Biochemistry, Biophysics, and Structural Biology Commons^™

Inference And Control In Regulatory Genomics, Siddharth Sharma

Biology and Medicine Through Mathematics Conference

No abstract provided.

Fluorescent Probes And Functionalized Nanoparticles For Bioimaging: Synthesis, Photophysical Properties And Applications, Xinglei Liu

Dissertations

The development of new organic molecular probes with excellent photophysical properties and high fluorescence quantum yields is of considerable interest to many research areas including one- and two-photon fluorescence microscopy, fluorescence-based sensing methodologies, and cancer therapy. Series of organic linear-/non-linear optical molecules including squaraine derivatives, and fluorene derivatives as well as other bioconjugates are designed and synthesized during the doctoral study for the aim of ion detection (Chapter 5), photo dynamic therapy, and deep-tissue imaging (Chapter 4). These optical probes are capable of absorbing light in the near infrared (NIR) window and thus have deeper penetration and cause less photodamage …

Design And Assessment Of Small Molecules As Free Radical Scavengers And Potential Multi-Target Therapeutic Agents Against Alzheimer’S Disease, Diabetes And Cancer, William Horton

Graduate Doctoral Dissertations

Complex diseases such as Alzheimer’s disease (AD), diabetes and cancer are difficult to manage with single target treatment approaches and unfortunately, they are wide-spread. For example, over 16 million people are expected to have AD in the US by 2050, thus new therapeutic approaches have to be developed. Multi-functional drug candidates have gained increasing popularity in treating complex diseases. The impact of oxidative stress in almost every disease progression makes them essential components in therapies for complex diseases. Endogenous systems typically maintain redox homeostasis within the cell, but in the diseased state these systems fail to alleviate oxidative stress. Supplementation …

Identification Of A Tola Protein Binding Site For Bacterial Toxins, Monica Ferrante

Honors Projects

Group A colicins are proteinaceous bacteriocins encoded by plasmids that exploit the cellular envelope protein TolA to translocate the cell wall barrier and cellular envelope of the bacterium Escherichia coli. These colicins offer protocols for studying certain protein-protein interactions involved in such membrane transport functions. Previous experimentations suggest the carboxyl-terminal domain of TolA protein contains specific amino acid binding regions required for the translocation of group A colicins into E. coli. The amino acid sequence of this domain varies between E. coli and other gram-negative bacterial species. It has been suggested that this diversity could be utilized to …

Structural And Functional Characterization Of Plant And Fungal Lov Proteins, Jameela Lokhandwala

Chemistry Theses and Dissertations

The plant blue light photoreceptor proteins Flavin binding Kelch F-box protein-1 (FKF1) and LOV Kelch protein-2 (LKP2) play an important role in maintaining circadian rhythmicity and photo-periodic flowering responses. These proteins along with light sensitive Light Oxygen Voltage (LOV) domain contain F-box and Kelch repeat domains. Therefore, these proteins control blue light mediated degradation of various protein targets to regulate circadian rhythmicity, growth, and photo-periodic flowering. Blue-light excitation of these proteins leads to formation of a cysteinyl-flavin adduct, which then decays depending upon various factors. Therefore, spectral studies were conducted to measure the kinetics of light–dark recovery. Size Exclusion Chromatography …

Cyclic Urethane: A Versatile Handle For Synthetic Peptide Applications, Hader E. Elashal

Seton Hall University Dissertations and Theses (ETDs)

While peptides have impeccable potential due to their biological and therapeutic abilities, they are inherently limited in clinical practice due to their instability towards proteolysis and poor bioavailability. In the past few years peptidomimetics have emerged as a powerful class of compounds that overcomes the shortcomings associated with peptides. Peptidomimetics essentially mimic a natural peptide or protein in its chemical composition, structure and its ability to perform a biologically relevant role. In addition to increased stability and bioavailability, peptidomimetics can also have increased receptor binding affinity and selectivity, thereby making these mimics lead compounds in the field of drug design …

Comparative Biochemical Analysis Of Uhrf Proteins Reveals Molecular Mechanisms That Uncouple Uhrf2 From Dna Methylation Maintenance, Robert M. Vaughan, Bradley M. Dickson, Evan M. Cornett, Joseph S. Harrison, Brian Kuhlman, Scott B. Rothbart

College of the Pacific Faculty Articles

UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties. While UHRF1 and UHRF2 diverge in their …

Effect Of Bmp Treatment On Periostin Gene Expression In Pre-Osteoblastic Mc3t3-E1 Mouse Cells, Vincent Lee Khang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Periostin is a secreted, extracellular matrix (ECM) protein widely expressed within collagen-rich fibrous connective tissues of the body including the periodontal ligament (PDL), bone, skin, heart, and cornea. Periostin has been shown to serve many important regulatory functions including cell adhesion, cell motility, wound healing and of particular importance to the dental field, differentiation of osteoblasts. The deletion of periostin compromises osteoblast attachment to bone matrix and induces a reduction in mineralization and expression of bone markers, including type I collagen, osteocalcin, osteopontin and alkaline phosphatase. Periostin has also been shown to play a significant role in collagen fibrillogenesis by …

Transcriptional Silencing And Anti-Silencing Of Virulence Genes In The Bacterial Pathogen Shigella Flexneri: Virb, Dna Supercoiling, And The Histone-Like Nucleoid Structuring Protein, Michael Adam Picker

UNLV Theses, Dissertations, Professional Papers, and Capstones

Transcriptional silencing and anti-silencing affect many aspects of bacterial physiology, including virulence in bacterial pathogens. In Shigella species, a group of gram-negative pathogens that cause bacillary dysentery in humans, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences virulence genes found on the large virulence plasmid while VirB anti-silences these genes. However, the mechanistic details of their interplay are not fully understood. To elucidate their regulatory mechanisms, I use the icsP virulence locus, which shares a long intergenic region with the divergently transcribed ospZ gene (1535 bp from TSS to TSS). Prior to this work, two discrete H-NS binding regions had …

The Caspase Cascade During Hibernation In The Golden-Mantled Ground Squirrel, Spermophilus Lateralis, Michael David Treat

UNLV Theses, Dissertations, Professional Papers, and Capstones

In several human pathologies like heart attack, stroke, neurodegenerative diseases, and autoimmune disorders, widespread cell death, or apoptosis, is a major cause of organ dysfunction and death. Hibernating golden-mantled ground squirrels, Spermophilus lateralis, experience numerous conditions during the winter that are known to be pro-apoptotic in other mammal systems (e.g. extreme hypothermia, ischemia and reperfusion, acidosis, increased reactive oxygen species, bone and muscle disuse). However, studies suggest that hibernators may invoke a protective phenotype to limit widespread cell damage and loss during the hibernation season. Could regulating apoptosis provide protection against the harmful conditions experienced during the hibernation season? Could …

Characterization Of A Catalyst-Based Conversion Technique To Measure Total Particulate Nitrogen And Organic Carbon And Comparison To A Particle Mass Measurement Instrument, Chelsea E. Stockwell, Agnieszka Kupc, Bartlomiej Witkowski, Ranajit K. Talukdar, Yong Liu, Vanessa Selimovic, Kyle J. Zarzana, Kanako Sekimoto, Carsten Warneke, Rebecca A. Washenfelder, Robert J. Yokelson, Ann M. Middlebrook, James M. Roberts

Chemistry and Biochemistry Faculty Publications

The chemical composition of aerosol particles is a key aspect in determining their impact on the environment. For example, nitrogen-containing particles impact atmospheric chemistry, air quality, and ecological N deposition. Instruments that measure total reactive nitrogen (Nr Combining double low line all nitrogen compounds except for N2 and N2O) focus on gas-phase nitrogen and very few studies directly discuss the instrument capacity to measure the mass of Nr-containing particles. Here, we investigate the mass quantification of particle-bound nitrogen using a custom Nr system that involves total conversion to nitric oxide (NO) across platinum and molybdenum catalysts followed by NOĝ'O3 chemiluminescence …

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …

Melatonin-Micronutrients Osteopenia Treatment Study (Mots): A Translational Study Assessing The Effects Of Melatonin, Strontium Citrate, Vitamin D3 And Vitamin K2 On Bone Density, Bone Turnover Markers And Health-Related Quality Of Life In Postmenopausal Osteopenic Women Following A One-Year Double-Blind Randomized Placebo-Controlled Trial And On Osteoblast-Osteoclast Co-Cultures, Sifat Maria

Electronic Theses and Dissertations

Objective: The purpose of this study was to assess if a novel combination of melatonin and three other natural bone-aiding micronutrients: strontium citrate, vitamins D₃ and K₂ (MSDK) could improve bone health by modulating the activity of osteoblasts and osteoclasts in favor of balanced bone remodeling and by improving the overall health-related quality of life in postmenopausal osteopenic women.

Methods: The Melatonin-micronutrients Osteopenia Treatment Study (MOTS) is a translational research study that used both clinical and in vitro approaches to assess the efficacy of MSDK on bone health in women and to identify potential mechanisms for its effects. …

The Role Of Criticality Of Gene Regulatory Networks On Emergent Properties Of Biological Systems, Hyobin Kim

Graduate Dissertations and Theses

The relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied. However, the relationship between the criticality of GRNs and properties of multicellular organisms at a higher level has not been fully explored. Here we aim at revealing potential roles of the criticality of GRNs at a multicellular and hierarchical level, using a random Boolean network as a GRN. We perform three studies. Firstly, we propose a GRN-based morphogenetic model, and delve into the role of the criticality of GRNs in morphogenesis at a multicellular level. Secondly, we include …

Cloning And Characterization Of A Pyrethroid Pesticide Decomposing Esterase Gene, Est3385, From Rhodopseudomonas Palustris Psb-S, Xiangwen Luo, Deyong Zhang, Xuguo Zhou, Jiao Du, Songbai Zhang, Yong Liu

Entomology Faculty Publications

Full length open reading frame of pyrethroid detoxification gene, Est3385, contains 963 nucleotides. This gene was identified and cloned based on the genome sequence of Rhodopseudomonas palustris PSB-S available at the GneBank. The predicted amino acid sequence of Est3385 shared moderate identities (30–46%) with the known homologous esterases. Phylogenetic analysis revealed that Est3385 was a member in the esterase family I. Recombinant Est3385 was heterologous expressed in E. coli, purified and characterized for its substrate specificity, kinetics and stability under various conditions. The optimal temperature and pH for Est3385 were 35 °C and 6.0, respectively. This enzyme could …

Till Death Do Us Part: The Marriage Of Autophagy And Apoptosis., Katrina F Cooper

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Autophagy is a widely conserved catabolic process that is necessary for maintaining cellular homeostasis under normal physiological conditions and driving the cell to switch back to this status quo under times of starvation, hypoxia, and oxidative stress. The potential similarities and differences between basal autophagy and stimulus-induced autophagy are still largely unknown. Both act by clearing aberrant or unnecessary cytoplasmic material, such as misfolded proteins, supernumerary and defective organelles. The relationship between reactive oxygen species (ROS) and autophagy is complex. Cellular ROS is predominantly derived from mitochondria. Autophagy is triggered by this event, and by clearing the defective organelles effectively, …

Synthetic Routes To Bromo-Terminated Phosphonate Films And Alkynyl Pyridine Compounds For Click Coupling, Poornima Sunder

Departmental Honors & Graduate Capstone Projects

Click reactions are a highly versatile class of reactions that produce a diverse range of products. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) click reactions require an azide and a terminal alkyne and produce a coupled product that is “clicked” through a triazole ring that can have a variety of substituents. In this work, bromo-terminated phosphonate films on copper oxide surfaces were explored as the platform for click coupling, as the terminal azide needed for the reaction can be generated through an in situ SN2 reaction with a terminal bromo group. The reactions were characterized using model reactions in solution before being conducted …

An N-Terminal Acidic Domain In Β-Amylase2 Is Required For K+ Regulation., Jillian Breault

Senior Honors Projects, 2010-2019

In the chloroplasts of leaf mesophyll cells, β-amylase proteins (BAMs) are responsible for breaking down starch into maltose when the plant cannot undergo photosynthesis. BAM2, which was previously considered inactive, was recently shown to be active under stromal-like levels of salt and has optimal activity at 80mM KCl. In addition, BAM2 is active as a tetramer in vivo and displays sigmoidal kinetics due to a secondary binding site that is responsible for activating BAM2 when bound to starch. A hypothesized tetramer model was created using a homology model of a BAM2 monomer and the configuration of a crystallized sweet potato …

Searching For Potential Binding Partners Of Arabidopsis Β-Amylase9 Using Yeast 2-Hybridization, Sheikh Hossain

Senior Honors Projects, 2010-2019

In plants, starch is a major carbon and energy storage compound. Starch is made as a product of photosynthesis while plants are in light and is degraded at night. Our lab is interested in the cellular mechanism of starch degradation in plants and for our studies we use Arabidopsis thaliana as a model. β-amylases are primarily responsible for the hydrolysis of starch in plants and a total of nine β-amylases genes are encoded in Arabidopsis thaliana. These nine genes are identified as BAM1-9. BAM9 is located in the chloroplast where starch is located, and is present …

Molecular Mechanism Of Early Amyloid Self-Assembly Revealed By Computational Modeling, Mohtadin Hashemi

Theses & Dissertations

Protein misfolding followed by the formation of aggregates, is an early step in the cascade of conformational changes in a protein that underlie the development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive.

Here, we demonstrate that the hairpin fold, a structure found in the early folding intermediates of amyloid b, induces morphological and stability changes in the aggregates of Aβ(14-23) peptide. We structurally characterized the interactions of monomer and hairpin using extended molecular dynamics (MD) simulations, which revealed a novel intercalated type complex. …

Muc4 Based Immunotherapy For Pancreatic Cancer, Kasturi Banerjee

Theses & Dissertations

Pancreatic Cancer (PC) is a lethal disease claiming approximately 45000 lives in the US in 2018, and it establishes an elaborate immunosuppressive tumor microenvironment that aids in disease pathogenesis. Immunotherapy has emerged as a strategy to target tumor cells by reprogramming patient’s immune system. Challenges present in PC immunotherapy are: i) identifying a tumor-associated antigen that could be targeted, ii) identifying adjuvants that could efficiently deliver antigens, iii) eliciting robust anti-tumor responses and iv) overcoming peripheral tolerance and immunosuppression elicited by the tumor.

Firstly, we detected circulating autoantibodies to MUC4 present in PC patients and observed that IgM autoantibodies to …

Elucidation Of The Functions Of Neuropilin 2 In Osteoclasts In Promoting Prostate Cancer Bone Metastasis., Navatha S. Polavaram

Theses & Dissertations

Bone metastasis is one of the major clinical concerns that causes skeletal related malignancies and increased mortality. Bone is one of the preferred sites for metastatic prostate cancer. The metastatic prostate cancer cells interact with bone cells (osteoblasts and osteoclasts) resulting in an imbalance in the bone homeostasis leading to increased activation of osteoblasts over osteoclasts. Our preliminary data indicated a non-tyrosine kinase receptor Neuropilin 2 (NRP2) is expressed in osteoclasts induced by metastatic prostate cancer cells and acts as a negative regulator of osteoclast differentiation and function. We hypothesize that prostate cancer -induced NRP2 expression in osteoclasts is necessary …

Towards The Identification Of The Molecular Mechanism Responsible For Rpa:Rad52 Complex Formation, Lucas Struble

Theses & Dissertations

Human cells are routinely exposed to DNA-damaging conditions, from both external sources like ionizing radiation and internal sources like normal oxidative metabolism. Damage in the form of double strand breaks (DSBs) is especially problematic. DSBs occurring outside of replication forks can be repaired through two forms of homologous recombination. The first of these is genetic conversion involving either RPA, BRCA1, PALB2, BRCA2, and RAD51, or RPA, RAD52, RAD51, and other unknown factors. The second is single strand annealing involving RPA and RAD52. Familial breast cancers, among numerous others, are characterized by homozygous pathological mutations in the BRCA2 pathway and must …

Inhibition Of Rad52-Based Dna Repair For Cancer Therapy, Mona Al-Mugotir

Theses & Dissertations

Germline BRCA mutations underlay a significant risk for breast and ovarian cancer that increases in age. BRCA mutations are usually associated with the most aggressive subtypes of these cancers such as triple negative breast cancer and high-grade serous ovarian cancer. Conventional chemotherapeutic or hormonal therapies do not address the molecular deficiencies responsible for their resistance and there is a high rate of recurrence. Targeted therapy that can address the unique molecular features in these subtypes of cancer is the only way to cure the disease or, at the very least, improve patients’ quality of life.

Homologous recombination repair is an …

The Beta-Catenin/Muc1.Ct Interaction In Pancreatic Cancer, Edwin Wiest

Theses & Dissertations

MUC1 is overexpressed in over 90% of pancreatic cancer cases, and its interaction with beta-catenin promotes progression of the disease. Various in vitro and in vivo methods show that beta-catenin and MUC1 interact by way of the cytoplasmic tail of MUC1 (MUC1.CT). This interaction occurs in the membrane of pancreatic cancer cells but is found to a smaller extent in the nucleus as well. Biophysical methods suggest that MUC1 interacts with beta-catenin through a sequence of amino acids in the tail of MUC1 that sit very near the transmembrane domain of MUC1. In pancreatic ductal adenocarcinoma cells, it appears that …

Abcg5 And Abcg8: More Than A Defense Against Xenosterols, Shailendra B. Patel, Gregory A. Graf, Ryan E. Temel

Pharmaceutical Sciences Faculty Publications

The elucidation of the molecular basis of the rare disease, sitosterolemia, has revolutionized our mechanistic understanding of how dietary sterols are excreted and how cholesterol is eliminated from the body. Two proteins, ABCG5 and ABCG8, encoded by the sitosterolemia locus, work as obligate dimers to pump sterols out of hepatocytes and enterocytes. ABCG5/ABCG8 are key in regulating whole-body sterol trafficking, by eliminating sterols via the biliary tree as well as the intestinal tract. Importantly, these transporters keep xenosterols from accumulating in the body. The sitosterolemia locus has been genetically associated with lipid levels and downstream atherosclerotic disease, as well as …

Modeling And Analyzing An Optogenetic System For Photoactivatable Protein Dissociation, Anvin Thomas, James Schaff

Honors Scholar Theses

Computational modeling of cell-cell interactions can grant clues and can answer questions about an experiment, especially for observations about binding interactions and kinetics. This approach was used to investigate an interaction between a light-oxygen-voltage (LOV) domain and an engineered protein called Zdark (Zdk). The LOV domain is membrane-bound while Zdk is cytosolic. The LOV domain and Zdk bind strongly in dark (K_d 26.2 nM), and weakly upon exposure to blue light (K_d > 4 μM). Total internal reflection fluorescence (TIRF) images are acquired of Zdk, the fluorescent species bound to a mCherry tag, and the loss of fluorescence is …

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

Articles

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated with …