Biochemistry Commons^™

Atrial Fibrillation: Biophysics, Molecular Mechanisms, And Novel Therapies., Alexey V. Glukhov, Leonid V. Rosenshtraukh, Anamika Bhargava, Michele Miragoli, Bas J. D. Boukens

Anatomy and Regenerative Biology Faculty Publications

No abstract provided.

Bacterial Expression Of Plant Pyruvate Kinase, Kristina Fuller

STAR Program Research Presentations

Pyruvate kinases serve an important role in regulating glycolysis pathways. Different pyruvate kinase isozymes can dictate which of several different products will be formed during the final step of glycolysis. Being able to reliably copy active pyruvate kinases (PK) would allow study of the different isozymes, with the goal of eventually creating plants that are more nutritionally beneficial for humans. This study focused on improving the protocol for replicating each of two isolated PK isozymes from the model plant Arabidopsis thaliana. Previous attempts had resulted in the PK denaturing and consequently precipitating out of solution and so we manipulated the …

Species Preference Of Viral Deubiquitinating Proteases Toward Isg15 Through Structural And Enzymatic Characterization, Michelle Kay Deaton

Electronic Theses and Dissertations

Proteases from the Ovarian Tumor domain (OTU) superfamily of deubiquitinating enzymes (DUBs) are expressed by a range of RNA viruses. Viral OTUs (vOTUs) are found in nairoviruses such as Crimean Congo Hemorrhagic Fever virus (CCHFV), Nairobi sheep disease virus (NSDV), the Erve virus (ERVEV), and the Dugbe virus (DUGV), as well as in the areterivirus Porcine Reproductive and Respiratory Syndrome virus (PRRSV), among others. vOTUs, which interfere with host innate immune response through editing of host Ub and Ub-like molecules such as interferon stimulated gene 15 (ISG15), have been identified as a potential virulence factor through their role in evading …

Ph Dependence Of Cyanide And Imidazole Binding To The Heme Domains Of Sinorhizobium Meliloti And Bradyrhizobium Japonicum Fixl, Anil K. Bidwai, Angela J. Ahrendt, John S. Sullivan, Lidia B. Vitello, James E. Erman

Faculty Publications & Research

Equilibrium and kinetic properties of cyanide and imidazole binding to the heme domains of Sinorhizobium meliloti and Bradyrhizobium japonicum FixL (SmFixLH and BjFixLH) have been investigated between pH 5 and 11. K_D determinations were made at integral pH values, with the strongest binding at pH 9 for both ligands. K_D for the cyanide complexes of BjFixLH and SmFixLH is 0.15 ± 0.09 and 0.50 ± 0.20 μM, respectively, and 0.70 ± 0.01 mM for imido-BjFixLH. The association rate constants are pH dependent with maximum values of 443 ± 8 and 252 ± 61 …

Bacterial Death Results From Mutations Made In Translocation Peptide Of Leucyl-Trna Synthetase, Daniel M. Mcdonough, Layla N. Baykal, Mallory J. Banton, Rachel A. Hellmann-Whitaker

Bridges: A Journal of Student Research

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3' acceptor stem of tRNA 30 Å from the …

Bacterial Death Results From Mutations Made In Translocation Peptide Of Leucyl-Trna Synthetase, Daniel M. Mcdonough, Layla N. Baykal, Mallory J. Banton, Rachel A. Hellmann-Whitaker

Bridges: A Journal of Student Research

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3' acceptor stem of tRNA 30 Å from the …

Reversing Chromatin Accessibility Differences That Distinguish Homologous Mitotic Metaphase Chromosomes., Wahab A Khan, Peter K Rogan, Joan H M Knoll

Biochemistry Publications

BACKGROUND: Chromatin-modifying reagents that alter histone associating proteins, DNA conformation or its sequence are well established strategies for studying chromatin structure in interphase (G1, S, G2). Little is known about how these compounds act during metaphase. We assessed the effects of these reagents at genomic loci that show reproducible, non-random differences in accessibility to chromatin that distinguish homologous targets by single copy DNA probe fluorescence in situ hybridization (scFISH). By super-resolution 3-D structured illumination microscopy (3D-SIM) and other criteria, the differences correspond to 'differential accessibility' (DA) to these chromosomal regions. At these chromosomal loci, DA of the same homologous chromosome …

Validating A Method For Measuring Protein Domain And Lipid Binding Interactions Using Luciferase Fusion Proteins, Dezaray E. Thoen

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

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 …

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.

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.

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.

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

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 …

Transfer Rna Comes Of Age, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

"The year the journal RNA was founded was slated by some in scientific publishing to be the year that one particular type of RNA's run in the spotlight would end. In 1995 I had recently started as a post-doc with Dieter Söll at Yale when he came into the lab to solemnly inform us all that an editor at a certain (S)cience journal had just told him “we won't be publishing any more tRNA papers.” For a post-doc who had migrated across the Atlantic for the sole purpose of furthering his career by working on tRNA this was not great …

Introduction To Fifth Special Issue On Electroporation-Based Technologies And Treatments, Damijan Miklavčič, Lluis M. Mir, P. Thomas Vernier

Bioelectrics Publications

This special issue of the Journal of Membrane Biology contains reports on recent developments in the field of electroporation by participants in the International Workshop and Postgraduate Course on Electroporation-Based Technologies and Treatments held in November 2014 in Ljubljana. This was the eighth session of what is now an annual event, first organized in 2003.

In Situ Oh Generation From O2- And H2o2 Plays A Critical Role In Plasma Induced Cell Death, Dehui Xu, Dingxing Liu, Biqing Wang, Chen Chen, Zeyu Chen, Dong Li, Yanjie Yang, Hailan Chen, Michael G. Kong

Bioelectrics Publications

Reactive oxygen and nitrogen species produced by cold atmospheric plasma (CAP) are considered to be the most important species for biomedical applications, including cancer treatment. However, it is not known which species exert the greatest biological effects, and the nature of their interactions with tumor cells remains ill-defined. These questions were addressed in the present study by exposing human mesenchymal stromal and LP-1 cells to reactive oxygen and nitrogen species produced by CAP and evaluating cell viability. Superoxide anion (O₂-) and hydrogen peroxide (H₂O₂) were the two major species present in plasma, but their …

Picosecond To Terahertz Perturbation Of Interfacial Water And Electropermeabilization Of Biological Membranes, P. Thomas Vernier, Zachary A. Levine, Ming-Chak Ho, Shu Xiao, Iurii Semenov, Andrei G. Pakhomov

Bioelectrics Publications

Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, we need an understanding of the biophysical mechanisms underlying the responses that have been reported to these novel stimuli. We show here that subnanosecond (≤500 ps) electric pulses induce action potentials in neurons and cause calcium transients in neuroblastoma-glioma hybrid cells, and we report complementary molecular dynamics simulations of phospholipid bilayers in electric fields in which …

Diffuse, Non-Polar Electropermeabilization And Reduced Propidium Uptake Distinguish The Effect Of Nanosecond Electric Pulses, Iurii Semenov, Christian W. Zemlin, Olga N. Pakhomova, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Ca²⁺ activation and membrane electroporation by 10-ns and 4-ms electric pulses (nsEP and msEP) were compared in rat embryonic cardiomyocytes. The lowest electric field which triggered Ca²⁺ transients was expectedly higher for nsEP (36 kV/cm)than forms EP (0.09 kV/cm) but the respective doses were similar (190 and460 mJ/g). At higher intensities, both stimuli triggered prolonged firing in quiescent cells. An increase of basal Ca²⁺ level by N10 nM in cells with blocked voltage-gated Ca²⁺ channels and depleted Ca²⁺ depot occurred at 63 kV/cm (nsEP) or 0.14 kV/cm (msEP) and was regarded as electroporation threshold. These …

Connecting Proline Metabolism And Signaling Pathways In Plant Senescence, Lu Zhang, Donald F. Becker

Department of Biochemistry: Faculty Publications

The amino acid proline has a unique biological role in stress adaptation. Proline metabolism is manipulated under stress by multiple and complex regulatory pathways and can profoundly influence cell death and survival in microorganisms, plants, and animals. Though the effects of proline are mediated by diverse signaling pathways, a common theme appears to be the generation of reactive oxygen species (ROS) due to proline oxidation being coupled to the respiratory electron transport chain. Considerable research has been devoted to understand how plants exploit proline metabolism in response to abiotic and biotic stress. Here, we review potential mechanisms by which proline …

Chloroplast Lipid Transfer Processes In Chlamydomonas Reinhardtii Involving A Trigalactosyldiacylglycerol 2 (Tgd2) Ortholog, Jaruswan Warakanont, Chia-Hong Tsai, Elena J.S. Michel, George R. Murphy Iii, Peter Y. Hsueh, Rebecca L. Roston, Barbara B. Sears, Christoph Benning

Department of Biochemistry: Faculty Publications

In plants, lipids of the photosynthetic membrane are synthesized by parallel pathways associated with the endoplasmic reticulum (ER) and the chloroplast envelope membranes. Lipids derived from the two pathways are distinguished by their acyl-constituents. Following this plant paradigm, the prevalent acyl composition of chloroplast lipids suggests that Chlamydomonas reinhardtii (Chlamydomonas) does not use the ER pathway; however, the Chlamydomonas genome encodes presumed plant orthologs of a chloroplast lipid transporter consisting of TGD (TRIGALACTOSYLDIACYLGLYCEROL) proteins that are required for ER-tochloroplast lipid trafficking in plants. To resolve this conundrum, we identified a mutant of Chlamydomonas deleted in the TGD2 gene and characterized …

Phenotypic Screening Identifies Brefeldin A/Ascotoxin As An Inducer Of Lipid Storage In The Algae Chlamydomonas Reinhardtii, Nishikant Wase, Boqiang Tu, Paul N. Black, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

The use of microalgae as a biofuel feedstock is highly desired, but current methods to induce lipid accumulation cause severe stress responses that limit biomass and, thus oil yield. To address these issues, a high throughput screening (HTS) method was devised to identify chemical inducers of growth and lipid accumulation. Optimization was performed to determine the most effective cell density, DMSO and Nile Red (NR) concentrations to monitor growth and lipid accumulation. The method was tested using 1717 compounds from National Cancer Institute (NCI) Diversity Set III and Natural Products Set II in Chlamydomonas reinhardtii. Cells were inoculated at …