Biochemistry, Biophysics, and Structural Biology Commons^™

Biomuta And Bioxpress: Mutation And Expression Knowledgebases For Cancer Biomarker Discovery, Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Kashay

Biochemistry and Molecular Medicine Faculty Publications

Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated single-nucleotide variations, and BioXpress, a database of cancer-associated differentially expressed genes and microRNAs, differ from other disease-associated variation and expression databases primarily through the aggregation of data across many studies into a single source with a unified representation and annotation of functional attributes. Early versions of these resources were initiated by pilot funding for specific research …

Nanoparticle Targeting To The Central Nervous System, Emily Baker

Williams Honors College, Honors Research Projects

Drug delivery to the central nervous system is complicated by the blood-brain barrier, a vascular structure that prevents free diffusion of molecules into brain tissue. In this study, we examined the in vitro properties of a nanoparticle-based drug delivery system. We used several nanoparticle formulations, both LTP based and PLGA based, to test the cellular uptake and toxicity in microglial cells. Using immunofluorescence imaging, we show that LTP nanoparticles are taken up by microglia. We confirmed that our nanoparticle formulations are non-toxic by two cell viability assays. These results suggest that nanoparticle formulations may be a biocompatible method of delivering …

Dream Of A Conducive Learning Environment: One Dreem For All Medical Students!, Rehana Rehman, Kulsoom Ghias, Syeda Sadia Fatima, Mehwish Hussain, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To compare students' response assessed by Dundee Ready Educational Environment Measure on the basis of the year of study, gender and pre-medical educational background.Methods: This cross-sectional study was carried out at the Aga Khan University Medical College, Karachi, Pakistan, from June 2014 to March 2015, and comprised medical students. The average scores of Dundee Ready Educational Environment Measure scales and subscales were compared between gender and educational background. Responses were also compared on the basis of year of study.Results: Of the 416 participants, 184 (44%) were males and 232 (56%) were females. There were 100 (24%) students in the …

A New Model For Phd Elective Course, H R. Ahmad, Satwat Hashmi, M H. Mahmood

Department of Biological & Biomedical Sciences

No abstract provided.

Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor

Honors Theses

Molecular dynamics (MD) simulations and computational chemistry allow for an atomistic understanding of protein-protein and protein-ligand binding motifs. Through the use of MD, medicinally relevant complexes can be examined in detail unattainable by experimental methods. Within this work, systems pertinent to both Alzheimer’s Disease and HIV-1 are probed and thoroughly sampled to help elucidate potential therapeutic pathways. We used molecular dynamics and free energy estimations to gauge the affinity for the binary and ternary complexes of KLC1, APP and JIP1, three proteins all believed to be involved in the propagation of Alzheimer’s Disease. Two areas of thought exist suggesting that …

Myeloperoxidase-Mediated Protein Lysine Oxidation Generates 2- Aminoadipic Acid And Lysine Nitrile In Vivo, Hongqiao Lin, Bruce S. Levison, Jennifer A. Buffa, Ying Huang, Xiaoming Fu, Zeneng Wang, Valentin Gogonea, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

Recent studies reveal 2-aminoadipic acid (2-AAA) is both elevated in subjects at risk for diabetes and mechanistically linked to glucose homeostasis. Prior studies also suggest enrichment of protein-bound 2-AAA as an oxidative post-translational modification of lysyl residues in tissues associated with degenerative diseases of aging. While in vitro studies suggest redox active transition metals or myeloperoxidase (MPO) generated hypochlorous acid (HOCl) may produce protein-bound 2-AAA, the mechanism(s) responsible for generation of 2- AAA during inflammatory diseases are unknown. In initial studies we observed that traditional acid- or basecatalyzed protein hydrolysis methods previously employed to measure tissue 2-AAA can artificially generate …

Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista

Honors Undergraduate Theses

Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, …

Characterizing The Function Of The N-Terminal Domain Of Omi/Htra2, Christine Nguyen

Honors Undergraduate Theses

The yeast two-hybrid system was used to isolate and characterize protein interactors of the N-terminal domain of the serine protease Omi/HtrA2 (high temperature requirement protein A2) encompassing amino acids 31-133. This large domain of Omi/HtrA2 is usually cleaved and removed through autoproteolysis to produce the mature form of the protein. Whether the N-terminal domain has any function after its removal is unknown. Omi/HtrA2 is involved in a variety of diseases including cancers, neurodegenerative disorders, and metabolic disorders, but thus far, it is assumed that its normal function is the degradation of specific substrates. To characterize any potential function of Omi/HtrA2’s …

A Family Of Genus-Specific Rnas In Tandem With Dna-Binding Proteins Control Expression Of The Bada Major Virulence Factor Gene In Bartonella Henselae, Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson

Molecular Biosciences Faculty Publications

Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each …

Transposon-Mediated Stable Suppression Of Gene Expression In The Developing Chick Retina, Masaru Nakamoto, Chizu Nakamoto

Biology Faculty Publications

The embryonic chick has long been a favorite model system for in vivo studies of vertebrate development. However, a major technical limitation of the chick embryo has been the lack of efficient loss-of-function approaches for analyses of gene functions. Here, we describe a methodology in which a transgene encoding artificial microRNA sequences is introduced into embryonic chick retinal cells by in ovo electroporation and integrated into the genome using the Tol2 transposon system. We show that this methodology can induce potent and stable suppression of gene expression. This technique therefore provides a rapid and robust loss-of-function approach for studies of …

Exploring The Physics Of Proteins At Molecular Level By Neutron And X-Ray Scattering, Utsab Raj Shrestha

Wayne State University Dissertations

The protein structures revealed by the crystallographic studies have provided the valuable information over the years regarding their biological functions. However, such snapshots of protein fluctuations averaged over time may not be enough to fully capture the underlying biological phenomena. A deeper understanding of the protein dynamics is crucial for elucidating the structural pathways or the transition mechanism from the initial state to the final state necessary for regulating the physical and chemical processes. Hence, the biological activities and functions are mainly governed by the protein conformational dynamics. However, the direct correlation of a wide range of protein dynamics to …

Real-Time Investigation Of Bulky Lesion Bypass By Y-Family Dna Polymerase, Dpo4, Using Single Molecule Fret, Pramodha Liyanage

Wayne State University Dissertations

DNA is constantly exposed to various DNA damaging agents that are generated by various internal and external sources. Some of this damage may not be able to be repaired by cellular machineries causing DNA replication to be blocked. Once the replication fork is blocked by a DNA adduct, damage tolerance DNA polymerases, mainly Y-family, are able to restore the DNA replication by synthesizing past the DNA adduct. Benzo[a]pyrene (B[a]P) is one of the most studied environmental carcinogens. It is known to make covalent DNA adducts after metabolic activation and the bulkiness of the B[a]P adducts impose a strong barrier to …

Frnk Regulatory Complex Formation With Fak Is Regulated By Erk Mediated Serine 217 Phosphorylation, Taylor J. Zak

Dissertations

Focal adhesion kinase related non-kinase (FRNK) is an endogenous inhibitor of focal adhesion kinase (FAK) that has traditionally been used to inhibit FAK signaling in a variety of experiments and is also an important endogenous regulator of FAK signaling. More recently, FRNK has been shown to be of increasing importance in some pathologic conditions. Despite the increasing importance of FRNK, the molecular mechanism by which it functions remains unclear. In addition, FRNK contains several phosphorylation sites with unknown importance and function. Here I hypothesize that FRNK can inhibit FAK by binding directly to FAK within focal adhesions. Furthermore, I propose …

Characterization Of Quorum-Quenching Lactonases And Plp-Dependent Aminotransferases: Structure, Mechanism And Alternative Turnover, Romila Nina Mascarenhas

Dissertations

Cell-to-cell communication by bacteria is essential for the regulation of gene expression important in colonization, biofilm formation, virulence and other processes. This communication is called "quorum-sensing" and is mediated by small molecules called autoinducers. One major class of autoinducers used by gram-negative bacteria is N-acyl homoserine lactones (AHL's). Enzymes capable of disrupting this communication are called "quorum-quenching" catalysts and have proven to be invaluable biochemical tools for understanding quorum-sensing pathways. Quorum-quenching enzymes hold promise for application in anti-biofouling, agriculture, aquaculture, bioremediation and other synthetic biology settings. However, the mechanisms that these enzymes use to recognize and process their substrates are …

Isolation And Spectroscopic Characterization Of Zn(Ii), Cu(Ii), And Pd(Ii) Complexes Of 1,3,4-Thiadiazole-Derived Ligand, Dariusz Karcz, Arkadiusz Matwijczuk, Bozena Boron, Bernadette Creaven, Leszek Fiedor, Andrzej Niewiadomy, Mariusz Gagos

Articles

A series of complexes incorporating Zn(II), Cu(II), and Pd(II) ions, and 4-(5-heptyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (L1) as model ligand, was synthesized in order to examine the nature of potential interactions between biologically active ligands, 1,3,4-thiadiazoles and metal ions with proven biological relevance. The structures of the compounds isolated were characterized using a number of spectroscopic methods including IR, Uv–vis, AAS, steady state and time-resolved fluorescence (TRF). The results obtained suggest that the L1-Zn(II) and L1-Pd(II) complexes consist of one molecule of L1 and one acetate ion acting as ligands, while the L1-Cu(II) complex adapts a 2:1 (L1: metal) stoichiometry. The coordination of L1 …

Towards The Complete Proteinaceous Regulome Of Acinetobacter Baumannii, Leila G. Casella, Andy Weiss, Ernesto Pérez-Rueda, J Antonio Ibarra, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so …

The Role Of Oxidation-Sensitive Nociception And Epigenetics In Endometriosis-Associated Pain, Kristeena Ray Wright

Theses, Dissertations and Capstones

Endometriosis is an enigmatic disease that is associated with severe symptoms and consequences such as total hysterectomy. Upwards of 10% of women of reproductive age have endometriosis, most of whom are afflicted with chronic pelvic pain and/or infertility. Despite many treatment options available to endometriosis patients, there is no cure for this condition and recurrence of symptoms is extremely common. In CHAPTER 1, we describe the mechanisms involved in endometriotic pain and the currently available treatment strategies. Our laboratory has provided evidence for the role of oxidative stress in the etiology of endometriosis and its associated pain. In this dissertation …

Erk3 As A Braf-Regulated Tumor Suppressor Is A New Potential Cancer Target In Melanoma, Minyi Chen

Browse all Theses and Dissertations

Melanoma is the highest mortality rate skin cancer and the sixth most common cancer in the U.S..[1, 2] Arising from melanocytes, melanoma is known for frequent mutation of BRAF to its constitutive activation state BRAFV600E, thus over-activating its downstream MAPK targets ERK1/2 and contributing to melanoma progression.[3, 4, 5] ERK3, a less studied MAPK family protein which contributes to promoting lung, breast, cervical, head and neck (HNC) cancer metastasis, has also shown a correlation with upregulation of BRAF.[6, 7, 8, 9] However, the BRAF-ERK3 regulatory mechanism and the function of ERK3 in melanoma are still unclear. Here, we first elucidate …

Urinary Metabolomics To Detect Polycystic Kidney Disease At Early Stage, Amnah Mahmoud Obidan

Browse all Theses and Dissertations

Urinary metabolomics abilities in detection of biological effects (i.e., toxicity, disease) is compounded by high background variability. Previously, we showed mild kidney dysfunction was detectable under the stress imposed by furosemide (diuretic). Here we tested whether furosemide (FUR) can enhance the sensitivity to detect autosomal dominant polycystic kidney disease (ADPKD) at an early stage. ADPKD is one of the most common inherited renal disorders and is characterized by the growth of numerous cysts in the kidneys. Urinary metabolomics analyses, using nuclear magnetic resonance (NMR) spectroscopy, were conducted in control (WT) and diseased mice (RC) at 7 and 24 weeks of …

Identification Of Expression And Function Of The Glucagon-Like Peptide-1 Receptor In Gastrointestinal Smooth Muscle, Alexander T. May

Theses and Dissertations

In response to ingestion of nutrients, enteroendocrine L cells secrete the incretin hormone, glucagon-like peptide-1 (GLP-1), to enhance glucose-dependent insulin release. Therapies related to GLP-1 are approved for type 2 diabetes. The GLP-1 receptor (GLP-1R) is expressed in cells of the gastrointestinal tract and elsewhere. In pancreatic beta cells, GLP-1R are coupled to the Gs/cAMP/PKA pathway. The expression and function of GLP-1R in gastrointestinal smooth muscle are not known. Aim. To test the hypothesis that GLP-1 regulates smooth muscle function by acting on GLP-1R expressed on smooth muscle. Methods. Smooth muscle cells (SMC) were isolated and cultured. Expression of GLP-1R …

Novel Role Of The Nociceptin System As A Regulator Of Glutamate Transporter Expression In Developing Astrocytes, Logan Meyer

Theses and Dissertations

Our previous results showed that oligodendrocyte development is regulated by both nociceptin and its G-protein coupled receptor, the nociceptin/orphanin FQ receptor (NOPR). The present in vitro and in vivo findings show that nociceptin plays a crucial conserved role in both human and rodent brain astrocytes, regulating the levels of the glutamate/aspartate transporter GLAST/EAAT1. This nociceptin-mediated response takes place during a critical developmental window that coincides with astrocyte maturation and synapse formation. GLAST/EAAT1 upregulation by nociceptin is mediated by NOPR and the downstream participation of a complex signaling cascade that involves the interaction of several kinase systems, including PI-3K/AKT, mTOR and …

N-Alkyl 4-Methylamphetamine Enantiomers And The Implication For Potential Modulation Of Abuse Liability And Enhancement Of Psychoactive Drug Targeting., Ramsey Sitta

Theses and Dissertations

Drugs of abuse have a long history in humanity. Currently however, a subject of great interest is the phenylalkylamine family of drugs. Not only is the abuse liability of interest but also the potential therapeutic expansion of the capabilities of this family of drugs by utilizing the unique stereospecific effects of the newly discovered hybrid compounds. Based upon prior data of N-Alkyl 4-MA the enantiomers of N-Methyl, N-Ethyl, and N-Propyl were analyzed in hDAT, hNET, and hSERT. It was found that there was a negative correlation between chain length and potency and dopaminergic component. In agreement with the currently established …

Design, Synthesis And Biological Screening Of Novel Cucsinspired Estrone Analogues Towards Treatment Of Hepatocellular Carcinoma, Mater Hussen Mahnashi

Electronic Theses and Dissertations

Cucurbitacins (CUCS) are natural products with highly oxygenated tetracyclic triterpenes produced mostly by Cucurbitaceae family plant. They are known for their therapeutic efficiency with different biological activities, such as anti-inflammatory, hepatoprotective and anti-cancer. Hepatocellular carcinoma (HCC) is the third leading cause of death worldwide. Previous reports have shown the ability of CUCS to inhibit the growth of hepatocellular carcinoma cell lines (HepG-2) significantly. Structural activity relationship studies suggested the potential of the 23, 24 enone side chain of CUCS to bind to the Epidermal Growth Factor Receptor (EGFR). Due to the limited quantities of CUCS upon isolation and the challenges …

The Assembly Factor Pet117 Couples Heme A Synthase Activity To Cytochrome Oxidase Assembly, Nicholas G. Taylor, Samantha Swenson, Nicholas J. Harris, Edward M. Germany, Jennifer L. Fox, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme a is an essential metalloporphyrin cofactor of the mitochondrial respiratory enzyme cytochrome c oxidase (CcO). Its synthesis from heme b requires several enzymes, including the evolutionarily conserved heme a synthase (Cox15). Oligomerization of Cox15 appears to be important for the process of heme a biosynthesis and transfer to maturing CcO. However, the details of this process remain elusive, and the roles of any additional CcO assembly factors that may be involved remain unclear. Here we report the systematic analysis of one such uncharacterized assembly factor, Pet117, and demonstrate in Saccharomyces cerevisiae that this evolutionarily conserved protein is necessary for …

Examining Interactions Between Opsins And Carotenoid Biosynthetic Proteins In Halophilic Archaea, Alexandru M. Plesa

Honors Theses

Organisms have evolved numerous specialized molecules for constantly responding to environmental changes. Examples of such molecules are the light-driven proton-pump rhodopsins, such as bacteriorhodopsin (BR) and cruxrhodopsin (cR), and the carotenoid pigments, such as retinal and bacterioruberin. In halophilic Archaea, retinal can covalently bind bacterioopsin (BO) and cruxopsin (CO) to form the corresponding protein complexes, and its biosynthesis is indirectly controlled by the activity of the lycopene elongase (Lye) enzyme, which converts lycopene, a retinal precursor, to a form of bacterioruberin. Interestingly, opsins were shown to inhibit the activity of Lye, thereby promoting retinal biosynthesis and indirectly regulating the apoprotein-cofactor …

Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data, Michael Riffle, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, Daniel Jaschob, William S. Noble, Brook L. Nunn

OES Faculty Publications

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the …

Beyond Zar: The Use And Abuse Of Classification Statistics For Otolith Chemistry, C. M. Jones, M. Palmers, J. J. Schaffler

OES Faculty Publications

Classification method performance was evaluated using otolith chemistry of juvenile Atlantic menhaden Brevoortia tyrannus when assumptions of data normality were met and were violated. Four methods were tested [linear discriminant function analysis (LDFA), quadratic discriminant function analysis (QDFA), random forest (RF) and artificial neural networks (ANN)] using computer simulation to determine their performance when variable-group means ranged from small to large and their performance under conditions of typical skewness to double the amount of skewness typically observed. Using the kappa index, the parametric methods performed best after applying appropriate data transformation, gaining 2% better performance with LDFA performing slightly better …

Expression, Purification, And Characterization Of An Intrinsically Disordered Late Embryogenesis Abundant (Lea) Protein From Artemia Franciscana Utilizing Escherichia Coli And Nicotiana Tabacum, Md Fazlul Karim

Masters Theses

Anhydrobiosis is an astounding strategy that allows certain species (both animals and plants) to survive severe environmental conditions such as desiccation, extreme cold, or heat in the habitat. Despite the occurrence of several different molecular strategies, expression of highly hydrophilic polypeptides termed LEA proteins has been most conclusive identified as a requirement for the survival of plants and animals during periods of water stress such as freezing and drying. Several classification schemes for LEA proteins have been proposed and the brine shrimp, Artemia franciscana, is the only known animal that naturally expresses LEA proteins from three different classification groups …

Effects Of Asiatic Acid On Neurite Outgrowth In Neuro-2a Cells, Aishah Asiri

Masters Theses

Recently, medicinal plants from ancient Ayurvedic medicine have provided clues to the discovery of novel therapeutics for various diseases. In Ayurvedic medicine, a common Indian plant, Centella asiatica is highly regarded as a "rasayana" or nerve tonic. The Centella extract is used to ward off age-related dementia and to increase memory and intelligence. The mechanism by which Centella improves memory and learning and reduces the risk of dementia is unclear.

We recently tested the effects of asiatic acid, the main active component of Centella, on neuronal growth. We hypothesized that asiatic acid will promote neuronal growth and neurite network …

Enhancement Of The Physicochemical Properties Of Pt(Dien)(Nucleobase) (2+) For Hivncp7 Targeting, S. D. Tsotsoros, P. B. Lutz, A. G. Daniel, E. J. Peterson, R. E. F. De Paiva, E. Rivera, Y. Qu, C. A. Bayse, N. P. Farrell

Chemistry & Biochemistry Faculty Publications

Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]²⁺([PtN₄]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN₄ coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified …