Purification and Characterisation of a Protease (Tamarillin) from Tamarillo Fruit
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Phylogenetic Screening for Possible Novel
11 M060072591U NORTH-WEST UNIVERSITY tilt• YUNIBESITI YA BOKONE•BOPHIRIMA NOOROVVE S-UNIVERSITEIT PHYLOGENETIC SCREENING FOR POSSIBLE NOVEL ANTIBIOTIC PRODUCING ACTINOMYCETES FROM RHIZOSPHERIC SOIL SAMPLES COLLECTED FROM NGAKA MODIRI MOLEMA DISTRICT IN NORTH WEST PROVINCE, SOUTH AFRICA I BY MOBOLAJI FELICIA ADEGBOYE A thesis submitted in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY (BIOLOGY) DEPARTMENT OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE, AGRICULTURE AND TECHNOLOGY NORTH-WEST UNIVERSITY, MAFIKENG CAMPUS SOUTH AFRICA Supervisor: Professor Olubukola 0. Babalola 2014 LIBRARY o MAFIKENG CAMPUS CALL NO.: 2021 -02- 0 4 DECLARATION I, the undersigned, declare that this thesis submitted to the North-West University for the degree of Doctor of Philosophy in Biology in the Faculty of Science, Agriculture and Technology, School of Environmental and Health Sciences, and the work contained herein is my original work with exemption to the citations and that this work has not been submitted at any other University in partial or entirely for the award of any degree. Name: Mobolaji Felicia Adegboye Signature: .....~ •·· ··· ····· ·· .. ··············· ..... Date: .... ~S.. .. ....a~ ·1·· ·'.}Q~i; ... ............ .... DEDICATION This work is dedicated to Almighty God for His faithfulness over my life and for making my helpers to be many. ii ACKNOWLEDGEMENTS I would like to express my deepest thanks, gratitude and appreciation to my supervisor and mentor, Prof. Olubukola 0. Babalola for giving me the opportunity to pursue my doctoral degree under her supervision and for her encouragement, help and kind support. Her invaluable advice, suggestions, discussions and guidance were a real support to me. I acknowledge with honour and gratitude the International Foundation for Science (IFS) for research grant (F/5330-1 ), Connect Africa Scholarship Award, H3ABioNet/SANBio Scholarship and North-West University for offering me bursary/scholarship award to pursue the PhD degree. -
Exosomes Confer Chemoresistance to Pancreatic Cancer Cells By
FULL PAPER British Journal of Cancer (2017) 116, 609–619 | doi: 10.1038/bjc.2017.18 Keywords: chemoresistance; exosomes; pancreatic cancer; ROS; microRNA Exosomes confer chemoresistance to pancreatic cancer cells by promoting ROS detoxification and miR-155-mediated suppression of key gemcitabine-metabolising enzyme, DCK Girijesh Kumar Patel1, Mohammad Aslam Khan1, Arun Bhardwaj1, Sanjeev K Srivastava1, Haseeb Zubair1, Mary C Patton1, Seema Singh1,2, Moh’d Khushman3 and Ajay P Singh*,1,2 1Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA; 2Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA and 3Department of Interdisciplinary Clinical Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA Background: Chemoresistance is a significant clinical problem in pancreatic cancer (PC) and underlying molecular mechanisms still remain to be completely understood. Here we report a novel exosome-mediated mechanism of drug-induced acquired chemoresistance in PC cells. Methods: Differential ultracentrifugation was performed to isolate extracellular vesicles (EVs) based on their size from vehicle- or gemcitabine-treated PC cells. Extracellular vesicles size and subtypes were determined by dynamic light scattering and marker profiling, respectively. Gene expression was examined by qRT-PCR and/or immunoblot analyses, and direct targeting of DCK by miR-155 was confirmed by dual-luciferase 30-UTR reporter assay. Flow cytometry was performed to examine the apoptosis indices and reactive oxygen species (ROS) levels in PC cells using specific dyes. Cell viability was determined using the WST-1 assay. Results: Conditioned media (CM) from gemcitabine-treated PC cells (Gem-CM) provided significant chemoprotection to subsequent gemcitabine toxicity and most of the chemoresistance conferred by Gem-CM resulted from its EVs fraction. -
Integrative Systems Biology– Renal Diseases: a Road to a Holist View of Chronic Disease Mechanism
Integrative Systems biology– Renal Diseases: A road to a holist view of chronic disease mechanism Matthias Kretzler Div. Nephrology / Internal Medicine Computational Medicine and Bioinformatics University of Michigan Medical School The challenge in chronic disease • Descriptive disease categorization with multiple pathogenetic mechanisms § Problems of ‘mixed bag’ diseases: • Unpredictable disease course and response to therapy • Nephrology as an ‘art of trial and error’ • Shift in our disease paradigms: § Mechanism based patient management • Define the disease process active in the individual patient – Base prognosis on specific disease process – Target therapy to interfere with the mechanism currently destroying endorgan function Molecular Nephrology approach Clinical outcome research Genetics Molecular Pathology Molecular Epigenetics Phenotyping Genomics Functional Clinical research Disease Genomics Biobanks Proteomics Model systems Animal models Molecular interaction In vitro tissue culture model systems Organ culture and development Tower of Babylon: Search for the universal language for the medicine of the 21st century Pieter Bruegl: 1563. Kunsthistorisches Museum Wien Molecular Nephrology approach Clinical outcome research Genetics Molecular Pathology Molecular Epigenetics Phenotyping Genomics Functional Clinical research Disease Genomics Integrative Biobanks Proteomics Biology (Physiology) Model systems Animal models Molecular interaction of renal disease In vitro tissue culture model systems Organ culture and development Systems -
Tremblay Robinlee.Pdf
Expression and Characterisation ofa Gene Enc oding RbpD, an RNA- Bind ing Protein in Anabaena sp. strain PeC 7120 by Rob in lee Tremblay A lhesis submitted to the Scltool of Graduale Studies in partial fulfilment of the requirements fOl" the degree of Master of Science Department of BiochemistrylFacultyof Science Memorial University of Newfoundland January 2000 SI.JOM'S Newfoun dland Abs t ra ct The RNA-binding protein RbpD, from the cyano bacterium Anaba ena sp, strain Pe C 7120 was expressed in £Sch~ ric h ia coli and successfully purified using me IMPACT I system (New England Biolabs). The rbp D gene was cloned into the pCYBt expre ssion vector by using polymerase chain reaction to introduce Ndel and SapI restriction sites at the 5' end 3' ends of the gene respect ively. The 3'.-end mutagenesis also chan ged the stop codon into a cysteine codon. The resulting gene encoded a fusion protein consisting of RbpD, the Saccharomyces cerev isiae VMA intein and a chitin binding domain.. Expressi on of the fusion protein was observed in £ coli strain MCI061 but Western blot analysis using an intein-directed ant ibody indicated that significant in vivo fmeln-direcred splicing of the fusion protein occurred. We were unable to eliminate this problem; no fusion protein expression was observed in 8 other E coli strains tested. Wild -type RbpD was purified following binding of the fusion protein 10 a chitin column and overnight cleavage in the presence of a reducing agent, dlthicthrehc l. A number of modifications to the manufacturer' s purification protocol were found to be necessary for success ful purification. -
ANABOLISM III: Biosynthesis Amino Acids & Nucleotides
BI/CH 422/622 ANABOLISM OUTLINE: Photosynthesis Carbohydrate Biosynthesis in Animals Biosynthesis of Fatty Acids and Lipids Biosynthesis of Amino Acids and Nucleotides Nitrogen fixation nitrogenase Nitrogen assimilation Glutamine synthetase Glutamate synthase Amino-acid Biosynthesis non-essential essential Nucleotide Biosynthesis RNA precursors purines pyrimidines DNA precursors deoxy-nucleotides Biosynthesis of secondary products of amino acids ANABOLISM III: Biosynthesis Amino Acids & Nucleotides Dr. Kornberg: Lecture 04.26.17 (0:00-5:06) 5 min 1 Biosynthesis Amino Acids & Nucleotides How are Ribonucleic Acid Precursors So far: converted to Deoxyribonucleic Acid GMPàGDPàGTP Precursors? ….....and how is dTTP made? AMPàADPàATP 2’C-OH bond is directly reduced to 2’-H UMPàUDPàUTPà bond …without activating the carbon for CDPßCTP dehydration, etc.! catalyzed by ribonucleotide reductase Specific kinases, Non-specific kinase, e.g., UMP kinase, nucleoside GMP kinase, diphosphate kinase Very unique enzyme in all of biochemistry – use of free Adenylate kinase (works on both oxy- and radicals etc. deoxy-ribose GDPàdGDP nucleosides) Mechanism: Two H atoms are donated ADPàdADP by NADPH and carried by thioredoxin or glutaredoxin to the active site. UDPàdUDP –Substrates are the NDPs and the products CDPàdCDP are dNDP. Biosynthesis Amino Acids & Nucleotides Source of Reducing Structure of Ribonucleotide Reductase a2 are regulatory Electrons for and half the Ribonucleotide catalytic site; need to be reduced. Reductase b 2 are the other half (a b ) of the active site, 2 2 and the free- radical generators • NADPH serves as the electron donor. • Funneled through glutathione or JoAnne Stubbe thioredoxin pathways (1946– ) 2 •Most forms of enzyme have two catalytic/ regulatory subunits and two radical- generating subunits. -
Discovery of Industrially Relevant Oxidoreductases
DISCOVERY OF INDUSTRIALLY RELEVANT OXIDOREDUCTASES Thesis Submitted for the Degree of Master of Science by Kezia Rajan, B.Sc. Supervised by Dr. Ciaran Fagan School of Biotechnology Dublin City University Ireland Dr. Andrew Dowd MBio Monaghan Ireland January 2020 Declaration I hereby certify that this material, which I now submit for assessment on the programme of study leading to the award of Master of Science, is entirely my own work, and that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge breach any law of copyright, and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Signed: ID No.: 17212904 Kezia Rajan Date: 03rd January 2020 Acknowledgements I would like to thank the following: God, for sending me angels in the form of wonderful human beings over the last two years to help me with any- and everything related to my project. Dr. Ciaran Fagan and Dr. Andrew Dowd, for guiding me and always going out of their way to help me. Thank you for your patience, your advice, and thank you for constantly believing in me. I feel extremely privileged to have gotten an opportunity to work alongside both of you. Everything I’ve learnt and the passion for research that this project has sparked in me, I owe it all to you both. Although I know that words will never be enough to express my gratitude, I still want to say a huge thank you from the bottom of my heart. -
Anticancer Potential of Resveratrol, -Lapachone and Their Analogues
molecules Review Anticancer Potential of Resveratrol, β-Lapachone and Their Analogues 1, 2, Danielly C. Ferraz da Costa y, Luciana Pereira Rangel y , 3, 3, Mafalda Maria Duarte da Cunha Martins-Dinis y, Giulia Diniz da Silva Ferretti y, Vitor F. Ferreira 4 and Jerson L. Silva 3,* 1 Departamento de Nutrição Básica e Experimental, Instituto de Nutrição, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; [email protected] 2 Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; [email protected] 3 Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; [email protected] (M.M.D.d.C.M.-D.); [email protected] (G.D.d.S.F.) 4 Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Rio de Janeiro 24241-000, Brazil; [email protected]ff.br * Correspondence: [email protected] These authors contributed equally to this work. y Received: 31 December 2019; Accepted: 13 February 2020; Published: 18 February 2020 Abstract: This review aims to explore the potential of resveratrol, a polyphenol stilbene, and beta-lapachone, a naphthoquinone, as well as their derivatives, in the development of new drug candidates for cancer. A brief history of these compounds is reviewed along with their potential effects and mechanisms of action and the most recent attempts to improve their bioavailability and potency against different types of cancer. Keywords: resveratrol; β-lapachone; cancer 1. -
Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degenerations: Similarities in Genetic Background
diagnostics Review Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degenerations: Similarities in Genetic Background Eva Parobkova 1 and Radoslav Matej 1,2,3,* 1 Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer University Hospital, 14059 Prague, Czech Republic; [email protected] 2 Department of Pathology, First Faculty of Medicine, Charles University, and General University Hospital, 14059 Prague, Czech Republic 3 Department of Pathology, Third Faculty of Medicine, Charles University, and University Hospital Kralovske Vinohrady, 14059 Prague, Czech Republic * Correspondence: [email protected] Abstract: Amyotrophic lateral sclerosis (ALS) is a devastating, uniformly lethal progressive degen- erative disorder of motor neurons that overlaps with frontotemporal lobar degeneration (FTLD) clinically, morphologically, and genetically. Although many distinct mutations in various genes are known to cause amyotrophic lateral sclerosis, it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neuronal degeneration. Many of the gene mutations are in proteins that share similar functions. They can be grouped into those associated with cell axon dynamics and those associated with cellular phagocytic machinery, namely protein aggregation and metabolism, apoptosis, and intracellular nucleic acid transport. Analysis of pathways implicated by mutant ALS genes has provided new insights into the pathogenesis of both familial forms of ALS (fALS) and sporadic forms (sALS), although, regrettably, this has not yet yielded definitive treatments. Many genes play an important role, with TARDBP, Citation: Parobkova, E.; Matej, R. SQSTM1, VCP, FUS, TBK1, CHCHD10, and most importantly, C9orf72 being critical genetic players Amyotrophic Lateral Sclerosis and in these neurological disorders. -
Nucleotide Biosynthesis Links Glutathione Metabolism to Ferroptosis Sensitivity
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.14.452394; this version posted July 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Nucleotide Biosynthesis Links Glutathione Metabolism to Ferroptosis Sensitivity Amy Tarangelo1,3, Joon Tae Kim2, Jonathan Z. Long2, Scott J. Dixon1,4 1Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA 2Department of Pathology and Stanford ChEM-H, Stanford University School of Medicine 291 Campus Drive, Stanford, CA 94305, USA 3Current address: Children’s Medical Center Research Institute, UT Southwestern, 6000 Harry Hines Blvd, Dallas, TX 75235 4Contact: [email protected] Key words: Cell death, iron, p53, p21 Running title: Nucleotide metabolism and ferroptosis bioRxiv preprint doi: https://doi.org/10.1101/2021.07.14.452394; this version posted July 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Nucleotide synthesis is a metabolically demanding process essential for cell division. Several anti-cancer drugs that inhibit nucleotide metabolism induce apoptosis. How inhibition of nucleotide metabolism impacts non-apoptotic cell death is less clear. Here, we report that inhibition of nucleotide metabolism by the p53 pathway is sufficient to suppress the non-apoptotic cell death process of ferroptosis. -
Electron Transfer and Substrate Reduction in Nitrogenase
Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 5-2014 Electron Transfer and Substrate Reduction in Nitrogenase Karamatullah Danyal Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biochemistry Commons Recommended Citation Danyal, Karamatullah, "Electron Transfer and Substrate Reduction in Nitrogenase" (2014). All Graduate Theses and Dissertations. 2181. https://digitalcommons.usu.edu/etd/2181 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. ELECTRON TRANSFER AND SUBSTRATE REDUCTON IN NITROGENASE by Karamatullah Danyal A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biochemistry Approved: ________________________ _______________________ Lance C. Seefeldt Scott A. Ensign Major Professor Committee Member ________________________ _______________________ Alvan C. Hengge Sean J. Johnson Committee Member Committee Member ________________________ _______________________ Korry Hintze Mark R. McLellan Committee Member Vice President for Research and Dean of the School of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2014 ii Copyright © Karamatullah Danyal 2014 All Rights Reserved iii ABSTRACT Electron Transfer and Substrate Reduction in Nitrogenase by Karamatullah Danyal, Doctor of Philosophy Utah State University, 2014 Major Professor: Dr. Lance C. Seefeldt Department: Chemistry and Biochemistry Population growth over the past ~50 years accompanied by the changes in dietary habits due to economic growth have markedly increased the demand for fixed nitrogen. Aided by biological nitrogen fixation, the Haber-Bosch process has been able to fulfill these demands. -
Gene Metabolic Signature for Survival Prediction in Patients with Kidney Renal Clear Cell Carcinoma
www.aging-us.com AGING 2021, Vol. 13, No. 6 Research Paper Identification and validation of a two-gene metabolic signature for survival prediction in patients with kidney renal clear cell carcinoma Xudong Guo1, Zhuolun Sun2, Shaobo Jiang1, Xunbo Jin1, Hanbo Wang1 1Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China 2Department of Urology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, Guangdong, China Correspondence to: Hanbo Wang; email: [email protected], https://orcid.org/0000-0002-6095-8611 Keywords: kidney renal clear cell carcinoma, metabolism, nomogram, prognostic signature, The Cancer Genome Atlas Received: September 2, 2020 Accepted: October 22, 2020 Published: March 03, 2021 Copyright: © 2021 Guo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Metabolic reprogramming contributes to the high mortality of advanced stage kidney renal clear cell carcinoma (KIRC), the most common renal cancer subtype. This study aimed to identify a metabolism-related gene (MRG) signature to improve survival prediction in KIRC patients. We downloaded RNA sequencing data and corresponding clinical information for KIRC and control samples from The Cancer Genome Atlas database and identified, based on an MRG dataset in the Molecular Signatures Database, 123 MRGs with differential expression in KIRC. Following Cox regression analysis and least absolute shrinkage and selection operator selection, RRM2 and ALDH6A1 were identified as prognosis-related genes and used to construct a prognostic signature with independent prognostic significance. -
Molybdenum Hazards to Fish, Wildlife, and Invertebrates: a Synoptic Review
Biological Report 85(1.19) Contaminant Hazard Reviews August 1989 Report No. 19 MOLYBDENUM HAZARDS TO FISH, WILDLIFE, AND INVERTEBRATES: A SYNOPTIC REVIEW by Ronald Eisler U.S. Fish and Wildlife Service Patuxent Wildlife Research Center Laurel, MD 20708 SUMMARY The element molybdenum (Mo) is found in all living organisms and is considered to be an essential or beneficial micronutrient. However, the molybdenum poisoning of ruminants has been reported in at least 15 States and 8 foreign countries. Molybdenum is used primarily in the manufacture of steel alloys. Its residues tend to be elevated in plants and soils near Mo mining and reclamation sites, fossil-fuel power plants, and Mo disposal areas. Concentrations of Mo are usually lower in fish and wildlife than in terrestrial macrophytes. Aquatic organisms are comparatively resistant to Mo salts: adverse effects on growth and survival usually appeared only at water concentrations >50 mg Mo/l. But in one study, 50% of newly fertilized eggs of rainbow trout (Oncorhynchus mykiss) died in 28 days at only 0.79 mg Mo/l. High bioconcentration of Mo by certain species of aquatic algae and invertebrates--up to 20 grams of Mo/kg dry weight--has been recorded without apparent harm to the accumulator; however, hazard potential to upper trophic organisms (such as waterfowl) that may feed on bioconcentrators is not clear. Data on Mo effects are missing for avian wildlife and are inadequate for mammalian wildlife. In domestic birds, adverse effects on growth have been reported at dietary Mo concentrations of 200 mg Mo/kg, on reproduction at 500 mg/kg, and on survival at 6,000 mg/kg.