Annex: Preparation of Media and Reagents
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Exploring Small-Scale Chemostats to Scale up Microbial Processes: 3-Hydroxypropionic Acid Production in S
Lawrence Berkeley National Laboratory Recent Work Title Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae. Permalink https://escholarship.org/uc/item/43h8866j Journal Microbial cell factories, 18(1) ISSN 1475-2859 Authors Lis, Alicia V Schneider, Konstantin Weber, Jost et al. Publication Date 2019-03-11 DOI 10.1186/s12934-019-1101-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Lis et al. Microb Cell Fact (2019) 18:50 https://doi.org/10.1186/s12934-019-1101-5 Microbial Cell Factories RESEARCH Open Access Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae Alicia V. Lis1, Konstantin Schneider1,2, Jost Weber1,3, Jay D. Keasling1,4,5,6,7, Michael Krogh Jensen1 and Tobias Klein1,2* Abstract Background: The physiological characterization of microorganisms provides valuable information for bioprocess development. Chemostat cultivations are a powerful tool for this purpose, as they allow defned changes to one single parameter at a time, which is most commonly the growth rate. The subsequent establishment of a steady state then permits constant variables enabling the acquisition of reproducible data sets for comparing microbial perfor- mance under diferent conditions. We performed physiological characterizations of a 3-hydroxypropionic acid (3-HP) producing Saccharomyces cerevisiae strain in a miniaturized and parallelized chemostat cultivation system. The physi- ological conditions under investigation were various growth rates controlled by diferent nutrient limitations (C, N, P). Based on the cultivation parameters obtained subsequent fed-batch cultivations were designed. Results: We report technical advancements of a small-scale chemostat cultivation system and its applicability for reliable strain screening under diferent physiological conditions, i.e. -
Identification of Strains Isolated in Thailand and Assigned to the Genera Kozakia and Swaminathania
JOURNAL OF CULTURE COLLECTIONS Volume 6, 2008-2009, pp. 61-68 IDENTIFICATION OF STRAINS ISOLATED IN THAILAND AND ASSIGNED TO THE GENERA KOZAKIA AND SWAMINATHANIA Jintana Kommanee1, Somboon Tanasupawat1,*, Ancharida Akaracharanya2, Taweesak Malimas3, Pattaraporn Yukphan3, Yuki Muramatsu4, Yasuyoshi Nakagawa4 and Yuzo Yamada3,† 1Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; 2Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; 3BIOTEC Culture Collection, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand; 4Biological Resource Center, Department of Biotechnology, National Institute of Technology and Evaluation, Kisarazu 292-0818, Japan; †JICA Senior Overseas Volunteer, Japan International Cooperation Agency, Shibuya-ku, Tokyo 151-8558, Japan; Professor Emeritus, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan *Corresponding author, e-mail: [email protected] Summary Four isolates, isolated from fruit of sapodilla collected at Chantaburi and designated as CT8-1 and CT8-2, and isolated from seeds of ixora („khem” in Thai, Ixora species) collected at Rayong and designated as SI15-1 and SI15-2, were examined taxonomically. The four isolates were selected from a total of 181 isolated acetic acid bacteria. Isolates CT8-1 and CT8-2 were non motile and produced a levan-like mucous polysaccharide from sucrose or D-fructose, but did not produce a water-soluble brown pigment from D-glucose on CaCO3-containing agar slants. The isolates produced acetic acid from ethanol and oxidized acetate and lactate to carbon dioxide and water, but the intensity of the acetate and lactate oxidation was weak. Their growth was not inhibited by 0.35 % acetic acid (v/v) at pH 3.5. -
Tryptose Blood Agar Base
Tryptose Blood Agar Base Intended Use Principles of the Procedure Tryptose Blood Agar Base is used with blood in isolating, Tryptose is the source of nitrogen, carbon and amino acids in cultivating and determining the hemolytic reactions of fastidi- Tryptose Blood Agar Base. Beef extract provides additional ous microorganisms. nitrogen. Sodium chloride maintains osmotic balance. Agar is the solidifying agent. Summary and Explanation Investigations of the nutritive properties of tryptose demon- Supplementation with 5-10% blood provides additional growth strated that culture media prepared with this peptone were factors for fastidious microorganisms and is used to determine superior to the meat infusion peptone media previously used hemolytic patterns of bacteria. for the cultivation of Brucella, streptococci, pneumococci, me- Formula ningococci and other fastidious bacteria. Casman1,2 reported Difco™ Tryptose Blood Agar Base that a medium consisting of 2% tryptose, 0.3% beef extract, Approximate Formula* Per Liter 0.5% NaCl, 1.5% agar and 0.03% dextrose equaled fresh beef Tryptose .................................................................... 10.0 g infusion base with respect to growth of organisms. The small Beef Extract ................................................................. 3.0 g amount of carbohydrate was noted to interfere with hemolytic Sodium Chloride ......................................................... 5.0 g Agar ......................................................................... 15.0 g reactions, unless the medium was incubated in an atmosphere *Adjusted and/or supplemented as required to meet performance criteria. of carbon dioxide. Tryptose Blood Agar Base is a nutritious infusion-free basal Directions for Preparation from medium typically supplemented with 5-10% sheep, rabbit or Dehydrated Product horse blood for use in isolating, cultivating and determining 1. Suspend 33 g of the powder in 1 L of purified water. -
Insight Into the Resistome and Quorum Sensing System of a Divergent Acinetobacter Pittii Isolate from 1 an Untouched Site Of
bioRxiv preprint doi: https://doi.org/10.1101/745182; this version posted November 27, 2019. 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. 1 Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from 2 an untouched site of the Lechuguilla Cave 3 4 Han Ming Gan1,2,3*, Peter Wengert4 , Hazel A. Barton5, André O. Hudson4 and Michael A. Savka4 5 1 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 6 3220 ,Victoria, Australia 7 2 Deakin Genomics Centre, Deakin University, Geelong 3220 ,Victoria, Australia 8 3 School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, 9 Malaysia 10 4 Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA 11 5 Department of Biology, University of Akron, Akron, Ohio, USA 12 *Corresponding author 13 Name: Han Ming Gan 14 Email: [email protected] 15 Key words 16 Acinetobacter, quorum sensing, antibiotic resistance 17 18 Abstract 19 Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly 20 associated with soils, animal feeds and water. Some members of the Acinetobacter have been 21 implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the 22 whole genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine 23 location of the Lechuguilla Cave. -
Detection of Acid-Producing Bacteria Nachweis Von Säureproduzierenden Bakterien Détection De Bactéries Produisant Des Acides
(19) TZZ ¥ _T (11) EP 2 443 249 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/04 (2006.01) G01N 33/84 (2006.01) 19.11.2014 Bulletin 2014/47 (86) International application number: (21) Application number: 10790013.6 PCT/US2010/038569 (22) Date of filing: 15.06.2010 (87) International publication number: WO 2010/147918 (23.12.2010 Gazette 2010/51) (54) DETECTION OF ACID-PRODUCING BACTERIA NACHWEIS VON SÄUREPRODUZIERENDEN BAKTERIEN DÉTECTION DE BACTÉRIES PRODUISANT DES ACIDES (84) Designated Contracting States: (74) Representative: Isarpatent AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Patent- und Rechtsanwälte GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Friedrichstrasse 31 PL PT RO SE SI SK SM TR 80801 München (DE) (30) Priority: 15.06.2009 US 187107 P (56) References cited: 15.03.2010 US 314140 P US-A- 4 528 269 US-A- 5 098 832 US-A- 5 164 301 US-A- 5 601 998 (43) Date of publication of application: US-A- 5 601 998 US-A- 5 786 167 25.04.2012 Bulletin 2012/17 US-B2- 6 756 225 US-B2- 7 150 977 (73) Proprietor: 3M Innovative Properties Company • DARUKARADHYA J ET AL: "Selective Saint Paul, MN 55133-3427 (US) enumeration of Lactobacillus acidophilus, Bifidobacterium spp., starter lactic acid bacteria (72) Inventors: and non-starter lactic acid bacteria from Cheddar • YOUNG, Robert, F. cheese", INTERNATIONAL DAIRY JOURNAL, Saint Paul, Minnesota 55133-3427 (US) ELSEVIER APPLIED SCIENCE, BARKING, GB, • MACH, Patrick, A. -
Enterobacteriaceae Family (CRE), Is of Utmost Importance for the Enterobacteriaceae Management of Infected Or Colonized Patients
2013 iMedPub Journals THE INTERNATIONAL ARABIC JOURNAL Vol. 3 No. 3:5 Our Site: http://www.imedpub.com/ OF ANTIMICROBIAL AGENTS doi: 10.3823/737 Evaluation of Rula Al-Dawodi1,3, Rawan Liddawi1,3, Raed Ghneim1,3, Randa Kattan1,3, Issa Siryani1,3, Afaf Abu-Diab1, Riyad Meropenem, Ghneim1, Madeleine Zoughbi1,3, Abed-El-Razeq Issa1,3, Randa Al Qass1,3, Sultan Turkuman1, Hiyam Marzouqa1, and Imipenem and Musa Hindiyeh1,2,3* Ertapenem 1 Caritas Baby Hospital, 3 Palestinian Forum for Medical * Correspondence: Bethlehem, Palestine; Research (PFMR), Ramallah, Impregnated 2 Bethlehem University, Palestine Bethlehem, Palestine; [email protected] MacConkey * Musa Y Hindiyeh, Caritas Baby Hospital Bethlehem Agar Plates for Palestine. the Detection of Carbapenem Abstract Resistant Background: Rapid detection of carbapenem resistant bacteria, in particular, members of the Enterobacteriaceae family (CRE), is of utmost importance for the Enterobacteriaceae management of infected or colonized patients. Methods: Three carbapenems; meropenem, imipenem and ertapenem, with two different concentrations (0.5 mg/ml and 1.0 mg/ml), were impregnated in Mac- Conkey agar. The carbapenem impregnated MacConkey agar plates; ([Mac-Mem], [Mac-Imp] and [Mac-Ert]), were then evaluated for the detection of carbapenem resistant Gram-negative bacteria in particular the blaKPC producing Enterobacteria- ceae. The Limit of Detection (LOD) of the plates was determined in triplicate after serial logarithmic dilution of the bacterial strains in saline. This was followed by inoculating the plates and counting the colonies that grew after 24 hours of incu- bation. The specificity and the shelf-life of the plates were determined by testing the plates with six Extended Spectrum β-lactamases (ESBL) producing members of the Enterobacteriaceae family and one genus with the blaAmpC phenotype. -
Histopathology and Laboratory Features of Sexually Transmitted Diseases
Histopath & Labs for STIs Endo, Energy and Repro 2017-2018 HISTOPATHOLOGY AND LABORATORY FEATURES OF SEXUALLY TRANSMITTED DISEASES Dominck Cavuoti, D.O. Phone: 469-419-3412 Email: [email protected] LEARNING OBJECTIVES: • Identify the etiologic agents causing pelvic inflammatory disease and the pathologic changes they produce. • Discuss the characteristic clinical and pathologic findings caused by herpes simplex virus (HSV) infections: a. fever blisters b. genital herpes simplex virus infection c. disseminated neonatal HSV • Describe the pathologic changes produced by Treponema pallidum. • Describe the clinical features and pathologic changes produced by Chlamydia trachomatisand Neisseria gonorrhoeae • Describe the clinical and laboratory features of vaginal infections including: Trichomonas, Candida, and bacterial vaginosis. • Describe the clinical and laboratory features of ectoparasite infections PURPOSE OF THE LECTURE: 1. To describe the various agents of sexually transmitted diseases and their disease manifestations 2. To describe the pathologic features associated with STDs 3. To introduce some of the laboratory aspects of STDs TERMS INTRODUCED IN LECTURE: Condyloma lata Disseminated gonococcal infection Gummatous syphilis Lymphogranuloma venereum Pelvic inflammatory disease Rapid Plasma Reagin (RPR) Salpingitis Syphilis/endarteritis obliterans Venereal Disease Research Laboratory (VDRL) Treponema pallidum particle agglutination (TPPA) Histopath & Labs for STIs Endo, Energy and Repro 2017-2018 MAJOR CONCEPTS EMPHASIZED IN LECTURE I. Syphilis (Will be covered by Dr. Norgard in later lecture). II. Gonorrhea A. Causative agent: Neisseria gonorrhoeae, a Gram negative diplococcus. Humans are the only natural reservoir. Infection is acquired via direct contact with the mucosa of an infected person. The incubation period averages 2-5 days with a range of 1-14 days. -
Chemostat Culture for Yeast Experimental Evolution
Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press Protocol Chemostat Culture for Yeast Experimental Evolution Celia Payen and Maitreya J. Dunham1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195 Experimental evolution is one approach used to address a broad range of questions related to evolution and adaptation to strong selection pressures. Experimental evolution of diverse microbial and viral systems has routinely been used to study new traits and behaviors and also to dissect mechanisms of rapid evolution. This protocol describes the practical aspects of experimental evolution with yeast grown in chemostats, including the setup of the experiment and sampling methods as well as best laboratory and record-keeping practices. MATERIALS It is essential that you consult the appropriate Material Safety Data Sheets and your institution’s Environmental Health and Safety Office for proper handling of equipment and hazardous material used in this protocol. Reagents Defined minimal medium appropriate for the experiment For examples, see Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Ethanol (95%) Glycerol (20% and 50%; sterile) Yeast strain of interest Equipment Agar plates (appropriate for chosen strain) Chemostat array Assemble the apparatus as described in Miller et al. (2013) and Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Cryo deep-freeze labels Cryogenic vials Culture tubes Cytometer (BD Accuri C6) Glass beads, 4 mm (sterile; for plating yeast cells) Glass cylinder Kimwipes 1Correspondence: [email protected] © 2017 Cold Spring Harbor Laboratory Press Cite this protocol as Cold Spring Harb Protoc; doi:10.1101/pdb.prot089011 559 Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press C. -
Chocolate Agar Plate MP103 Intended Use for Isolation of Neisseria Gonorrhoeae from Chronic and Acute Gonococcal Infections
Chocolate Agar Plate MP103 Intended use For isolation of Neisseria gonorrhoeae from chronic and acute gonococcal infections. Composition** Ingredients Gms / Litre Proteose peptone 20.000 Dextrose 0.500 Sodium chloride 5.000 Disodium phosphate 5.000 Agar 15.000 After sterilization Sterile Lysed blood (at 80°C) 50.000 Vitamino Growth Supplement (FD025) 2 vials Final pH ( at 25°C) 7.3±0.2 **Formula adjusted, standardized to suit performance parameters Directions Either streak, inoculate or surface spread the test inoculum (50-100 CFU) aseptically on the plate. Principle And Interpretation Neisseria gonorrhoeae is a gram-negative bacteria and the causative agent of gonorrhea, however it is also occasionally found in the throat. The cultivation medium for gonococci should ideally be a rich nutrients base with blood, either partially lysed or completely lysed. The diagnosis and control of gonorrhea have been greatly facilitated by improved laboratory methods for detecting, isolating and studying N. gonorrhoeae. Chocolate Agar Base, with the addition of supplements, gives excellent growth of the gonococcus without overgrowth by contaminating organisms. G.C. Agar (M434) can also be used in place of Chocolate Agar Base, which gives slightly better results than Chocolate Agar (4). The diagnosis and control of gonorrhea have been greatly facilitated by improved laboratory methods for detecting, isolating and studying N. gonorrhoea. Interest in the cultural procedure for the diagnosis of gonococcal infection was stimulated by Ruys and Jens (9), Mcleod and co-workers (8), Thompson (7), Leahy and Carpenter (1), Carpenter, Leahy and Wilson (2) and Carpenter (10), who clearly demonstrated the superiority of this method over the microscopic technique. -
Macconkey Agar, CS, Product Information
MacCONKEY AGAR, CS (7391) Intended Use MacConkey Agar, CS is used for the isolation and differentiation of Gram-negative enteric bacilli from specimens containing swarming strains of Proteus spp. in a laboratory setting. MacConkey Agar, CS is not intended for use in the diagnosis of disease or other conditions in humans Product Summary and Explanation MacConkey Agar is based on the bile salt-neutral red-lactose agar of MacConkey.1 The original MacConkey medium was used to differentiate strains of Salmonella typhosa from members of the coliform group. Formula modifications improved growth of Shigella and Salmonella strains. These modifications include the addition of 0.5% sodium chloride, decreased agar content, altered bile salts, and neutral red concentrations. The formula modifications improved differential reactions between enteric pathogens and coliforms. MacConkey Agar, CS (“Controlled Swarming”) contains carefully selected raw materials to reduce swarming of Proteus spp., which could cause difficulty in isolating and enumerating other Gram-negative bacilli. Principles of the Procedure Enzymatic Digest of Gelatin, Enzymatic Digest of Casein, and Enzymatic Digest of Animal Tissue are the nitrogen and vitamin sources in MacConkey Agar, CS. Lactose is the fermentable carbohydrate. During Lactose fermentation a local pH drop around the colony causes a color change in the pH indicator, Neutral Red, and bile precipitation. Bile Salts and Crystal Violet are the selective agents, inhibiting Gram-positive cocci and allowing Gram-negative organisms to grow. Sodium Chloride maintains the osmotic environment. Agar is the solidifying agent. Formula / Liter Enzymatic Digest of Gelatin .................................................... 17 g Enzymatic Digest of Casein ................................................... 1.5 g Enzymatic Digest of Animal Tissue....................................... -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
Francisella Tularensis 6/06 Tularemia Is a Commonly Acquired Laboratory Colony Morphology Infection; All Work on Suspect F
Francisella tularensis 6/06 Tularemia is a commonly acquired laboratory Colony Morphology infection; all work on suspect F. tularensis cultures .Aerobic, fastidious, requires cysteine for growth should be performed at minimum under BSL2 .Grows poorly on Blood Agar (BA) conditions with BSL3 practices. .Chocolate Agar (CA): tiny, grey-white, opaque A colonies, 1-2 mm ≥48hr B .Cysteine Heart Agar (CHA): greenish-blue colonies, 2-4 mm ≥48h .Colonies are butyrous and smooth Gram Stain .Tiny, 0.2–0.7 μm pleomorphic, poorly stained gram-negative coccobacilli .Mostly single cells Growth on BA (A) 48 h, (B) 72 h Biochemical/Test Reactions .Oxidase: Negative A B .Catalase: Weak positive .Urease: Negative Additional Information .Can be misidentified as: Haemophilus influenzae, Actinobacillus spp. by automated ID systems .Infective Dose: 10 colony forming units Biosafety Level 3 agent (once Francisella tularensis is . Growth on CA (A) 48 h, (B) 72 h suspected, work should only be done in a certified Class II Biosafety Cabinet) .Transmission: Inhalation, insect bite, contact with tissues or bodily fluids of infected animals .Contagious: No Acceptable Specimen Types .Tissue biopsy .Whole blood: 5-10 ml blood in EDTA, and/or Inoculated blood culture bottle Swab of lesion in transport media . Gram stain Sentinel Laboratory Rule-Out of Francisella tularensis Oxidase Little to no growth on BA >48 h Small, grey-white opaque colonies on CA after ≥48 h at 35/37ºC Positive Weak Negative Positive Catalase Tiny, pleomorphic, faintly stained, gram-negative coccobacilli (red, round, and random) Perform all additional work in a certified Class II Positive Biosafety Cabinet Weak Negative Positive *Oxidase: Negative Urease *Catalase: Weak positive *Urease: Negative *Oxidase, Catalase, and Urease: Appearances of test results are not agent-specific.