Table Of ContentCurrent 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
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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).
