan Daniel Berkowitz

Publicly Accessible Penn Dissertations

The central hypothesis of molecular biology depicts RNA as an intermediary conveyor of genetic information. RNA is transcribed from DNA and translated to proteins, the molecular machines of the cell. However, many RNAs do not encode protein and instead function as molecular machines themselves. The most famous examples are ribosomal RNAs and transfer RNAs, which together form the core translational machinery of the cell. Many other non-coding RNAs have been discovered including catalytic and regulatory RNAs. In many cases RNA function is tightly linked to its secondary structure, which is the collection of hydrogen bonds between complimentary RNA sequences that ...


Contributions Of Sequence And Structure To Ligand Selectivity In Class Ii Cobalamin Riboswitches, Samantha M. Webster Jan 2016

Contributions Of Sequence And Structure To Ligand Selectivity In Class Ii Cobalamin Riboswitches, Samantha M. Webster

Undergraduate Honors Theses

Riboswitches are gene regulatory elements found in the 5’-untranslated region of many bacterial genes. The direct binding of small molecule ligands induces conformational changes in the RNA that influence downstream expression machinery and determine the transcription or translation of an attached gene. Cobalamin riboswitches, which bind coenzyme-B12 and other cobalamin variants, are divided into two distinct classes. Cbl-I riboswitches contain a large peripheral element that limits riboswitch binding to only coenzyme-B12 (adenosylcobalamin, or AdoCbl). Cbl-II riboswitches do not contain the same peripheral element, and were originally thought to only bind smaller species of cobalamin (including methylcobalamin, or ...


Novel Functions Of The Survival Motor Neuron Protein, Eric William Ottesen Jan 2016

Novel Functions Of The Survival Motor Neuron Protein, Eric William Ottesen

Graduate Theses and Dissertations

The Survival Motor Neuron (SMN) protein is a multi-functional protein that participates in a wide variety of critical pathways. Low levels of SMN cause spinal muscular atrophy (SMA), the most common genetic cause of infant mortality. While the role of SMN in the assembly of small nuclear ribonucleoproteins (snRNPs) has been well characterized, many of its other diverse functions have not been thoroughly explored. Here, we examine the critical role of SMN in the growth and development of male mammalian sex organs. We show that low levels of SMN in a mild mouse model of SMA cause impaired testis development ...


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 ...