Basic Biotechniques for Bioprocess and Bioentrepreneurship

520 Pages·2023·27.972 MB·English

by  Arvind Kumar Bhatt, Ravi Kant Bhatia, Tek Chand Balla

Basic Biotechniques for Bioprocess
and Bioentrepreneurship
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Basic Biotechniques
for Bioprocess
and Bioentrepreneurship
Edited By
Arvind Kumar Bhatt
Department of Biotechnology, Himachal Pradesh University, India
Ravi Kant Bhatia
Department of Biotechnology, Himachal Pradesh University, India
Tek Chand Bhalla
Department of Biotechnology, Himachal Pradesh University, India
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Contents
Contributors xv 7.5 Cultivationofanaerobic
Foreword xix microorganisms 16
Preface xxi 7.6 Intracellularbacterialculture 17
8. Conclusion 17
References 17
Part I
Isolation, screening and culture
2. Screening strategies
maintenance
ChayanikaPutatunda,PreetiSolanki,
1. Isolation of microorganisms 1 ShrutiPathania,AnilKumar,and
AbhishekWalia
MahinderKumarGupta
1. Introduction 23
1. Introduction 3 2. Conventionalstrainscreening
2. Clinicallyimportantmicroorganisms 3 techniques 24
2.1 Siteforisolation 3 2.1 Culture-dependentmethods 24
2.2 Sampling 4 2.2 Conventionalscreeningof
3. Agriculturallyimportantmicroorganisms 4 antimicrobials 24
3.1 Preliminaryassessment 9 3. Alternativecultivationmethods 25
3.2 Identificationofsitesandsample 4. Molecularmethodofmicrobialstrain
collection 9 screeningstrategies 26
3.3 Storageandpretreatmentofsoil 4.1 Randomlyamplifiedpolymorphic
samples 9 DNA 27
4. Dairyrelatedmicroorganisms 10 4.2 Restrictionfragmentlength
4.1 Samplecollection 10 polymorphism 29
4.2 Preservationofsamples 10 4.3 Pulsefieldgelelectrophoresis 29
5. Extremophiles 11 4.4 Amplifiedfragmentlength
5.1 Thermophiles 11 polymorphism 29
5.2 Psychrophiles 11 4.5 RioPrinter 30
5.3 Alkaliphiles/acidophiles 11 4.6 Multilocussequencetyping 30
5.4 Piezophiles 12 4.7 MALDI-TOF 31
5.5 Radiophiles 12 5. High-throughputscreeningtechniques 31
5.6 Xerophiles 12 5.1 AdvantagesofHTStechnology 32
5.7 Metallophiles 13 5.2 Analyticalmeasurement 32
5.8 Halophiles 13 6. “Omics”-basedscreeningtechniques 33
5.9 Microaerophiles 13 7. Virtualscreeningstrategies 36
6. Transportofsamples 13 8. Somepotentialapplicationofnovel
7. Industriallyimportantmicroorganisms 14 screeningstrategies 40
7.1 Sourcesofmicroorganisms 14 8.1 Inmedicineanddrugdiscovery 40
7.2 Enrichmentandisolation 14 8.2 Environmentalapplications 40
7.3 Cultivationofmicroorganisms 14 9. Conclusionsandfutureperspectives 41
7.4 Cultivationofextremophiles 16 References 41
v
vi Contents
3. Identification, morphological, 4. Microbial activity and productivity
biochemical, and genetic enhancement strategies
characterization of
ShashiKantBhatia,VijayKumar,
microorganisms
VirenderKumar,RaviKantBhatia,
andYung-HunYang
NiveditaSharma,NishaSharma,
ShakshiSharma,PushpinderSharma,and 1. Introduction 85
BinduDevi
2. Isolationofmicrobes 85
1. Introduction 47 3. Statisticaldesignforcultureandreaction
2. Isolationofmicroorganisms 47 conditionoptimization 86
2.1 Methodsofisolation 47 4. Inductionstrategy 87
3. Identificationofmicrobes 52 5. Immobilization 88
3.1 Principlesoftaxonomy 52 5.1 Adsorption 90
3.2 Strategiesusedtoidentify 5.2 Covalentbinding 91
microbes 53 5.3 Entrapment 91
3.3 Morphologyofbacteria 59 5.4 Cross-linking 91
3.4 Morphologyoffungi 61 5.5 Othermethodsofimmobilization 92
4. Biochemicalcharacterizationof 6. Mutagenesisforenhancementof
microbes 63 enzymeactivityandproductivity 92
4.1 Indoletest 63 6.1 Physicalandchemicalmutagenesis 93
4.2 Methylredtest 63 6.2 Directedevolution 95
4.3 VogesProskauertest 63 6.3 Sitedirectedmutagenesis 95
4.4 Citratetest 65 7. Metabolicengineering 95
4.5 Triplesugar-iron(TSI)agar 7.1 Improvementofmicrobesfor
test 65 utilizationofcarbonsource 96
4.6 Carbohydratefermentationtest 67 7.2 Constructionofnewmetabolic
4.7 Oxidativefermentative(O-F) pathway 96
test 68 7.3 Increasedcofactorproductionand
4.8 Aminoaciddecarboxylasetest 69 regeneration 96
4.9 Litmusmilktest 69 7.4 Improvementofrobustnessto
4.10 Hydrogensulfidetest 70 stress 98
4.11 O-nitrophenyl-β-D-galactopyranoside 8. Co-culturestrategy 98
(ONPG)test 70 9. Conclusion 99
4.12 Phenylalaninedeaminasetest 72 Acknowledgment 99
4.13 Catalasetest 72 References 99
4.14 Oxidasetest 73
4.15 Gelatinhydrolysistest 73 5. Culture maintenance,
4.16 Starchhydrolysistest 74 preservation, and strain
4.17 Lipidhydrolysistest 74 improvement
4.18 DNAhydrolysistestor
AmanKumar,SrijanaMukhia,AnilKumar,
deoxyribonuclease(DNase)test 74
KiranDindhoria,NehaBaliyan,and
4.19 Coagulasetest 75 RakshakKumar
5. Geneticcharacterizationof
microorganisms 75 1. Introduction 105
5.1 Microorganismswhosestudyis 2. Culturemediafordifferent aspects 106
2.1 Classificationbyphysicalnature 106
encompassedbymicrobial
2.2 Classificationbychemical
genetics 75
composition 106
5.2 DeterminationofDNA
2.3 Classificationbypurpose/
sequences 76
functionaluse 107
5.3 Microbialfingerprinting
3. Sterilizationtechniques 108
methods 79
6. Conclusion 82 3.1 Heatsterilization 108
References 82 3.2 Gassterilization 110
Contents vii
3.3 Sterilizationbyradiation 110 3.2 Materialusedinrotorconstruction 138
3.4 Filtersterilization 110 3.3 Varioustypesofcentrifugation
4. Maintenanceandpreservationofpure technique 138
cultures 111 3.4 Typesofcentrifuges 138
4.1 Metabolicallyactivemethods 112 3.5 Separationmethodsindifferenttypes
4.2 Metabolicallyinactivemethods 112 ofcentrifugation 139
4.3 Microbialculturecollections 114 3.6 Applicationsofcentrifugation
5. Strainimprovement 114 techniques 142
5.1 Characteristicsofanimprovedstrain 116 3.7 Careofcentrifugationequipment 142
5.2 Methodsformicrobialstrain 3.8 Safetyaspectswhileoperatinga
improvement 117 centrifuge 142
6. Conclusion 120 References 142
Acknowledgment 120
References 120
8. Spectroscopy—Principle, types,
and applications
Part II
SwetaSinha,ChristineJeyaseelan,
Laboratory techniques & GunjanSingh,TanyaMunjal,and
DebaratiPaul
instrumentation
1. Introduction 145
6. Biomolecules: Types, 2. Generaltypesofspectra 145
homogenization, bead beater, 2.1 Continuousspectra 145
2.2 Discretespectra 145
sonication
3. Principleofspectroscopy 146
ArshadJawed 3.1 Opticalinstrumentsinspectroscopy 147
3.2 Howspectroscopydifferentfrom
1. Introduction 125
spectrometry 147
2. Classificationofcelldisruption
4. Typesofspectroscopy 147
processes 126
4.1 Ultravioletandvisiblespectroscopy 147
2.1 Physicaldisruptionmethods 127
4.2 Infraredspectroscopy 150
2.2 Chemicaldisruption 127
4.3 Massspectrometry 155
2.3 Large-scalecelldisruption:
4.4 Nuclearmagneticresonance(NMR)
Thebeadmill 128
spectroscopy 158
3. Conclusion 130
5. Conclusion 162
References 130
References 162
7. Centrifugation: Basic principle, 9. Protein purification: Basic
types principles and techniques
GauravSood,MinakshiSharma, AllaSingh,KrishanKumar,
andRajeshKaushal DharamPaulChaudhary,NeerajKumar,
andDeepakPandey
1. Introduction 133
2. Basicprinciplesofcentrifugation, 1. Introduction 165
centrifugalforce,andsedimentation 2. Needofproteinpurificationand
coefficient 133 determinationofproteinidentity 165
2.1 Calculationofcentrifugalforce 134 3. Basicprinciplesofproteinpurification 166
2.2 Calculationofangularvelocity 134 4. Otherconsiderations 168
2.3 Calculationofrelativecentrifugal 5. Alternativesystems 168
field(RCF) 135 6. Importanceofrecombinantprotein
2.4 Sedimentationcoefficient 135 market 169
3. Instrumentationofacentrifuge 136 7. Conclusion 169
3.1 Typesofrotors 137 References 170
viii Contents
10. Chromatography: Basic principle, 3. IsolationofRNA 198
types, and applications 3.1 Guanidiumthiocyanate-based
isolationofRNA 199
MaheshKumarGupta
3.2 TRIzolreagentisolation 199
andPradipKumarBiswas
4. PCRandprimerdesigning 199
1. Basicprinciple 173 4.1 PrimerdesignforPCR 199
2. Generaltermsusedinchromatography 174 4.2 Polymerasechainreaction 200
3. Typesofchromatography 174 4.3 Parametersforprimerpairdesign 200
3.1 Liquidchromatography 174 4.4 Primerdesigntips 201
3.2 Affinitychromatography 176 4.5 Probesdesigntips 201
3.3 Ion-exchangechromatography 177 4.6 Productamplicons 202
3.4 Sizeexclusionchromatography 5. SubmissionofsequencetoGenBank 202
(gelfiltrationchromatography) 180 6. Phylogeneticanalysis 203
3.5 Hydrophobicinteraction 6.1 Methodsofphylogeneticanalysis 203
chromatographyandreversephase 6.2 Character-basedmethods 204
chromatography(hydrophobic 6.3 Calculationofthedegreeof
surfacearea) 181 divergence 205
3.6 Multimodalormixed-mode 6.4 Molecularclockhypothesis 205
chromatography(multiple 6.5 Advantagesofphylogeneticanalysis 205
properties) 181 6.6 Modernmethodsinphylogenetic
References 182 analysis 205
7. Conclusion 206
11. Electrophoresis: Basic principle, References 206
types, and applications
13. RDTand genetic engineering:
BabitaRanaandGopalKrishnaJoshi Basic of RDT method, PCR, and
application
1. Introduction 183
2. Typesofelectrophoresis 183
KomaljeetGill,ShivantiNegi,NeerjaRana,
2.1 Gelelectrophoresis 183 andPankajKumar
2.2 Zoneelectrophoresis 189
1. Introduction 207
2.3 Freeflowelectrophoresis 189
2. RecombinantDNAtechnology 208
2.4 Capillaryelectrophoresis 191
3. GeneticengineeringandRDT
3. Conclusion 192
differences 209
References 192
4. Polymerasechainreaction 209
4.1 Denaturation 209
Part III 4.2 Primerannealing 209
4.3 Elongation 210
Genomic and proteomic analysis
4.4 ApplicationsofPCR 210
5. RDT/geneticengineeringlinkageto
12. DNA, RNA isolation, primer bioentrepreneurship 212
designing, sequence submission, 6. Threepillarsofbioentrepreneurship 213
and phylogenetic analysis 7. RecombinantDNAtechnology
market-growthandtrends 214
RupaliSharma,ShashwatSharad,
8. RDTlinkedbioentrepreneurshipin
GillipsieMinhas,DeepRajSharma,
thehealthsector 214
KulsajanBhatia,andNeelKamalSharma
9. RDTlinkedbioentrepreneurshipin
1. Introduction 197 foodandagriculturesector:Helping
2. IsolationofDNA 197 tofeedtheworld 215
2.1 Phenol-chloroformextraction 10. Industrialandenvironmental
ofDNA 197 bioentrepreneurship 215
2.2 Detergent-basedisolationofDNA 198 11. Conclusion 215
2.3 Density-gradientcentrifugation 198 References 216
Contents ix
14. Protein sequence analysis 6.10 Fleksy 250
6.11 ParaDockS 251
DeepakSharmaandAbhishekChaudhary
6.12 FLIPDock 251
1. Introduction 217 6.13 PharmDock 251
2. Proteomics 217 6.14 FRED 251
3. Bioinformaticstoolsforprotein 6.15 RosettaLigand 251
sequenceanalysis 218 6.16 FlexibleCDOCKER 251
3.1 DynamicBayesiannetworks 219 6.17 LigandFit 251
3.2 Supportvectormachines 219 6.18 rDock 252
3.3 Neuralnetwork 219 6.19 LeadFinder 252
4. Sequencealigningprograms 220 6.20 GalaxyDock2 252
4.1 Basiclocalalignmentsearchtool 220 6.21 MS-DOCK 252
4.2 FASTA 220 6.22 BetaDock 252
4.3 Clustal 221 6.23 EADock 252
4.4 Otherprograms 221 6.24 FLOG 253
5. Alignment-freesequenceanalysis 221 6.25 Hammerhead 253
6. Conclusion 221 6.26 SwissDock 253
References 222 6.27 DockingServer 253
6.28 1-ClickDocking 253
15. Computationalstrategiesandtools 6.29 DOCKBlaster 253
for protein tertiary structure 6.30 BLINDDockingServer 254
prediction 6.31 ParDOCK 254
6.32 FlexPepDock 254
RajKumarandAjaySharma 6.33 ClusPro 254
6.34 PatchDock 254
1. Introduction 225
6.35 MEDOCK 254
2. Homologymodeling 225
6.36 BSP-SLIM 254
3. Foldrecognition/threading 227
6.37 BioDrugScreen 255
4. Abinitioproteinstructureprediction 236
6.38 KinDOCK 255
5. Hybridmethodsandcurrenttrendin
6.39 idTarget 255
proteinstructureprediction 237
6.40 Pose&Rank 255
6. Conclusion 238
7. Futureprospects 255
References 238
8. Conclusion 256
References 256
16. Docking strategies
ArushiSharmaand 17. A beginner’s guide to measuring
RagothamanM.Yennamalli
binding affinity during
1. Introduction 243 biomolecular interactions
2. Scoringfunctions 245
HannahI.Martin,VidushiAgnihotri,
3. Protein-liganddockingstrategies 246
RagothamanM.Yennamalli,andAurijitSarkar
4. Protein-proteindockingstrategies 247
5. Protein-nucleicaciddockingstrategies 248 1. Introduction 259
6. Differentsoftwareandtoolsusedfor 2. Anintroductiontomajormethodsof
docking 249 detectingprotein-ligandcomplexes 261
6.1 AutoDock 249 2.1 Fluorescenceassays 261
6.2 AutoDockVina 249 2.2 Differentialscanningfluorimetry(DSF) 263
6.3 DOCK 249 2.3 Isothermaltitrationcalorimetry 264
6.4 GOLD 249 2.4 Surfaceplasmonresonance 265
6.5 GLIDE 250 2.5 Nuclearmagneticresonance
6.6 GlamDock 250 spectroscopy 266
6.7 FlexAID 250 2.6 Frontalaffinitychromatography 268
6.8 iGEMDOCK 250 3. Conclusion 269
6.9 FlexX 250 References 269