Biochemistry, Biophysics, and Structural Biology Commons^™

Platination Kinetics: Insight Into Rna-Cisplatin Interactions As A Probe For Rna Microenvironments, Gayani Dedduwa-Mudalige

Wayne State University Dissertations

RNAs are crucial for many cellular functions. Thus, studying ligand-RNA interactions and their dynamics in response to changes in the surrounding environment is important. In spite of the well-known DNA coordination, current research also indicates cisplatin binding to RNA. Kinetic studies of rRNA platination reactions are largely unexplored. This research was conducted to achieve two objectives. First, a broad kinetic study was carried out to investigate the cisplatin-rRNA interactions. The structure, function, and ligand interactions depend on RNA microenvironments. Second, the application of platination kinetics as a tool to interrogate RNA electrostatic environments was explored.

Three model rRNA hairpins from …

Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. Mcintosh, Eptisam Lambu, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson

Student Research Posters

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. The Mu, Delta, and Kappa (MOP, DOP, KOP) opioid receptors are particularly intriguing members of this receptor family as they are the targets involved in many neurobiological diseases such as addiction, pain, stress, anxiety, and depression. Recently we discovered that the aaptamine class of marine sponge derived natural products exhibit selective agonist activity in vitro for the DOP versus MOP receptor. Our findings may explain …

Functional Transcranial Doppler Ultrasound For High Temporal Resolution Measurement Of Lateralization In Visual Memory And Visual Search Cognitive Tasks, B. Hage, M. Alwatban, E. Barney, M. Mills, M. Dodd, E. Truemper, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Functional transcranial Doppler ultrasound (fTCD) is a noninvasive sensing modality that measures blood flow velocities in cerebral arteries (CBFV) with high temporal resolution. Few studies have examined the relationship of CBFV change during visual search and visual memory cognitive tasks. Here a protocol to compare lateralization between these two similar tasks using fTCD is demonstrated. Thirteen healthy volunteers were shown visual scenes on a computer and performed visual search and visual memory tasks while CBFV in the bilateral middle cerebral arteries was monitored with fTCD. Each subject completed 40 trials, consisting of baseline, calibration, instruction, and task periods. Lateralization was …

The Significance Of Crispr/Cas9-Directed Cul3 Knockout On Human Colorectal Cancer Cells, Zoe A. Lautz

Departmental Honors Projects

Cancer, the second leading cause of death in the US, is caused by mutations in select genes that alter cellular function leading to uncontrolled proliferation. Understanding the specific genes that drive cancer can lead to the generation of novel cancer therapies. To identify novel genes that drive cancer in the colon (CRC), lungs, and ovaries in mice, Starr et al. employed a transposon-based insertional mutagenesis system. One of the genes identified, APC, is mutated in 70-80% of human CRCs. CUL3, suspected to be a general driver gene, was discovered in the lung cancer screen. CUL3 was analyzed for its role …

Tissue-Specific Splice Variants Of Hare/Stabilin-2 Are Expressed In Bone Marrow, Lymph Node, And Spleen, Amanda K. Hare, Edward N. Harris

Department of Biochemistry: Faculty Publications

The hyaluronan receptor for endocytosis (HARE), or Stabilin-2, is the mammalian endocytic clearance receptor for HA, heparin, advanced glycation end-products, acetylated and oxidized low-density lipoproteins and collagen N-terminal propeptides. This large 2551 amino acid receptor is encoded by a gene that covers over 180 kbp on human chromosome 12 and is predicted to be composed of 69 exons. Due to the expression profile of this gene and the number of exons it contains, we hypothesized that splice variants of stab2 are encoded in these tissues. In addition, a correlation between alternative splice variants and cancer progression has been shown in …

Hyaluronidase Hyal1 Increases Tumor Cell Proliferation And Motility Through Accelerated Vesicle Trafficking, Caitlin O Mcatee, Abigail R. Berkebile, Christian Elowsky, Teresa Fangman, Joseph J. Barycki, James K. Wahl Iii, Oleh Khalimonchuk, Naava Naslavsky, Steve Caplan, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

Background: Hyal1 is a turnover enzyme for hyaluronan that accelerates metastatic cancer by increasing cell motility.

Results: Hyal1-overexpressing cells have a higher rate of endocytosis that impacts cargo internalization and recycling.

Conclusion: The higher rate of vesicle trafficking increases motility receptor function and nutrient uptake.

Significance: This novel mechanism implicates Hyal1 trafficking in multiple signaling events during tumor progression.

Advantages Of Distributed And Parallel Algorithms That Leverage Cloud Computing Platforms For Large-Scale Genome Assembly, Phil Kumari, Raja Mazumder, Vahan Simonyan, Konstantinos Krampis

Biochemistry and Molecular Medicine Faculty Publications

Background: The transition to Next Generation sequencing (NGS) sequencing technologies has had numerous applications in Plant, Microbial and Human genomics during the past decade. However, NGS sequencing trades high read throughput for shorter read length, increasing the difficulty for genome assembly. This research presents a comparison of traditional versus Cloud computing-based genome assembly software, using as examples the Velvet and Contrail assemblers and reads from the genome sequence of the zebrafish (Danio rerio) model organism.

Results: The first phase of the analysis involved a subset of the zebrafish data set (2X coverage) and best results were obtained using …

Targeting Metastatic Breast Cancer: Problems And Potential [Version 1; Referees: 5 Approved], Sarah Deasy, Karol Szczepanek, Kent Hunter

Biochemistry and Molecular Medicine Faculty Publications

Breast cancer is one of the leading causes of cancer-related mortality of women in the United States. Since the majority of cancer deaths are due to metastases rather than the primary tumor, a better understanding of the biological mechanisms that lead to metastatic disease is critical to reduce breast cancer associated mortality. Current adjuvant therapies use the same broadly cytotoxic and targeted strategies against metastases as are used against the primary tumor. However, resistance to chemotherapy due to the cellular dormancy, high genotypic and phenotypic heterogeneity between primary tumor and metastases as well as among individual metastases, and the limitations …

Anti-Inflammatory Effect Of 1,3,5,7-Tetrahydroxy-8-Isoprenylxanthone Isolated From Twigs Of Garcinia Esculenta On Stimulated Macrophage., Dan-Dan Zhang, Hong Zhang, Yuan-Zhi Lao, Rong Wu, Jin-Wen Xu, Ferid Murad, Ka Bian, Hong-Xi Xu

Biochemistry and Molecular Medicine Faculty Publications

Garcinia Linn. plants having rich natural xanthones and benzophenones with anti-inflammatory activity attracted a great deal of attention to discover and develop them as potential drug candidates. Through screening targeting nitric oxide accumulation in stimulated macrophage, we found that 1,3,5,7-tetrahydroxy-8-isoprenylxanthone (TIE) had potential anti-inflammatory effect. To understand how TIE elicits its anti-inflammatory activity, we uncovered that it significantly inhibits the production of nitric oxide (NO) and prostaglandin E2 (PGE2) in LPS/IFNγ-stimulated RAW264.7 cells. In further study, we showed that TIE reduced the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), two key molecules responsible for the production of …

Composition, Taxonomy And Functional Diversity Of The Oropharynx Microbiome In Individuals With Schizophrenia And Controls., Eduardo Castro-Nallar, Matthew L Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G Severance, Faith B Dickerson, Jennifer R Schroeder, Robert H Yolken, Keith A Crandall

Computational Biology Institute

The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls …

Nitric Oxide Generating/Releasing Materials, Honying Liang, Parimala Nacharaju, Adam J. Friedman, Joel Friedman

Dermatology Faculty Publications

Harnessing the impressive therapeutic potential of nitric oxide (NO) remains an ongoing challenge. This paper describes several of the current strategies both with respect to the underlying chemistry and physics and to the applications where they have shown promise. Included in this overview are molecular systems such as NONOates that release NO through chemical reactions and delivery vehicles such as nanoparticles that can generate, store, transport and deliver NO and related bioactive forms of NO such as nitrosothiols. Although there has been much positive movement, it is clear that we are only at the early stages of knowing how to …

Cytosolic Fe-S Cluster Protein Maturation And Iron Regulation Are Independent Of The Mitochondrial Erv1/Mia40 Import System, Hatice K. Ozer, Adrienne C. Dlouhy, Jeremy D. Thornton, Jingjing Hu, Yilin Liu, Joseph J. Barycki, Janneke Balk, Caryn E. Outten

Department of Biochemistry: Faculty Publications

Background: The mitochondrial sulfhydryl oxidase Erv1 is implicated in cytosolic iron-sulfur protein maturation and iron regulation.

Results: An erv1 yeast strain used in previous iron metabolism studies is glutathione-deficient, and erv1/mia40 mutants with sufficient glutathione do not exhibit iron-related defects.

Conclusion: Iron homeostasis is independent of Erv1/Mia40 function. Significance: The unexplained role of Erv1 in yeast iron metabolism is resolved.

A Protective Role Of Autophagy In A Drosophila Model Of Friedreich's Ataxia (Frda), Luan Wang

Wayne State University Dissertations

Friedreich’s ataxia (FRDA) is an inherited autosomal recessive neurodegenerative disease. It affects 1 in every 50,000 people in central Europe and North America. FRDA is caused by deficiency of Frataxin, an essential mitochondrial iron chaperone protein, and the associated oxidative stress damages. Autophagy, a housekeeping process responsible for the bulk degradation and turnover of long half-life proteins and organelles, is featured by the formation of double-membrane vacuoles and lysosomal degradation. Previous researches indicate that Danon’s disease, the inherited neural disorder disease that shares similar symptoms with FRDA, is due to the malfunction of autophagy. Based on this, we raise the …

Cellulose Degradation: A Therapeutic Strategy In The Improved Treatment Of Acanthamoeba Infections, Sahreena Lakhundi, Ruqaiyyah Siddiqui, Naveed Ahmed Khan

Department of Biological & Biomedical Sciences

Acanthamoeba is an opportunistic free-living amoeba that can cause blinding keratitis and fatal brain infection. Early diagnosis, followed by aggressive treatment is a pre-requisite in the successful treatment but even then the prognosis remains poor. A major drawback during the course of treatment is the ability of the amoeba to enclose itself within a shell (a process known as encystment), making it resistant to chemotherapeutic agents. As the cyst wall is partly made of cellulose, thus cellulose degradation offers a potential therapeutic strategy in the effective targeting of trophozoite encased within the cyst walls. Here, we present a comprehensive report …

Severe Ovarian Hyperstimulation Syndrome Complicated By Stenotrophomonas Maltophilia Peritonitis: A Case Report And Literature Review, Abdul Rehman, Noor Ul-Ain Baloch, Muhammad Awais

Department of Biological & Biomedical Sciences

Ovarian hyperstimulation syndrome (OHSS) is an iatrogenic disorder resulting from ovulation induction. Although the occurrence of this disorder is rare, it can be potentially life-threatening in its most severe forms. We herein present the case of a young nulliparous woman who presented with features of abdominal compartment syndrome and was subsequently diagnosed with severe OHSS. All physicians, in particular critical care doctors, must be aware of this rare, but potentially life-threatening iatrogenic disorder.

Stress Management In Cyst-Forming Free-Living Protists: Programmed Cell Death And/Or Encystment, Naveed Ahmed Khan, Junaid Iqbal, Ruqaiyyah Siddiqui

Department of Biological & Biomedical Sciences

In the face of harsh conditions and given a choice, a cell may (i) undergo programmed cell death, (ii) transform into a cancer cell, or (iii) enclose itself into a cyst form. In metazoans, the available evidence suggests that cellular machinery exists only to execute or avoid programmed cell death, while the ability to form a cyst was either lost or never developed. For cyst-forming free-living protists, here we pose the question whether the ability to encyst was gained at the expense of the programmed cell death or both functions coexist to counter unfavorable environmental conditions with mutually exclusive phenotypes.

Pcdh19 Expression In Normal And Regenerating Adult Zebrafish Retinas, Kristin N. Forkapa Ms.

Williams Honors College, Honors Research Projects

My Honors Research Project will test the function of the N-cadherin molecule on the zebrafish optic nerve regeneration. N-cadherin is a member of the cadherin superfamily. Cadherins are cell adhesion molecules important for animal development and maintenance of adult structures. Unlike mammals, fish and amphibians have the ability to regenerate their optic nerve after damages. Molecular mechanisms underlying the optic nerve regeneration are still under intense investigation. Studies in Dr. Liu’s laboratory showed that expression of several cadherins, including N-cadherin, was greatly increased during adult zebrafish optic nerve regeneration, suggesting that cadherins may be involved in the optic nerve regeneration …

Isolation Of Microbial Nrps And Pks Gene Clusters For Natural Product Isolation, Danielle N. O'Hara

Honors Theses

Greater than 99% of microbes living in the environment are uncultivable due to their complex nutrient and temperature requirements for growth. These microorganisms present a potential source of natural products that could be developed for biotechnological and pharmaceutical uses. Microorganisms with phosphopantetheinyl transferase (PPTase) activity are of high interest due to the role PPTase plays in activating non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. These gene clusters produce multi-enzymatic, multi-domain megasynthases that produce complex natural products utilized by the host organism for selective advantages. This study isolated genomic DNA from soil samples collected from the University of …

Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill

Wayne State University Dissertations

Outbreaks of advanced antibiotic-resistant strains of microbes have hastened the need to identify new viable molecular targets for the development of novel anti-infectives. For this purpose, helix 69 (H69, or m3a 19-nucleotide (nt) hairpin motif that is highly conserved throughout phylogeny and rich in modified nucleotides, including pseudouridine () and 3-methylpseudouridine (m3) was chosen as a potential target. Helix 69, which is located in domain IV of Escherichia coli 23S ribosomal RNA (rRNA), undergoes conformational changes when in close proximity to the decoding region of 16S rRNA and transfer RNAs (tRNAs) in the peptidyl-transferase center (PTC). Functionally, the exact biological …

Increased Body Mass Index May Lead To Hyperferritinemia Irrespective Of Body Iron Stores, Faiza Alam, Abdul Shakoor Memon, Syeda Sadia Fatima

Department of Biological & Biomedical Sciences

Objective: Obesity causes subclinical inflammation which results in the secretion of various bioactive peptides that are key players in metabolic regulation of iron homeostasis. We sought to establish correlation of one such peptide (ferritin) with marker of subclinical inflammation (CRP) in various BMI.
Methods: Total 150 subjects between the ages of 20-60 years were included in the cross-sectional study conducted at Basic Medical Sciences Institute, Jinnah Post Graduate Medical Centre, Karachi, Pakistan. Body Mass Index (BMI) was calculated by weight (kg) /height (m(2)). The given values were used as reference for Group A: normal weight (18.0-22.9 kg/m2), Group B: overweight …

Prevalence Of Obesity And Overweight, Its Clinical Markers And Associated Factors In A High Risk South-Asian Population, Faridah Amin, Syeda Sadia Fatima, Najmul Islam, Anwar H. Gilani

Department of Biological & Biomedical Sciences

Background: Obesity is a global epidemic, which is a risk factor for cardiovascular diseases and metabolic abnormalities. It is measured by body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), body fat (BF) distribution and abdominal fat mass, each having its own merits and limitations. Variability in body composition between ethnic groups in South-Asians is significant and may not be truly reflected by BMI alone, which may result in misclassification. This study therefore, aims to determine the frequency of obesity, body fat composition and distribution, in a high risk population of an urban slum of Karachi, Pakistan. This survey …

How Pakistan's Media Spreads The Message About Reproductive And Sexual Health, Syed H. Abidi, Muhammad Raees, Syed Ali

Department of Biological & Biomedical Sciences

Abstract, issue, and pagination are not provided by the author/publisher

Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy, Anwesha Sarkar

Wayne State University Dissertations

Atomic Force Microscopy (AFM) provides superior imaging resolution and the ability to measure forces at the nanoscale. It is an important tool for studying a wide range of bio-molecular samples from proteins, DNA to living cells. We developed AFM measurement procedures to measure protein interactions on live cells at the single molecular level. These measurements can be interpreted by using proper statistical approaches and can yield important parameters about ligand-receptor interactions on live cells. However, the standard theory for analyzing rupture force data does not fit the experimental rupture force histograms. Most of the experimental measurements of rupture force data …

Cardiolipin Regulates Mitophagy Through The Pkc Pathway, Zheni Shen

Wayne State University Dissertations

Cardiolipin (CL), the signature phospholipid of mitochondrial membranes, is important for cardiovascular health. Perturbation of CL metabolism is implicated in cardiovascular disease (CVD). The link between CL and CVD may be explained by the physiological roles of CL in pathways that are cardioprotective, such as autophagy/mitophagy and the mitogen-activated protein kinase (MAPK) pathways. My dissertation work focuses on elucidating how CL influences mitophagy and MAPK pathways.

crd1Δ was synthetically lethal/sick with the general autophagy mutants atg8Δ, atg18Δ and mitophagy mutant atg32Δ, suggesting that autophagy/mitophagy may be deficient in cells lacking CL. Microscopic examination of mitophagy revealed decreased translocation of GFP-tagged …

Regulation Of Cxcr4 Intracellular Trafficking By Ubiquitin, Justine Elizabeth Kennedy

Dissertations

G protein-coupled receptor (GPCR) sorting into the degradative pathway is important for attenuating signaling. Perturbations in this process can manifest in a variety of diseases. Upon agonist activation of the chemokine receptor CXCR4, a GPCR, it is rapidly ubiquitinated, internalized to endosomes and sorted for degradation in lysosomes via the endosomal sorting complex required for transport (ESCRT) pathway. This process culminates in attenuation of CXCR4 signaling. CXCR4 overexpression and increased CXCR4 signaling have been associated with several pathologies including immune deficiency disorders and over 23 cancers. Yet the mechanisms governing the regulation of CXCR4 signaling remain elusive.

CXCR4 is ubiquitinated …

Eliminating Acute Myeloid Leukemia Stem Cells By Targeting The Niche Microenviromnent: Co-Inhibition Of Tnf/Il1- Jnk And Nf-Κb, Andrew Volk

Dissertations

Leukemia Stem Cells (LSCs) from Acute Myeloid Leukemia (AML) require the activity of the transcription factor NF-kB to maintain stemness and drive tumor formation. Blocking NF-kB can preferentially eliminate LSCs in vitro with minimal effects on healthy Hematopoietic Stem and Progenitor Cells (HSPCs), making NF-kB a compelling target for anti-leukemia therapies. However, blocking NF-kB in vivo can only extend survival for a short period of time before transplanted mice succumb to the disease. I propose this is due to components of the in vivo niche supporting LSC survival and compensating for the inhibition of NF-kB.

I observed patients with partially …

Application Of Lipid Styryl Dye For Staining Intracytoplasmic Membranes In Gram-Negative Bacteria, Theodore J. Hammer

Williams Honors College, Honors Research Projects

Intracytoplasmic membranes are structures that form within cells which help facilitate a variety of different metabolic processes. This feature of intracellular membranes makes them particularly valuable for studying compartmentalization and cell dynamics in bacteria. In the past, transmission electron microscopy has been the primary method for imaging bacteria with intracytoplasmic membranes. Because transmission electron microscopy takes images of a cell in fixed slices, it’s impossible to follow a cell’s growth and development over time. Fluorescence microscopy is a particularly effective method of measurement that can combat these issues when evaluating live bacterial cells. Here, standard biochemical laboratory procedures were used …

Inhibition Of Shp2 Suppresses Mutant Egfr-Induced Lung Tumors In Transgenic Mouse Model Of Lung Adenocarcinoma, Valentina E. Schneeberger, Yuan Ren, Noreen Luetteke, Qingling Huang, Liwei Chen, Harshani R. Lawrence, Nicholas J. Lawrence, Eric B. Haura, John M. Koomen, Domenico Coppola, Jie Wu

Molecular Biosciences Faculty Publications

Epidermal growth factor receptor (EGFR) mutants drive lung tumorigenesis and are targeted for therapy. However, resistance to EGFR inhibitors has been observed, in which the mutant EGFR remains active. Thus, it is important to uncover mediators of EGFR mutant-driven lung tumors to develop new treatment strategies. The protein tyrosine phosphatase (PTP) Shp2 mediates EGF signaling. Nevertheless, it is unclear if Shp2 is activated by oncogenic EGFR mutants in lung carcinoma or if inhibiting the Shp2 PTP activity can suppress EGFR mutant-induced lung adenocarcinoma. Here, we generated transgenic mice containing a doxycycline (Dox)-inducible PTP-defective Shp2 mutant (tetO-Shp2CSDA). Using the rat Clara …

The Νsaα Specific Lipoprotein Like Cluster (Lpl) Of S. Aureus Usa300 Contributes To Immune Stimulation And Invasion In Human Cells, Minh Thu Nguyen, Beatrice Kraft, Wenqi Yu, Dogan Doruk Demicrioglu, Tobias Hertlein, Marc Burian, Mathias Schmaler, Klaus Boller, Isabelle Bekeredjian-Ding, Knut Ohlsen, Birgit Schittek, Friedrich Götz

Molecular Biosciences Faculty Publications

All Staphylococcus aureus genomes contain a genomic island, which is termed νSaα and characterized by two clusters of tandem repeat sequences, i.e. the exotoxin (set) and 'lipoprotein-like' genes (lpl). Based on their structural similarities the νSaα islands have been classified as type I to IV. The genomes of highly pathogenic and particularly epidemic S. aureus strains (USA300, N315, Mu50, NCTC8325, Newman, COL, JH1 or JH9) belonging to the clonal complexes CC5 and CC8 bear a type I νSaα island. Since the contribution of the lpl gene cluster encoded in the νSaα island to virulence is unclear to date, we deleted …

Regulation Of Vldl Trafficking By Orp 10, Philip A. Wessels

HIM 1990-2015

Of the challenges facing the improvement of human health, none has taken the forefront quite like the endeavor to discover novel treatments for heart disease. As heart disease has now become the leading cause of death throughout the world [1], the medical community has made incredible strides in the mission to treat atherosclerosis which is the major contributor to heart disease. Very Low Density Lipoproteins (VLDL) are secreted by the liver and subsequently converted to Low Density Lipoproteins (LDL). Many factors contribute to the narrowing of the arterial walls, however oxidized LDL is the main factor that leads to the …