W2017 MB230 Lab Manual
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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. -
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. -
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. -
Microbiology Laboratory Exercises Third Edition 2020
MICROBIOLOGY Laboratory Exercises Third Edition Keddis & Rauschenbach 2020 Photo Credits (in order of contribution): Diane Davis, Ines Rauschenbach & Ramaydalis Keddis Acknowledgements: Many thanks to those in the Department of Biochemistry and Microbiology, Rutgers University, who have through the years inspired our enthusiasm for the science and teaching of microbiology, with special thanks to Diane Davis, Douglas Eveleigh and Max Häggblom. Safety: The experiments included in this manual have been deemed safe by the authors when all necessary safety precautions are met. The authors recommend maintaining biosafety level 2 in the laboratory setting and using risk level 1 organisms for all exercises. License: This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 International License Microbiology Laboratory Exercises Third Edition 2020 Ramaydalis Keddis, Ph.D. Ines Rauschenbach, Ph.D. Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey CONTENTS PAGE Introduction Schedule ii Best Laboratory Practices Iii Working in a Microbiology Laboratory iv Exercises Preparation of a Culture Medium 1 Culturing and Handling Microorganisms 3 Isolation of a Pure Culture 5 Counting Bacterial Populations 8 Controlling Microorganisms 10 Disinfectants 10 Antimicrobial Agents: Susceptibility Testing 12 Hand Washing 14 The Lethal Effects of Ultraviolet Light 15 Selection of Fungi from Air 17 Microscopy 21 Morphology and Staining of Bacteria 26 Microbial Metabolism 30 Enzyme Assay 32 Metabolic -
Examination of Zoonotic Bacterial Pathogens in Canine and Feline Raw Meat-Based Diets
F.P.J. van Bree, Utrecht University, 2016 Paper Paper Examination of zoonotic bacterial pathogens in canine and feline raw meat-based diets F.P.J. van Bree, P.A.M. Overgaauw The feeding of raw meat-based diets (RMBD) to companion animals has become increasingly popular in recent years. However, such diets were demonstrated to be possibly contaminated with various zoonotic bacterial species in several studies and so the feeding of these diets could pose a risk to both animal and human health. Data about the situation in the Netherlands, or Europe in general are not available. Therefore, the purpose of this study was to evaluate the contamination of commercial RMBDs available in the Netherlands with zoonotic bacterial pathogens. Thirty-five commercial RMBDs were evaluated via bacterial culture for Escherichia coli O157:H7, extended- spectrum beta-lactamase (ESBL-)producing E. coli, Listeria monocytogenes and Salmonella spp.. E. coli O157:H7 was isolated from eight (23%) products, ESBL-producing E. coli from twenty- eight (80%) products, L. monocytogenes from nineteen (54%) products, other Listeria spp. from fifteen (43%) products, and Salmonella spp. from seven (20%) products. The results of this study demonstrate the need to pay attention to the potential of RMBDs to be a source for zoonotic bacterial pathogens in the Netherlands. These diets cannot be ruled out as a possible source for bacterial infections in both humans and animals and therefore companion animal owners should be informed about the associated risks. Keywords: raw meat-based diet; BARF; E. coli O157; ESBL; Listeria monocytogenes; Salmonella; public health In recent years it has become increasingly popular among of them are intended to provide for a complete diet for dogs dog and cat owners to feed raw meat-based diets (RMBD), and/or cats. -
Maintenance of Bacterial Strains
Maintenance of Bacterial Strains Short-term growth and maintenance The simplest method for obtaining strains is to order them from a microbiological supply company. Presque Isle, Ward, and Carolina Biological (see “Resources” page of the Microbes Web site: www.umsl.edu/~microbes) are economical sources of strains that are commonly used in the classroom. Another possible source is a local college or university that teaches a microbiology lab course. If they have strains already prepared for their class, they will probably be willing to provide you with a culture. This is probably not a reasonable ongoing source of strains, but can be useful in an emergency. For short-term maintenance and use, it is best to streak bacteria on some type of rich agar petri plate, such as nutrient agar. Label and date the plate on the bottom of the plate. Streak from the source culture using good sterile technique. The quadrant streak method (see the article on quadrant streaking) is good for obtaining well-isolated colonies. Incubate the plate only until good colonies have formed. Do not leave the culture in the incubator beyond that time, or the cells will die on the plate. Store the plate in the refrigerator. It will keep for about a month. For class use, it is best to streak a fresh plate 2-3 days before the strain will be needed for class. Use the fresh plate as the source of cultures for the class. For broth cultures for a class, it is best to grow a larger volume culture in a flask (if possible, with shaking) overnight and then dispense aliquots of the master culture into sterile test tubes using a sterile pipette. -
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. -
Thesis Evaluations That Increase Value for Pork
THESIS EVALUATIONS THAT INCREASE VALUE FOR PORK EXPORT PRODUCTS Submitted by Dan Sewald Department of Animal Sciences In partial fulfillment of the requirements For the degree of Master of Science Colorado State University Fort Collins, Colorado Fall 2017 Master’s Committee: Advisor: Dale R. Woerner Keith E. Belk Gary Mason Copyright by Dan Robert Sewald 2017 All Rights Reserved ABSTRACT EVALUATIONS THAT INCREASE VALUE FOR PORK EXPORT PRODUCTS Experiment 1: An evaluation of the suitability of porcine lung tissue for human consumption This study was conducted to provide evidence of the safety of pork lungs for human consumption via an assessment of prevalence of potentially pathogenic bacteria and infectious agents. Specifically, the goal was to collect evidence that could be used to petition the current regulation disallowing use of pork lungs for human food. Pork lungs have been labeled by the U.S. Meat Export Federation as a widely consumed product across Asia as well as South and Central America. It was believed that there is profit potential in saving pork lungs and exporting them to specified countries. Pork lungs must first be deemed safe and edible before they can be sold on the export market. Lungs (N = 288) were collected from a total of six federally inspected young market barrow/gilt or sow processing facilities. In an attempt to obtain a representative sample of production at each facility on a given day, lungs were randomly selected throughout the entire production day. All collected lungs were removed and processed using aseptic techniques to prevent any exogenous contamination. Lung samples were tested for the presence of pathogens and other physical contamination. -
Wooden Sticks for Plaque Streaking and Microbiological Inoculation
ISSN 1519-6984 (Print) ISSN 1678-4375 (Online) THE INTERNATIONAL JOURNAL ON NEOTROPICAL BIOLOGY THE INTERNATIONAL JOURNAL ON GLOBAL BIODIVERSITY AND ENVIRONMENT Original Article Wooden sticks for plaque streaking and microbiological inoculation might be more cost- effective, but is its large scale use feasible? Quality control methods and proof of concept Métodos de controle de qualidade e prova de conceito para a utilização de palitos de madeira em microbiologia podem ser mais econômicas, mas seu uso em larga escala é viável? Método de controle de qualidade e prova de conceito D. M. Castro e Silvaa* and N. S. Adiwardanab aInstituto Adolfo Lutz – IAL, São Paulo, SP, Brasil bInstituto de Infectologia Emilio Ribas, São Paulo, SP, Brasil Abstract The loop is a material classically used in the laboratory for the purpose of plate streaking and handling biological materials. However, metal loops techniques might be time consuming, considering the amount of time spent to guarantee its cooling process through each inoculation. Furthermore, plastic loops may also represent environmental issues during its production and discard process and can also represent higher costs for the laboratory. Thus, in situations of limited resources, even the simplest materials can be restricted due to logistical and budgetary issues, especially in developing countries. Inspired by demands like these, facing an occasional shortage of supply of laboratory plastic handles, we hereby present a quality control for sterilization methods and cost-effectiveness studies towards the use of wooden sticks in a Latin American country and we discuss the possibility of the large-scale use of this technique. Keywords: microbiology; bacteriology; plaque inoculation; wood; waste management. -
Study of Equipment's Used in Microbiology : Spirit Lamp, Inoculation Loop, Hot Air Oven, Laminar Air Flow (Laf) and Incubato
Study of some equipments Spirit lamp, Inoculation Loop, Hot Air Oven, Laminar Air Flow (LAF) and Incubator By Dr.S.V.Patil, Head, Department of Botany Bhusawal Arts, Science and P.O. Nahata Commerce college,1 Bhusawal Spirit Lamp Alcohol lamp Used for heating , sterilization and combustion. Ethyl alcohol or spirit used as a fuel. Used to proudest open fire. Made of glass, brass, aluminum. Chemical or biological reaction need to heat to get desired product. Flame is limitated i.e. ( 5 centimeters) in height. Lower temp. than glass flame. Flame sterilization of laboratory equipments. 2 Inoculation Loop Aseptic transfer. Loop consists of insulation Handle. screw device at the top. Heat resistance nichrome or platinum wire. Approximately 3 inch long. Wire end is bent round to form a loop. It sterilized by using heating or flaming until it is red hot. Loop mainly used transfer( sub culture) form liquid culture. 3 Hot Air Oven Used for Sterilizing. glassware, petri dishes, test tube, pipettes, metal instrument. Consist of isolated cabinet which held at a constant temp. Sterilization completed 150 – 180 c for 2-4 hrs. Fan fitted in hot air to circulating at a constant temp. Normal sterilization at 160 0C 4 Laminar Air Flow Its allowed to working for long period. Made up of stainless steel with no gaps or joint. PRINCIPLE – based on flow of current to create uniform velocity along parallel line, which helps in transforming microbial culture in aseptic condition to avoid the dust and contamination. Working - filter pad a fan and HEPA filter ( High Efficiency Particulate Air) 5 Fan suck the air through the filter pad where dust is trapped Prefiltered air has to pass the HEPA filter where contamination fungi, bacteria, dust are removed Ultraclean air which is free from fungal & bacterial contamination flows at the velocity of about 27 ± 3 m/minute through work area UV lamp is fitted in working area 6 Before starting work, LAF is put on for 10 – 15 minute. -
Experiment 4 Aseptic Cult-Ure Technique
I EXPERIMENT 4 ASEPTIC CULT-URE I TECHNIQUE I I Structure I 4.1 Introduction I Objectives I 4.2 Experiment I 4.1.1 Principle I 4.1.2 Observations I 4.3 Precautions I 4.1 INTRODUCTION I I In previous experiments you learned that microorganisms thrive pretty much I everywhere. It is far too easy to contaminate your lab cultures and experiments with stray microorganisms from the air, the countertop, or your tools. It is also possible to I expose your surroundings or ycurself'to a possible pathogen. In this lab exercise, you wrll I learn to transfer microbiological cultures from one medium to a second sterile medium without contamination of the culture, sterile medium, or the surroundings. I I Objectives I After studying and performing this experiment, you should be able to: I • know how to handle microorganisms, tubed media, plated media, and inoculating I tools such as loops, needles, or swabs etc.; I • leai n how to transfer bacteria from test tubes or broth and agar; and I • learn how to transfer bacteria from Petri plates. I 4.2 EXPERIMENT I I 4.2.1 Principle I Aseptic technique is a method that prevents the introduction of unwanted organisms into I an environment. In order to protect sterile broth, media, plates, slants etc. from I contamination we must practice aseptic i.e. sterile techniques to protect our material from contamination. By using aseptic technique only sterile surface touches other sterile I surface and exposure to the non sterile environment is minimized. I Though, observingaseptic technique is the most important instruction for any micrcbiology I experiment, some common circumstances will be discussed in this practical to make you aware of aseptic techniques. -
Bacterial Typing and Identification Based on Fourier Transform
Bacterial Typing and Identication Based on Fourier Transform Infrared Spectroscopy Huayan Yang Ningbo University Fangling Wu Ningbo University Fuxin Xu Ningbo University Keqi Tang Ningbo University Chuanfan Ding Ningbo University Haimei Shi ( [email protected] ) Ningbo University Shaoning Yu ( [email protected] ) Ningbo University Method Article Keywords: Bacteria,Typing , Identication, Fourier Transform Infrared Spectroscopy Posted Date: February 14th, 2020 DOI: https://doi.org/10.21203/rs.2.23337/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/50 Abstract Fourier transform infrared (FT-IR) spectroscopy is a label-free and highly sensitive technique that provides complete information on the chemical composition of biological samples. The bacterial FT-IR signals are extremely specic and highly reproducible ngerprint-like patterns, making FT-IR an ecient tool for bacterial typing and identication. Due to the low cost and high ux, FT-IR has been widely used in hospital hygiene management for infection control, epidemiological studies, and routine bacterial determination of clinical laboratory values. However, the typing and identication accuracy could be affected by many factors, and the bacterial FT-IR data from different laboratories are usually not comparable. A standard protocol is required to improve the accuracy of FT-IR-based typing and identication. Here, we detail the principles and procedures of bacterial typing and identication based on FT-IR spectroscopy, including bacterial culture, sample preparation, instrument operation, spectra collection, spectra preprocessing, and mathematical data analysis. Without bacterial culture, a typical experiment generally takes <2 h. Introduction 1. Introduction 1.1 overview Ecient typing and identication of bacteria is important for many applications in microbiology1-3.