Molecular Biology Commons^™

Restriction And Characterization Of Human Breast Cancer Using A Three-Dimensional Embryonic Stem Cell Model, Bridget Mooney

Legacy Theses & Dissertations (2009 - 2024)

Human breast cancer is currently the highest diagnosed form of cancer and the second leading cause of cancer-related deaths in American women. Triple negative breast cancer is of the basal subtype and displays the worst prognosis owing to its highly metastatic properties. Current treatments focused on eradicating breast tumors in lieu of or following local therapy include chemotherapy, hormonal therapy, and targeted therapy. Hormonal therapy is not an option for triple negative breast cancer as it does not contain hormone receptors and there are currently no approved biological targeted therapies. Chemotherapy has proven unsuccessful because triple negative breast cancer is …

Beta-Sheet Forming Peptides By Design : Control Of Folding And Applications, Gaius Takor

Legacy Theses & Dissertations (2009 - 2024)

The focus of the present research is the synthesis of polypeptides for the study of protein folding and misfolding and for the development of novel polypeptide-based optical antennas in nanotechnology. It is hypothesized that simple polypeptides can be used as models to mimic in vivo folding of globular proteins. Desired repetitive polypeptides were genetically encoded and expressed in E. coli using conventional methods and characterized using a variety of spectroscopic (including circular dichroism (CD), deep UV resonance Raman (DUVRR), UV-vis and fluorescence) and microscopic (atomic force microscopy (AFM) and transmission electron microscopy (TEM)) techniques. The polypeptides predominantly formed bilayer, fibrillar …

Effects Of High Voltage Nanosecond Electric Pulses On Eukaryotic Cells (In Vitro): A Systematic Review, Tina Batista Napotink, Matej Reberšek, P. Thomas Vernier, Babara Mali, Damijan Miklavčič

Bioelectrics Publications

For this systematic review, 203 published reports on effects of electroporation using nanosecond high-voltage electric pulses (nsEP) on eukaryotic cells (human, animal, plant) in vitro were analyzed. A field synopsis summarizes current published data in the field with respect to publication year, cell types, exposure configuration, and pulse duration. Published data were analyzed for effects observed in eight main target areas (plasma membrane, intracellular, apoptosis, calcium level and distribution, survival, nucleus, mitochondria, stress) and an additional 107 detailed outcomes. We statistically analyzed effects of nsEP with respect to three pulse duration groups: A: 1–10 ns, B: 11–100 ns and C: …

Contribution Of Cx3cr1/Fractalkine (Cx3cl1) Axis To The Progression Of Non-Small Cell Lung Cancer (Nsclc), Rhonda Prince

Wayne State University Theses

A thesis is presented on the characterization of the contribution of the chemokine axis, CX_3CR1/Fractalkine, to the progression of Non-Small Cell Lung Cancer (NSCLC). Cancer is the second leading cause of death in the United States, and Lung cancer is one of the four leading causes of the disease. Carcinoma cells, unlike their normal counterparts, gain the ability to express chemokine receptors. Understanding if/how this gain of expression contributes to the progression of cancer could provide a lucrative therapeutic target. Goals of the study include investing if the NSCLC cell line A549, an adenocarcinoma cell line, express the chemokine receptor …

Characterization Of The Yeast Cysteine Desulfurase Complex Within The Mitochondrial Fe-S Cluster Biogenesis, Dulmini Pabasara Barupala

Wayne State University Dissertations

Disrupted iron homeostasis within the human body materializes as various disorders. Pathophysiology of many of them relates to iron induced oxidative damage to key cellular components caused by iron accumulation within the tissues. Pertaining to the growing occurrence, cost of patient care and devastating burden associated with these diseases, the call for understanding the role of iron homeostasis within these disorders becomes inevitable. Being an abundant iron containing cofactor, the role of Fe-S clusters in cellular iron homeostasis is indisputable in the case of Friedreich’s ataxia, a disease caused by a deficiency in the protein frataxin that is indispensable during …

A Requirement For Y841 In Jak3 Enzymatic Activity And Hematopoietic Cancers, George Steven Martinez

Open Access Theses & Dissertations

A medical need exists for successfully treating people afflicted with leukemia, especially those who develop drug resistant forms. Relapse leukemia cases are particularly high within Hispanic populations where this disease is among the most frequently occurring cancer. Fourteen somatic mutations have been reported in Janus tyrosine kinase 3 (Jak3), including M511I and A573V, from patients with various forms of leukemia. To monitor drug sensitivity, a model system was developed. Indeed, many of these mutations have been shown to possess transforming ability in cell lines such as the IL-3 dependent pro-B cell line Ba/F3. As such, Ba/F3 cells were transformed to …

Characterization Of Hemerythrin-Like Protein Rv2633c, Michelle D. Cherne

Honors Undergraduate Theses

Hemerythrin-like protein Rv2633c is a small 18 kDa protein that is expressed in Mycobacterium tuberculosis (Mtb). Sequence analysis of Rv2633c predicts the presence of a hemerythrin-like domain, which binds dioxygen using a µ-oxo-bridge (Fe-O-Fe), rather than a heme group. Though it is noticeably upregulated during macrophage infection and during in vitro acidification, the role of Rv2633c in Mtb survival has yet to be elucidated. This project aims to characterize the function of Rv2633c by studying the in vitro response of the recombinant protein to conditions present in the macrophage lysosome, such as reduced oxygen levels or the …

Aptameric Sensors: In Vitro Selection Of Dna That Binds Bromocresol Purple, Derek B. Miller

Honors Undergraduate Theses

Aptamers being used as sensors is an emerging field that has capabilities of being tomorrow’s diagnostic tools. As aptameric sensors have become more popular, their visualization systems have been limited. The majority of today’s aptameric sensors require expensive machinery such as a fluorometer in order to visualize results. We propose a system that will cut the need for instrumentation and be detected via the naked eye. With the selection of an aptamer to bind the pH indicating dye bromocresol purple (BCP) this may be achieved. When rendered active, the binding towards BCP will facilitate a color change from yellow to …

Enabling Method To Design Versatile Biomaterial Systems From Colloidal Building Blocks, Shalini Saxena, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Development of materials with fine spatial control over topographical, mechanical, or chemical features has been investigated for a variety of applications. Here we present a method to fabricate an array of polyelectrolyte constructs including two-dimensionally and three-dimensionally patterned assemblies using both compressible and incompressible colloidal building blocks. This method eliminates prior constraints associated with specific chemistries, and can be used to develop modular, multi-component, patterned assemblies. In particular, development of constructs were investigated using microgels, which are colloidally stable hydrogel microparticles, polystyrene (PS) beads, and PS-microgel core-shell building blocks in conjunction with the polycation poly(ethyleneimine) (PEI). The topography, mechanical properties, …

A Chiroptical Molecular Sensor For Ferrocene, Marco Agnes, Andrea Nitti, Douglas A. Vander Griend, Daniele Dondi

University Faculty Publications and Creative Works

A homochiral, square-shaped, D2 symmetrical nanosized metal-linked macrocycle is able to form stable complexes with ferrocene in polar solvents, with detection achieved by means of multiple outputs (optical/chiroptical spectroscopies and cyclic voltammetry). Selective sensing using chiroptical spectroscopy in the presence of interfering analytes is demonstrated.

Elucidating Proteasome Catalytic Subunit Composition And Its Role In Proteasome Inhibitor Resistance, Kimberly C. Carmony

Theses and Dissertations--Pharmacy

Proteasome inhibitors bortezomib and carfilzomib are FDA-approved anticancer agents that have contributed to significant improvements in treatment outcomes. However, the eventual onset of acquired resistance continues to limit their clinical utility, yet a clear consensus regarding the underlying mechanisms has not been reached.

Bortezomib and carfilzomib are known to target both the constitutive proteasome and the immunoproteasome, two conventional proteasome subtypes comprising distinctive sets of catalytic subunits. While it has become increasingly evident that additional, ‘intermediate’ proteasome subtypes, which harbor non-standard mixtures of constitutive proteasome and immunoproteasome catalytic subunits, represent a considerable proportion of the proteasome population in many cell …

Towards Elucidation Of The Mechanism Of Biological Nanomotors, Zhengyi Zhao

Theses and Dissertations--Pharmacy

Biological functions such as cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging, and cell entry all involve biomotor-driven DNA translocation. In the past, the ubiquitous biological nanomotors were classified into two categories: linear and rotation motors. In 2013, we discovered a third type of biomotor, revolving motor without rotation. The revolving motion is further found to be widespread among many biological systems. In addition, the detailed sequential action mechanism of the ATPase ring in the phi29 dsDNA packaging motor has been elucidated: ATP binding induces a conformational entropy alternation of ATPase …

Molecular And Biochemical Signaling Underlying Arabidopsis-Bacterial/Virus/Fungal Interactions, Mohamed H. El-Shetehy

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is a form of inducible defense response triggered upon localized infection that confers broad-spectrum disease resistance against secondary infections. Several factors are known to regulate SAR and these include phenolic phytohormone salicylic acid (SA), phosphorylated sugar glycerol-3-phosphate (G3P), and dicarboxylic acid azelaic acid (AzA). This study evaluated a role for free radicals nitric oxide (NO) and reactive oxygen species (ROS) in SAR. Normal accumulation of both NO and ROS was required for normal SAR and mutations preventing NO/ROS accumulation and/or biosynthesis compromised SAR. A role for NO and ROS was further established using pharmacological approaches. Notably, …

Repositioning Of Drugs Using Open-Access Data Portal Dtome: A Test Case With Probenecid (Review), Mohammad U. Ahmed, Dylan J. Bennett, Tze-Chen Hsieh, Barbara B. Doonan, Saba Ahmed, Joseph M. Wu

NYMC Faculty Publications

The one gene-one enzyme hypothesis, first introduced by Beadle and Tatum in the 1940s and based on their genetic analysis and observation of phenotype changes in Neurospora crassa challenged by various experimental conditions, has witnessed significant advances in recent decades. Much of our understanding of the association between genes and their phenotype expression has benefited from the completion of the human genome project, and has shown continual transformation guided by the effort directed at the annotation and characterization of human genes. Similarly, the idea of one drug‑one primary disease indication that traditionally has been the benchmark for the labeling and …

Computational Studies Of Paradifluorobenzene Cations And Hydrogen Cyanide Molecule, John C. Rowe Iv

Honors Theses

Polycyclic aromatic hydrocarbons (PAHs) are hypothesized to comprise a significant portion of interstellar carbon identified from the Diffuse Interstellar Bands (DIBs). Gas phase cation-molecule reactions between compounds that previously existed as weakly bound species provides the best explanation for the emergence of PAHs in the interstellar medium (ISM). In this work, we use computational methods to characterize one of these weakly-bound systems. We discovered that intramolecular charge distribution (calculated using the Natural Population Analysis) dictate the complexes formed between a paradifluorobenzene cation and either one or two HCN molecules. Additionally, the relative stabilities of the complexes and the binding energies …

Characterization Of Catecholamine Receptors And Transporters In Murine Macrophages, Elizabeth Gonye

Honors Theses

Macrophages are a critical part of the immune response. When circulating monocytes move into tissues they differentiate int macrophages to mount the first line of defense against pathogens.

Calcium (Ii) Catalyzed Nitrone Additions, Elizabeth A. Congdon

Honors Theses

Calcium(II) complexes have be shown to be successful catalysts for nitrone reactions. The addition of n-­‐methyl and n-­‐phenyl nitrones to donor-­‐acceptor cyclopropanes was achieved with calcium triflate (Ca(OTf). Differentially substituted tetrahydro-­‐1,2-­‐oxazines were synthesized in good to excellent yields. Calcium triflate was also found to catalyze the addition of silyl enol ethers to n-­‐phenyl nitrones along the Mukaiyama-­‐Mannich addition pathway. B-­‐amino carbonyls were synthesized from a variety of substituted nitrones. Bulky and cyclic silyl enol ethers were also found to be reactive, the products of which were isolated in good to excellent yields.

Impact Of Vector Range Expansion On Pathogen Transmission Dynamics Of Lyme Disease In Southwestern Virginia, Bishan Bhattarai

Honors Theses

Blacklegged ticks, Ixodes scapularis is the primary vector of Lyme disease in eastern United States. Borrelia Burgdorfei, the etiological agent of Lyme disease is transferred by ticks of Ixodes species. In recent years, its congener, Ixodes affinis has been expanding its range northwards from its southern population. We were interested in studying how the introduction of this new vector affected the interaction between the pathogen genotype and the host. We hypothesized that differential host use by I. affinis and I. scapularis would partly explain observed differences in B. burgdorferi infection prevalence and genotypic structure in southeastern Virginia. The result …

Novel Cell Penetrating Peptide-Adaptors Effect Intracellular Delivery And Endosomal Escape Of Protein Cargos, John C. Salerno, Verra M. Ngwa, Scott J. Nowak, Carol A. Chrestensen, Allison N. Healey, Jonathan L. Mcmurry

Faculty Articles

The use of cell penetrating peptides (CPPs) as biomolecular delivery vehicles holds great promise for therapeutic and other applications, but development has been stymied by poor delivery and lack of endosomal escape. We have developed a CPP-adaptor system capable of efficient intracellular delivery and endosomal escape of user-defined protein cargos. The cell penetrating sequence of HIV transactivator of transcription was fused to calmodulin, which binds with subnanomolar affinity to proteins containing a calmodulin binding site. Our strategy has tremendous advantage over prior CPP technologies because it utilizes high affinity noncovalent, but reversible coupling between CPP and cargo. Three different cargo …

Chlamydia Trachomatis Transformants Show A Significant Reduction In Rates Of Invasion Upon Removal Of Key Tarp Domains, Christopher Parrett

Electronic Theses and Dissertations

Chlamydia trachomatis is an obligate, intracellular bacterium which is known to cause multiple human infections including nongonococcal urethritis (serovars D-K), lymphogranuloma venereum (serovars L1, L2, L3) and trachoma (serovars A-C). The infectious form of the bacterium, called the elementary body (EB), harbors a type III secreted effector known as Tarp (translocated actin recruiting phosphoprotein) which is a candidate virulence factor and is hypothesized to play a role in C. trachomatis' ability to invade and grow within epithelial cells in a human host. C. trachomatis L2 Tarp harbors five unique protein domains which include the Phosphorylation Domain, the Proline Rich Domain, …

Comparative Proteomic Analysis Of Extracellular Vesicles From Prostate Cancer-Derived Cell Lines, Gloria Polanco

Open Access Theses & Dissertations

Prostate cancer (PCa) is the leading non-cutaneous malignancy and the second deadliest among American men. PCa mortality rates among African American men are much higher than any other ethnic group, and the same is true for men of African ancestry world-wide. There is also a lack of reliable diagnostic markers and effective treatment options. Extracellular vesicles (EVs) have been observed to play an important role in cancer processes such as promotion of tumor growth and metastasis. They are also a promising source of diagnostic markers. This study addresses these problems by studying the proteome of EVs derived from PCa cells …

Identification And Characterization Of Small Molecules Targeting Fkbp52 As A Novel Treatment For Prostate Cancer, Naihsuan C. Guy

Open Access Theses & Dissertations

Prostate cancer (PCa) is one of the most commonly diagnosed diseases and the second leading cause of cancer deaths among men worldwide. Its growth is dependent upon androgen receptor (AR) signaling and the mainstay for treatment is hormone-ablation therapy using antiandrogens and/or androgen-deprivation therapies (ADT). Treatment of PCa with antiandrogens and/or ADT are initially effective; they act to repress the AR by directly competing with androgens for the ligand binding domain (LBD) and prevent activation of the receptor resulting in tumor regression. Unfortunately, the resistance to these treatments invariably emerges and results in a much more aggressive form of tumor …

Defining And Characterizing The Step In The Hiv-1 Viral Life Cycle Affected By Fullerene Derivatives, Zachary Sean Martinez

Open Access Theses & Dissertations

Fullerene derivatives, both C60 and C70, were synthesized and characterized to test their activity against HIV-1 infection. The derivatives tested have previously been reported to inhibit HIV-1 replication and/or in vitro activity of reverse transcriptase. It was found that viruses produced in the presence of low micromolar concentrations of most of these fullerene derivatives exhibit a reduction in viral infectivity greater than 99%. Quantification of virion-associated viral RNA and p24 indicates that RNA packaging and viral production were unremarkable in these viruses. These compounds did not affect infectivity of mature virions, indicating no effect on the early steps of the …

Elucidating The Molecular Mechanism Of Action By Which Rs1-208b Induces Apoptosis In Hematological Cancers, Ruben Israel Calderon

Open Access Theses & Dissertations

The 26S proteasome has been successfully targeted to treat multiple myeloma. However, the effect can sometimes be reversed as cells acquire resistance to chemotherapy. Recently, combining proteasome inhibitors with indirect proteasome inhibitors has been proposed in order to delay and even reverse resistance. Small molecules derived from 4-piperidinone that maintain an unsaturated β-carbonyl group are thought to interact with the thiol group of catalytically active cysteine residues in deubiquitinases that associate with the 26S proteasome, effectively inhibiting the proteasome.

RS1-208b was selected following a high-throughput screening of a small library of 4-piperidinone derived curcumin structural analogs due to its selectivity …

Vascularization In Interconnected 3d Printed Ti-6al-4v Foams With Hydrogel Matrix For Biomedical Bone Replacement Implants, Victor Correa

Open Access Theses & Dissertations

Abstract:

Vascularization or angiogenesis on newly implanted metal orthopedic implants has remained a challenge in the field of tissue engineering. In this research, an interconnected foam structure of Ti-6Al-4V was micro-fabricated by Electron Beam Melting (EBM) technique. The foam in question has a density of 1.77g/cm3 with 60% porosity and a tensile strength of 18GPa. An Extracellular Matrix based hydrogel was added as an aqueous matrix to the foam in question. Hypoxia mimetic stress has been closely related to many wound healing biomedical applications as it increases survival and proliferation molecular signals. To that end, increased expression of Hypoxia-Inducible Factor-1α …

Effects Of Synthetic Ligands On Heterodimer Pairs Regarding Full-Length Human Pparα, Rxrα And Lxrα, Emily Delman

Browse all Theses and Dissertations

Nuclear receptor study is critically relevant in therapeutic medicine since the intricate details of disease states pertaining to atherosclerosis and diabetes are poorly understood. Three nuclear receptors of interest regulate target genes pertaining to cholesterol and fatty acid regulation, linking these receptors to therapeutic medicine. The first is the peroxisome proliferator-activated receptor alpha (PPARa), which resides in liver and muscle, coordinating lipoprotein and fatty acid homeostasis [1]. Cholesterol homeostasis is dictated by the liver X receptor alpha (LXRa), targeting genes pertaining to the kidney, intestine, liver and adipose tissues [2]. A common partner receptor to PPARa and LXRa is known …

Instability At Trinucleotide Repeat Dnas, Rujuta Yashodhan Gadgil

Browse all Theses and Dissertations

Trinucleotide repeats (TNRs) are sequences prone to formation of non-B DNA structures and mutations; undergo expansions in vivo to cause various inherited neurodegenerative diseases. Hairpin structures formed during DNA replication or repair can cause replication fork stalling and if left unrepaired could cause single or double strand DNA breaks. To test and study this hypothesis we have devised a novel two color marker gene assay to detect DNA breaks at TNRs. By inducing replication stress our results show that TNRs are prone to DNA strand breaks and it is dependent on the repeat tract length. Double strand breaks at structured …

Investigation Of Mutations In Nuclear Genes That Affect The Atp Synthase, Russell Dsouza

Wayne State University Dissertations

The F1 domain is the catalytic subunit of the mitochondrial ATP synthase. Studies with respiratory-deficient yeast identified ATP1 and ATP2 as nuclear genes encoding the alpha and beta subunits, respectively, of the mitochondrial F1-ATPase. The mutations in the atp1 and atp2 genes were cloned and sequenced, and they appear to affect the ATP synthase. Most yeast strains with mutations in the or the subunit primarily show an F1 assembly defective phenotype. This feature is similar to the assembly-defective mutants missing the chaperones required for assembly of the F1 oligomer or either the alpha/beta subunits.

Some of the atp2 and atp1 …

Insights Into De Novo Fes-Cluster Biogenesis Via The Eukaryotic Fes-Cluster (Isc) Pathway In Vitro, Stephen Paul Dzul

Wayne State University Dissertations

Fe-S clusters are iron-containing cofactors utilized by numerous proteins within several biological pathways essential to life. In eukaryotes, the primary pathway for Fe-S cluster production is the iron-sulfur cluster (ISC) pathway. The eukaryotic ISC pathway, localized primarily within the mitochondria, has been best characterized within Saccharomyces cerevisiae. In yeast, de novo Fe-S cluster formation is accomplished through coordinated assembly of the substrates iron and sulfur on the primary scaffold assembly protein “Isu1”. The sulfur used for cluster assembly is provided by the cysteine desulfurase “Nfs1”, a protein that works in union with its accessory protein “Isd11”. Frataxin “Yfh1” helps direct …

Effective Drug Treatment Induces Drug Resistance Through Rapid Genome Alteration-Mediated Cancer Evolution, Steven Horne

Wayne State University Dissertations

The central paradox associated with current cancer therapeutic strategies is initially effective treatment, which eliminates a high tumor cell count, consistently results in successful drug resistance. Mathematical and evolutionary modeling have previously suggested that therapeutic intervention could provide selective pressure for the expansion of resistant variants. Drug-related stress has been associated with genome chaos, a common phenomenon in cancer characterized as rapid, stochastic genomic fragmentation and reorganization. Since cancer represents an evolutionary process, analysis within the context of genome-mediated cancer evolution can shed light on this key problem of therapeutics. We propose that genomic change is a general response to …