Biochemistry, Biophysics, and Structural Biology Commons^™

Creation Of An Immunodeficient Hla-Transgenic Mouse (Humamice) And Functional Validation Of Human Immunity After Transfer Of Hla-Matched Human Cells, Yang Zeng, Bingrun Liu, Marie-Therese Rubio, Xinyue Wang, David M. Ojcius, Ruoping Tang, Antoine Durrbach, Zhitao Ru, Yusen Zhou, Yu-Chun Lone

All Dugoni School of Dentistry Faculty Articles

Research on human immunology has been hindered by the lack of optimal small animal models, given that the protective immune responses of human and non-human species show significant differences. However, due to ethical constraints[1] and the high cost of clinical trials, it is urgent to improve the current animal models that can mimic faithfully human physiology, particularly the human immune system (HIS). HIS mice had been generated recently by engrafting human hematopoietic stem cells (hHSCs) or human peripheral mononuclear cells (hPBMCs) into highly immuno-deficient mice such as NSG, NOG or NRG mice. However, a major experimental drawback for studies using …

Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3a And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer., S Deivendran, Hezlin Marzook, T R Santhoshkumar, Rakesh Kumar, M Radhakrishna Pillai

Biochemistry and Molecular Medicine Faculty Publications

Despite a recognized role of DNA methyltransferase 3a (DNMT3a) in human cancer, the nature of its upstream regulator(s) and relationship with the master chromatin remodeling factor MTA1, continues to be poorly understood. Here, we found an inverse relationship between the levels of MTA1 and DNMT3a in human cancer and that high levels of MTA1 in combination of low DNMT3a status correlates well with poor survival of breast cancer patients. We discovered that MTA1 represses DNMT3a expression via HDAC1/YY1 transcription factor complex. Because IGFBP3 is an established target of DNMT3a, we investigated the effect of MTA1 upon IGFBP3 expression, and found …

Metastasis-Associated Protein 1 Is An Upstream Regulator Of Dnmt3Α And Stimulator Of Insulin-Growth Factor Binding Protein-3 In Breast Cancer, S Deivendran

Biochemistry and Molecular Medicine Faculty Publications

Despite a recognized role of DNA methyltransferase 3a (DNMT3a) in human cancer, the nature of its upstream regulator(s) and relationship with the master chromatin remodeling factor MTA1, continues to be poorly understood. Here, we found an inverse relationship between the levels of MTA1 and DNMT3a in human cancer and that high levels of MTA1 in combination of low DNMT3a status correlates well with poor survival of breast cancer patients. We discovered that MTA1 represses DNMT3a expression via HDAC1/YY1 transcription factor complex. Because IGFBP3 is an established target of DNMT3a, we investigated the effect of MTA1 upon IGFBP3 expression, and found …

Oxidation Of Substituted Catechols At The Air-Water Interface: Production Of Carboxylic Acids, Quinones, And Polyphenols, Elizabeth A. Pillar, Marcelo I. Guzman

Chemistry Faculty Publications

Anthropogenic activities contribute benzene, toluene, and anisole to the environment, which in the atmosphere are converted into the respective phenols, cresols, and methoxyphenols by fast gas-phase reaction with hydroxyl radicals (HO(•)). Further processing of the latter species by HO(•) decreases their vapor pressure as a second hydroxyl group is incorporated to accelerate their oxidative aging at interfaces and in aqueous particles. This work shows how catechol, pyrogallol, 3-methylcatechol, 4-methylcatechol, and 3-methoxycatechol (all proxies for oxygenated aromatics derived from benzene, toluene, and anisole) react at the air-water interface with increasing O3(g) during τc ≈ 1 μs contact time and contrasts their …

Testing Effectiveness Of Aqueous Phases From Struvite And Hydroxyapatite Mineral Precipitation As Algal Nutrient Sources, Aaron Lyons

Virginias Collegiate Honors Council Conference

As interest in algal biofuel grows, the need to explore diverse nutrient sources for growing algae becomes apparent. Struvite and Hydroxyapatite (HAP) were precipitated after flash hydrolysis. The leftover aqueous phase (AP) could serve as nutrients source for algae cultivation and the potential reuse of this waste stream is promising. To test this, 12 bottles of Scenedemus sp., four of Struvite, four of HAP, and four control AM-14 synthetic media were cultivated. 10% of the Phosphorus in the synthetic media was replaced with phosphorous from the struvite AP, and 10% of the nitrogen in the synthetic media was replaced …

Validation Of The Pre-B Cell Receptor As A Therapeutic Target In B Cell Precursor Acute Lymphoblastic Leukemia, Michael Frank Erasmus

Biomedical Sciences ETDs

This dissertation is built upon the fundamental idea that the pre-B cell receptor (pre-BCR) is important to leukemia cell survival and a logical therapeutic target in B cell precursor acute lymphoblastic leukemia (BCP-ALL). The pre-BCR is expressed early at a specific stage during B cell development where it plays a central role in survival of healthy B lymphocytes. This receptor is composed of the membrane heavy chain (mIgμ) associated with surrogate light chain components, 5 and VpreB. Through the use of advanced imaging modalities, in particular two-color single particle tracking (SPT), we showed that pre-BCRs formed transient, homotypic interactions. These …

Therapeutic Modulation Of Cancer Metabolism With Dichloroacetate And Metformin, Nathan Patrick Ward

USF Tampa Graduate Theses and Dissertations

The robust glycolytic metabolism of glioblastoma multiforme (GBM) has proven them susceptible to increases in oxidative metabolism induced by the pyruvate mimetic dichloroacetate (DCA). Recent reports demonstrate that the anti-diabetic drug metformin enhances the damaging oxidative stress associated with DCA treatment in cancer cells. We sought to elucidate the role of metformin’s reported activity as a mitochondrial complex I inhibitor in the enhancement of DCA cytotoxicity in the VM-M3 model of GBM. We demonstrated that metformin potentiated DCA-induced superoxide production and that this was required for enhanced cytotoxicity towards VM-M3 cells with the combination. Similarly, rotenone enhanced oxidative stress resultant …

Ultraviolet Radiation Reduces Desmosine Cross-Links In Elastin, Basant Dhital, Philip Durlik, Pratikkumar Rathod, Farhana Gul-E-Noor, Zhixiao Wang, Cheng Sun, Emmanuel J. Chang, Boris Itin, Gregory S. Boutis

Publications and Research

Elastic fibers, a major component of the extracellular matrix of the skin, are often exposed to ultraviolet (UV) radiation throughout mammalian life. We report on an in vitro study of the alterations in bovine nuchal ligament elastic fibers resulting from continuous UV-A exposure by the use of transmission electron microscopy (TEM), histology, mass spectrometry, and solid state 13C NMR methodologies. TEM images reveal distinct cracks in elastic fibers as a result of UV-A irradiation and histological measurements show a disruption in the regular array of elastic fibers present in unirradiated samples; elastic fibers appear shorter, highly fragmented, and thinner after …

Uncovering Transcriptional Activators And Targets Of Hsf-1 In Caenorhabditis Elegans, Jessica Brunquell

USF Tampa Graduate Theses and Dissertations

In order to survive, cells must be able to cope with a variety of environmental stressors. The heat shock response (HSR) is a pro-survival mechanism employed by cells in response to protein denaturing stress, such as heat. Since its discovery in 1960, the heat shock response has been found to be regulated by the transcription factor heat shock factor 1 (HSF1). During periods of increased stress, HSF1 undergoes a multi-step process of activation that involves homotrimerization, DNA-binding, and post-translational regulatory modifications, all of which ultimately function to control the transcription of chaperone genes. These chaperone genes encode molecular chaperone proteins …

Quantitative Evaluation Of Clinostomum Marginatum Distribution In The Fish Host (Perca Flavescens): Investigation Of The Impact On Functional Performance, Doiba Ki Eshofonie, Precious Freeman

Student Scholar Showcase

Doiba Eshofonie & Precious Freeman

Mentor: Takashi Maie

2017 Student Scholar Showcase

Quantitative evaluation of Clinostomum marginatum distribution in the fish host (Perca flavescens): Investigation of the impact on functional performance

Clinostomum marginatum is a trematode commonly found in freshwater fish. The adult C. marginatum stays in its definitive avian host’s mouth and throat. It releases eggs upon contact in water and the eggs hatch into a free-swimming miracidia, which infects an aquatic snail as the first intermediate host. The miracidia, then, develops into a cercaria and leaves the snail to find a fish as its second intermediate …

Tracking The Sexual Assault Kit Backlog, Kallie Crawford, Lyndsie Ferrara

Undergraduate Research and Scholarship Symposium

The backlog of untested sexual assault kits is a national problem. Numerous federal funding opportunities offer the forensic science and law enforcement communities valuable resources needed to test the kits, but issues still remain. The majority of resources are focused on the collection and testing of sexual assault kits, but the tracking of the kits has not been a primary focus. This research highlights improvements that can be made to better understand the current backlog and improve the future processing and tracking of kits. Given the lack of a universal evidence tracking database among agencies, tracking sexual assault kits seems …

Inquiry Into Perilipin-5a Expression In Triacylglycerol Rich Vs Normal Fed Mouse Tissue, Kobi Agyepong

Undergraduate Honors Thesis Projects

The steep rise in both childhood and adult obesity over the past three decades has moved to the forefront of public consciousness in recent years. This development has generated a marked increase in general health awareness and lifestyle changes for a vast number of individuals, most notably in the form of increased physical activity and diet alterations. The latter point is especially salient in a biochemical context, because of the myriad factors that can result in “fat accumulation”. Chief among these factors is the Perilipin 5A gene, (known as PLIN5A) which encodes the protein Perilipin 5A of the Perilipin family …

Construction And Comparison Of The Recombinant Strains Of Synechocystis Sp. Pcc 6803 Able To Grow On Wood Sugars, Saurabh Jayant Ranade

Theses and Dissertations

The wood sugars present in the lignocellulosic biomass can be used to support microbial growth to synthesize a number of value added products. The objective of this research was to metabolically engineer model cyanobacterium Synechocystis to enable it to harvest carbon and energy stored in the wood sugars in addition to the light energy. In the xylose-specific work, we generated five Synechocystis strains that heterologously expressed XylAB enzymes, which mediate xylose catabolism, either in combination with or without one of four xylose transporters, namely XylE, XylFGH, GalP, or Glf. In terms of dry biomass accumulation and xylose consumption, the strains …

Molecular Mass Of L-Arginine-Based Potentially Carcinogenic Heterocyclic Amines, Irene S. Hwang

Honors Theses

Investigation of cancer-inducing molecules in cooked foods has led to the discovery of mutagenic heterocyclic amines (HCAs) in meat. The amino acids creatin(in)e and L-phenylalanine form the precursors for these HCAs. Recent research here at Andrews University have found similar mutagenic HCAs produced from plant-based proteins when L-arginine, rather than creatin(in)e, is substituted in high temperature reactions (simulated cooking) with L-phenylalanine. Our research focused on developing HPLC methods to isolate individual candidates that are then screened for mutagenicity via the Ames test. Mass spectroscopy methods were also developed to identfy the molecular structure of these lead mutagenic L-arginine-based HCAs.

Fluorescence Analysis Of Pamam Dendrimers, Ansel Nam

Honors Theses

Despite their lack of conjugation, polyamidoamine (PAMAM) dendrimers are intrinsically fluorescent, and this fluorescent is somewhat manipulable through altering the dendrimer's solvent. This level of fluorescence is dependent on a number of the dendrimer's qualities: the pH of the solvent, the mass percent concentration of the dendrimer in solvent, and the generation size of the dendrimer. In past studies, fluorescent intensity increased as generation size increased and pH decreased. Thus, this research project will attempt to replicate those results as well as further analyze the efficiency of fluorescence of PAMAM dendrimer in comparison to fluorescein.

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

International Collaboration And New Technology Reveal Rare Genes That Determine Height, Nicolle Dauphinee

Thinking Matters Symposium Archive

Height is a phenotype, an observable trait of the genes that we inherit from our parents. It's a polygenic trait, meaning it is controlled by 2 or more genes. Because it is so easy to measure, it is an ideal characteristic to help us understand other polygenic traits. So far, genome-wide association studies (GWAS) have identified 700 common variants that determine a person's height. New discoveries have been made by the international group called Genetic Investigation of Anthropometric Traits (GIANT), revealing 83 genetic mutations that have additional effects on a person's height.¹

The Effects Of Carrier Ligands On Cisplatin Binding To Cysteine And Methionine, Adam C.R Smith

Masters Theses & Specialist Projects

We have reacted several derivatives of the anticancer drug cisplatin with N-acetyl-Lcysteine (N-AcCys) and N-acetyl-L-methionine (N-AcMet), which are two of the primary amino acid targets of platinum. NMR spectroscopy was used to monitor the reactions and determine the effect the different ligands would have on the platinum reactivity. Several of the platinum compounds were tested at pH of 4 and 7, and with platinum:amino acid ratios of 1:1, 2:1 and 1:2. Competition reactions between cysteine and methionine were done to confirm which would react with the platinum compound first. [Pt(dien)(NO3)]+ reacts faster with methionine than with cysteine at both pH …

The Statistical Dynamics Of Nonequilibrium Control, Grant Murray Rotskoff '09

Doctoral Dissertations

Living systems, even at the scale of single molecules, are constantly adapting to changing environmental conditions. The physical response of a nanoscale system to external gradients or changing thermodynamic conditions can be chaotic, nonlinear, and hence difficult to control or predict. Nevertheless, biology has evolved systems that reliably carry out the cell’s vital functions efficiently enough to ensure survival. Moreover, the development of new experimental techniques to monitor and manipulate single biological molecules has provided a natural testbed for theoretical investigations of nonequilibrium dynamics. This work focuses on developing paradigms for both understanding the principles of nonequilibrium dynamics and also …

Analysis Of Hiv-1 Quasispecies Sequences Generated By High Throughput Sequencing (Hts) Using Hive, Naila Gulzar, Bhavna Hora, Konstantinos Karagiannis, Krista Smith, Feng Gao, Raja Mazumder

GW Research Days 2016 - 2020

The high level of genetic variability of Human Immunodeficiency Virus type 1 (HIV-1) is caused by the low fidelity of its replication machinery. This leads to evolution of swarm-like viral populations often described as quasispecies. High throughput sequencing (HTS) technology provides higher resolution over Sanger sequencing, enabling detection of low frequency variant genomes. However, quasispecies analysis is still a challenge due to the systematic noise, introduced by HTS technology. This leads to the increase in type I errors (also known as false positives) and the underlying genetic diversity, which can lead to mathematically insolvable type II errors (also known as …

Development Of An In Vivo Assay For Acetyl-Coa Carboxylase Using 1,3,6,8- Tetrahydroxynapthalene Synthase, Sarah Bond

Honors Capstones

No abstract provided.

Synthesis, Kinetic And Catalytic Studies Of Manganese Complexes With Corrole And Porphyrin Ligands, Haleh Jeddi

Masters Theses & Specialist Projects

High-valent transition metal-oxo intermediates play a significant role in the catalytic cycle of the ubiquitous cytochrome P450 enzymes and in biomimetic catalytic systems. In this work, manganese(III) porphyrin and corrole systems (2) were synthesized and characterized by UV-vis absorbance and 1H-NMR, matching literaturereported spectroscopic data. Manganese(V)-oxo corroles (3) and a manganese(IV)-oxo porphyrin (4) were successfully generated by chemical oxidation using mchloroperoxybenzoic acid (m-CPBA), and their oxidation reactions with organic reductants were comparatively investigated. Results from single-turnover kinetic studies indicate that in the tris(pentafluorophenyl)corrole system (3a), the active oxidizing intermediate differs in different solvents. The active oxidizing intermediate in acetonitrile is …

Effects Of Binding Affinity Between Bovine Serum Albumin And Platinum Drugs, Nathan Puckett

Masters Theses & Specialist Projects

Platinum complex drugs such as cisplatin have been used as highly successful chemotherapy drugs since the 1970s. We are interested in how the ligands attached to cisplatin analogs influences their reactivity with biologically relevant targets along with time and amount. For this study, reactions were conducted to determine the reactivity between different platinum compounds and the protein bovine serum albumin. Various platinum compounds with different ligands were reacted in varying amounts with albumin in ammonium acetate buffer for either 1 hour, 4 hours, or 24 hours. Each reaction was quenched after the designated reaction time by dialysis and the platinum …

Correlated Mutation In The Evolution Of Catalysis In Uracil Dna Glycosylase Superfamily, Bo Xia, Yingling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N. Dominy, Weiguo Cao

Publications

Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG …

Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier

Mechanical & Aerospace Engineering Faculty Publications

We extend the multiscale spatiotemporal heat map strategies originally developed for interpreting molecular dynamics simulations of well-structured proteins to liquids such as lipid bilayers and solvents. Our analysis informs the experimental and theoretical investigation of electroporation, that is, the externally imposed breaching of the cell membrane under the influence of an electric field of sufficient magnitude. To understand the nanoscale architecture of electroporation, we transform time domain data of the coarse-grained interaction networks of lipids and solvents into spatial heat maps of the most relevant constituent molecules. The application takes advantage of our earlier graph-based activity functions by accounting for …

A Balanced Approach To Adaptive Probability Density Estimation, Julio Kovacs, Cailee Helmick, Willy Wriggers

Mechanical & Aerospace Engineering Faculty Publications

Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes. Our tests on simulated data show that BADE exhibits equal or better accuracy than existing methods, and visual tests …

Quantifying Cyanide Inhibition Of Nitrification And Developing Cost-Effective Treatment Processes, Germano M. Salazar-Benites

Civil & Environmental Engineering Theses & Dissertations

All wastewater treatment plants that operate multiple hearth furnaces (MHF) and are required to nitrify must manage the inhibitory effects of free cyanide (HCN, CN-) in the scrubber return flows due to inhibitory impacts on nitrifying bacteria.

HRSD Boat Harbor Treatment Plant (BHTP) a 25 MGD facility consisting of primary and secondary treatment, employs an anoxic selector process for nitrification and partial denitrification and operates a MHF. There is a desire to improve TN removal performance at BHTP due to an annual mass-based bubble permit limit on a combined discharge from seven HRSD plants, and there are no discharge limitations …

Natural Killer (Nk) Cells And Their Involvement In Different Types Of Cancer. Current Status Of Clinical Research, Isadora Zaharescu, Adina D. Moldovan, Cristiana Tanase

Journal of Mind and Medical Sciences

Natural killer cells are the main agents of innate immunity. Since 1970, various studies have repeatedly confirmed their involvement in decreasing local tumor growth and also decreasing the risk of metastasis, due to their cytotoxic effects and also through the release of immunostimulatory cytokines such as IFN-gamma. In the 1990s, several studies demonstrated the existence of certain inhibiting and stimulating receptors of these cells, leading to the concept of “induced self”, thus explaining why tumors with MHC-1 are destroyed and autologous cells without it are saved out. Recognition and destruction of tumor cells by the NK cells are the result …

Reactivity Of Ketyl And Acetyl Radicals From Direct Solar Actinic Photolysis Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The variable composition of secondary organic aerosols (SOA) contributes to the large uncertainty for predicting radiative forcing. A better understanding of the reaction mechanisms leading to aerosol formation such as for the photochemical reaction of aqueous pyruvic acid (PA) at λ ≥ 305 nm can contribute to constrain these uncertainties. Herein, the photochemistry of aqueous PA (5-300 mM) continuously sparged with air is re-examined in the laboratory under comparable irradiance at 38° N at noon on a summer day. Several analytical methods are employed to monitor the time series of the reaction, including (1) the derivatization of carbonyl (C═O) functional …

Exploring The Use Of Free Bioinformatics Modules In An Introductory Biochemistry Course, Charlsey Dodgen, Uzezi Uwerosuo, Chulhee Kang, Cathy Lee

Georgia Journal of Science

Although bioinformatics, the use of computational science to study biology, has become imperative in many areas of the biological sciences and related career paths, introductory biochemistry courses may disregard practical knowledge on bioinformatics. For this reason, we merged a hands-on activity module into an undergraduate biochemistry course in two ways. First, we incorporated bioinformatics modules for building phylogenetic trees by aligning the active sites of 10 chosen related α-amylase enzymes using freely available data. Secondly, we chose three of those 10 α-amylase enzymes to compare the 3D structure of their active sites. This module gives the students an opportunity to …