Biochemistry, Biophysics, and Structural Biology Commons^™

The Development Of Bioaffinity-Based Concepts For On-Site Forensic Analyses : Blood, Sweat, And ... Fingerprints?, Crystal Huynh

Legacy Theses & Dissertations (2009 - 2024)

There have been many advances in forensic science over the recent years, but a majority of the tests currently preformed are still heavily reliant upon laboratory-based processes. This means that valuable pieces of information are left unexamined until a crime scene has been completely processed and evidence is moved to a crime lab. In some cases, the evidence may even be left in a queue due to backlogs from previous cases. The delay resulting from the time necessary for crime scene processing and transportation, as well as additional time spent waiting on lab equipment availability, hinders an investigator’s ability to …

Genetically Engineered Polypeptides As Biomimetic Light Harvesting Optical Antenna, Jason P. Seeley

Legacy Theses & Dissertations (2009 - 2024)

Natural resources useful for the generation of energy are limited. The development of efficient materials capable of utilizing the abundant free solar radiation is of considerable interest. Utilization of otherwise wasted energy sources, including solar radiation, is a progressive step in the quest for sustainable energy. Solar radiation incident upon the earth’s surface exceeds current energy requirements and motivates scientists to investigate and develop functional devices and nanomaterials including light harvesting complexes (LHC) capable of capturing solar radiation for energy conversion and storage.

Methionine Sulfoximine: A Novel Anti Inflammatory Agent, Tyler Peters

Wayne State University Dissertations

ABSTRACT

METHIONINE SULFOXIMINE: A NOVEL ANTI-INFLAMMATORY AGENT

by

TYLER J. PETERS

October 2018

Advisor: William Brusilow

Major: Biochemistry and Molecular Biology

Degree: Doctor of Philosophy

The glutamine synthetase inhibitor methionine sulfoximine (MSO), shown previously to prevent death caused by an inflammatory liver response in mice, was tested on in vitro production of cytokines by mouse peritoneal macrophages triggered with lipopolysaccharide (LPS). MSO significantly reduced the production of Interleukin 6 (IL-6) and Tumor Necrosis Factor Alpha (TNFα) at 4 and 6 hours after LPS-treatment. This reduction did not result from decreased transcription of IL-6 and TNFα genes, and therefore appeared to …

Computational Design Of Levansucrase For Production Of Tailor-Made Length Levan-Type Fructo-Oligosaccharides, Pongsakorn Kanjanatanin

Chulalongkorn University Theses and Dissertations (Chula ETD)

Levansucrase (LS) is an exocellular fructosyltransferase catalyzing the hydrolysis of sucrose and polymerization of levan and levan-type fructo-oligosaccharides (LFOs) that have various potentials in pharmaceutical and biological applications such as prebiotics and anticancer agents. LFOs with the chain length of 5 (LFO5 or GF4) showed inhibition activity against the SW480 colorectal cell lines up to about 83%. Although LFO5 has beneficial properties, the ability to produce LFO5 in large quantity is still limited. This study aimed to explore conformational diversity and elucidate the structural and molecular properties of LFO5, LFO10 and LFO15 as well as to redesign the active site …

Algae Biofuel Triacylglyceride Transesterification Optimization, Erik Ferenczy

Senior Honors Theses

Algae biofuels may hold the key to solving the problem of fossil fuel consumption by being comparable in content, renewable, and carbon-neutral. Many biofuel researchers and corporations have undertaken to increase the production rate or capacity of triacylglycerides (TAG), the fat precursor to biodiesel fuel produced by algae, in algae cultures and published articles documenting their findings. This research is devoted to evaluating the effect of water that may be present in samples on the conversion efficiency of TAG into fatty acid methyl esters (FAME), commonly referred to as biodiesel. Therefore, that efficiency was studied to find the water content …

Split Deoxyribozyme Probe For Efficient Detection Of Highly Structured Rna Targets, Sheila Raquel Solarez

Honors Undergraduate Theses

Transfer RNAs (tRNAs) are known for their role as adaptors during translation of the genetic information and as regulators for gene expression; uncharged tRNAs regulate global gene expression in response to changes in amino acid pools in the cell. Aminoacylated tRNAs play a role in non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosynthesis. ^[1] tRNAs have a highly stable structure that can present a challenge for their detection using conventional techniques. ^[2] To enable signal amplification and lower detection limits, a split probe - split deoxyribozyme (sDz or BiDz) probe, which …

Discovery Of Novel Muraymycin Antibiotics And Insight Into The Biosynthetic Pathway, Zheng Cui

Theses and Dissertations--Pharmacy

New antibiotics with novel targets or mechanisms of action are needed to counter the steady emergence of bacterial pathogens that are resistant to antibiotics used in the clinic. MraY, a promising novel target for antibiotic development, initiates the lipid cycle for the biosynthesis of peptidoglycan cell wall, which is essential for the survival of most, if-not-all, bacteria. MraY is an enzyme that catalyzes the transfer and attachment of phospho-MurNAc-pentapeptide to a lipid carrier, undecaprenylphosphate. Muraymycins are recently discovered lipopeptidyl nucleoside antibiotics that exhibit remarkable antibiotic activity against Gram-positive as well as Gram-negative bacteria by inhibiting MraY. We conducted a thorough …

Surface And Structural Modification Of Carbon Electrodes For Electroanalysis And Electrochemical Conversion, Yan Zhang

Theses and Dissertations--Chemistry

Electrocatalysis is key to both sensitive electrochemical sensing and efficient electrochemical energy conversion. Despite high catalytic activity, traditional metal catalysts have poor stability, low selectivity, and high cost. Metal-free, carbon-based materials are emerging as alternatives to metal-based catalysts because of their attractive features including natural abundance, environmental friendliness, high electrical conductivity, and large surface area. Altering surface functionalities and heteroatom doping are effective ways to promote catalytic performance of carbon-based catalysts. The first chapter of this dissertation focuses on developing electrode modification methods for electrochemical sensing of biomolecules. After electrochemical pretreatment, glassy carbon demonstrates impressive figures-of-merit in detecting small, redox-active …

Comparative Toxicology Of Nio And Ni(Oh)₂ Nanoparticles, Melissa Hope Cambre

Masters Theses

“Understanding the potential toxicity of nanoparticles (NPs) is important to ensure that these new products do not impose harmful effects to human and environmental health. Paper I is a literature review in which we discuss characteristics of nanomaterials, with an emphasis on transition metal oxide nanoparticles that influence cytotoxicity. Identification of those properties may lead to the design of more efficient and safer nanosized products for various industrial purposes and provide guidance for assessment of human and environmental health risk. We then investigate biochemical and molecular mechanisms of cytotoxicity that include oxidative stress-induced cellular events and alteration of the pathways …

Initial Functional Characterization Of Bfo 2291 And Bfo 2294 From Tannerella Forsythia; Degraders Of Chondroitin Sulfate A, Rony Eshaque, Rony Eshaque

Theses and Dissertations (Comprehensive)

Periodontitis is characterized by the inflammation of the periodontal tissues in response to bacterial action. The Global Burden of Disease (GBD) 2010 study shows that periodontitis ranks 6^thin the global prevalence of oral health conditions and affects 11% of the world population. It is initiated by the formation of biofilms containing different types of bacteria. These biofilms exist as dental plaque and contain three types of bacteria called Tannerella forsythia, Porphyromonasgingivalis, and Treponema denticola. These three types of bacteria are strongly associated with periodontitis and they are termed as the Red complex. The main focus of the …

Enhanced Hot Electron Lifetimes In Quantum Wells With Inhibited Phonon Coupling, Hamidreza Esmaielpour, Vincent R. Whiteside, Herath P. Piyathilaka, Sangeetha Vijeyaragunathan, Bin Wang, Echo Adcock-Smith, Kenneth P. Roberts, Tetsuya D. Mishima, Michael B. Santos, Alan D. Bristow, Ian R. Sellers

Faculty & Staff Scholarship

Hot electrons established by the absorption of high-energy photons typically thermalize on a picosecond time scale in a semiconductor, dissipating energy via various phonon-mediated relaxation pathways. Here it is shown that a strong hot carrier distribution can be produced using a type-II quantum well structure. In such systems it is shown that the dominant hot carrier thermalization process is limited by the radiative recombination lifetime of electrons with reduced wavefunction overlap with holes. It is proposed that the subsequent reabsorption of acoustic and optical phonons is facilitated by a mismatch in phonon dispersions at the InAs-AlAsSb interface and serves to …

Esope-Equivalent Pulsing Protocols For Calcium Electroporation: An In Vitro Optimization Study On 2 Cancer Cell Models, Stefania Romeo, Anna Sannino, Maria Rosaria Scarfi, P. Thomas Vernier, Ruggero Cadossi, Julie Gehl, Olga Zeni

Bioelectrics Publications

Reversible electroporation is used to increase the uptake of chemotherapeutic drugs in local tumor treatment (electrochemotherapy) by applying the pulsing protocol (8 rectangular pulses, 1000 V/cm, 100 µs) standardized in the framework of the European Standard Operating Procedure on Electrochemotherapy multicenter trial. Currently, new electrochemotherapy strategies are under development to extend its applicability to tumors with different histology. Electrical parameters and drug type are critical factors. A possible approach is to test pulse parameters different from European Standard Operating Procedure on Electrochemotherapy but with comparable electroporation yield (European Standard Operating Procedure on Electrochemotherapy-equivalent protocols). Moreover, the use of non-toxic drugs …

Dynamic Control Of Particle Separation In Deterministic Lateral Displacement Separator With Viscoelastic Fluids, Yuke Li, Hongna Zhang, Yongyao Li, Xiaobin Li, Jian Wu, Shizhi Qian, Fengchen Li

Mechanical & Aerospace Engineering Faculty Publications

We proposed an innovative method to achieve dynamic control of particle separation by employing viscoelastic fluids in deterministic lateral displacement (DLD) arrays. The effects of shear-thinning and elasticity of working fluids on the critical separation size in DLD arrays are investigated. It is observed that each effect can lead to the variation of the critical separation size by approximately 40%. Since the elasticity strength of the fluid is related to the shear rate, the dynamic control can for the first time be easily realized through tuning the flow rate in microchannels.

Targeting The Cellular Redox Environment: A Novel Approach For The Treatment Of Hematopoietic Neoplasms, Dustin W. Carroll

Theses and Dissertations--Toxicology and Cancer Biology

Hematopoietic stem cells (HSCs) that function to maintain the hematopoietic compartment through self-renewal and differentiation capacities, as well as their downstream progeny, are susceptible to transformation resulting in the generation of the leukemic stem cell (LSC). Chief in the factors that control HSC regulation and protection of the HSC compartment is the cellular redox environment. Deregulation of the Hematopoietic Stem/Progenitor Cell (HSPC) redox environment results in loss of HSPC function and exhaustion. The characteristic developments of HSPC exhaustion via exposure to redox stress closely mirror phenotypic traits of hematopoietic malignancies, presenting the HSPC/LSC redox environment as a potential therapeutic target. …

Influence Of Dietary Ractopamine And Supranutritional Supplementation Of Vitamin E On Proteome Profile Of Postmortem Beef Longissimus Lumborum Muscle, Hyun Mok Kim

Theses and Dissertations--Animal and Food Sciences

The effects of dietary ingredients on the proteome profile of postmortem beef longissimus lumborum (LL) muscle were evaluated. In the first experiment, the influence of dietary ractopamine on the whole-muscle proteome of beef LL was examined. Five proteins were differentially abundant between ractopamine-fed (RAC) and non-ractopamine fed (CON) groups. The differentially abundant proteins were over-abundant in RAC and were related to muscle structure development (F-actin-capping protein subunit beta-2 and PDZ and LIM domain protein-3), chaperone (heat shock protein beta-1), oxygen transportation (myoglobin), and glycolysis (L-lactate dehydrogenase A chain). These findings indicated that ractopamine influences the abundance of proteins associated with …

Size-Dependent Inhibitory Effects Of Antibiotic Drug Nanocarriers Against Pseudomonas Aeruginosa, Feng Ding, Preeyaporn Songkiatisak, Pavan Kumar Cherukuri, Tao Huang, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Multidrug membrane transporters (efflux pumps) are responsible for multidrug resistance (MDR) and the low efficacy of therapeutic drugs. Noble metal nanoparticles (NPs) possess a high surface-area-to-volume ratio and size-dependent plasmonic optical properties, enabling them to serve both as imaging probes to study sized-dependent MDR and as potential drug carriers to circumvent MDR and enhance therapeutic efficacy. To this end, in this study, we synthesized three different sizes of silver nanoparticles (Ag NPs), 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm, functionalized their surface with a monolayer of 11-amino-1-undecanethiol (AUT), and covalently conjugated them with antibiotics (ofloxacin, Oflx) …

Altering Oligomerization Of Epha2 Via Mutations In The Intracellular Domain, Ryan W. Lingerak

Williams Honors College, Honors Research Projects

Eph receptor tyrosine kinases (RTKs) are activated by membrane-bound ligands called ephrins. Eph RTKs are divided into two subclasses, each activated by a specific classes of the ligand ephrin. The overexpression of Eph receptors is correlated to cancer cell metastasis in several different types of cancers. Studies with the EphA2 extracellular domain (ECD) and ephrinA1 ligand have shown that upon binding of ephrin to the receptor, EphA2 undergoes increased oligomerization and activation. This indicates that oligomerization is intimately connected to kinase activity. High resolution crystal structures of the EphA2 ECD have revealed some details of these ligand bound oligomers, as …

Integrated Immunoassays On Paper/Polymer Hybrid Microfluidic Devices For Low-Cost Detection Of Disease Biomarkers, Sanjay Sharma Timilsina

Open Access Theses & Dissertations

Infectious diseases and cancers have been the major cause of global death and disability causing a significant impact on global health and economies. Enzyme-linked immunosorbent assay (ELISA) is one of the most widely used laboratory diagnostic methods for infectious diseases and cancer. ELISA detects proteins based on their binding to immobilized antibodies or antigen. Even though most ELISAs performed today in 96-well plates are well suited for high throughput assays, performing ELISA in low-resource settings is limited by several factors, such as long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we have developed multiple simple, miniaturized …

The Structural And Functional Study Of The Human Mitochondrial Hsp60 Chaperonin In Neurodegenerative Diseases, Jinliang Wang

Open Access Theses & Dissertations

Proteins are essential elements that are responsible for a variety of cellular activities within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules. After protein synthesis in the ribosome, the unfolded protein need to fold into their unique compact structures so that they can perform their full biological functions. The biologically active structure of a protein is referred to the native-state of the protein with biological activity. The process of protein folding is one of the most important and challenging research topics of contemporary biochemistry, especially for its central role …

Antibiotic Effects Of Dimethyl Sulfoxide And Synthetic Polyphenols On E. Coli Cells, Camila Cardenas

Theses and Dissertations

There is increasing interest in polyphenols due to their potential medicinal and antibiotic applications. Naturally occurring polyphenols, such as curcumin, have garnered tremendous attention. However, synthetic polyphenols commonly used in biochemistry experiments have not been sufficiently explored. The purpose of this study is to determine the effect of dimethyl sulfoxide on the cellular uptake of synthetic polyphenols. Three synthetic polyphenols (Phenol Red, Congo Red, and Bromophenol Blue) were tested for their antibiotic properties and compared to the antibiotic activity of curcumin. Our results show that phenol red does not interact with the bacterial membrane even in the presence of 30% …

Sporadic Appearance Of Paralytic Spongiform Neurodegeneration In A Colony Of Inbred Mice Is Associated With Cns Retrovirus Expression, Magdalene Durbak

Williams Honors College, Honors Research Projects

Abstract

Exogenous and endogenous retroviruses (RV) have been known to induce vacuolar central nervous system neuropathology. Two mice which were juvenile inbred Rocky Mountain White (IRW), showed signs of spontaneous degenerate motor neuron disease. Signs included wasting, unkempt fur, adduction reflex upon tail elevation, kyphosis, and stilted gait by postnatal day 18 (P18). Brains and spinal cords were examined with H&E staining and stained with a broadly reactive retrovirus antibody. When compared to brains of mice with normal vacuolar pathology as well as mice infected with prototypic non-neurovirulent RV, Fr57E and prototypic neurovirulent RV FrCasE, the subject showed less severity …

Mutations In Rhodopsin Transmembrane Helix 5 And Dimerization Interface, Margaret Pinkevitch

Williams Honors College, Honors Research Projects

G protein coupled receptors (GPCRs) are membrane proteins with many functional roles. This family of receptors is expansive, with several subfamilies. Here, a member of subfamily A, rhodopsin (Rho) is studied. Mutations in rhodopsin have been linked to the disease retinitis pigmentosa (RP). Some of these mutations have been found to disrupt the dimerization/oligomerization of Rho at the TM4/TM5 proposed dimerization interface, causing pathogenesis of RP. In this study, two mutations of transmembrane helix 5 were investigated for changes in dimerization and stability, cell trafficking, and signaling. It was found that the V209M and F220C mutations did not result in …

Alternative Strategies To Inhibit Lysine Methyltransferases And Deubiquitinases In Human Cancers, Nicholas Spellmon

Wayne State University Dissertations

X-ray crystallography is the gold standard method for imagining macromolecules to atomic resolution. Three dimensional data is central to understanding the molecular mechanism how DNA, RNA and proteins function in biological events. Structural insights into these events provide a molecular window to visualize how biological molecules influence human health. Visualizing the architecture of these molecules set the stage for rational and selective drug design. The following dissertation utilizes biochemical and biophysical tools, including X-ray crystallography, to shed light on poorly understood mechanisms related to SMYD2 activity and regulation, USP10 architecture and function, and PDZ-RhoGEF dimerization. SMYD2 is one member of …

Detection Of Semi-Polar Vitamins And Nutrients In Biological Samples, Jennifer Janovick

Williams Honors College, Honors Research Projects

Metabolomics is used to examine metabolite fluctuations in biological systems and enables the diagnosis of metabolic disorders and the identification of new therapeutic targets.¹ Liquid chromatography-mass spectrometry (LC-MS) was utilized to develop a new method using a T3 column to separate small molecule nutrients and vitamins in a tissue sample. Initial tests of column performance used standard solutions; the amount of metabolites identified and the elution profile of these metabolites was examined. Both the standard solution and sample of brain tissue were tested with the final method developed. Six metabolites were identified in the standard and 31 were identified …

Controlling Platelet Secretion To Modulate Hemostasis And Thrombosis, Smita Joshi

Theses and Dissertations--Molecular and Cellular Biochemistry

Upon vascular injury, activated blood platelets fuse their granules to the plasma membrane and release cargo to regulate the vascular microenvironment, a dynamic process central to platelet function in many critical processes including hemostasis, thrombosis, immunity, wound healing, angiogenesis etc. This granule- plasma membrane fusion is mediated by a family of membrane proteins- Soluble N-ethyl maleimide Attachment Receptor Proteins(SNAREs). SNAREs that reside on vesicle (v-SNAREs) /Vesicle-Associated Membrane Proteins(VAMPs) interact with target/t-SNAREs forming a trans-bilayer complex that facilitates granule fusion. Though many components of exocytic machinery are identified, it is still not clear how it could be manipulated to prevent …

The Abiotic Stress Response Of Hydroponic Vetiver Grass (Chrysopogon Zizanioides L.) To Acid Mine Drainage And Its Potential For Environmental Remediation, Jef Kiiskila

Dissertations, Master's Theses and Master's Reports

Mining activities can generate acid mine drainage (AMD), an acidic discharge that contains elevated sulfate (SO₄^2-), soluble metals, and orange-yellow metal-containing particulates. AMD imposes ecological risks from metal toxicity and physical stress, which may physically spread to nearby water sources or biologically through bioaccumulation. Current methods for AMD treatment, such as chemical or passive biological treatments, are often non-sustainable. Chemical treatments can be expensive and create large amounts of secondary waste, whereas biological treatments like anaerobic wetlands require continuous maintenance through input of organic nutrients. The end goal of this research is to develop a cost-efficient and …

Modulation Of Electron Transport By Metformin In Cardiac Protection: Role Of Complex I, Ahmed Abdul Hussein Mohsin

Theses and Dissertations

Modulation of mitochondrial complex I during reperfusion reduces cardiac injury. Complex I exists in two structural states: active (A) and deactive (D) with transition from A→D during ischemia. Reperfusion reactivates D→A with an increase in ROS production. Metformin preserves the D-Form. Our aim was to study the contribution of maintenance of deactivation of complex I during early reperfusion by metformin to protect against ischemia reperfusion injury. Our results showed that metformin decreased H9c2 cardiomyoblast apoptosis and total cell death following simulated ischemia for six hours followed by reoxygenation for twenty four hours compared to untreated cells. Reactive oxygen species (ROS) …

Total Mercury Determination In Muscle And Liver Tissue Samples From Brazilian Amazon Fish Using Slurry Sampling, João Vitor De Queiroz, José Cavalcante Souza Vieira, Izabela Da Cunha Bataglioli, Alis Correia Bittarello, Camila Pereira Braga, Grasieli De Oliveira, Cilene Do Carmo Federici Padilha, Pedro De Magalhães Padilha

Department of Biochemistry: Faculty Publications

This paper presents a slurry sampling method for total mercury determination by graphite furnace atomic absorption spectrometry (GFAAS) in tissue of fish from the Amazon. The tissue samples were lyophilized and macerated, and then the slurry samples were prepared by putting 20 mg of tissue, added to a solution containing Triton X-100, Suprapur HNO₃, and zirconium nitrate directly in sampling vials of a spectrometer. Mercury standard solutions were prepared under the same conditions as the slurry samples. The slurry samples and the mercury standard solutions were sonicated for 20 s. Twenty microliters of slurry samples were injected into …

Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing …

Towards The Synthetic Design Of Camelina Oil Enriched In Tailored Acetyl-Triacylglycerols With Medium-Chain Fatty Acids, Sunil Bansal, Hae Jin Kim, Gunnam Na, Megan E. Hamilton, Edgar B. Cahoon, Chaofu Lu, Timothy P. Durrett

Department of Biochemistry: Faculty Publications

The ability to manipulate expression of key biosynthetic enzymes has allowed the development of genetically modified plants that synthesise unusual lipids that are useful for biofuel and industrial applications. By taking advantage of the unique activities of enzymes from different species, tailored lipids with a targeted structure can be conceived. In this study we demonstrate the successful implementation of such an approach by metabolically engineering the oilseed crop Camelina sativa to produce 3-acetyl-1,2-diacyl-sn-glycerols (acetyl-TAGs) with medium-chain fatty acids (MCFAs). Different transgenic camelina lines that had been genetically modified to produce MCFAs through the expression of MCFA-specific thioesterases and …