Current Developments in Biotechnology and Bioengineering. Foundations of Biotechnology and Bioengineering PDF
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Current Developments in Biotechnology and Bioengineering Foundations of Biotechnology and Bioengineering Edited by Ashok Pandey, Jose´ Anto´nio Couto Teixeira AMSTERDAM l BOSTON lHEIDELBERG lLONDON lNEWYORK lOXFORD PARIS l SANDIEGO lSANFRANCISCOlSINGAPORE lSYDNEYl TOKYO Elsevier Radarweg29, POBox211,1000 AEAmsterdam,Netherlands TheBoulevard,LangfordLane,Kidlington, OxfordOX51GB,United Kingdom 50HampshireStreet,5thFloor,Cambridge, MA02139,United States Copyright©2017 ElsevierB.V. Allrights reserved. Nopartofthispublication maybereproducedortransmittedinanyform orbyany means, electronicormechanical,including photocopying,recording,oranyinformation storage andretrievalsystem,without permissioninwritingfromthepublisher.Detailsonhowto seekpermission,furtherinformation aboutthePublisher’s permissions policiesandour arrangements withorganizations suchastheCopyrightClearance CenterandtheCopyright LicensingAgency,canbefoundatourwebsite:www.elsevier.com/permissions. 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LibraryofCongress Cataloging-in-Publication Data Acatalog recordforthisbook isavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-Publication Data Acataloguerecord forthis bookisavailablefromtheBritishLibrary ISBN:978-0-444-63668-3 ForinformationonallElsevierpublications visitourwebsiteathttps://www.elsevier.com/ Publisher:JohnFedor AcquisitionEditor:Kostas Marinakis EditorialProjectManager:Anneka Hess ProductionProjectManager: MohanapriyanRajendran Designer:GregHarris TypesetbyTNQBooksandJournals List of Contributors T.Q. Aguiar University of Minho, Braga, Portugal M.R. Aires-Barros Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, Lisbon, Portugal A.M. Azevedo InstituteforBioengineeringandBiosciences(IBB),InstitutoSuperior Técnico, Universidade de Lisboa, Av. Rovisco Pais, Lisbon, Portugal L. Domingues University of Minho, Braga, Portugal B. Fernandes University of Minho, Braga, Portugal P. Gunasekaran Madurai Kamaraj University, Madurai, Tamil Nadu, India P. Jauregi University of Reading, Reading, United Kingdom A. Mota University of Minho, Braga, Portugal C. Oliveira University of Minho, Braga, Portugal L. Pastrana INLeInternationalIberianNanotechnologyLaboratory,Braga,Portugal J. Rajendhran Madurai Kamaraj University, Madurai, Tamil Nadu, India K.B. Ramachandran Indian Institute of Technology Madras, Chennai, India S. Ramalingam Anna University, Chennai, India J.L. Rodrigues University of Minho, Braga, Portugal L.R. Rodrigues University of Minho, Braga, Portugal T. Satyanarayana University of Delhi South Campus, New Delhi, India ix x List of Contributors B. Singh Maharshi Dayanand University, Rohtak, India S. Srinivasan Madurai Kamaraj University, Madurai, Tamil Nadu, India A. Vicente University of Minho, Braga, Portugal About the Editors Ashok Pandey ProfessorAshokPandeyisEminentScientistattheCenterof Innovative and Applied Bioprocessing, Mohali (a national institute under the Department of Biotechnology, Ministry of Science and Technology, Government of India), and former chief scientist and head of the Biotechnology DivisionattheCSIR’sNationalInstituteforInterdisciplinary Science and Technology at Trivandrum. He is an adjunct professor at Mar Athanasios College for Advanced Studies Thiruvalla,Kerala,andatKalasalingamUniversity,Krishnan Koil, Tamil Nadu. His major research interests are in the areas of microbial, enzyme, and bioprocess technology, which span various programs, including biomass to fuels and chemicals, probiotics and nutraceuticals, industrial enzymes, solid-state fermentation, etc. He has more than 1100 publications and communications, which include 16 patents, 50+ books, 125 book chapters,and425originalandreviewpapers,withanhindexof75andmorethan23,500 citations (Google Scholar). He has transferred several technologies to industries and has been an industrial consultant for about a dozen projects for Indian and international industries. Professor Pandey is the recipient of many national and international awards and fellowships, which include Elected Member of the European Academy of Sciences and Arts, Germany; Fellow of the International Society for Energy, Environment and Sustainability; Fellow of the National Academy of Science (India); Fellow of the Biotech Research Society, India; Fellow of the International Organization of Biotechnology and Bioengineering;FellowoftheAssociationofMicrobiologistsofIndia;honorarydoctorate degree from the Universite´ Blaise Pascal, France; Thomson Scientific India Citation Laureate Award, United States; Lupin Visiting Fellowship; Visiting Professor at the Universite´ Blaise Pascal, France, the Federal University of Parana, Brazil, and the E´cole Polytechnique Fe´de´rale de Lausanne, Switzerland; Best Scientific Work Achievement Award, Government of Cuba; UNESCO Professor; Raman Research Fellowship Award, CSIR;GBF,Germany,andCNRS,Francefellowships;YoungScientistAward;andothers. He was chairman of the International Society of Food, Agriculture and Environment, Finland (Food & Health) during 2003e04. He is the Founder President of the Biotech xi xii About the Editors Research Society, India (www.brsi.in); International Coordinator of the International Forum on Industrial Bioprocesses, France (www.ifibiop.org); chairman of the InternationalSocietyforEnergy,Environment&Sustainability(www.isees.org);andvice president of the All India Biotech Association (www.aibaonline.com). Professor Pandey iseditor-in-chiefofBioresourceTechnology,HonoraryExecutiveAdvisoroftheJournalof Water Sustainability and Journal of Energy and Environmental Sustainability, subject editoroftheProceedingsoftheNationalAcademyofSciences(India),andeditorialboard member of several international and Indian journals, and also a member of several national and international committees. Jose´ Anto´nio Couto Teixeira Jose´ Anto´nio Couto Teixeira is currently a Professor (“Professor Catedra´tico”) at the Biological Engineering Department,UniversityofMinho,Portugal(since2000).He has a degree in Chemical Engineering from the University of Porto (1980) and a Ph.D. in Chemical Engineering also from the University of Porto (1988). He has been involved in various management activities, being Head of the DepartmentofBiologicalEngineering,UniversityofMinho, 2000e2012, and Head of the Biological Engineering Research Center, 2012e2015. His main research interests are industrial biotechnology (bioprocess development for the transformation of lignocellulosic materials into second-generation bioethanol and chemicals, valorization of agroindustrial residues, and bioreactor development, including new design bioreactors and continuous processing) and food biotechnology (nonconventional food processing, edible films for packaging, process development for productionofprebiotics).Hewasresponsibleorcoresponsibleforthesupervision of31 Ph.D. theses and 20 postdoctoral researchers and has been the coordinator of 32 sci- entific research projects, 7 of which were international. Jose´ Teixeira was awarded the StimulustoExcellence,2006,fromtheFundac¸a˜oparaaCieˆnciaeaTecnologia;theSeeds of Science in Engineering and Technology, 2011, from Cieˆncia Hoje;, and the Scientific Merit Award, Universidade do Minho, 2015. He is the coeditor of the books Reactores Biolo´gicosdFundamentos e Aplicac¸o˜es (in Portuguese), Engineering Aspects of Milk and DairyProducts, andEngineeringAspectsofFoodBiotechnologyandthe author/coauthor of over 400 peer-reviewed papers (see http://orcid.org/0000-0002-4918-3704). Preface This book is a part of the comprehensive series Current Developments in Biotechnology and Bioengineering (Editor-in-chief: Ashok Pandey), comprising nine volumes, and presents a collection of chapters dealing with the foundations of biotechnology and bioengineering. Biotechnology has been part of human activities for more than 10,000years and its impor- tance has been increasing with human development. Nowadays, biotechnology has an enormous impact on our everyday life and is a key technology for industry, health, envi- ronment, food, and other areas of activity. Biotechnology, according to the Organization of Economic Co-operation and Development, is defined as “the application of scientific and engineeringprinciplestotheprocessingofmaterialsbybiologicalagents.”Inbiotechnology, intact organisms, such as yeast, bacteria, or microalgae, or their components, such as en- zymes, are used to manufacture useful products and provide services. This makes clear the multidisciplinary character of biotechnology and the importance of professionals from different areas of knowledge interacting and understanding one another so that the full potential of biotechnology can be exploited. This book comprises eight chapters: the first and second chaptersare dedicated to the fundamentalsofmicrobiologyandbiochemistry;fromthethirdtothefifth,topicsaddressed arefocusedongenetics,molecularbiology,andgeneticandmetabolicengineering;Chapters 6 and 7 deal with the most important engineering operations in biotechnology; and, finally, Chapter 8 reviews methods and tools in synthetic biology. Chapter 1 gives an overview of the basic aspects of microbiology, including microbial metabolism,anditsrole invariousindustrial bioprocesses; in Chapter2themainbiological molecules are introduced, such as proteins, carbohydrates, lipids, and nucleic acids, including their chemical structures, properties, and importance in biotechnological and bioengineering developments such as genetic engineering and bioprocesses. This chapter also points out advances in areas such as proteomics and genetic engineering, and their relevance to advances in the discovery of new drugs and treatment of diseases is discussed. The basic concepts of the fundamental units of life, encompassing DNA replication, transcription, and gene regulation, are discussed in Chapter 3. Other vital biological phe- nomena such as transformation, conjugation, transduction, recombination, and horizontal genetransfer arealsopresentedin thischapter.Themajortechniquesin molecularbiology, suchasblotting,polymerasechainreaction,andsequencingtechnologies,arealsodescribed. Chapter4compilesinformationontheprinciplesofgeneticengineering,describingnotonly the basic techniques used in molecular biology and the basics of recombinant DNA tech- nology,butalsopresentingmorerecentdevelopmentsonthesetechniques,aswellasup-to- dateinsilicotools.InChapter5,metabolicengineeringisthetopicconsidered,andthemajor steps involved in metabolic engineeringdanalysis and synthesisdare described. Metabolic flux analysis and its importance to bioprocess development are also addressed. Chapters 6 and 7 deal with the most relevant engineering topics in biotechnologyd bio-reactionengineeringanddownstreamprocessing.Chapter6presentsthebasicconcepts of biocatalyst (cell and enzymes) kinetics and the main bioreactor types and operation modes, as well as a comprehensive approach regarding the monitoring of various xiii xiv Preface bio-reactions and control strategies. In Chapter 7, themost commonly used unit operations in the downstream processing of biotechnology products are described, and relevant considerations in designing a purification strategy are discussed. Finally, in Chapter 8, the relevance of synthetic biology in the improvement of biotechnology is presented together with a review of the tools and methods used. Wehopethatthisbook willbeofgreatvalueto engineers,microbiologists, geneticists, and others in providing key life science and engineering aspects of the development of biotechnology and bioengineering. We would like to acknowledge the reviewers for their valuablecommentsto improvethefinalquality ofthechaptersincludedin this volume.We thank Dr. Kostas Marinakis, Book Acquisition Editor; Ms. Anneka Hess; and the entire pro- ductionteamatElsevierfortheirhelpandsupportinbringingoutthisvolume.Withouttheir commitment, efficiency, and dedicated work, this volume could not have ever been accomplished. Editors Ashok Pandey Jose´ Anto´nio Couto Teixeira 1 Basic Microbiology B. Singh1, T. Satyanarayana2,* 1MAHARSHI DAYANAND UNIVERSITY, ROHTAK, INDIA; 2UNIVERSITY OF DELHI SOUTH CAMPUS, NEW DELHI, INDIA 1.1 Introduction Microbiology was initially focused on the causes of infectious diseases but now includes practical applications of the science. A large number of scientists have made significant contributions to the development of microbiology. There is no evidence for the exact discoveryofmicroorganisms,but themicroscopewasavailable inthemid-1600s. Robert Hooke,anEnglishscientist,initiallyobservedmicroorganisms.AntonievanLeeuwenhoek madeseveralobservationsofmicroscopicorganismsduringthe1670sandhecalledthem animalcules. He was the first to provide accurate descriptions of protozoa, fungi, and bacteria. During this period, the theory of spontaneous generation was disputed by Francesco Redi by proving that fly maggots do not arise from decaying meat when the meat is covered to prevent the entry of flies. LouisPasteurexperimentallyprovedthatbacterialgrowthisthemainreasonforsour taste in wine and dairy products. Pasteur also disproved the theory of spontaneous generationusingswan-neckedflasksfilledwithbroth.Hisworkalsoprovidedsupportfor the belief that microorganisms are in the air and can cause diseases. Pasteur postulated the germ theory of disease, but he did not prove this theory unequivocally. Later this theory was proved by the German scientist Robert Koch by cultivating anthrax bacilli frominfectedanimals.Heinjectedpureculturesofthebacilliintomice,whichresultedin anthrax. All these findings are collectively called Koch’s postulates (Fig. 1.1). During his work with staphylococci, Alexander Fleming (1929) observed the inhibition of bacterial growth by a mold that was identified as Penicillium notatum [21]. Selman Abraham Waksman discovered over 20 antibiotics along with the well-known streptomycin. During the era of discovery of microbes (1625e1850) many agents of various infec- tious diseases were identified. The treatment of infected people was not, however, known well, except for some precautionary measures. Antibiotics were introduced after World War II, which resulted in a decline in cases of pneumonia, tuberculosis, menin- gitis, syphilis, and other diseases. With the development of the electron microscope in the1940s,theknowledgeandunderstanding ofviruseswerepossible.Thedevelopment *CorrespondingAuthor. CurrentDevelopmentsinBiotechnologyandBioengineering:FoundationsofBiotechnologyandBioengineering http://dx.doi.org/10.1016/B978-0-444-63668-3.00001-9 1 Copyright©2017ElsevierB.V.Allrightsreserved. 2 CURRENT DEVELOPMENTS IN BIOTECHNOLOGY AND BIOENGINEERING FIGURE 1.1 The steps of Koch’s postulates used to relate a specific microorganism to a specific disease. (A)Microorganismsareobservedinasickanimaland(B)cultivatedinthelab.(C)Theorganismsareinjectedinto ahealthyanimal,and(D)theanimaldevelopsthedisease.(E)Theorganismsareobservedinthesickanimaland (F)reisolatedinthelab.Adaptedfromhttp://www.cliffsnotes.com/sciences/biology/microbiology/. ofvaccinesduringthedecade1950e60ledtothecontrolofviraldiseases suchaspolio, measles, mumps, and rubella. Modernmicrobiologyhasexpandedintomanyfieldsofhumanendeavorsuchasthe developmentofpharmaceuticalproducts,theuseofqualitycontrolmethodsinfoodand dairy products, the control of pathogens in drinking water, and the industrial applica- tions of microorganisms. Microbes have been employed in the production of vitamins, amino acids, enzymes, growth supplements, and several others. They are also useful in the manufacture of fermented foods such as dairy products (sour cream, yogurt, buttermilk)aswellasotherfoods/beverages(pickles,sauerkraut,bread,wines,beer,and other alcoholic beverages).
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