Biochemistry, Biophysics, and Structural Biology Commons^™

Dikar-Induced Synthetic Lethality In A Drosophila Model Of Cag Repeat Diseases Does Not Result From An Expression Feedback Loop, Daniel Camacho

Honors Scholar Theses

Human CAG repeat diseases manifest themselves through the common pathology of neurodeneration. This pathological link is attributed to the property shared by all nine of these diseases: an expanded polyglutamine (polyQ) tract. The most evident result of polyQ expansion is protein aggregation, and it is believed that this phenomenon is partly responsible for conferring cytotoxic properties on the mutated protein. Apart from sequestering the mutated protein, cellular aggregates are able to incorporate native proteins via polyQ-mediated aggregation, thus disrupting important cellular pathways. Using Drosophila melanogaster as a disease model, researchers have been able to compile collections of these so-called disease …

Investigations In Enhancing The Reproducibility Of Implantable Amperometric Glucose Biosensors For Mass Production, Dipesh Manharbhai Patel

Honors Scholar Theses

Implantable glucose sensors for Diabetes management should possess several attributes such as linearity, sensitivity, selectivity, long life time and should elicit no negative tissue response. Based on this, the UConn implantable glucose sensor team has developed a 5-layer sensor architecture that simultaneously affords the aforementioned requirements. However, the large scale production of these 5-layer sensors is inhibited by the lack of high sensor-to-sensor reproducibility. Herein, we investigate the origin of sensor-to-sensor irreproducibility and develop methodologies for large-scale fabrication of these devices.

Broad Spectrum Systemic Acquired Resistance In Amblystegium Serpens, Christina A. Tatara

Undergraduate Honors Thesis Collection

Systemic acquired resistance (SAR) is a well-characterized defense mechanism in vascular plants where initial exposure to a pathogen induces resistance throughout the plant to subsequent attacks by a wide range of pathogens. A similar SAR-like mechanism has recently been documented in a nonvascular plant, the moss Amblysregium serpens, but it has not been thoroughly characterized. Currently only one pathogen, the oomycete Pythium irregulare, has been shown to trigger SAR in this or any other nonvascular plant. I have observed and characterized the interactions between A. serpens and two other alleged moss pathogens, the ascomycetes Acrosporium sympodiale and Botrytis cinerea. Using …

N→Π* Interactions Of Amides And Thioamides: Implications For Protein Stability, Robert W. Newberry, Brett Vanveller, Ilia A. Guzei, Ronald T. Raines

Brett VanVeller

Carbonyl–carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor–acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor–acceptor orbital interactions rather than dipole–dipole interactions.

Temperature Dependence Of Transcription Initiation In Archaea, Ming-Hsiao Wu

Student Research Symposium

TFB1 and TFB2 are two Transcription Factor B (TFB) found in Pyrococcus furious (Pfu), a hyperthermophile archaeon. TFB1 is the primary TFB in Pfu, and highly conserved with eukaryotic TFIIB. TFB2 lacks some residues in B-reader region which interacts with promoter DNA and recognizes the transcription start site. Exposure to heat-shock increases the mRNA level of Pfu TFB2 in vivo; however, mRNA level of Pfu TFB1 stays the same. In Pfu, different TFBs may be used for regulating transcription. It is hypothesized that TFB2 is involved in heat-shock reaction and increases the transcription efficiency of heat-shock promoters. In our in …

Spectroscopic Studies Of Cu2+ And Zn2+ Binding To Prodigiosin Analogs, Karen Chichetu, Papireddy Kancharla, Shilah Bonnett, Kevin Reynolds

Student Research Symposium

Prodigiosins are a family of secondary metabolites that were first isolated from the bacterium Serratia marascens. These natural compounds are red pigmented and characterized by a tri-pyrrole skeleton with a C-4 methoxy group. They have been reported to have good biological properties that include anticancer, antimalarial, antimicrobial and immunosuppressive activities. We have synthesized analogs of the natural prodigiosins (prodiginines) to produce a library of biologically active compounds which have improved biological activity and reduced cytotoxicity in human cells. In this work we studied the interaction between prodiginines and Cu2+ and Zn2+ using UV and Mass Spectroscopy techniques. Early results show …

Finding Rna-Dna Hybrid Viruses, Jeremy Filip, Geoffery S. Diemer, Kenneth M. Stedman

Student Research Symposium

Until extremely recently it was thought that recombination between DNA and RNA viruses was practically nonexistent. The discovery of the "RNA-DNA Hybrid Virus" (RDHV) genome in a metavirome from a hightemperature acidic lake changed this view (Diemer and Stedman, 2012). We, and others, have discovered multiple examples of this recombination "hiding in plain sight" in multiple both published and unpublished metagenomes from many different environments and recent publications (Rosario et al., 2012 a Tae Woong Whon et al, 2012, Mitsuhiro Yoshida et al., 2013, and several others through personal communication). Comparing the proteins within these hybrid viruses against each other …

Polyethylenimine-Enhanced Alumina Nanoscale Adjuvant For Cancer Vaccine, Naoko Uno, Haiyan Li, Hong-Ming Hu, Jun Jiao

Student Research Symposium

Aluminum oxide nanoparticles (Al2O3 NPs) have been shown to increase the efficiency of cell-mediated immune response. Specifically, CD8 and CD4 immune response is required for T cell activation by dendritic cells. These nanoparticles, when functionalized with peptides and other molecules, can be used as vaccine in cancer treatment. In this study, Al2O3 NPs were attached to E6/E7 proteins. HPV-induced cervical cancer expresses E6/E7 antigens. E6/E7 proteins were attached using surface modification of the Al2O3 NPs; different types of molecules were tested to see which adhered the highest amount of protein and produced the strongest cell response. Protein measurements were done …

The Sustainability Of Coffee Brewing, Richard F Simmerman

Faculty Publications and Other Works -- Chemical and Biomolecular Engineering

In short, over 8.25 million tons of coffee are produced world-wide annually (2009). Remarkably, only two different species of coffee are cultivated to reach almost the entire crop, Coffea canephora (robusta) and C. arabica (arabica). Arabica coffee is a tetraploid, that takes 9 months to ripen, yields 1500-3000 kg beans/ha, has an optimum temperature 15-24°C, an optimal rainfall need of 1500-2000 mm, an optimum altitude 1000-2000 m, is much more susceptible to disease and parasites, with a caffeine content per bean of 0.8-1.4%. Robusta coffee is a diploid, that takes 11 months to ripen, yields 2300-4000 kg beans/ha, …

Molecular Characterization Of A Patient Presumed To Have Prader-Willi Syndrome, Marina Falaleeva, Carlos R. Sulsona, Horst R. Zielke, Kathleen M. Currey, Pierre De La Grange, Vahid Aslanzadeh, Daniel J. Driscoll, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

Prader-Willi syndrome (PWS) is caused by the loss of RNA expression from an imprinted region on chromosome 15 that includes SNRPN, SNORD115, and SNORD116. Currently, there are no mouse models that faithfully reflect the human phenotype and investigations rely on human post-mortem material. During molecular characterization of tissue deposited in a public brain bank from a patient diagnosed with Prader-Willi syndrome, we found RNA expression from SNRPN, SNORD115, and SNORD116 which does not support a genetic diagnosis of Prader-Willi syndrome. The patient was a female, Caucasian nursing home resident with history of morbid obesity (BMI 56.3) and mental retardation. She …

Eastern Kentucky Farmer's Willingness To Grow Biomass For Emergy Production, Austin P. Jacobs

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Austin P. Jacobs in May of 2013.

From Gibbons To Gymnasts: A Look At The Biomechanics And Neurophysiology Of Brachiation In Gibbons And Its Human Rediscovery, Emma Et Pennock

Student Works

This conference paper serves to examine the evolutionary linkages of a brachiating ancestor in humans, the biomechanical and neurophysiology of modern day brachiators, and the human rediscovery of this form of locomotion. Brachiation is arguably one of the most metabolically effective modes of travel by any organism and can be observed most meritoriously in Gibbons. The purpose of the research conducted for this paper was to encourage further exploration of the neurophysiological similarities and differences between humans and non-human primates. The hope is that in spurring more interest and research in this area, further possibilities for rehabilitating brain injury will …

The Unavoidable Threat Of Aggregation: Implications For Folding And Function Of A Β-Rich Protein, Mylene Hazelle Anne Ferrolino

Open Access Dissertations

Protein aggregation has been implicated in several catastrophic diseases (neurodegeneration, diabetes, ALS) and its complexity has also become a major obstacle in large-scale production of protein-based therapeutics. Despite the generic behavior of proteins to aggregate, only a few globular proteins have known aggregation mechanisms. At present, there have been no clear connections between a protein folding, function and aggregation. We have tackled the challenge of understanding the links between a protein's natural tendency to fold and function with its propensity to misfold and aggregate. Using a predominantly beta-sheet protein whose in vitro folding has been explored in detail: cellular retinoic …

Structure-Function Analysis Of Human Integrator Subunit-4, Anupama Sataluri

Dissertations & Theses (Open Access)

Structure-function analysis of human Integrator subunit 4

Anupama Sataluri

Advisor: Eric. J. Wagner, Ph.D.

Uridine-rich small nuclear RNAs (U snRNA) are RNA Polymerase-II (RNAPII) transcripts that are ubiquitously expressed and are known to be essential for gene expression. snRNAs play a key role in mRNA splicing and in histone mRNA expression. Inaccurate snRNA biosynthesis can lead to diseases related to defective splicing and histone mRNA expression. Although the 3′ end formation mechanism and processing machinery of other RNAPII transcripts such as mRNA has been well studied, the mechanism of snRNA 3′ end processing has remained a mystery until the recent …

Manipulating Aktivated Metabolism Via Mtorc1, Ivan Von Hack Prestinary

HIM 1990-2015

Although poorly understood, normal cells and cancerous cells of the same type exhibit different patterns of nutrient consumption, processing and utility of metabolic substrates. Differences in substrate uptake, preference, and alternately emphasized metabolic pathways offer opportunities for selective targeting of cancer versus stroma. This may be accomplished by using a sequential approach of nutrient deprivation and pharmaceutical perturbation of metabolic pathways to inhibit cellular proliferation. The purpose of this study was to investigate the effects of restricting glucose and glutamine concentrations, in vitro, to levels that resemble a potential human fasting state. The mammalian target of rapamycin (mTOR), a mediator …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

Understanding The Origins Of Product Specificity Of Protein Methyltransferases From Qm/Mm Md And Free Energy Simulations, Yuzhuo Chu

Doctoral Dissertations

Protein lysine methyltransferases (PKMTs) catalyze the methylation of certain lysine residues on histone tails using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Regulation of chromatin structure and gene expression through histone lysine methylation depends on the degree of methylation. Therefore, it is of importance to understand the features of PKMTs that control how many methyl groups would be added to the target lysine (product specificity). In my dissertation, I have applied quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations to understand the origin of the product specificities of SET8, GLP and their mutants. The relative free energy barriers …

Role Of Retinoids In The Regulation Of Hepatic Glucose And Lipid Metabolism, Rui Li

Doctoral Dissertations

The liver plays an important role in controlling glucose and lipid homeostasis. Metabolic abnormalities such as obesity and type 2 diabetes are often associated with profound changes in the expression of genes involved in hepatic glucose and lipid metabolism. Dietary nutrients provide us with macronutrients for energy and micronutrients for maintenance of general health. However, the effects of individual micronutrients on the development of metabolic diseases are unknown. Sterol regulatory element binding protein-1c (SREBP-1c) is the master regulator of fatty acid synthesis, and glucokinase (GK) is the key enzyme in glucose metabolism. Based on the preliminary results from our laboratory …

Quorum Sensing And Metabolism In Marine Environments, Amanda May

Doctoral Dissertations

Quorum sensing (QS) is a phenomenon that allows bacteria to communicate with each other. Small molecules known as autoinducers are synthesized and released by bacteria, and once enough members of the community are around to ensure survival, i.e. quorum, a phenotype, e.g. bioluminescence, is expressed. There are two types of QS molecules, intra- and inter-species.

S-4,5-Dihydroxy-2,3-pentanedione (DPD) is a byproduct of the activated methyl cycle which recycles methionine. This has led to the discussion as to whether DPD is a metabolic byproduct or is the interspecies signal as proposed previously. The detection and quantitation of DPD however, has not …

Characterization Of Field Evolved Resistance To Transgenic Cry1fa Maize In Spodoptera Frugiperda (J. E. Smith), Siva Rama Krishna Jakka

Doctoral Dissertations

Transgenic Bt crops expressing Cry and Vip toxins from Bacillus thuringiensis (Bt) have been increasingly planted to manage insect pest damage on agricultural crops. The high adoption of Bt-based insecticidal technologies suggests an increase selection pressure for the evolution of resistance in insect populations. So far, nine insect species have developed field evolved resistance to Bt crops, yet the mechanisms involved in field evolved resistance are unknown. In the present study, the resistance mechanism in field evolved resistance to maize producing Cry1Fa in Spodoptera frugiperda collected in fields from Puerto Rico was characterized. High levels of resistance to …