Biochemistry Commons^™

Synthetic Pathways For Potential Platinum 1,10-Phenanthroline Compounds, Jacob Young

Mahurin Honors College Capstone Experience/Thesis Projects

There are extremely important uses for platinum when it comes to the treatment of cancers and dementias. One potential therapeutic combines platinum with a structure known as phenanthroline. This platinum phenanthroline structure is normally extremely water-insoluble, rendering it difficult to study and use in biological systems. The Williams’ Biochemistry Laboratory endeavored to find a simpler synthetic pathway for a water-soluble phenanthroline product. While unsuccessful in identifying a product as of yet, many synthetic pathways have been ruled out, and more hypothetical pathways are being formulated for testing.

Among the strategies analyzed are varying solvent, reagents, apparatus, methodology, and temperature in …

Analyzing Single Ion Channel Activity In A Lipid Bilayer, David Ruiter, Loren Haarsma

Summer Research

Bilayers of lipid molecules form the basis of the cell membranes in living organisms. An ion channel is a type of molecule that can temporarily open a channel in a lipid bilayer in order to allow specific ions in and out. Problems with ion channels and their interactions with lipid bilayers are associated with several diseases, including osteoporosis. Carefully controlling the type of lipid in the bilayer, and its temperature, gives us tools to study the basic biophysics of these systems

Effects Of Resin Chemistries On The Selective Removal Of Industrially Relevant Metal Ions Using Wafer-Enhanced Electrodeionization, Humeyra B. Ulusoy Erol, Christa N. Hestekin, Jamie A. Hestekin

Chemical Engineering Faculty Publications and Presentations

Wafer-enhanced electrodeionization (WE-EDI) is an electrically driven separations technology that occurs under the influence of an applied electric field and heavily depends on ion exchange resin chemistry. Unlike filtration processes, WE-EDI can be used to selectively remove ions even from high concentration systems. Because every excess ion transported increases the operating costs, the selective separation offered by WE-EDI can provide a more energy-efficient and cost-effective process, especially for highly concentrated salt solutions. This work reports the performance comparison of four commonly used cation exchange resins (Amberlite IR120 Na⁺, Amberlite IRP 69, Dowex MAC 3 H⁺, and …

Development Of A Dna Biosensor Using Crispr/Dcas9 On A Graphene Oxide Surface For Detecting Antibiotic Resistance Genes, Wendy Cecil

Mahurin Honors College Capstone Experience/Thesis Projects

Antibiotic resistance is a rapidly spreading global threat to human health. Previously in our lab, we developed a simple method for facile detection of antibiotic resistance genes (ARGs) in bacteria. This DNA detection system takes advantage of the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeat and CRISPRAssociated Protein). We designed CRISPR in complex with nuclease deactivated Cas9 (dCas9) on graphene oxide (GO) sheets conjugated with Cas9 antibodies. Single guide RNA (sgRNA) was customized to program dCas9 for target DNA binding. sgRNA was covalently labeled with fluorescein to provide fluorescence signal. Graphene oxide (GO) is utilized for its quenching properties …

Synthesis And Biological Evaluation Of Grp94 Selective Inhibitors, Zach Priebe, Kyler Pugh, Brian S. J. Blagg

Summer Research

Grp94 is one of four chaperones which belong to the Heat Shock Protein 90 (Hsp90) family. Hsp90 isoforms exist as homodimers and assist in the folding and maturation of over 400 client proteins. These proteins are highly sought-after therapeutic targets as they are known to chaperone misfolded proteins involved in various signaling pathways. During the protein folding cycle, ATP binds to the N-Terminal domain of Hsp90, which allows nascent polypeptides to undergo maturation. To prevent the folding and maturation of oncogenic proteins, researchers developed N-terminal inhibitors to prevent ATP binding. Unfortunately, these inhibitors (termed pan-inhibitors) were not isoform selective, which …

Substrate Profiling Of The Epigenetic Erasers Hdac1 And Lsd1, Herath Mudiyansela Gedara Kavinda Eranga Herath

Wayne State University Dissertations

Regulators of chromatin structure have emerged as a key driver of transcriptional responses inside the cell. Two such groups of regulators, histone writers and erasers; the proteins, that add or remove histone post translational modifications (PTMs), have become the central players in chromatin structure. Thus, the aberrant expression of writers and erasures is a hallmark in human diseases. For example, overexpression of the erasures histone deacetylase1 (HDAC1) and lysine specific demethylase1 (LSD1) had been reported in many cancers. Currently, HDAC inhibitors have been used successfully for cancer treatment and several inhibitors targeting LSD1 are in clinical trial. To date, apart …

Developing Inhibitors Of Uchl5 Deubiquitinase In The Proteasome, Harshani Sewvandi Gurusingha Arachchige

Wayne State University Dissertations

Ubiquitin proteasomal system (UPS) plays a vital role in maintaining protein homeostasis by eliminating misfolded and damaged proteins in a eukaryotic cell. Target proteins to be degraded are modified by poly-ubiquitination, which leads to degradation by 26S proteasome. Before entering the 20S catalytic subunit, the 19S regulatory particle is responsible for binding, unfolding, and deubiquitinating the target protein. Based on the nature of the polyubiquitin tag, removal of the ubiquitin is performed by the deubiquitinases (DUBs) associated with the proteasome.Ubiquitin carboxyl-terminal hydrolase isozyme L5 (UCHL5) is one of the three DUBs in the proteasome. UCHL5 regulates many cellular functions and …

The Inhibition Of Growth Of S. Cerevisiae, U. Maydis, And M. Lychinidis-Dioicae By Apiaecea Plant Extracts, Jackson M Hoffman, Jared Scott, David Schultz Phd

Undergraduate Arts and Research Showcase

The Apiaceae family of plants contains over 3,500 species, many of which are used as food crops: vegetables (carrot, parsnip, celery, etc.), herbs (cilantro, fennel, dill, etc.), and spices (cumin, anise, caraway, etc.). Many spices have been shown to exhibit antimicrobial properties against both bacteria and fungi. We set out to determine if the Apiaceae spice extracts currently used in our lab for anticancer studies exhibit any antimicrobial properties. Ethanolic extracts were made from several Apiaceae seeds: Apium graveolens (celery), Cuminum cyminum (cumin), Anethum graveolens(dill), Foeniculum vulgare (fennel), Coriandrum satvium (coriander), Pimpinella ansium (anise), Trachyspermum ammi (ajwain), Carum carvi …

Teaching Metabolism In Upper-Division Undergraduate Biochemistry Courses Using Online Computational Systems And Dynamical Models Improves Student Performance, Christine S. Booth, Changsoo Song, Michelle E. Howell, Achilles Rasquinha, Aleš Saska, Resa M. Helikar, Sharmin M. Sikich, Brain A. Couch, Karin Van Dijk, Rebecca Roston, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Understanding metabolic function requires knowledge of the dynamics, interdependence, and regulation of metabolic networks. However, multiple professional societies have recognized that most undergraduate biochemistry students acquire only a surface-level understanding of metabolism. We hypothesized that guiding students through interactive computer simulations of metabolic systems would increase their ability to recognize how individual interactions between components affect the behavior of a system under different conditions. The computer simulations were designed with an interactive activity (i.e., module) that used the predict–observe–explain model of instruction to guide students through a process in which they iteratively predict outcomes, test their predictions, modify the interactions …

Long Non-Coding Rna Meg3 Deficiency Impairs Glucose Homeostasis And Insulin Signaling By Inducing Cellular Senescence Of Hepatic Endothelium In Obesity, Xiao Cheng, Mohamed Sham Shihabudeen Haider Ali, Matthew Moran, Martonio Ponte Viana, Sarah L. Schlichte, Matthew C. Zimmerman, Oleh Khalimonchuk, Mark W. Feinberg, Xinghui Sun

Department of Biochemistry: Faculty Publications

Obesity-induced insulin resistance is a risk factor for diabetes and cardiovascular disease. However, the mechanisms underlying endothelial senescence in obesity, and how it impacts obesity-induced insulin resistance remain incompletely understood. In this study, transcriptome analysis revealed that the long non-coding RNA (lncRNA) Maternally expressed gene 3 (Meg3) is one of the top differentially expressed lncRNAs in the vascular endothelium in diet-induced obese mice. Meg3 knockdown induces cellular senescence of endothelial cells characterized by increased senescence-associated β–galactosidase activity, increased levels of endogenous superoxide, impaired mitochondrial structure and function, and impaired autophagy. Moreover, Meg3 knockdown causes cellular senescence of hepatic endothelium in …

Integrative Network Analyses Of Transcriptomics Data Reveal Potential Drug Targets For Acute Radiation Syndrome, Robert Moore, Bhanwar Lal Puniya, Robert Powers, Chittibabu Guda, Kenneth W. Bayles, David Berkowitz, Tomas Helikar

Department of Biochemistry: Faculty Publications

Recent political unrest has highlighted the importance of understanding the short- and long-term effects of gamma-radiation exposure on human health and survivability. In this regard, effective treatment for acute radiation syndrome (ARS) is a necessity in cases of nuclear disasters. Here, we propose 20 therapeutic targets for ARS identified using a systematic approach that integrates gene co-expression networks obtained under radiation treatment in humans and mice, drug databases, disease-gene association, radiation-induced differential gene expression, and literature mining. By selecting gene targets with existing drugs, we identified potential candidates for drug repurposing. Eight of these genes (BRD4, NFKBIA, CDKN1A, TFPI, MMP9, …

Root Nrt, Nir, Amt, Gs, Gogat And Gdh Expression Levels Reveal No Andaba Mediated Drought Tolerance In Brassica Juncea L., Seema Sahay, Luis Robledo-Arratia, Katarzyna Glowacka, Meetu Gupta

Department of Biochemistry: Faculty Publications

Little is known about the interactive effects of exogenous nitric oxide (NO) and abscisic acid (ABA) on nitrogen (N) metabolism and related changes at molecular and biochemical levels under drought stress. The present study highlights the independent and combined effect of NO and ABA (grouped as “nitrate agonists”) on expression profiles of representative key genes known to be involved in N-uptake and assimilation, together with proline metabolism, N–NO metabolism enzyme’s activity and nutrient content in polyethylene glycol (PEG) treated roots of Indian mustard (B. juncea cv. Varuna). Here we report that PEG mediated drought stress negatively inhibited growth performance, as …

Lysosomal Slc46a3 Modulates Hepatic Cytosolic Copper Homeostasis, Jung-Hwan Kim, Tsutomu Matsubara, Jaekwom Lee, Cristina Fenollar-Ferrer, Kyungreem Han, Donghwan Kim, Shang Jia, Christopher J. Chang, Heejung Yang, Tomokazu Nagano, Kristopher W. Krausz, Sun Hee Yim, Frank J. Gonzalez

Department of Biochemistry: Faculty Publications

The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) causes hepatic toxicity associated with prominent lipid accumulation in humans. Here, the authors report that the lysosomal copper transporter SLC46A3 is induced by TCDD and underlies the hepatic lipid accumulation in mice, potentially via effects on mitochondrial function. SLC46A3 was localized to the lysosome where it modulated intracellular copper levels. Forced expression of hepatic SLC46A3 resulted in decreased mitochondrial membrane potential and abnormal mitochondria morphology consistent with lower copper levels. SLC46A3 expression increased hepatic lipid accumulation similar to the known effects of TCDD exposure in mice and humans. The TCDD-induced hepatic triglyceride accumulation was significantly …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Association Of The Malate Dehydrogenase‑Citrate Synthase Metabolon Is Modulated By Intermediates Of The Krebs Tricarboxylic Acid Cycle, Joy Omini, Izabela Wojciechowska, Aleksandra Skirycz, Hideaki Moriyama, Toshihiro Obata

Department of Biochemistry: Faculty Publications

Mitochondrial malate dehydrogenase (MDH)-citrate synthase (CS) multi-enzyme complex is a part of the Krebs tricarboxylic acid (TCA) cycle ‘metabolon’ which is enzyme machinery catalyzing sequential reactions without diffusion of reaction intermediates into a bulk matrix. This complex is assumed to be a dynamic structure involved in the regulation of the cycle by enhancing metabolic flux. Microscale Thermophoresis analysis of the porcine heart MDH-CS complex revealed that substrates of the MDH and CS reactions, NAD+ and acetyl-CoA, enhance complex association while products of the reactions, NADH and citrate, weaken the affinity of the complex. Oxaloacetate enhanced the interaction only when it …

An In Vivo Inducible Expression System To Determine Antibacterial Activity Of Peptides, Rabiul Islam

Wayne State University Dissertations

The threat of bacterial resistance throughout the world has created tremendous challenges to clinicians. Some bacterial species have acquired resistance to not only single antibiotics, but also to multiple compounds, which is called multidrug resistance. Since the early discovery of resistance to penicillin, scientists have been developing new drugs to combat antibiotic resistance. In some cases, it took less than a decade to develop resistance to a new antibiotic. The World Health Organization (WHO) reported several deadly multi-drug-resistant bacteria, some of which cause life-threating illnesses. Each year more than 35,000 people in the United States die from antibiotic-resistant bacterial infections. …

Machine Learning And Bioinformatic Insights Into Key Enzymes For A Bio-Based Circular Economy, Japheth E. Gado

Theses and Dissertations--Chemical and Materials Engineering

The world is presently faced with a sustainability crisis; it is becoming increasingly difficult to meet the energy and material needs of a growing global population without depleting and polluting our planet. Greenhouse gases released from the continuous combustion of fossil fuels engender accelerated climate change, and plastic waste accumulates in the environment. There is need for a circular economy, where energy and materials are renewably derived from waste items, rather than by consuming limited resources. Deconstruction of the recalcitrant linkages in natural and synthetic polymers is crucial for a circular economy, as deconstructed monomers can be used to manufacture …

Structural Analysis Of Neutralizing Epitopes Of The Sars-Cov-2 Spike To Guide Therapy And Vaccine Design Strategies, Maxwell T. Finkelstein , '22, Adam G. Mermelstein , '21, Emma Parker Miller , '22, Paul C. Seth , '22, Erik-Stephane D. Stancofski , '21, Daniela Fera

Chemistry & Biochemistry Faculty Works

Coronavirus research has gained tremendous attention because of the COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus (nCoV or SARS-CoV-2). In this review, we highlight recent studies that provide atomic-resolution structural details important for the development of monoclonal antibodies (mAbs) that can be used therapeutically and prophylactically and for vaccines against SARS-CoV-2. Structural studies with SARS-CoV-2 neutralizing mAbs have revealed a diverse set of binding modes on the spike’s receptor-binding domain and N-terminal domain and highlight alternative targets on the spike. We consider this structural work together with mAb effects in vivo to suggest correlations between structure …

Purification And Activity Analysis Of A Highly Active Recombinant Catalase From Psychrophilic Bacterium Psychrobacter Cryohaloentis, Andrew Stewart

Honors Program Theses

To date, the genus Psychrobacter includes 37 recognized bacterial species isolated from different sources ranging from Siberian permafrost (P. cryohalolentis) to seal feces (P. lutiphocae). Due to its diverse ecological niches, several species belonging to the genus have different enzymatic activities with potential applications in bioremediation and the food industry. In this study, a bioprospecting approach was used to perform a in depth analysis of a Psychrobacter-like bacterial strain isolated from goose feces (designated as Psychrobacter unknown). The phylogenetic analysis of 16S rRNA gene and homologous sequence studies suggest that the strain may represent a novel species of the Psychrobacter …

The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes

Honors Theses

The internal recycling phosphorus in freshwater lake bottom sediments represents a significant source of hypolimnetic phosphorus (P) release for many of Maine’s lakes. In summer months, Maine lakes often thermally stratify and the lake hypolimnion develops anoxia, leading to a reduction in redox potential at the sediment-water interface. These reducing conditions facilitate the reductive dissolution of ferric iron, and, since phosphorus is often present in freshwater lake sediments as solid FeOOH-PO₄ complexes, results in release of soluble phosphorus into the water column. Our current study presents field and laboratory data from sediment fractionation extractions designed to quantify concentrations of …