Biochemistry Commons^™

Fam129b Phosphorylation And Its Effect On Membrane Localization In Confluent Hela Cells, Lakshmi Thompil Somasekharan

Wayne State University Theses

Phosphorylation and de-phosphorylation of many proteins is a key regulator of cellular life. It maintains cellular activity through an array of signaling pathways like cell division, proliferation and growth. However, Overexpression or mutations by the constitutive activation of phosphorylation machinery disrupt the balance in the cell, driving the inappropriate activation or deactivation of the cellular processes it controls. FAM129B is a protein whose activity is partly maintained by phosphorylation and dephosphorylation at the six serine residues at the C-terminal. FAM129B is expressed highly in many forms of cancer and its main function is to suppress apoptosis and enhances cancer cell …

Design, Synthesis And Analysis Of Potential Photo-Activatable Cathepsin K Inhibitors, Khalin Evania Nisbett

Wayne State University Theses

Abstract

DESIGN, SYNTHESIS AND ANALYSIS OF POTENTIAL PHOTO-ACTIVATABLE CATHEPSIN K INHIBITORS

by

KHALIN NISBETT

May 2017

Advisor: Dr. Jeremy Kodanko

Major: Chemistry

Degree: Master of Science

Tightly regulated cysteine CA proteases play a major role in maintaining the homeostasis within cells. Subsequently, when these proteases are dysregulated and mislocalized they disrupt healthy cell dynamics and contribute to many life-threatening pathologies such arteriosclerosis, osteoporosis and cancer. As such many pharmaceutical companies and research teams are highly interested in these proteases as targets. One emergent strategy is the spatiotemporal control of biological processes. In relation to this, a series of spatiotemporally controlled …

Elucidating Structure, Function, And Small Molecular Interactions Of Human Immunodeficiency Virus And Chikungunya Virus, Kristin Nicole Slater

Wayne State University Theses

Abstract HIV-1:

Human immunodeficiency virus-1 (HIV-1) is a widespread, incurable retrovirus known to cause

immunodeficiency and a shortened life span. Despite successful treatment methods, HIV-1

frequently mutates, resulting in antiviral resistance. Many therapies target the HIV-1 protease

(PR), which is responsible for cleaving the viral polyprotein essential for its life cycle. HIV-1 PR

often evades treatment by way of mutations and less commonly through residue insertions. We

have identified a clinical isolate with a five residue insertion between residues 28 and 29.

Through molecular dynamics simulations we analyzed the protease protein structure and

determined that the residue insertion created a …

Primate Proteomic Composition Of Seminal Plasma And Prostate-Specific Transglutaminase Activity In Relation To Sexual Selection., Amanda M.C. Zielen

Electronic Theses and Dissertations

Humans (Homo sapiens), chimpanzees (Pan troglodytes), and gorillas (Gorilla gorilla) have diverse mating systems with varying levels of sperm competition. Several seminal plasma genes have been claimed to evolve under positive selection, while others are altered or lost. This study aims to identify biologically relevant differences among seminal plasma proteomes of primates in relation to mating systems and previous genomic studies. Seminal plasma from three individuals of each species were run in triplicate in shotgun liquid chromatography – tandem mass spectrometry (LC-MS/MS) and confirmed with Western blots. Over 7,000 peptides were identified across all …

The Human Mitochondrial Chaperonin: It Takes Two Single-Rings To Tango, Adrian Sergio Enriquez

Open Access Theses & Dissertations

The human mitochondrial chaperonin is a macromolecular machine that catalyzes the proper folding and assembly of newly imported mitochondrial proteins into their biologically active state. It is composed of two proteins from the highly conserved heat shock protein family, hsp10 and hsp60, that assemble into large oligomeric complexes responsible for mediating the folding of non-native polypeptides in an ATP dependent manner. In addition to its innate role in protein folding, human mitochondrial hsp60 has been implicated in numerous moonlighting cellular activities that have been linked to diseases conditions such as cancer and neurodegeneracy. In light of its cellular importance, the …

Using Low-Coherence Interferometry To Monitor Cell Invasion In An In-Vitro Model System, Behnaz Davoudi Nasab

Honors Undergraduate Theses

In an optically random system, such as naturally occurring and man-made media, light undergoes pronounced multiple scattering. This phenomenon has shown a remarkable potential in characterizing complex materials. In this regime, scattering occurs from each individual center of the scattering and independent scattering events lead to multiple light scattering. This phenomenon is often described as a random walk of photons and can be modeled in terms of a diffusion equation based on the radiative transfer theory. In this thesis, we used optical path-length spectroscopy (OPS), which is an experimental method to obtain the path-length probability density of the propagating light …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

The E. Coli Protein Ybgl: A Novel Dna Repair Enzyme?, Mason H. Conen, Brooke D. Martin, Kent Sugden, Savannah Whitfield

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Cr(V) is a carcinogen that oxidizes guanine aggressively to form spiroiminodihydantion (Sp) and guanidinohydantoin (Gh), both of which contain an unusual hydantoin moiety that cause G→T transversion mutations at a high rate. Endonuclease VIII (nei) can recognize and excise these oxidation products from DNA and is translated as one of five protein products of the Nei operon in Escherichia coli (E. coli). However, the functions of the other four proteins remain unknown. To address this gap in knowledge, we focused on one of the four that immediately precedes nei, the ybgL protein. Previous work by our group has suggested a …

Investigation Of The Mechanism Of Action For Mithramycin And The Biosynthesis Of L-Rednose In Saquayamycins, Stevi Weidenbach

Theses and Dissertations--Pharmacy

Natural products continue to be a major chemical lead matter for drug discovery due to their diverse chemical structures and bioactivities. Clinically significant natural products include anti-cancer and anti-infective compounds and while many more of these compounds show promising bioactivity, their clinical relevance is often limited by toxicity or poor solubility. Combinatorial biosynthesis can be employed to modify existing chemical scaffolds towards reducing these limitations. To fully take advantage of these biochemical tools, it is important to understand the biosynthesis and mechanism of action of the molecules.

Saccharides in glycosylated natural products provide specific interactions with cellular targets and are …

Ligands Of Therapeutic Utility For The Liver X Receptors., Rajesh Komati, Dominick Spadoni, Shilong Zheng, Jayalakshmi Sridhar

Faculty and Staff Publications

Liver X receptors (LXRs) have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. …

Chemical Profiling And Chemical Standardization Of Vitex Negundo Using 13c Nmr, Fabian M. Dayrit, Lolita G. Lagurin, John Daniel J. Magsalin, Anthony R. Zosa

Chemistry Faculty Publications

Chemical profiling and standardization of the defatted methanol extract of the leaves of Vitex negundo L. were carried out using 13C nuclear magnetic resonance (NMR) analysis followed by chemometric analysis of the chemical shift data. Chemical profile was obtained using a k-means cluster profile and chemical standardization which was achieved using a multivariate control chart. The V. negundo samples were made up of four groups: the training set, submitted samples from production farms, commercial samples, such as tablets, capsules and teas, and experimental samples (samples which were allowed to degrade). Four groups were generated in k-means cluster, which generally corresponded …

Exosomes Serve As Novel Modes Of Tick-Borne Flavivirus Transmission From Arthropod To Human Cells And Facilitates Dissemination Of Viral Rna And Proteins To The Vertebrate Neuronal Cells, Wenshuo Zhou, Michael Woodson, Biswas Neupane, Fengwei Bai, Michael B. Sherman, Kyung H. Choi, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Molecular determinants and mechanisms of arthropod-borne flavivirus transmission to the vertebrate host are poorly understood. In this study, we show for the first time that a cell line from medically important arthropods, such as ticks, secretes extracellular vesicles (EVs) including exosomes that mediate transmission of flavivirus RNA and proteins to the human cells. Our study shows that tick-borne Langat virus (LGTV), a model pathogen closely related to tick-borne encephalitis virus (TBEV), profusely uses arthropod exosomes for transmission of viral RNA and proteins to the human- skin keratinocytes and blood endothelial cells. Cryo-electron microscopy showed the presence of purified arthropod/neuronal exosomes …

End-To-End Molecular Communication Channels In Cell Metabolism: An Information Theoretic Study, Zahmeeth Sayed Sakkaff, Jennie L. Catlett, Mikaela Cashman, Massimiliano Pierobon, Nicole R. Buan, Myra B. Cohen, Christine A. Kelley

Department of Biochemistry: Faculty Publications

The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and …

Portulaca Oleracea Extract Can Inhibit Nodule Formation Of Colon Cancer Stem Cells By Regulating Gene Expression Of Notch Signal Transduction Pathway, Li Chen

Dissertations, Master's Theses and Master's Reports

The main aim of this study was to investigate the effects of Portulaca oleracea extract on tumor formation in colon cancer stem cells and chemotherapy sensitivity. In addition, this study analyzed the genetic changes within the Notch signal transduction pathway associated with the effects of the extracts. Serum-free cultures of colon cancer cells (HT-29) and HT-29 stem cells were treated with the chemotherapeutic drug 5-FU to assess sensitivity. Injections of the stem cells were also given to BALB/c mice to confirm tumor growth and characteristics. In addition, the effect of different concentrations of P. oleracea extract was tested on the …

Heterologous Expression And Purification Of Full-Length Human Polybromo-1 Protein, Sarah Hopson

Dissertations, Master's Theses and Master's Reports

Over the past decade, it has become apparent that the human polybromo-1 protein (BAF180) has a critical role in cancer. BAF180 is known to be a driver mutation in clear cell renal cell carcinoma, where it has been found to be mutated in approximately 40% of cases. Mutations have also been found in several other cancers, including intrahepatic cholangiocarcinomas and epithelioid sarcomas. BAF180 is the chromatin targeting subunit of the PBAF (Polybromo-associated BRG1-associated factor) chromatin remodeling complex, a role facilitated by its nine domains: six bromodomains, which recognize and bind to acetylated lysines on histones; two BAH (bromo-adjacent homology) domains, …

Hyper-Activation Of Pp60(Src) Limits Nitric Oxide Signaling By Increasing Asymmetric Dimethylarginine Levels During Acute Lung Injury, Sanjiv Kumar, Xutong Sun, Satish Kumar Noonepalle, Qing Lu, Evgeny Zemskov, Ting Wang, Saurabh Aggarwal, Christine Gross, Shruti Sharma, Ankit A. Sesai, John D. Catravas

Bioelectrics Publications

The molecular mechanisms by which the endothelial barrier becomes compromised during lipopolysaccharide (LPS) mediated acute lung injury (ALI) are still unresolved. We have previously reported that the disruption of the endothelial barrier is due, at least in part, to the uncoupling of endothelial nitric oxide synthase (eNOS) and increased peroxynitrite-mediated nitration of RhoA. The purpose of this study was to elucidate the molecular mechanisms by which LPS induces eNOS uncoupling during ALI. Exposure of pulmonary endothelial cells (PAEC) to LPS increased pp60^Src activity and this correlated with an increase in nitric oxide (NO) production, but also an increase in …

Toward Biochemical Conversion Of Lignocellulose On-Farm: Pretreatment And Hydrolysis Of Corn Stover In Situ, Alicia A. Modenbach, Sue E. Nokes, Michael D. Montross, Barbara L. Knutson

Biosystems and Agricultural Engineering Faculty Publications

High-solids lignocellulosic pretreatment using NaOH followed by high-solids enzymatic hydrolysis was evaluated for an on-farm biochemical conversion process. Increasing the solids loadings for these processes has the potential for increasing glucose concentrations and downstream ethanol production; however, sequential processing at high-solids loading similar to an on-farm cellulose conversion system has not been studied. This research quantified the effects of high-solids pretreatment with NaOH and subsequent high-solids enzymatic hydrolysis on cellulose conversion. As expected, conversion efficiency was reduced; however, the highest glucose concentration (40.2 g L^-1), and therefore the highest potential ethanol concentration, resulted from the high-solids combined pretreatment …

Sex Differences In The Subjective Effects Of Oral Δ9-Thc In Cannabis Users, Jessica S. Fogel, Thomas H. Kelly, Philip M. Westgate, Joshua A. Lile

Behavioral Science Faculty Publications

Previous studies suggest that there are sex differences in endocannabinoid function and the response to exogenous cannabinoids, though data from clinical studies comparing acute cannabinoid effects in men and women under controlled laboratory conditions are limited. To further explore these potential differences, data from 30 cannabis users (N=18 M, 12 F) who completed previous Δ⁹-tetrahydrocannabinol (Δ⁹-THC) discrimination studies were combined for this retrospective analysis. In each study, subjects learned to discriminate between oral Δ⁹-THC and placebo and then received a range of Δ⁹-THC doses (0, 5, 15 and a “high” dose of …

Metabolic Reprogramming Of Human Lung Cancer Cells And Ex Vivo Tissues Revealed By Uhr-Ftms Analysis Of Small Amino And Carboxyl Metabolites, Ye Yang

Theses and Dissertations--Toxicology and Cancer Biology

Studies were carried out to understand how human lung cancer cells and human ex vivo lung cancer tissues that are metabolically reprogramed compared with analogous non-cancer cells or non-cancer tissues. A Stable isotope resolved metabolomics (SIRM) approach was used to fulfill this aim by employing ¹³C, ²H or ¹⁵N labeled metabolic precursors like ¹³C₆-Glc, ¹³C₂-Gly, ²H₂-Gly, ²H₃-Ser, ¹³C₅, ¹⁵N₂-Gln to trace the flow of the labeled atoms into the down stream metabolic network. NMR and mass spectrometry are two …

Synthesis And Characterization Of Amide Linked Triazolyl Glycolipids As Molecular Hydrogelators And Organogelators, Guijun Wang, Anji Chen, Hari P. R. Mangunuru, Jayasudhan Reddy Yerabolu

Chemistry & Biochemistry Faculty Publications

Carbohydrate based small molecular gelators are important classes of compounds which can form useful soft materials with many practical applications. Although many different types of effective gelators have been reported, the rational design of a molecular hydrogelator is still challenging. In this research, we combined the structural features of two classes of monosaccharide based molecular gelators and obtained a new class of glycolipids that can function as molecular gelators. These new compounds were synthesized by introducing a triazole functional group to a protected 2-glucosamine through Cu(i) catalyzed azide/alkyne cycloaddition reaction (CuAAC). A series of eighteen new glycolipids containing 4,6-O …