Molecular Biology Commons^™

Isolation Of Cancer Stem Cells From Adult Glioblastoma Multiforme, Xianpeng Yuan, James Curtin, Yizhi Xiong, Gentao Liu, Sebastian Waschsmann-Hogiu, Daniel Farkas, Keith Black, John Yu

Articles

Glioblastoma multiforme (GBM) is the most common adult primary brain tumor and is comprised of a heterogeneous population of cells. It is unclear which cells within the tumor mass are responsible for tumor initiation and maintenance. In this study, we report that brain tumor stem cells can be identified from adult GBMs. These tumor stem cells form neurospheres, possess the capacity for self-renewal, express genes associated with neural stem cells (NSCs), generate daughter cells of different phenotypes from one mother cell, and differentiate into the phenotypically diverse populations of cells similar to those present in the initial GBM. Having a …

Rhodobacter Capsulatus Porphobilinogen Synthase, A High Activity Metal Ion Independent Hexamer, David Bollivar

Scholarship

No abstract provided.

Phylogenetic Analysis Of The Formin Homology 2 Domain, Henry N. Higgs, Kevin J. Peterson

Dartmouth Scholarship

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the …

On Thacker's Biomedia (2004), Nicholas Ruiz Iii

Reconstruction: Studies in Contemporary Culture

[First paragraph]

Only we could have done it. The Code (DNA and its analogs, etc.) that we perhaps only narrate, never forgetting all of the fictions that narration portends, today consciously edits the text that evolution has edited unconsciously for eons. Thacker considers how humans -- perhaps little more than interactive Code, manipulate the Code -- with the technology of the Code. No other faction of Code has yet to make such heady ‘gains.’ Where posthumanity was always a literary endeavor, a literary bypass, out of instrumental science and into fictive states, it now is a technical endeavor, encompassing a …

Paradigm Shifts And New Worldviews: Kuhn, Laudan And Discovery In Molecular Biology, Priya Venkatesan

Reconstruction: Studies in Contemporary Culture

[Editors' Introduction]

The author poses an alternate set of ideas concerning paradigms, normal science, research traditions and scientific revolution on the basis of the unique and inherently distinctive development of molecular biology and genetics; for, a new set of conceptual tools concerning scientific progress are required for an adequate understanding of how biological processes were elucidated under the scientific auspices of the central dogma of the genetic code. This essay concentrates on a limited study of three aspects in genetics: the study of chromosome structure, dynamics and function, reverse transcriptases, and the discovery of RNA catalysts. In attempting to analyze …

Cloning And Functional Analysis Of The Putative Tetracycline Resistance Gene Hp1165 In Helicobacter Pylori, Yuhuan Li

All-Inclusive List of Electronic Theses and Dissertations

Tetracycline has been used in combination with other antibiotics in treatment of Helicobacter pylori infection. However, tetracycline resistance has developed in clinical isolates of H. pylori, rendering treatment failure. Mutations in the 16S rRNA gene have been reported to mediate tetracycline resistance in some patient isolates. Nevertheless, the diversity of tetracycline resistance cases suggests multiple genes are involved. HPl 165, a putative tetracycline resistance gene in the genome of H. pylori 26695, displays 49.8% identity to the tetracycline efflux gene tetA (P) from Clostridium perfringens. To determine the function of the HPl 165 gene and gain a better understanding of …

Pv1 Is A Key Structural Component For The Formation Of The Stomatal And Fenestral Diaphragms, Radu V. Stan, Eugene Tkachenko, Ingrid R. Niesman

Dartmouth Scholarship

PV1 is an endothelial-specific integral membrane glycoprotein associated with the stomatal diaphragms of caveolae, transendothelial channels, and vesiculo-vacuolar organelles and the diaphragms of endothelial fenestrae. Multiple PV1 homodimers are found within each stomatal and fenestral diaphragm. We investigated the function of PV1 within these diaphragms and their regulation and found that treatment of endothelial cells in culture with phorbol myristate acetate (PMA) led to upregulation of PV1. This correlated with de novo formation of stomatal diaphragms of caveolae and transendothelial channels as well as fenestrae upon PMA treatment. The newly formed diaphragms could be labeled with anti-PV1 antibodies. The upregulation …

The Importance Of A Critical Protonation State And The Fate Of The Catalytic Steps In Class A Β-Lactamases And Penicillin-Binding Proteins, Dasantila Golemi-Kotra, Samy O. Meroueh, Choonkeun Kim, Sergei B. Vakulenko, Alexey Bulychev, Ann J. Stemmler, Timothy L. Stemmler, Shahriar Mobashery

Biochemistry and Molecular Biology Faculty Publications

b-Lactamases and penicillin-binding proteins are bacterial enzymes involved in antibiotic resistance to b-lactam antibiotics and biosynthetic assembly of cell wall, respectively. Members of these large families of enzymes all experience acylation by their respective substrates at an active-site serine as the first step in their catalytic activities. A Ser-X-X-Lys sequence motif is seen in all these proteins and crystal structures demonstrate that the side chain functions of the serine and lysine are in contact with one another. Three independent methods were used in this report to address the question of the protonation state of this important lysine (Lys73) in the …

Pcr And 16s Rdna Sequencing For Identifying And Comparing Gram-Negative Bacteria, Molly Truax

Honors Capstones

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

The C. Elegans Heterochronic Gene Lin-46 Affects Developmental Timing At Two Larval Stages And Encodes A Relative Of The Scaffolding Protein Gephyrin, A. S.-R. Pepper, Jill E. Mccane, Kevin Kemper, Dennis Au Yeung, Rosalind C. Lee, Victor Ambros, Eric G. Moss

Dartmouth Scholarship

The succession of developmental events in the C. elegans larva is governed by the heterochronic genes. When mutated, these genes cause either precocious or retarded developmental phenotypes, in which stage-specific patterns of cell division and differentiation are either skipped or reiterated, respectively. We identified a new heterochronic gene, lin-46, from mutations that suppress the precocious phenotypes caused by mutations in the heterochronic genes lin-14 and lin-28. lin-46 mutants on their own display retarded phenotypes in which cell division patterns are reiterated and differentiation is prevented in certain cell lineages. Our analysis indicates that lin-46 acts at a step immediately downstream …

Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal

Department of Biological & Biomedical Sciences

No abstract provided.

Photoreactive Bicyclic Amino Acids As Substrates For Mutant Escherichia Coli Phenylalanyl-Trna Synthetases, Thomas Bentin, Ramin Hamzavi, Jahan Salomonsson, Hervé Roy, Michael Ibba, Peter E. Nielsen

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Unnatural amino acids carrying reactive groups that can be selectively activated under non-invasive biologically benign conditions are of interest in protein engineering as biological tools for the analysis of protein-protein and protein-nucleic acids interactions. The double ring system phenylalanine analogues benzofuranylalanine and benzotriazolylalanine were synthesized, and their photolability was tested by UV irradiation at 254, 320, and 365 nm. Although both showed photo reactivity, benzofuranylalanine appeared as the most promising compound because this amino acid was activated by UVA (long wavelength) irradiation. These amino acids were also tested for in vitro charging of tRNA^Phe and for protein mutagenesis via …

Mer1p Is A Modular Splicing Factor Whose Function Depends On The Conserved U2 Snrnp Protein Snu17p, Marc Spingola, Javier Armisen, Manuel Ares

Biology Department Faculty Works

Mer1p activates the splicing of at least three pre‐mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C‐terminal KH‐type RNA‐binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N‐terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5′ splice site as key elements in Mer1p‐activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns …

Divergence In Non-Cognate Amino Acid Recognition Between Class I And Class Ii Lysyl-Trna Synthetases, Jeffrey D. Levengood, Sandro F. Ataide, Hervé Roy, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Lysine insertion during coded protein synthesis requires lysyl-tRNA^Lys, which is synthesized by lysyl-tRNA synthetase (LysRS). Two unrelated forms of LysRS are known: LysRS2, which is found in eukaryotes, most bacteria, and a few archaea, and LysRS1, which is found in most archaea and a few bacteria. To compare amino acid recognition between the two forms of LysRS, the effects of l-lysine analogues on aminoacylation were investigated. Both enzymes showed stereospecificity toward the l-enantiomer of lysine and discriminated against noncognate amino acids with different R-groups (arginine, ornithine). Lysine analogues containing substitutions at other positions were generally most effective as …

Altered Phosphorylation Of [Beta]-Catenin In Glucocorticoid Treated 235-1 Rat Pituitary Tumor Cells, Susie K. Saunders

Theses, Dissertations and Capstones

Beta-catenin is an essential cell adhesion and signaling protein, associated with high prolactin levels in rat pituitary tumor cells. It has been shown that phosphorylation affects the location and activity of b-catenin. Glycogen synthase kinase (GSK3-b) is a serine-threonine kinase that phosphorylates b-catenin on N-terminal residues, targeting it for proteasomal degradation. Studies have shown that C-terminal tyrosine phosphorylation decreases the association of b-catenin with cadherin. In 235-1 rat pituitary tumor cells, our lab has shown that the glucocorticoid analog dexamethasone (Dex) decreases the half- life of b-catenin while increasing the activity of GSK3-b. The current study was undertaken to examine …

Molecular Typing Of Mycobacterial Isolates Cultured From The Tissue Of Inflammatory Bowel Disease (Crohn's Disease) Patients, Leanne M. Adams

Electronic Theses and Dissertations

The role of Mycobacterium avium subsp paratuberculosis (MAP) in the etiology and pathogenesis of inflammatory bowel disease (IBD) including Crohn's Disease (CD), has been investigated. The fastidious characteristics and cross reactivity of MAP with other members in Mycobacteria have produced significant challenges in their detection and identification. In this two year pilot study, an array of three PCR molecular assays based on the detection of sequences from the16S rRNA, IS1245, and IS900 genes, belonging to members of the MAC, have been developed and optimized into a common protocol to be used as a rapid and accurate diagnostic tool regarding M. …

Extracullular Atp Regulates Il-1beta Release From Microglial Cells Via Purinergic Receptor After In Vitro Trauma, Chengya Liang

Electronic Theses and Dissertations

Traumatic brain injury (TBI) induces a state of microglialactivation, which includes upregulation of macrophage functions and release inflammatory mediators such as certain inflammatory cytokines. Current literature suggests that interleukin-1Beta is an important cytokine mediator, which is dramatically increased after brain injury. Previous studies indicate that ATP is released by traumatically injured astrocytes and serves as a cell-to-cell mediator through purinergic receptors after in vitro injury. However, the mechanism of interleukin-1Beta release after traumatic brain injury remains poorly defined and is difficult to study using in vivo models. Using an in vitro model for traumatic brain injury (cell strain or stretch), …

Evaluation Of Multiple Models To Distinguish Closely Related Forms Of Disease Using Dna Microarray Data: An Application To Multiple Myeloma, Johanna S. Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J. Crowley

Pomona Faculty Publications and Research

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is …

Actr/Aib1 Functions As An E2f1 Coactivator To Promote Breast Cancer Cell Proliferation And Antiestrogen Resistance, Maggie C. Louie, June X. Zou, Alina Rabinovich, Hong-Wu Chen

Collected Faculty Scholarship

Overexpression or amplification of ACTR (also named AIB1, RAC3, p/CIP, TRAM-1, and SRC-3), a member of the p160 family of coactivators for nuclear hormone receptors, has been frequently detected in multiple types of human tumors, including breast cancer. However, its role in cancer cell proliferation and the underlying mechanism are unclear. Here, we show that overexpression of ACTR not only enhances estrogen-stimulated cell proliferation but also, more strikingly, completely negates the cell cycle arrest effect by tamoxifen and pure antiestrogens. Unexpectedly, we found that ACTR directly interacts, through its N-terminal domain, with E2F1 and is recruited to E2F target gene …

Integrated Allosteric Regulation In The S. Cerevisiae Carbamylphosphate Synthetase – Aspartate Transcarbamylase Multifunctional Protein, Valã©Rie Serre, Bernadette Penverne, Jean-Luc Souciet, Serge Potier, Hedeel Guy, David Evans, Patrick Vicart, Guy Hervã©

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

The S. cerevisiae carbamylphosphate synthetase – aspartate transcarbamylase multifunctional protein catalyses the first two reactions of the pyrimidine pathway. In this organism, these two reactions are feedback inhibited by the end product UTP. In the present work, the mechanisms of these integrated inhibitions were studied.

Results

The results obtained show that the inhibition is competitive in the case of carbamylphosphate synthetase and non-competitive in the case of aspartate transcarbamylase. They also identify the substrate whose binding is altered by this nucleotide and the step of the carbamylphosphate synthetase reaction which is inhibited. Furthermore, the structure of the domains …

Survival Of Mycobacterium Avium Subspecies Paratuberculosis In The Pol, John Rumsey

Electronic Theses and Dissertations

Mycobacterium avium subspecies paratuberculosis (map) is an intracellular pathogen that is known to parasitize macrophages and monocytes. Map infiltrates gastrointestinal tract host tissue where it is the known etiological agent of johne's disease in ruminants and implicated in the etiology of crohn's disease in humans. Map's ability to survive within macrophages enables it to disseminate throughout the rest of the host, possibly infecting other circulating blood leukocytes. In this study, the survival and fate of map strain atcc 43015 (human isolate) following phagocytosis was determined using in vitro murine macrophage cell line j774a.1 and polymorphonuclear cells (pmnc's) from five crohn's …

Can Martian Life Exist Under Dry Conditions?, Michael Kendrick

Inquiry: The University of Arkansas Undergraduate Research Journal

Recently, we have begun to hear more and more about news coming from Mars. With the recent confirmation of evidence of liquid water in Mars' past, evidence indicating liquid water in Mars' present, and as many missions planned for this decade and the next than have successfully reached the planet in the last 40 years, life on Mars is beginning to become a more relevant issue in our study of the planet. Although there have been no indications of multicellular life on Mars, there may be a possibility of microbial life in the subsurface. Since it appears that all of …

Characterization Of Protein Prenyltransferases And Protein Prenylation In Plasmodium Falciparum, Thiago Gaspar Dasilva

Electronic Theses and Dissertations

Malaria kills at least one million people each year, mostly children - a death every 30 seconds. Almost one half of the world population is at risk from malaria. Antimalarial drugs are the only means for the treatment of about 500 million annual global malaria cases. Because of prevalent drug-resistance it is extremely urgent to identify new drug targets. Many proteins involved in eukaryotic signal transduction and cell cycle progression undergo post-translational lipid modification by a prenyl group. Protein prenyltransferases, which catalyze the post-translational prenyl modification, have been established as a target for anticancer therapy. Research done in our laboratory …

Molecular Cloning And Characterization Of Two Mouse Peroxisome Proliferator-Activated Receptor Alpha (Ppara) Regulated Peroxisomal Acyl-Coa Thioesterases., Maria Westin, Mary Hunt, Stefan Alexson

Articles

Peroxisomes are organelles that function in the b-oxidation of very-long and long-chain acyl-CoAs, bile acid-CoA intermediates, prostaglandins, leukotrienes, thromboxanes, dicarboxylic fatty acids, pristanic acid and xenobiotic carboxylic acids. The very long- and long-chain acyl-CoAs are mainly chain-shortened and then transported to mitochondria for further metabolism. We have now identified and characterized two peroxisomal acyl- CoA thioesterases, named PTE-Ia and PTE-Ic, which hydrolyze acyl-CoAs to the free fatty acid and coenzyme A. PTE-Ia and PTE-Ic show 82% sequence identity at amino acid level and a putative peroxisomal type 1 targeting signal of –AKL was identified at the carboxy-terminal end of both …

Stimulation Of Capacitative Calcium Entry In Hl-60 Cells By Nanosecond Pulsed Electric Fields, Jody A. White, Peter F. Blackmore, Karl H. Schoenbach, Stephen J. Beebe

Bioelectrics Publications

Nanosecond pulsed electric fields (nsPEFs) are hypothesized to affect intracellular structures in living cells providing a new means to modulate cell signal transduction mechanisms. The effects of nsPEFs on the release of internal calcium and activation of calcium influx in HL-60 cells were investigated by using real time fluorescent microscopy with Fluo-3 and fluorometry with Fura-2. nsPEFs induced an increase in intracellular calcium levels that was seen in all cells. With pulses of 60 ns duration and electric fields between 4 and 15 kV/cm, intracellular calcium increased 200-700 nM, respectively, above basal levels (similar to100 nM), while the uptake of …

Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.

Mathematics & Statistics Faculty Publications

Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.

Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …

Dissecting The Loci Of Low-Level Quinine Resistance In Malaria Parasites, Michael T. Ferdig, Roland A. Cooper, Jianbing Mu, Bingbing Deng, Deirdre A. Joy, Xin-Zhuan Su, Thomas E. Wellems

Biological Sciences Faculty Publications

Quinine (QN) remains effective against Plasmodium falciparum, but its decreasing efficacy is documented from different continents. Multiple genes are likely to contribute to the evolution of QN resistance. To locate genes contributing to QN response variation, we have searched a P. falciparum genetic cross for quantitative trait loci (QTL). Results identify additive QTL in segments of chromosomes (Chrs) 13, 7 and 5, and pairwise effects from two additional loci of Chrs 9 and 6 that interact, respectively, with the QTL of Chrs 13 and 7. The mapped segments of Chrs 7 and 5 contain pfcrt, the determinant of …

Possible Use Of P20 Antigen In Serodiagnosis Of Inflammatory Bowel Disease, Shinchieh Yang

Electronic Theses and Dissertations

Crohn's disease (CD) is an idiopathic, chronic, relapsing inflammatory disorder, which is most commonly involved terminal ileum and colon. The incidence and prevalence of CD has dramatically increased during the last 50 years; however, the etiology and mechanism of this disorder remain unveiled. Besides genetic susceptibility, recent integrated researches investigated the role of environmental triggers such as microflora, measles viruses and mycobacteria in the pathogenesis of CD. The association between M. avium subsp paratuberculosis (MAP) and CD has been heightened because of clinical resemblance to Johne's disease (JD), a granulomatous enteritis in ruminants caused by MAP. Isolation of MAP from …

Aminoacyl-Trnas: Setting The Limits Of The Genetic Code, Michael Ibba, Dieter Söll

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNAs (aa-tRNAs) are simple molecules with a single purpose—to serve as substrates for translation. They consist of mature tRNAs to which an amino acid has been esterified at the 3′-end. The 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases (aaRSs, of which there are two classes), one for each amino acid of the genetic code (Ibba and Söll 2000). This would be fine if it were not for the fact that such a straightforward textbook scenario is not true in a single known living organism. aa-tRNAs lie at the heart of gene expression; they interpret …

Evaluation Of Immunogenicity Of Transgenic Chloroplast Derived Protect, Vijay Koya

Electronic Theses and Dissertations

Anthrax, a fatal bacterial infection is caused by Bacillus anthracis, a gram-positive, spore forming, capsulated, rod shaped organism. Centers for Disease Control (CDC) lists anthrax as Category A biological agent due to its severity of impact on human health, high mortality rate, acuteness of the disease and potential for delivery as a biological weapon. The currently available human vaccine in the United States (AVA anthrax vaccine adsorbed) is prepared from Alum adsorbed formalin treated supernatant culture of toxigenic, non-encapsulated strain of Bacillus anthracis with the principle component being protective antigen (PA83). Evaluation of anthrax vaccine given to nearly 400,000 US …