DOCSLIB.ORG

Investigating the Potential of Biosurfactants in the Control of Tooth Infections

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Investigating the Potential of Biosurfactants in the Control of Tooth Infections Investigating the Potential of Biosurfactants in the Control of Tooth Infections A thesis submitted to Cardiff University in fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) 2019 Zahraa Amer Hashim College of Biomedical and Life Sciences School of Dentistry Cardiff University Declaration This work has not been submitted in substance for any other degree or award at this or any other university or place of learning, nor is being submitted concurrently in candidature for any degree or other award. Signed :............................................. (Zahraa Amer Hashim) Date:................ Statement 1 This thesis is being ubmitted in partial fulfillment of the requirements for the degree of PhD. Signed :............................................. (Zahraa Amer Hashim) Date:................ Statement 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. Other sources are acknowledged by explicit references. The views expressed are my own. Signed :............................................. (Zahraa Amer Hashim) Date:................ Statement 3 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signed :............................................. (Zahraa Amer Hashim) Date:................ Statement 4: Previously Approved Bar on Access I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loans after expiry of a bar on access previously approved by the Academic Standards & Quality Committee. Signed :............................................. (Zahraa Amer Hashim) Date:................ ii Dedication to IRAQ in general, NINAVA in particular I dedicate this thesis iii Acknowledgements First and foremost, I praise ALLAH, the almighty for granting me the opportunity, capability and providing me with patience to complete this Thesis. Pursuing my PhD has been an incredible challenge especially when I suddenly found myself alone raising three children away from my family whom themselves were in danger. This journey would not have been possible to be completed successfully without the help and support of those around me. I owe a huge deal of gratitude to my main supervisor: Prof. Rachel Waddington, I can see your advice as a reality now while I am putting all together “PhD is a sequential acquisition of knowledge”. Thank you for your patience, understanding and continuous guidance and support. I would like also to thank my secondary supervisor Dr. Melanie Wilson for her tremendous advice, generous support and being friendly along the study time and to Prof. Jean-Yves Maillard, my third supervisor, for his shrewdness, kindness and valuable feedback and advice. I must include thanks to the Higher Committee for Education Development (HCED) in Iraq for the financial support to get this degree. My praise goes to all the technicians, staff and colleagues in the Oral and Biomedical Department, especially Dr. Wayne Ayre, Dr. Amr Alraies, Dr. Ahmed Al-Qarakhli, Dr. Daniel Morse and Dr. Steven Avery for their training and advice; Dr. Sarah Youde and Dr. Maria Stack for assistance in molecular biology and tissue culture; Lucy Marsh and Dr. Sarah Bamford in the microbiology lab; Hayley Pincott and Sue Wozniak in the pathology lab, as has the advice of Dr. Adam Jones; Wendy Rowe for her training and help with imaging; Dr Kate Heesom, facility director of University of Bristol Proteomics Facility and Dr Ian Brewis, Central Biotechnology Services (CBS) operational director for help in running Mass spectrometry. There have been many others who have lent a hand, an ear or a piece of equipment along the way, and I am very lucky to have worked with such a supportive group of people. To Nadia Alaidaroos, Uzma Ghulam, Jabur Khan, Vildan Celiksoy and to all other unnamed friends, I highly appreciated your support and being a part of my life here in Cardiff. A special thank you to my parents for your love, reassurance and continued support. I will always be indebted to what you have done for me throughout my life and for the patience and understanding you have demonstrated throughout my academic endeavours away from home. To my other family and friends who I have not mentioned here, thank you for your additional support and encouragement. My wonderful children: Zakariya, Zainab and little Asma thank you for giving me love, company and happiness, thank you for your patience on those days and weekends when I was conducting experiments, feeding cells or killing bugs returning back home late instead of being with you, I LOVE you. iv Presentations Work from this thesis has been presented at the following meetings: Speaking of Science, Cardiff, 5th May 2016 “Investigate the potential of probiotics and their products in endodontic infections” Zahraa Hashim, Melanie J Wilson, Jean-Yves Maillard, Rachel Waddington Oral Microbiology and Immunology Group (OMIG) meeting, Wales, 9th- 11th March 2016 “Investigating the potential for probiotic micro-organisms and biosurfactants in preventing pathogenic infection” Zahraa Hashim, Daniel J Morse, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington School of Medicine and Dentistry Postgraduate Research Day, Cardiff, November 2016 “Assessment of Biosurfactants from Lactobacillus plantarum to Fight Endodontic Infection” Zahraa Hashim, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington CITER annual scientific meeting, Cardiff, September 2017 “Assessment of Biosurfactants from Lactobacillus plantarum to Fight Endodontic Infection” Zahraa Hashim, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington BSODR annual general meeting, Plymouth, September 2017 “Biosurfactants from Lactobacillus plantarum to Fight Endodontic Infection” Zahraa Hashim, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington IADR/PER General Session-London, England “Assessing the Potential of Novel Biosurfactants in Treating Pulpal Infection” Zahraa Hashim, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington v 17th Annual Conference of the UK Society for Biomaterials, 28th -29th Jun 2018 Bath “Assessment of Biosurfactants from Lactobacillus plantarum to Fight Endodontic Infection” Zahraa Hashim, Jean-Yves Maillard, Melanie J Wilson, Rachel J Waddington vi Abstract A shift from the “doomed” organ concept of an exposed pulp to the concept of hope and retrieval has been recently adopted with the introduction of vital pulp therapy. Microbial contamination of the capped pulp is the main cause of therapy failure and is a fundamental challenge of contemporary endodontics. Biosurfactants are tensioactive microbe-derived molecules with a potential antimicrobial/antiadhesive activity. This project aimed to investigate the role of biosurfactants, specifically probiotic-derived ones and a commercial- sourced rhamnolipid (Sigma Aldrich), as novel endodontic antimicrobial therapies that can aid in reducing the incidence of infection and endodontic failure. Of five probiotic strains studied, Lactobacillus plantarum demonstrated significant antimicrobial activity against three Streptococcus anginosus group members; S. anginosus, S. constellatus and S. intermedius and against Enterococcus faecalis. A cell-bound biosurfactant (Lp-BS) was successfully extracted from the potential probiotic L. plantarum. Biochemical characterisation identified Lp-BS as a glycoprotein molecule that was capable of reducing surface tension and emulsifying hydrocarbons. For the endodontic pathogens studied, Lp-BS demonstrated no antibacterial activity up to concentrations of 50 mg/ml, but displayed significant antiadhesive potential at 20 mg/mL. Proteomic analysis revealed a rich heterogeneous proteinaceous nature of Lp-BS mixture and importantly identified three adhesin-like proteins raising the possibility for applications in pathogenic bacterial adhesion interference. Ten mg/ml Lp-BS induced high levels of apoptosis in pulpal fibroblasts at 24 h, resulting in significant reduction in cell number. No significant differences were reported in cell counts or histology of pulp tissue treated with 0.625-10 mg/mL Lp-BS in comparison to the controls, over a 24 h time period. Subsequent incubation with 10 mg/mL for 48 h revealed obvious pulp tissue toxicity. Partial purification of Lp-BS by means of size-exclusion chromatography resulted in five elution pools with the first fraction determined to retain the biosurfactant activity; this fraction can be further investigated for antimicrobial/antiadhesive effects. Rhamnolipid demonstrated substantial antimicrobial effect with minimum inhibitory concentrations determined to be 0.097 mg/mL against S. anginosus, 0.048 mg/mL against S. constellatus and S. intermedius and 50 mg/mL against E. faecalis. Rhamnolipid also reduced attachment of S. anginosus and S. intermedius to an abiotic surface. Of importance, rhamnolipid was shown to tolerate serum concentrations ≤ 5 % v/v. However, above this concentration inactivation of rhamnolipid effect was demonstrated. Application of rhamnolipid to rodent ex-vivo tooth model infected with S. anginosus and S. constellatus demonstrated significant antimicrobial activity and a mild immune response of pulp tissue in response to treatment was documented. This work provides the foundation for further investigation on Lp-BS adhesin-like proteins as a novel endodontic antiadhesive therapy. Furthermore, the cost-effective rhamnolipid with its
Load more

Recommended publications
  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • SUPPLEMENTARY INFORMATION in Silico Signature Prediction
    SUPPLEMENTARY INFORMATION In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia coli Strains Maryam Javadi, Mana Oloomi*, Saeid Bouzari Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran http://www.genominfo.org/src/sm/gni-15-69-s001.pdf Supplementary Table 6. Aalphabetic abbreviation and description of putative conserved domains Alphabetic Abbreviation Description 17 Large terminase protein 2_A_01_02 Multidrug resistance protein 2A0115 Benzoate transport; [Transport and binding proteins, Carbohydrates, organic alcohols] 52 DNA topisomerase II medium subunit; Provisional AAA_13 AAA domain; This family of domains contain a P-loop motif AAA_15 AAA ATPase domain; This family of domains contain a P-loop motif AAA_21 AAA domain AAA_23 AAA domain ABC_RecF ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase ABC_SMC_barmotin ATP-binding cassette domain of barmotin, a member of the SMC protein family AcCoA-C-Actrans Acetyl-CoA acetyltransferases AHBA_syn 3-Amino-5-hydroxybenzoic acid synthase family (AHBA_syn) AidA Type V secretory pathway, adhesin AidA [Cell envelope biogenesis] Ail_Lom Enterobacterial Ail/Lom protein; This family consists of several bacterial and phage Ail_Lom proteins AIP3 Actin interacting protein 3; Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity Aldose_epim_Ec_YphB Aldose 1-epimerase, similar to Escherichia coli YphB AlpA Predicted transcriptional regulator [Transcription] AntA AntA/AntB antirepressor AraC AraC-type
    [Show full text]
  • Supplemental Methods
    Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
    The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Modulation of the Camp Levels with a Conserved Actinobacteria Phosphodiesterase 2 Enzyme Reduces Antimicrobial Tolerance in Mycobacteria
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.26.267864; this version posted August 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase 2 enzyme reduces antimicrobial tolerance in mycobacteria 3 4 Michael Thomson1, Kanokkan Nunta1, Ashleigh Cheyne1, Yi liu1, Acely Garza-Garcia2 and 5 Gerald Larrouy-Maumus1† 6 7 1MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, 8 Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK 9 2The Francis Crick Institute, London NW1 1AT, United Kingdom. 10 11 †Corresponding author: 12 13 Dr Gerald Larrouy-Maumus 14 MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty 15 of Natural Sciences, Imperial College London, London, SW7 2AZ, UK 16 Telephone: +44 (0) 2075 947463 17 E-mail: [email protected] 18 19 20 1 e ag P 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.26.267864; this version posted August 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 21 Abstract 22 Antimicrobial tolerance (AMT) is the gateway to the development of antimicrobial resistance 23 (AMR) and is therefore a major issue that needs to be addressed. 24 The second messenger cyclic-AMP (cAMP), which is conserved across all taxa, is involved 25 in propagating signals from environmental stimuli and converting these into a response.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0058468 A1 Mickeown (43) Pub
    US 20120058468A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0058468 A1 MickeoWn (43) Pub. Date: Mar. 8, 2012 (54) ADAPTORS FOR NUCLECACID Related U.S. Application Data CONSTRUCTS IN TRANSMEMBRANE (60) Provisional application No. 61/148.737, filed on Jan. SEQUENCING 30, 2009. Publication Classification (75) Inventor: Brian Mckeown, Oxon (GB) (51) Int. Cl. CI2O I/68 (2006.01) (73) Assignee: OXFORD NANOPORE C7H 2L/00 (2006.01) TECHNOLGIES LIMITED, (52) U.S. Cl. ......................................... 435/6.1:536/23.1 Oxford (GB) (57) ABSTRACT (21) Appl. No.: 13/147,159 The invention relates to adaptors for sequencing nucleic acids. The adaptors may be used to generate single stranded constructs of nucleic acid for sequencing purposes. Such (22) PCT Fled: Jan. 29, 2010 constructs may contain both strands from a double stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) (86) PCT NO.: PCT/GB1O/OO160 template. The invention also relates to the constructs gener ated using the adaptors, methods of making the adaptors and S371 (c)(1), constructs, as well as methods of sequencing double stranded (2), (4) Date: Nov. 15, 2011 nucleic acids. Patent Application Publication Mar. 8, 2012 Sheet 1 of 4 US 2012/0058468 A1 Figure 5' 3 Figure 2 Figare 3 Patent Application Publication Mar. 8, 2012 Sheet 2 of 4 US 2012/0058468 A1 Figure 4 End repair Acid adapters ligate adapters Patent Application Publication Mar. 8, 2012 Sheet 3 of 4 US 2012/0058468 A1 Figure 5 Wash away type ifype foducts irrirrosilise Type| capture WashRE products away unbcure Pace É: Wash away unbound rag terts Free told fasgirre?ts aid raiser to festible Figure 6 Beatre Patent Application Publication Mar.
    [Show full text]
  • Trna-Derived Fragments: Mechanisms Underlying Their Regulation of Gene Expression and Potential Applications As Therapeutic Targets in Cancers and Virus Infections
    Theranostics 2021, Vol. 11, Issue 1 461 Ivyspring International Publisher Theranostics 2021; 11(1): 461-469. doi: 10.7150/thno.51963 Review tRNA-derived fragments: Mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections 1,2 1 1 1 1 2 Xiuchong Yu , Yaoyao Xie , Shuangshuang Zhang , Xuemei Song , Bingxiu Xiao and Zhilong Yan 1. Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China. 2. Department of Gastrointestinal Surgery, Ningbo First Hospital, Ningbo University, Ningbo 315010, China. Corresponding authors: E-mail: [email protected], or [email protected]; Tel: +86-574-87600758; Fax: +86-574-87608638. © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.08.14; Accepted: 2020.10.02; Published: 2021.01.01 Abstract tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre-tRNAs or mature tRNAs. Based on the incision loci, tRFs are classified into several types: tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. Some tRFs participate in posttranscriptional regulation through microRNA-like actions or by displacing RNA binding proteins and regulating protein translation by promoting ribosome biogenesis or interfering with translation initiation. Other tRFs prevent cell apoptosis by binding to cytochrome c or promoting virus replication.
    [Show full text]
  • 1 SUPPLEMENTARY INFORMATION 1 2 an Archaeal Symbiont
    1 SUPPLEMENTARY INFORMATION 2 3 An archaeal symbiont-host association from the deep terrestrial subsurface 4 5 Katrin Schwank1, Till L. V. Bornemann1, Nina Dombrowski2, Anja Spang2,3, Jillian F. Banfield4 and 6 Alexander J. Probst1* 7 8 9 1 Group for Aquatic Microbial Ecology (GAME), Biofilm Center, Department of Chemistry, 10 University of Duisburg-Essen, Germany 11 2Department of Marine Microbiology and Biogeochemistry (MMB), Royal Netherlands Institute 12 for Sea Research (NIOZ), and Utrecht University, Den Burg, Netherlands 13 3Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE- 14 75123, Uppsala, Sweden 15 4 Department for Earth and Planetary Sciences, University of California, Berkeley, USA 16 17 *to whom the correspondence should be addressed: 18 Alexander J. Probst 19 University of Duisburg-Essen 20 Universitätsstrasse 4 21 45141 Essen 22 [email protected] 23 24 25 Content: 26 1. Supplementary Methods 27 2. Supplementary Tables 28 3. Supplementary Figure 29 4. References 30 31 32 33 1. Supplementary methods 34 Phylogenetic analysis 35 Hmm profiles of the 37 maker genes used by the phylosift v1.01 software [1, 2] were queried 36 against a representative set of archaeal genomes from NCBI (182) and the GOLD database (3) as 37 well as against the huberarchaeal population genome (for details on genomes please see 38 Supplementary Data file 1) using the phylosift search mode [1, 2]. Protein sequences 39 corresponding to each of the maker genes were subsequently aligned using mafft-linsi v7.407 [3] 40 and trimmed with BMGE-1.12 (parameters: -t AA -m BLOSUM30 -h 0.55) [4].
    [Show full text]
  • The Quest for Novel Extracellular Polymers Produced by Soil-Borne Bacteria
    Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. Bioprospecting: The quest for novel extracellular polymers produced by soil-borne bacteria A thesis presented in partial fulfilment of the requirements for the degree of Master of Science In Microbiology at Massey University, Palmerston North, New Zealand Jason Smith 2017 i Dedication This thesis is dedicated to my dad. Vaughan Peter Francis Smith 13 July 1955 – 27 April 2002 Though our time together was short you are never far from my mind nor my heart. ii Abstract Bacteria are ubiquitous in nature, and the surrounding environment. Bacterially produced extracellular polymers, and proteins are of particular value in the fields of medicine, food, science, and industry. Soil is an extremely rich source of bacteria with over 100 million per gram of soil, many of which produce extracellular polymers. Approximately 90% of soil-borne bacteria are yet to be cultured and classified. Here we employed an exploratory approach and culture based method for the isolation of soil-borne bacteria, and assessed their capability for extracellular polymer production. Bacteria that produced mucoid (of a mucous nature) colonies were selected for identification, imaging, and polymer production. Here we characterised three bacterial isolates that produced extracellular polymers, with a focus on one isolate that formed potentially novel proteinaceous cell surface appendages. These appendages have an unknown function, however, I suggest they may be important for bacterial communication, signalling, and nutrient transfer.
    [Show full text]
  • Electronic Supplementary Information S10
    Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information S10. Up and downregulated genes of ACR3 and TIP-ACR3 compared to control roots all exposed to 0.1 mM As III . HYBRIDIZATION 4: LIST OF UP-REGULATED GENES Fold Change Probe Set ID ([0.1 ACR3] vs [0.1-HR]) Blast2GO description Genbank Accessions C228_s_at 48.018467 N.tabacum cysteine-rich extensin-like protein-4 mRNA EB683071 C1359_at 32.31786 Proteinase inhibitor I3, Kunitz legume, Kunitz inhibitor ST1-like DW004832 EB430244_x_at 22.426174 unknow EB430244 C10896_at 21.463442 dir1 (defective in induced resistance 1) lipid binding JF275847.1 BP528597_at 21.445984 Mitochondrial DNA BP528597 C10933_x_at 20.347004 Solanum nigrum clone 82 organ-specific protein S2 (OS) EB443218 TT31_B05_s_at 17.260008 Proteinase inhibitor I3, Kunitz legume, Kunitz inhibitor ST1-like C3546_s_at 17.171844 fasciclin-like arabinogalactan protein 2 EB451563 C8455_at 16.855278 Defective in induced resistance 2 protein (DIR2) BP530866 C11687_at 16.618454 galactinol synthase EB432401 BP136836_s_at 15.364014 Nicotiana tabacum mitochondrial DNA BP136836 BP525701_at 15.137816 Nicotiana tabacum mitochondrial DNA BP525701 EB682942_at 14.943408 Hop-interacting protein THI101 EB682942 BP133164_at 14.644844 Nicotiana tabacum mitochondrial DNA BP133164 AY055111_at 14.570147 Nicotiana tabacum pathogenesis-related protein PR10a AY055111 TT08_C02_at 14.375496 BP526999_at 14.374481 Nicotiana tabacum mitochondrial DNA BP526999 CV017694_s_at
    [Show full text]