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Full-Text Articles in Molecular Biology

The Sumo-Stress Response (Ssr) In Normal And Cancerous Cells, Rui Yin May 2019

The Sumo-Stress Response (Ssr) In Normal And Cancerous Cells, Rui Yin

Undergraduate Honors Theses

SUMO (Small Ubiquitin-like Modifier) is a small protein that becomes reversibly attached to a large number of proteins. While research has firmly established SUMO’s importance in modulating protein interactions, activation, targeting, and half-life, little is known about its role in the SUMO-Stress Response (SSR), a phenomenon that involves a rapid increase in SUMOylation in response to cellular stress. Here I describe the use of kmUTAG-fl, a novel fluorescent SUMO trapping UTAG protein, to characterize and study how the SSR unfolds in normal and carcinogenic tissue culture cells. Specifically, fixed cells were stained with the SUMO-conjugate specific kmUTAG-fl reagent to ...


Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs May 2016

Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs

Undergraduate Honors Theses

In order to elucidate the biological processes that occur in everyday life, chemical biologists have developed technologies that allow the study of a various biological systems. Bioorthogonal chemistry is an ever-growing technology that involves performing chemical reactions with biological systems that do not rely on existing biological chemistries. In this work we attempt to develop and characterize novel bioorthognal chemistries that further expand the utility of this field. Additionally, we explore the utility of fluorescent probes in labeling applications. Finally, we attempt to create novel methods of control for a gene-editing protein using light as a mechanism of regulation.


The Pseudophosphatase Mk-Styx Colocalizes To Aggresomes, Veronica L. Nagle May 2016

The Pseudophosphatase Mk-Styx Colocalizes To Aggresomes, Veronica L. Nagle

Undergraduate Honors Theses

MK-STYX [MAPK (mitogen-activated protein kinase) phosphoserine/threonine/tyrosine-binding protein] is a pseudophosphatase member of the dual-specificity family subfamily of protein tyrosine phosphatases. MK-STYX lacks the essential cysteine in its signature motif required for catalytic activity. However, mutations to “restore” the signature motif result in a catalytically active phosphatase, MK-STYXactive (F1). We reported that MK-STYX interacts with G3BP-1 [Ras-GAP (GTPAse-activating protein) SH3 (Src homology 3) domain binding protein-1], and inhibits stress granule (SG) formation implicating the pseudophosphatase MK-STYX in the stress response pathway. SGs are large structures in which untranslated mRNAs accumulate and may serve as sites of mRNA sorting ...


Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla May 2016

Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla

Undergraduate Honors Theses

With the advent of chemoselective reactions and unnatural amino acids (UAAs), the fields of molecular biology and organic synthesis are merging. Researchers are developing synthetic tools and producing small molecules that are able to affect and investigate large biomolecules and complex living systems. This thesis undertakes a survey of synthetic techniques to develop novel tools that can be employed to address a variety of relevant biological questions. Specifically, we are investigating alternatives and improvements to caging groups, including photoreversible azobenzene UAAs and an UAA caging group possessing a bioorthogonal handle. Also, we are developing a novel system to undergo copper-free ...


Characterizing Importin Binding To Thyroid Hormone Receptor Α1, Emma Lynn Mcgregor Apr 2016

Characterizing Importin Binding To Thyroid Hormone Receptor Α1, Emma Lynn Mcgregor

Undergraduate Honors Theses

Thyroid hormone, or T3, is essential in many bodily functions, from early development to the maintenance of health in adults. It is crucial for growth and skeletal development, development of the nervous system, cell differentiation, and maintenance of metabolic balance. The thyroid hormone receptor, TR, is a major mediator of thyroid hormone action. TR is a transcription factor and able to activate or repress transcription depending on the binding of its ligand, T3. There are two isoforms of TR, encoded by different genes: TRα and TRβ. Each of these isoforms have multiple alternative splicing products.

While TR’s ...


Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens Apr 2016

Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens

Undergraduate Honors Theses

One way to study disease is to model specific biological reactions or processes involved in the generation of the disease in terms of a system of differential equations. The equations, called kinetic rate laws, are often non-linear and high order, making them difficult to solve. By approximating equations in complex biological networks as linear first order reactions, we can solve large sets of equations using computational software, such as MATLAB, to determine general trends in the change of molecular concentrations over time. These trends can tell us details about the disease and direct us toward areas worthy of further investigation ...


Unnatural Amino Acids In Proteins For Development Of Novel Biochemical Tools, Jordan Villa May 2015

Unnatural Amino Acids In Proteins For Development Of Novel Biochemical Tools, Jordan Villa

Undergraduate Honors Theses

Unnatural amino acids (UAAs) permit the incorporation of novel biochemical functionalities into proteins. This expansion of the genetic code has enabled enhanced spatial and temporal control of protein activity and conferred novel protein reactivity. This study examines the incorporation of three UAAs: fluoro-tyrosine, ortho-nitrobenzyl-tyrosine, and propargyloxy-phenylalanine towards various applications. Each UAA was successfully incorporated into a protein of interest (GFP or PRMT1) to facilitate the desired manipulation of protein function. The resulting alterations to GFP fluorescence, PRMT1 activity, or immobilization using Glaser-Hay bioconjugation demonstrate the success and practicality of the utilization of UAAs in the development of novel biochemical tools.


Characterization Of Pseudophosphatase Mk-Styx-Induced Neuronal Differentiation In Pc12 Cells, Dallas A. Banks Apr 2015

Characterization Of Pseudophosphatase Mk-Styx-Induced Neuronal Differentiation In Pc12 Cells, Dallas A. Banks

Undergraduate Honors Theses

MK-STYX [MAPK (mitogen activated protein kinase) phosphoserine/threonine/tyrosine binding protein] is a pseudophosphatase member of the MAPK phosphatase family. Though structurally related to the MAPK phosphatases, MK-STYX lacks the nucleophilic cysteine and histidine residues essential for catalysis. Despite its lack of catalytic activity, MK-STYX maintains its ability to bind to phosphorylated proteins, but not dephosphorylating them. This thesis focuses on further characterizing the role of MK-STYX in PC12 neuronal differentiation. The PC12 cell line is widely used as a model to study neuronal differentiation. Our previous data demonstrated that MK-STYX induces neuronal differentiation in PC12 cells. The results presented ...


The Role Of Mk-Styx In The Eif2alpha Stress Response Pathway, Alex Mcfarland Apr 2014

The Role Of Mk-Styx In The Eif2alpha Stress Response Pathway, Alex Mcfarland

Undergraduate Honors Theses

The pseudophosphatase MK-STYX (mitogen activated kinase phosphoserine/threonine/tyrosine binding protein) is a member of the MAPK phosphatases (MKP) dual specificity phosphatase family. However, it has the residues FSX5R, instead of HCX5R in its signature active motif. We previously reported that MK-STYX interacts with the RNA binding protein G3BP1 (Ras-GTPase SH3 domain binding protein-1) in the stress response pathway. During the stress response, mRNA translation is halted. Cytoplasmic compartments known as stress granules form around mRNA and RNA binding proteins, such as G3BP1, until the cell determines their fate. Dephosphorylation of G3BP1 at S149 induces stress ...


Identifying Sumo Protease Targets And Investigating E3 Ligase Interactions, Mark Guillotte Jan 2014

Identifying Sumo Protease Targets And Investigating E3 Ligase Interactions, Mark Guillotte

Dissertations, Theses, and Masters Projects

No abstract provided.


Investigating Heat Shock Protein 70 As A Binding Partner Of Mk-Styx, And The Role Of Mk-Styx In Neuronal Differentiation, Lauren Elizabeth Rusnak Jan 2013

Investigating Heat Shock Protein 70 As A Binding Partner Of Mk-Styx, And The Role Of Mk-Styx In Neuronal Differentiation, Lauren Elizabeth Rusnak

Dissertations, Theses, and Masters Projects

No abstract provided.


Spe-7, A Novel Regulator Of Msp Assembly In C Elegans Spermatocytes, Kari Lynn Messina Jan 2012

Spe-7, A Novel Regulator Of Msp Assembly In C Elegans Spermatocytes, Kari Lynn Messina

Dissertations, Theses, and Masters Projects

No abstract provided.


An Investigation Of The Polymorphic Arss Gene Of Helicobacter Pylori, Daniel Ross Hallinger Jan 2011

An Investigation Of The Polymorphic Arss Gene Of Helicobacter Pylori, Daniel Ross Hallinger

Dissertations, Theses, and Masters Projects

No abstract provided.


The Sumo-Targeted Ubiquitin Ligase Subunit Slx5 Functional Interacts With The Sumo E3 Ligase Siz1, Jason William Westerbeck Jan 2011

The Sumo-Targeted Ubiquitin Ligase Subunit Slx5 Functional Interacts With The Sumo E3 Ligase Siz1, Jason William Westerbeck

Dissertations, Theses, and Masters Projects

No abstract provided.


Sumo-Dependent Substrate Targeting Of The Sumo Protease Ulp1, Zachary Cole Elmore Jan 2011

Sumo-Dependent Substrate Targeting Of The Sumo Protease Ulp1, Zachary Cole Elmore

Dissertations, Theses, and Masters Projects

No abstract provided.


Understanding The Origins, Dispersal, And Evolution Of Bonamia Species (Phylum Haplosporidia) Based On Genetic Analyses Of Ribosomal Rna Gene Regions, Kristina M. Hill Jan 2011

Understanding The Origins, Dispersal, And Evolution Of Bonamia Species (Phylum Haplosporidia) Based On Genetic Analyses Of Ribosomal Rna Gene Regions, Kristina M. Hill

Dissertations, Theses, and Masters Projects

No abstract provided.


Molecular Marker Development For The Discrimination Of Atlantic And Pacific Blue Marlin (Makaira Nigricans), Laurie Sorenson Jan 2011

Molecular Marker Development For The Discrimination Of Atlantic And Pacific Blue Marlin (Makaira Nigricans), Laurie Sorenson

Dissertations, Theses, and Masters Projects

No abstract provided.


The Pax-5 Gene Is Alternatively Spliced In Trout B Cells, Raaj Mahendra Talauliker Jan 2010

The Pax-5 Gene Is Alternatively Spliced In Trout B Cells, Raaj Mahendra Talauliker

Dissertations, Theses, and Masters Projects

No abstract provided.


Assessing Genetic Variation Within And Among Native Populations And Hatchery Stocks Of Crassostrea Ariakensis Using Microsatellite Markers, Jie Xiao Jan 2009

Assessing Genetic Variation Within And Among Native Populations And Hatchery Stocks Of Crassostrea Ariakensis Using Microsatellite Markers, Jie Xiao

Dissertations, Theses, and Masters Projects

Assessing genetic variation within and among native populations and hatchery stocks of Crassostrea ariakensis using microsatellite markers In response to the dramatic decline of eastern oyster (Crassostrea virginica) populations in the Chesapeake Bay, introduction of the non-native Asian oyster Crassostrea ariakensis has been proposed. Currently several hatchery stocks of C. ariakensis, derived from a few wild populations along the coast of Japan and China, are being maintained in U.S. hatcheries in the Pacific northwest and on the east coast. In recent years, as the risks of the proposed introduction are being assessed, these hatchery animals have been widely used ...


The Relationship Between Antibody Redox Structure And Affinity In Rainbow Trout, Jianmin Ye Jan 2008

The Relationship Between Antibody Redox Structure And Affinity In Rainbow Trout, Jianmin Ye

Dissertations, Theses, and Masters Projects

Teleost immunoglobulin M (IgM), an 800 kDa tetramer, possesses considerable structural diversity due to the non-uniform disulfide polymerization of its halfmeric or monomeric subunits. However, to date, no plausible functional role for this diversity has been demonstrated or proposed. This research was, therefore, designed to investigate the possible functional role(s) for this diversity using the trout model. The possible relationship between this structural diversity and affinity was specifically addressed. The relationship between high levels of disulfide polymerization and high affinity was demonstrated by selective immunoadsorption and analysis of antibodies isolated during the process of affinity maturation. A pivotal determinative ...


Analysis Of Sequence Variation At Two Helicobacter Pylori Genetic Loci Potentially Involved In Virulence, George Warren Liechti Jan 2008

Analysis Of Sequence Variation At Two Helicobacter Pylori Genetic Loci Potentially Involved In Virulence, George Warren Liechti

Dissertations, Theses, and Masters Projects

No abstract provided.


A Molecular Phylogeny Of The Genus Bonamia Based On Sequence Data Of The Ribosomal Rna (Rrna) Gene Complex, Delonna M. White Jan 2008

A Molecular Phylogeny Of The Genus Bonamia Based On Sequence Data Of The Ribosomal Rna (Rrna) Gene Complex, Delonna M. White

Dissertations, Theses, and Masters Projects

No abstract provided.


A Molecular Analysis Of Atlantic Menhaden (Brevoortia Tyrannus) Stock Structure, Abigail J. Lynch Jan 2008

A Molecular Analysis Of Atlantic Menhaden (Brevoortia Tyrannus) Stock Structure, Abigail J. Lynch

Dissertations, Theses, and Masters Projects

Atlantic menhaden is an ecologically and economically important species along the U.S. east coast. As a filter-feeder and key prey fish, it provides a critical link between primary production, phytoplankton, and larger piscivorous predators, such as striped bass, bluefish, and weakfish. The species is also the target of one of the largest commercial fisheries in the country. Menhaden are assessed as a single, coastwide stock, and recent assessments indicate that it is not overfished. However, there is very limited population genetics data to support the assumption of a single stock. Additionally, the recent consolidation of the fishery and localization ...


A Molecular Study Of The Mitochondrial Genome And Invasions Of The Veined Rapa Whelk, Rapana Venosa, Emily A. Chandler Jan 2007

A Molecular Study Of The Mitochondrial Genome And Invasions Of The Veined Rapa Whelk, Rapana Venosa, Emily A. Chandler

Dissertations, Theses, and Masters Projects

No abstract provided.


A Molecular Technique For Specific Identification Of Western Atlantic Ocean Scombrids And An Analysis Of A Larval Scombrid Assemblage Off The Kona Coast Of Hawaii, Melissa A. Paine Jan 2006

A Molecular Technique For Specific Identification Of Western Atlantic Ocean Scombrids And An Analysis Of A Larval Scombrid Assemblage Off The Kona Coast Of Hawaii, Melissa A. Paine

Dissertations, Theses, and Masters Projects

No abstract provided.


Effects Of Overexpressing Alternative Isoform Pax-5e In Vivo, Suzanne Elizabeth Cole Jan 2004

Effects Of Overexpressing Alternative Isoform Pax-5e In Vivo, Suzanne Elizabeth Cole

Dissertations, Theses, and Masters Projects

No abstract provided.


Characterization Of The Xgat-1 Gene In Xenopus Laevis, Lisa Layne August Jan 2003

Characterization Of The Xgat-1 Gene In Xenopus Laevis, Lisa Layne August

Dissertations, Theses, and Masters Projects

No abstract provided.


Synalpheus Shrimp From Carrie Bow Cay, Belize. Systematics, Phylogenetics And Biological Observations (Crustacea: Decapoda: ; Alpheidae), Ruben Rios Gonzalez Jan 2003

Synalpheus Shrimp From Carrie Bow Cay, Belize. Systematics, Phylogenetics And Biological Observations (Crustacea: Decapoda: ; Alpheidae), Ruben Rios Gonzalez

Dissertations, Theses, and Masters Projects

Snapping shrimp in the family Alpheidae are remarkably abundant in coral reef ecosystems worldwide. The second most speciose genus, Synalpheus , includes species usually small and reclusive, and their general morphology is notably uniform, yet the number of species is staggeringly high, as is the intraspecific variability. These features have contributed to a poorly resolved taxonomic status, as evidenced both by recurring lumping and splitting of species and by lack of proper definition of several common species. I examined western Atlantic species of Synalpheus in the large and regionally dominant "Gambarelloides group of species", an informal but widely used guild within ...


Genetic Variation Within And Among The Suminoe Oyster (Crassostrea Ariakensis) Populations And Stocks As Assessed By Molecular Markers, Qian Zhang Jan 2003

Genetic Variation Within And Among The Suminoe Oyster (Crassostrea Ariakensis) Populations And Stocks As Assessed By Molecular Markers, Qian Zhang

Dissertations, Theses, and Masters Projects

No abstract provided.


A Mycobacterium-Inducible Nramp In Striped Bass Morone Saxatilis, Erin Jeffrey Burge Jan 2003

A Mycobacterium-Inducible Nramp In Striped Bass Morone Saxatilis, Erin Jeffrey Burge

Dissertations, Theses, and Masters Projects

In mammals, the natural resistance-associated macrophage protein 1 gene, Nramp1, plays a major role in resistance to mycobacterial infections. Chesapeake Bay (USA) striped bass, Morone saxatilis, are currently experiencing an epizootic of mycobacteriosis that threatens the health of this ecologically and economically important species. This dissertation characterizes an Nramp gene in this species (MsNramp ) and provide evidence for induction following Mycobacterium exposure. The striped bass MsNramp gene and 554 amino acid sequence contain all the signal features of the Nramp family, including a topology of 12 transmembrane domains (TM), the transport protein specific 'binding-protein-dependent transport system inner membrane component signature ...