Biochemistry, Biophysics, and Structural Biology Commons^™

Interfamily Variation In Amphibian Early Life-History Traits: Raw Material For Natural Selection?, Gareth R. Hopkins, Brian G. Gall, Susannah S. French, Edmund D. Brodie Jr.

Biology Faculty Publications

The embryonic development and time to hatching of eggs can be highly adaptive in some species, and thus under selective pressure. In this study, we examined the underlying interfamily variation in hatching timing and embryonic development in a population of an oviparous amphibian, the rough-skinned newt (Taricha granulosa). We found significant, high variability in degree of embryonic development and hatching timing among eggs from different females. Patterns of variation were present regardless of temperature.We also could not explain the differences among families by morphological traits of the females or their eggs. This study suggests that the variation necessary for natural …

Spontaneous Cooperative Assembly Of Replicative Catalytic Rna Systems, Nilesh Vaidya

Dissertations and Theses

The RNA World hypothesis proposes a period of time during the origins of life in which RNA molecules were the only source of both genotypes and phenotypes. Although a vast amount of evidence has been obtained in support of this hypothesis, a few critical demonstrations are lacking. A most crucial one is a demonstration of self-replication of RNA molecule from prebiotic soup. Previously in the Lehman laboratory, it has been demonstrated that a 198-nucleotide molecule derived from the Azoarcus group I intron can self-assemble from up to four fragments of RNA via recombination. Furthermore, the covalent full-length molecules are catalytically …

Determination Of An Interaction Between Nipped B-Like Protein And Mll, Adam Robert Marek

Master's Theses

The Mixed Lineage Leukemia (MLL) protein serves as a positive transcriptional regulator during hematopoietic and embryonic development. The MLL gene can undergo chromosomal translocations producing leukemia-causing fusions that retain the MLL amino-terminus, including the repression domain. A recent yeast two-hybrid screening used the MLL repression domain as bait and yielded nine positive clones of Nipped B-like (NIPBL).

NIPBL is a crucial member of the cohesin complex, which functions in the segregation of sister chromatids during cell division. However, recent evidence suggests the cohesin complex can also function as a transcriptional regulator.

In this study, we wanted to confirm this interaction …

Characterization Of The Coca Chemokine Receptor Four Agonist Activity Of Ubiquitin, Daniel M. Staren

Master's Theses

Ubiquitin has previously been identified as another natural agonist of CXC chemokine receptor 4 (CXCR4). In addition, recent evidence suggests that ubiquitin may activate CXCR4 through a binding site on the receptor, which is distinct from the binding site for the cognate ligand stromal cell-derived factor (SDF)-1α. The cellular consequences of ubiquitin induced CXCR4 activation, however, are still poorly defined and a side-by-side comparison of CXCR4 mediated functions after activation with SDF-1α and ubiquitin is lacking. Such information will be instrumental to better understand the physiological function of CXCR4 and to further define its role as a therapeutic target in …

Signals From Intraventricular Depth Electrodes Can Control A Brain-Computer Interface, Jerry J. Shih, Dean J. Krusienski

Electrical & Computer Engineering Faculty Publications

A Brain-Computer Interface (BCI) is a device that enables severely disabled people to communicate and interact with their environments using their brain waves. Most research investigating BCI in humans have used scalp-recorded electroencephalography (EEG). We have recently demonstrated that signals from intracranial electrocorticography (ECoG) and stereotactic depth electrodes (SDE) in the hippocampus can be used to control a BCI P300 Speller paradigm. We report a case in which stereotactic depth electrodes positioned in the ventricle were able to obtain viable signals for a BCI. Our results demonstrate that event-related potentials from intraventricular electrodes can be used to reliably control the …

Molecular Characterization And Tissue-Specific Gene Expression Of Dermacentor Variabilis Α-Catenin In Response To Rickettsial Infection, Piyanate Sunyakumthorn, Natthida Petchampai, Michael T. Kearney, Daniel E. Sonenshine, Kevin R. Macaluso

Biological Sciences Faculty Publications

Alpha catenin is a cytoskeleton protein that acts as a regulator of actin rearrangement by forming an E-cadherin adhesion complex. In Dermacentor variabilis, a putative α-catenin (Dvα-catenin) was previously identified as differentially regulated in ovaries of ticks chronically infected with Rickettsia montanensis. To begin characterizing the role(s) of Dvα-catenin during rickettsial infection, the full-length Dvα-catenin cDNA was cloned and analysed. Comparative sequence analysis demonstrates a 3069-bp cDNA with a 2718-bp open reading frame with a sequence similar to Ixodes scapularis α-catenin. A portion of Dvα-catenin is homologous to the vinculin-conserved domain containing a putative …

Development Of An In-Cell Förster Resonance Energy Transfer Technique To Study Protein Structure Inside Living Cells, Victoria Lynn Murray

Wayne State University Dissertations

The goal of my thesis is to develop an in-cell fluorescence technique that allows for measurement of the distances between fluorescence acceptors and donors within a protein or between two proteins inside the correct intracellular compartment of living cells. The successful achievement of this goal will allow us to obtain high-resolution structural information from a protein, one key step towards high-resolution structural biology of proteins inside the living cell.

To achieve this goal, we will apply the fluorescence resonance energy transfer (FRET) technique to the specifically labeled proteins inside the cells. Our rationale is to specifically label the protein(s) of …

The Role Of R7 Regulators Of G Protein Signaling In The Retina, Hoon Shim

Theses and Dissertations

The R7 regulators of G protein signaling (R7 RGS), namely RGS6, RGS7, RGS9 and RGS11, are expressed in the retina along with its binding partner Gβ5. The RGS9-1 isoform is expressed only in retinal photoreceptors and rate-limits the recovery of rod phototransduction by acting as a member of the transducin GAP complex (RGS9-1/Gβ5L/R9AP). The Gβ5L isoform is also only expressed in retinal photoreceptors and acts by stabilizing the GAP complex. The Gβ5S isoform differs from Gβ5L by the absence of exon 1 due to alternative splicing and is expressed in many other retinal cells. Gβ5L is barely detectable in RGS9-/- …

Identifying Sortase A Variants With Higher Catalytic Effeciency, Muna Suliman

Theses and Dissertations

In the past two decades, the field of protein engineering has evolved rapidly to include new genetic and chemical techniques to alter protein function. Protein engineering seeks to improve enzyme properties through powerful methods that specifically incorporate novel or improved function in proteins. One such method is protein ligation, which is used to selectively link synthetic and recombinant polypeptides. Due to the limitations of current protein labeling techniques, simple site-specific modification methods remain in high demand. Use of enzyme-based labeling has been the focus of various studies because of its substrate specificity. Sortase-mediated transpeptidation is one approach that has been …

Structure And Dynamics Of The P53 Transactivation Domain Binding To Mdm2 And Rpa70, Anne Terese Powell

USF Tampa Graduate Theses and Dissertations

The tumor suppressor protein, p53, is mutated or dysregulated in nearly all human cancers(1). The amino terminal domains are essential for transcriptional activation in stressed cells and play a vital role in cell cycle regulation, apoptosis and senescence. The transactivation (TAD) and proline rich domains in this region are dynamic and intrinsically disordered; lacking stable secondary or tertiary structure. This region contains multiple binding sites; arguably, the most significant of these is for p53's negative regulator, the E3 ligase, MDM2. An important, but less understood interaction involving the single stranded DNA binding protein, RPA70A, is hypothesized to be involved in …

Cloning Of The Gene, Purification As Recombinant Protein And Functional Characterization Of Leishmania Mexicana Cytochrome B5 Reductase, Ala Azhari

USF Tampa Graduate Theses and Dissertations

Leishmania are protozoan parasites that are transmitted by a sand fly vector. These parasites affect not only humans but also wild animals including domestic dogs and rodents, which form an additional challenge and public health problem to control the disease. Leishmaniasis is an important disease with worldwide distribution, including Saudi Arabia, the Middle East, and other tropical and subtropical areas around the world. Due to the expansion of irrigation and agricultural activities, more exposure to sand fly occurs, which leads to the expansion of leishmaniasis infections as newly emerging disease.

Emerging drug resistance in leishmaniasis is an additional problem, contributed …

Stable Carbon Isotope Discrimination By Rubisco Enzymes Relevant To The Global Carbon Cycle, Amanda J. Boller

USF Tampa Graduate Theses and Dissertations

Five different forms of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO; IA, IB, IC, ID, II), the carboxylase of the Calvin-Benson-Bassham cycle (CBB), are utilized by plants, algae and autotrophic bacteria for carbon fixation. Discrimination against ¹³C by RubisCO is a major factor dictating the stable carbon isotopic composition (δ¹³C = {[¹³C/¹²C sample/¹³C/¹²C standard] - 1} X 1000) of biomass. To date, isotope discrimination, expressed as ε values (={[¹²k/¹³k] - 1} X 1000; ¹²k and ¹³k …

Aberrant Sialylation Alters Cardiac Electrical Signaling, Andrew Ednie

USF Tampa Graduate Theses and Dissertations

In the heart, electrical signaling is responsible for its rhythmicity and is necessary to initiate muscle contraction. The net electrical activity in a cardiac myocyte during a contraction cycle is observed as the action potential (AP), which describes a change in membrane potential as a function of time. In ventricular cardiac myocytes, voltage-gated sodium channels (Nav) and voltage-gated potassium channels (Kv) play antagonistic roles in shaping the AP with the former initiating membrane depolarization and the latter repolarizing it. Functional changes in the primary cardiac Nav isoform, Nav 1.5, or any one of the many Kv isoforms expressed in the …

Lipid Raft Formation And Peptide-Lipid Interactions In Myelin Model Membranes, Ashtina R. Appadu

Theses and Dissertations (Comprehensive)

Multiple sclerosis (MS), a demyelinating disease affecting 75,000 Canadians and almost 400,000 Americans, is one of the most prevalent diseases in young adults. Unfortunately, there exist no known cures to date and the pathways involved in the progression of the disease remain relatively obscure. The demyelination process triggered by the onset of MS, affects the lipid composition of the myelin membrane and causes a loss in viable myelin which can in turn greatly impact the proper functioning of the central nervous system (CNS). The cholesterol content of myelin fluctuates during MS and consequently this could affect the fluidity as well …

Proteomic Analysis Of The Highly Detergent Resistant Radial Component Of Myelin, Vatsal M. Patel

Theses and Dissertations (Comprehensive)

The wrapping of multiple layers of myelin membrane sheets around an axon plays an important role in normal neuronal function. In the central nervous system (CNS), oligodendrocytes are responsible for forming multiple myelin internodes which consist of lipids and proteins. Within these regions, there are various membrane microdomains including the radial component/tight junctions. The radial component is a junctional complex believed to stabilize the myelin membranes in the CNS myelin. In this study, the radial component from bovine and mouse myelin was isolated using differential detergent extraction. A highly detergent resistant fraction, containing previously identified proteins of the radial component …

A Novel Method Of Studying Ion Formation And Fragmentation Using A Modified Time-Of-Flight Mass Spectrometer, David S. Ames

Dissertations and Theses @ UNI

Laser desorption has been an important tool in mass spectrometry. It has been known that an order of magnitude more neutrals than ions are produced during laser desorption. A Time-Of-Flight Mass Spectrometer with an infinitely adjustable acceleration region was constructed to map the population distribution of neutral ion precursors and metastable ions in the flight tube. Desorption was performed by using a nitrogen UV laser at 337 nm. Experiments conclude that the majority of post-source ionization of neutrals occurs approximately 2.5 cm from the sample-laser interface. The intensity of ions tapers rapidly out to 6.0 cm, however ions were detected …

Development Of Capillary Electrophoresis For The Analysis Of Phenolics And Glucoraphanin In Brassica Oleracea, Iris Lee

Theses: Doctorates and Masters

Capillary electrophoresis (CE) has been used increasingly more over the last decade in the area of food analysis. Numerous food products and food components have been analysed using this technique because of its high efficiency and short separation times. However, the inherent lack of detection sensitivity in CE combined with the complex matrices present in many food samples, especially those of plant origins, is one of the contributing factors to the limited development on CE in this particular area of food analysis. In this project, the potential of CE as a tool in the analysis of vegetables belonging to the …

Spt5 Affects The Rate Of Mrna Degradation And Physically Interacts With Ccr4 But Does Not Control Mrna Deadenylation, Yajun Cui, Yueh-Chin Chiang, Palaniswamy Viswanathan, Darren J. Lee, Clyde L. Denis

New Hampshire Agricultural Experiment Station Publications

The CCR4-NOT complex has been shown to have multiple roles in mRNA metabolism, including that of transcriptional elongation, mRNA transport, and nuclear exosome function, but the primary function of CCR4 and CAF1 is in the deadenylation and degradation of cytoplasmic mRNA. As previous genetic analysis supported an interaction between SPT5, known to be involved in transcriptional elongation, and that of CCR4, the physical association of SPT5 with CCR4 was examined. A two-hybrid screen utilizing the deadenylase domain of CCR4 as a bait identified SPT5 as a potential interacting protein. SPT5 at its physiological concentration was shown to immunoprecipitate CCR4 and …

Design And Synthesis Of Cationic Steroid Antimicrobial Compounds, Synthesis Of Glycolipids Recognized By Natural Killer T Cells And Development Of Tlr-1, Tlr-6 Heterodimer Binders And Studies Of Their Immunology Activities, Yanshu Feng

Theses and Dissertations

Cationic steroid antimicrobial agents (CSAs) are a family of bile acid derivatives. These compounds are amphiphilic and mimic endogenous antimicrobial peptides. The antimicrobial activities of CSA-13 have been investigated and due to portent bactericidal activities and low toxicity, a large amount of CSA-13 is demanded for clinic trails and other antimicrobial applications. During our studies, we optimized the synthetic route of CSA-13, so that it can be prepared at the kilogram, even in tons scale. We investigated three routes and one of them is suitable for industry, because only recrystallization is needed in the synthesis. Natural killer T cells (NKT …

Synthesis Of Resveratrol Esters And Aliphatic Acids., Stanley Mofor Jing

Electronic Theses and Dissertations

Resveratrol (RV) is a naturally occurring phytoalexin of the stilbenoid family produced by some plant species, and present in grape skin, peanuts, and red wine. It has been found to exhibit anti-cancer, anti-inflammatory, anti-viral, anti-aging, cardio protective, and anti-oxidant properties. Bioavailability is a huge setback that limits the potentials of RV. As a result, efforts have been made to design and synthesize RV esters and aliphatic acids in an attempt to increase its bioavailability, solubility in water, and possibly improving its biological activities. Resveratrol esters, 3,5,4'-triacetyloxystilbene (2) and Methyl 1,1',1''- (3,4',5-stilbenyl)-1,6-hexanedioate (3) have been synthesized. Compound 3 is a new …