Microorganisms play an important role in the maintenance of the ecosystem structure and function. Bacteria constitute the major part of the microorganisms and possess tremendous potential in many important applications from environmental clean up to the drug discovery. Much advancement has been taken place in the field of research on bacterial systems. This book summarizes the experimental setups required for applied microbiological studies. Important background information, representative results, step by step protocol in this book will be of great use to the students, early career researchers as well as the academicians. The book describes many experiments covering the basic microbiological experiments to the applications of microbial systems for advanced research. Researchers in any field who utilize bacterial systems will find this book very useful. In addition to microbiology and bacteriology, this book will also find useful in molecular biology, genetics, and pathology and the volume should prove to be a valuable laboratory resource in clinical and environmental microbiology, microbial genetics and agricultural research. Unique features • Easy to follow by the users as the experiments have been written in simple language and step-wise manner. • Role of each reagents to be used in each experiment have been described which will help the beginners to understand quickly and design their own experiment. • Each experiment has been equipped with the coloured illustrations for proper understanding of the concept. • Trouble-shootings at the end of each experiment will be helpful in overcoming the problems faced by the users. • Flow-chart of each experiment will quickly guide the users in performing the experiments.
Author: Surajit Das,Hirak Ranjan Dash
Research on the microbial colonization of the aerial and subterranean tissues of plants has shown an extensive scale of interactions between the hosts and a range of microbes, including bacteria and fungi. Intercellular spaces, vascular systems and even single cells can be inhabited by these endophytic microbes. Of the bacterial endophytes, only a small percentage is harmful to the plant; most are neutral, opportunistic or beneficial. These plant-based bacteria can have various important functions throughout the life cycle of the plant; some promote plant growth and development, others protect the plant from diseases. This ability to be able to protect plants from diseases has catalyzed numerous laboratories to search for new bacteria that could be utilized instead of the traditional plant-protective agents. Because two or more interacting organisms are involved, research and the eventual application of suitable bio-controlling microbes are challenging and often require specific skills and equipment. The purpose of this book is to provide a comprehensive review for those who are interested in the research and biotechnological applications of plant-associated bacteria. It also provides a compilation of current work conducted on plant-bacteria interactions.
Part A: Bacteria
Author: Seppo Sorvari,Anna Maria Pirttilä
Publisher: Seppo Sorvari
Molecular Microbiology Laboratory, second edition, is designed to teach essential principles and techniques of molecular biology and microbial ecology to upper-level undergraduates majoring in the life sciences and to develop students' scientific writing skills. A detailed lab preparation manual for instructors and teaching assistants accompanies the lab book and contains a general discussion of scientific writing and critical reading as well as detailed instructions for preparation and peer review of lab reports. Each experimental unit is accompanied by a number of additional writing exercises based upon primary journal articles. Exposes students to the new molecular-based techniques Provides faculty with an authoritative, accessible resource for teaching protocols The only manual to incorporate writing exercises, presentation skills and tools for reading primary literature into the curriculum Based on a successful course for which the author won a teaching award New to this Edition: - Presents a real-world study of bacterial populations in the environment in the final experiment - Provides an overview of molecular biology in a new review chapter - Demonstrates how to design an experiment and how to interpret the results - Covers grant proposal writing and how panels review proposals - Presents guidance on public speaking and preparing PowerPoint presentations - Includes tutorials on three widely used software packages
A Writing-intensive Course
Author: Walt Ream,Bruce Gellar,Janine Trempy,Katherine Field
Publisher: Academic Press
Concerns over dwindling fossil fuel reserves and impending climate changes have focused attention worldwide on the need to discover alternative, sustainable energy sources and fuels. Biofuels, already produced on a massive industrial scale, are seen as one answer to these problems. However, very real concerns over the effects of biofuel production on food supplies, with some of ht recent increases in worldwide food costs attributable to biofuel production, have lead to the realization that new, non-food substrates for biofuel production must be bought online. This book is an authoritative, comprehensive, up-to-date review of the various options under development for the production of advanced biofuels as alternative energy sources. A general overview and introductory chapters for each section place the field in the context as well as provide essential basic notions for the more general reader. Accomplished, internationally recognized experts carrying out research on individual focus areas contribute specific technical chapters detailing present progress and future prospects.
Author: Patrick C. Hallenbeck
Publisher: Springer Science & Business Media
A rich array of methods and discussions of productive microbial processes. • Reviews of the newest techniques, approaches, and options in the use of microorganisms and other cell culture systems for the manufacture of pharmaceuticals, industrial enzymes and proteins, foods and beverages, fuels and fine chemicals, and other products. • Focuses on the latest advances and findings on the current state of the art and science and features a new section on the microbial production of biofuels and fine chemicals, as well as a stronger emphasis on mammalian cell culture methods. • Covers new methods that enhance the capacity of microbes used for a wide range of purposes, from winemaking to pharmaceuticals to bioremediation, at volumes from micro- to industrial scale.
Author: Richard H. Baltz,Arnold L. Demain,Julian E. Davies
Publisher: American Society for Microbiology Press
Around the World, metal pollution is a major problem. Conventional practices of toxic metal removal can be ineffective and/or expensive, delaying and exacerbating the crisis. Those communities dealing with contamination must be aware of the fundamentals advances of microbe-mediated metal removal practices because these methods can be easily used and require less remedial intervention. This book describes innovations and efficient applications for metal bioremediation for environments polluted by metal contaminates.
Author: Surajit Das,Hirak Ranjan Dash
Publisher: CRC Press
Synthetic Biology: A Lab Manual is the first manual for laboratory work in the new and rapidly expanding field of synthetic biology. Aimed at non-specialists, it details protocols central to synthetic biology in both education and research. In addition, it provides all the information that teachers and students from high schools and tertiary institutions need for a colorful lab course in bacterial synthetic biology using chromoproteins and designer antisense RNAs. As a bonus, practical material is provided for students of the annual international Genetically Engineered Machine (iGEM) competition. The manual is based upon a highly successful course at Sweden's Uppsala University and is coauthored by one of the pioneers of synthetic biology and two bioengineering postgraduate students. An inspiring foreword is written by another pioneer in the field, Harvard's George Church: “Synthetic biology is to early recombinant DNA as a genome is to a gene. Is there anything that SynBio will not impact? There was no doubt that the field of SynBio needed ‘A Lab Manual’ such as the one that you now hold in your hands.” Read about the interview with the authors! Contents:Introduction:What is Synthetic Biology, Exactly?The iGEM OutbreakA Synthetic Biology Lab ManualGenes, Chromoproteins and Antisense RNAs:E. coli DNA: Chromosomes, Plasmids and Copy NumberCoupling of Transcription and Translation in BacteriaPromoter and Terminator for TranscriptionRibosome Binding Site (RBS)Codon BiasChromoproteinsSmall Regulatory RNAs (sRNAs)Lab Rooms and Equipment:The Physical Lab SpacesEquipmentSafety is Priority #1:FiresChemicalsBiological Safety and DisposalDangerous EquipmentLab Course Projects:Time and ResourcesProject Overview and Learning ObjectivesThe Lab NotebookLab Section 1. Preparation of Chemical Solutions and Agar PlatesLab Section 2. Coloring Bacteria by Adding a Promoter to a Chromoprotein GeneLab Section 3: Rational Engineering of Chromoprotein Expression LevelLab Section 4. Other ExperimentsThe “Dreaded” ExamProtocols:IntroductionProtocol 1. Preparation of Solutions and Agar PlatesProtocol 2. Overnight Cultures with Antibiotics, and Glycerol StocksProtocol 3. BioBrick™ 3A Assembly and Gel AnalysisProtocol 4. Agarose Gel ElectrophoresisProtocol 5. Preparation of Competent E. coli Cells Using CaCl2Protocol 6. Transformation of CaCl2-Competent E. coli CellsProtocol 7. Bacterial Re-Streaking TechniquesProtocol 8. Lysis of E. coli Cells with LysozymeProtocol 9. Polymerase Chain Reaction (PCR)Protocol 10. Inverse PCR MutagenesisProtocol 11. Colony PCRProtocol 12. Gibson AssemblyAdvanced Methods:Flow Cytometry and Cell SortingRecombination in Plasmids and the ChromosomeElectrocompetent CellsThe International Genetically Engineered Machine (iGEM) Competition:How to Start an iGEM TeamUppsala iGEM 2011 — Show Color with ColorUppsala iGEM 2012 — Resistance is FutileUppsala iGEM 2013 — Lactonutritious — It's DeliciousAppendices Readership: Students and researchers in biotechnology, cell/molecular biology and genetics. Keywords:Synthetic Biology;Genetic Engineering;DNA Cloning;Polymerase Chain Reaction;Molecular Biology;Laboratory;Biobrick;Chromoprotein;Manual;CourseReviews: It provides an introductory workflow for common techniques and would be of definite use to educators wanting to bring synthetic biology into the classroom or for motivated undergraduate students with the desire to start thir own iGEM team.” Synthetic Biology See Full Review
A Lab Manual
Author: Josefine Liljeruhm,Erik Gullberg,Anthony C Forster
Publisher: World Scientific
This manual is an indispensable tool for introducing advanced undergraduates and beginning graduate students to the techniques of recombinant DNA technology, or gene cloning and expression. The techniques used in basic research and biotechnology laboratories are covered in detail. Students gain hands-on experience from start to finish in subcloning a gene into an expression vector, through purification of the recombinant protein. The third edition has been completely re-written, with new laboratory exercises and all new illustrations and text, designed for a typical 15-week semester, rather than a 4-week intensive course. The "project" approach to experiments was maintained: students still follow a cloning project through to completion, culminating in the purification of recombinant protein. It takes advantage of the enhanced green fluorescent protein - students can actually visualize positive clones following IPTG induction. Cover basic concepts and techniques used in molecular biology research labs Student-tested labs proven successful in a real classroom laboratories Exercises simulate a cloning project that would be performed in a real research lab "Project" approach to experiments gives students an overview of the entire process Prep-list appendix contains necessary recipes and catalog numbers, providing staff with detailed instructions
A Classroom Laboratory Manual
Author: Sue Carson,Susan Carson,Heather Miller,D. Scott Witherow
Publisher: Academic Press
Designed for advanced undergraduate students, graduate students, and environmental professionals, this book builds upon the tremendous success of the previous editions with a comprehensive and up-to-date discussion of environmental microbiology as a discipline that has greatly expanded in scope and interest over the past several decades. From terrestrial and aquatic ecosystems to urban and indoor environments, this edition relates environmental microbiology to a variety of life science, ecology, and environmental science topics including biogeochemical cycling, bioremediation, environmental transmission of pathogens, microbial risk assessment, and drinking water treatment and reuse. The final chapter highlights several emerging issues including microbial remediation of marine oil spills, microbial contributions to global warming, impact of climate change on microbial infectious disease, and the development of antibiotic-resistant bacteria. New chapters on: Microbial Diversity and Interactions in Natural Ecosystems (previous chapter on bacterial diversity expanded to include microbial ecology and interactions) Bioinformation and ‘Omic’ Approaches for Characterization of Environmental Microorganisms Microbial Source Tracking Land Application of Organic Residuals: Municipal Biosolids and Animal Manures Recycled Water Treatment and Reuse Global Emerging Microbial Issues in the Anthropocene Era Updates to Other Chapters: Cultural Methods: new cutting-edge approaches for isolating difficult-to-culture microorganisms Nucleic Acid-Based Methods: new text and graphics for a variety of methods including microarrays, quantitative PCR, and metagenomics Aquatic Environments: completely revised chapter Microorganisms and Metal Pollutants: new material on metal speciation and bioremediation Microorganisms and Organic Pollutants: updated discussion on anaerobic degradation of halogenated compounds and bioaugmentation-based remediation of contaminated groundwater Microbial Communication: new sections on bacterial communication with eukaryotic hosts New graphics, case studies, and information boxes throughout More Features: Introductory chapters provide foundational background in microbiology, microbial environments, and methodologies Presents state-of-the-art research results with key, recent references to document information Emphasizes critical information using "Information Boxes" throughout Includes real-world case studies to illustrate concepts, along with frequent use of graphics, cartoons and photographs Offers questions at the end of each chapter designed to test key concepts Lecture slides available for instructors online
Author: Ian L. Pepper,Charles P. Gerba,Terry J. Gentry
In response to the field's need for an introductory text, the authors have distilled the vast and scattered literature relating to the biotechnology of microbial secondary metabolites. General biology, biosynthesis, the search for novel metabolites, and techniques for strain improvement are all discussed to provide undergraduate and graduate students with a concise, readable overview of the field.
Author: G. Lancini,R. Lorenzetti
Publisher: Springer Science & Business Media
A first source for traditional methods of microbiology as well as commonly used modern molecular microbiological methods. • Provides a comprehensive compendium of methods used in general and molecular microbiology. • Contains many new and expanded chapters, including a section on the newly important field of community and genomic analysis. • Provides step-by-step coverage of procedures, with an extensive list of references to guide the user to the original literature for more complete descriptions. • Presents methods for bacteria, archaea, and for the first time a section on mycology. • Numerous schematics and illustrations (both color and black and white) help the reader to easily understand the topics presented.
Author: C. A. Reddy,Terry J. Beveridge,John A. Breznak,George Marzluf
Publisher: American Society for Microbiology Press
Laboratory Manual for Biotechnology provides the basic laboratory skills and knowledge to pursue a career in biotechnology. The manual, written by four biotechnology instructors with over 20 years of teaching experience, incorporates instruction, exercises, and laboratory activities that the authors have been using and perfecting for years. These exercises and activities serve to engage and help you understand the fundamentals of working in a biotechnology laboratory. Building skills through an organized and systematic presentation of materials, procedures, and tasks, the manual will help you explore overarching themes that relate to all biotechnology workplaces. The fundamentals in this manual are critical to the success of research scientists, scientists who develop ideas into practical products, laboratory analysts who analyze samples in forensic, clinical, quality control, environmental, and other testing laboratories.
Author: Lisa A. Seidman,Mary Ellen Kraus,Diana Brandner,Jeanette Mowery
Publisher: Benjamin Cummings
The development of CRISPR-Cas technology is revolutionizing biology. Based on machinery bacteria use to target foreign nucleic acids, these powerful techniques allow investigators to edit nucleic acids and modulate gene expression more rapidly and accurately than ever before. Featuring contributions from leading figures in the CRISPR-Cas field, this laboratory manual presents a state-of-the-art guide to the technology. It includes step-by-step protocols for applying CRISPR-Cas-based techniques in various systems, including yeast, zebrafish, Drosophila, mice, and cultured cells (e.g., human pluripotent stem cells). The contributors cover web-based tools and approaches for designing guide RNAs that precisely target genes of interest, methods for preparing and delivering CRISPR-Cas reagents into cells, and ways to screen for cells that harbor the desired genetic changes. Strategies for optimizing CRISPR-Cas in each system--especially for minimizing off-target effects--are also provided. Authors also describe other applications of the CRISPR-Cas system, including its use for regulating genome activation and repression, and discuss the development of next-generation CRISPR-Cas tools. The book is thus an essential laboratory resource for all cell, molecular, and developmental biologists, as well as biochemists, geneticists, and all who seek to expand their biotechnology toolkits.
Author: University Jennifer Doudna,Prashant Mali
University of California, Los Angeles. Introduction to bacterial genetics, including laboratory methods, for advanced students and beginning researchers. Handbook with plastic spiral-bound laboratory manual.
A Laboratory Manual and Handbook for Escherichia Coli and Related Bacteria
Author: Jeffrey H. Miller
Publisher: CSHL Press
With millions of different bacterial species living in soil, the microbial community is extremely complex, varying at very small scales. Microbe-driven functions are essential for most processes in soil. Thus, a better understanding of this microbial diversity will be invaluable for the management of the various soil functions. Nucleic Acids and Proteins in Soil combines traditional approaches in soil microbiology and biochemistry with the latest techniques in molecular microbial ecology. Included are methods to analyse the presence and importance of nucleic acids and proteins both inside and outside microbial cells, the horizontal gene transfer which drives bacterial diversity, as well as soil proteomes. Further chapters describe techniques such as PCR, fingerprinting, the challenging use of gene arrays for structural and functional analysis, stable isotope probing to identify in situ metabolic functions, and the use of marker and reporter genes in soil microbial ecology.
Author: Paolo Nannipieri,Kornelia Smalla
Publisher: Springer Science & Business Media
Principles of Laboratory Food Microbiology serves as a general laboratory guide for individuals in quality control, quality assurance, sanitation, and food production who need to increase their knowledge and skills in basic and applied food microbiology and food safety. This is a very useful book for food industry personnel with little or no background in microbiology or who need a refresher course in basic microbiological principles and laboratory techniques. Focusing on basic skill-building throughout, the book provides a review of basic microbiological techniques — media preparation, aseptic techniques, dilution, plating, etc. — followed by analytical methods and advanced tests for food-borne pathogens. It reviews basic microbiology techniques to evaluate the microbiota of various foods and enumerate indicator microorganisms. It emphasize on conventional cultural techniques. It also focuses on procedures for detecting pathogens in food, offering students the opportunity to practice cultural and biochemical methods. The final section discusses beneficial microorganisms and their role in food fermentations, concentrating on lactic acid bacteria, acetic acid bacteria and yeast. It provides an ideal text companion for an undergraduate or graduate laboratory course, offering professors an authoritative frame of reference for their own supplementary materials and to the food processing industry personnel, Government and private organization linked with food processing and microbial quality of the processed product. The book is an essential text for microbiologists working in the food industry, quality assurance personnel and academic researchers.
Author: Neelima Garg,K. L. Garg,K. G. Mukerji
Publisher: I. K. International Pvt Ltd
This edition features the exact same content as the traditional text in a convenient, three-hole-punched, loose-leaf version. Books a la Carte also offer a great value for your students--this format costs 35% less than a new textbook. Versatile, comprehensive, and clearly written, this competitively priced laboratory manual can be used with any undergraduate microbiology text--and now features brief clinical applications for each experiment, and a new experiment on hand washing. Microbiology: A Laboratory Manual is known for its thorough coverage, descriptive and straightforward procedures, and minimal equipment requirements. A broad range of experiments helps to convey basic principles and techniques. Each experiment includes an overview, an in-depth discussion of the principle involved, easy-to-follow procedures, and lab reports with review and critical thinking questions. Ample introductory material and laboratory safety instructions are provided.
A Laboratory Manual
Author: James Cappuccino,Natalie Sherman
Publisher: Benjamin-Cummings Publishing Company
This book provides a timely review of strategies for coping with polluted ecosystems by employing bacteria, fungi and algae. It presents the vast variety of microbial technologies currently applied in the bioremediation of a variety of anthropogenic toxic chemicals, mining and industrial wastes and other pollutants. Topics covered include: microbe-mineral interactions, biosensors in environmental monitoring, iron-mineral transformation, microbial biosurfactants, bioconversion of cotton gin waste to bioethanol, anaerobe bioleaching and sulfide oxidation. Further chapters discuss the effects of pollution on microbial diversity, as well as the role of microbes in the bioremediation of abandoned mining areas, industrial and horticultural wastes, wastewater and sites polluted with hydrocarbons, heavy metals, manganese and uranium.
Author: Lala Behari Sukla,Nilotpala Pradhan,Sandeep Panda,Barada Kanta Mishra
The most definitive manual of microbes in air, water, and soil and their impact on human health and welfare. • Incorporates a summary of the latest methodology used to study the activity and fate of microorganisms in various environments. • Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments. • Features a section on biotransformation and biodegradation. • Serves as an indispensable reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.
Author: Christon J. Hurst,Ronald L. Crawford,Jay L. Garland,David A. Lipson
Publisher: American Society for Microbiology Press
Aimed at research scientists and biotechnologists, this book is an essential reading for those working with extremophiles and their potential biotechnological application. Here, we provide a comprehensive and reliable source of information on the recent advances and challenges in different aspects of the theme. Written in an accessible language, the book is also a recommended as reference text for anyone interested in this thriving field of research. Over the last decades, the study of extremophiles has provided ground breaking discoveries that challenge our understanding of biochemistry and molecular biology. In the applied side, extremophiles and their enzymes have spawned a multibillion dollar biotechnology industry, with applications spanning biomedical, pharmaceutical, industrial, environmental, and agricultural sectors. Taq DNA polymerase (which was isolated from Thermus aquaticus from a geothermal spring in Yellowstone National Park) is the most well-known example of the potential biotechnological application of extremophiles and their biomolecules. Indeed, the application of extremophiles and their biologically active compounds has opened a new era in biotechnology. However, despite the latest advances, we are just in the beginning of exploring the biotechnological potentials of extremophiles.
Advances and Challenges
Author: Pabulo H Rampelotto