Table Of ContentBiotechnology in Healthcare, Volume 1
Technologies and Innovations
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Biotechnology in
Healthcare, Volume 1
Technologies and Innovations
Edited by
Debmalya Barh Ph.D
Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied
Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
Department of Genetics, Laboratory of Cellular & Molecular Genetics, Ecology & Evolution,
Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte,
CEP, 31270-901, Brazil
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Dedication
I dedicate this book to my little princess Vaibhavi.
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Contents
Listofcontributors xiii 2.3 Materialsofthree-dimensionalprinting 30
Abouttheeditor xvii 2.4 Three-dimensionalprintinginsurgical
Preface xix planningandmedicaleducation 31
2.5 Three-dimensionalprintinginoraland
1. Overview of healthcare maxillofacialsurgery 32
biotechnology 1 2.6 Three-dimensionalprintingin
orthopedics 33
AimanTanveer,KanchanYadav,ShrutiDwivedi,
2.7 Three-dimensionalprintingin
SupriyaGupta,PramodK.YadavandDineshYadav
neurosurgery 33
1.1 Introduction 1 2.8 Bioprintingtissueandorganfabrication 35
1.2 Genomics 1 2.9 Three-dimensionalprintingin
1.2.1 Geneticscreeningandtesting 3 pharmaceuticalindustry 36
1.2.2 Diagnosisofgeneticdisorders 3 2.10 Futureofthree-dimensionalprinting 36
1.2.3 Pharmacogenomicsand
2.10.1 Limitationsofthree-dimensional
epigenomics 6
printings 37
1.2.4 Personalizedmedicine 6
2.11 Conclusion 37
1.3 Transcriptomics 7
References 37
1.3.1 Toolsoftranscriptomics 7
1.3.2 Transcriptomicsindiseasediagnosis 9
1.3.3 Transcriptomeprofilingindrug
3. Synthetic biology in healthcare:
discovery 10
technologies and applications 41
1.4 Proteomics 10
1.4.1 Toolsandtechniquesinthe MubashirHassan,AnamNaz,AmmaraSiddique,
proteomics-basedstudy 10 SabaShahzadi,SalahudDin,ZainabYaseen,
1.4.2 Biomarkerdiscovery 13 SawairaNaqvi,QinzaAli,FaryalMehwishAwan
1.4.3 Drugdevelopment 13 andAqsaIkram
1.5 Metabolomics 14
3.1 Introduction 41
1.5.1 Toolsandtechniquesin
3.1.1 Cell-freesystemsandapplications 41
metabolomicsstudy 16
3.2 TechnologiesforsyntheticDNA,proteins,
1.5.2 Metabolomicsintreatmentofcancer,
andorganisms 41
neurological,andpsychiatric
disorders 18 3.2.1 Syntheticbiology-basedDoggybone
1.5.3 Individualizedmetabolomics 20 DNAtechnologyanditsusesin
1.6 Conclusion 20 vaccinesandDNA-based
Acknowledgments 20 genetherapyproducts 41
References 20 3.2.2 DevelopmentoflineardbDNA
vaccineconstruct 42
2. Three-dimensional printing in 3.3 Gen9technology—microfluidicdevicesand
healthcare 27 methodsforgenesynthesis 42
3.3.1 DNAsynthesisandscaleup
YusufIzci
(BioFabplatform) 42
2.1 Introduction 27 3.3.2 Technologiesforsyntheticgenomes 43
2.2 Three-dimensionalprintingtechnology 3.3.3 Syntheticbiologytocreatean
(hardwareandsoftware) 27 artificialmembrane-bindingprotein 43
vii
viii Contents
3.3.4 Pathwayrewiringwithadaptersand 4. Nanotechnology in healthcare:
scaffolds 44 nanoparticles for diagnostic and
3.3.5 SyntheticDNAfordevelopingnew therapy 55
antibiotics 44
3.3.6 SyntheticDNAforamino-acid TugbaTezcanandChia-HsienHsu
replacement 44
4.1 Introduction 55
3.3.7 Syntheticproteinstechnologies 45
4.2 Classificationandpropertiesof
3.3.8 Technologiestocreatesynthetic
nanoparticles 56
organisms 45
4.2.1 Goldnanoparticles 56
3.3.9 Syntheticbiologyapplicationsin
4.2.2 Magneticnanoparticles 57
diagnostics 46
4.2.3 Quantumdots 57
3.4 Transcriptional,posttranslational,and
4.2.4 Carbonnanostructures 58
hybridbiosensingandapplications 46
4.2.5 Polymericnanoparticles 58
3.4.1 Transcriptionalbiosensing 46
4.3 Nanoparticle-basedbiosensorsfor
3.4.2 Posttranslationalbiosensing 46
medicaldiagnosis 59
3.4.3 Hybridbiosensing 46
4.3.1 Plasmonicbiosensors 59
3.5 Applications 46
4.3.2 QD-basedbiosensors 60
3.5.1 Paper-baseddiagnostic 47
4.3.3 Carbonnanostructure-based
3.5.2 Syntheticbiologyapplicationsfor
biosensors 61
drugdiscoveryandtherapy 47
4.4 Nanoparticle-basedtherapyandimaging 61
3.5.3 Drug-targetidentification
4.4.1 Targeteddrugdelivery 62
(syntheticpathwaysandsystems) 48
4.4.2 Bioimagingandphotothermal
3.5.4 Drugdiscovery 48
therapy 63
3.5.5 Therapeutictreatment
4.4.3 Nanoparticlesintheclinic 64
(syntheticbiologydevices) 48
4.5 Conclusionandfutureperspective 65
3.5.6 Therapeuticdelivery 48
References 65
3.6 Syntheticbiologyforcreatinglivingsystems
toproducesmallmolecules,forinstance,
5. Analysis and applications of
aspirin,thatcharacteristicallycomefrom
chemicalratherthanthebiological sequencing in healthcare 71
processes 49
MaloyjoJoyrajBhattacharjeeand
3.6.1 CodeEvolver-likeprotein-engineering
BasantK.Tiwary
synthetic-biologyplatformtocreate
uniqueenzymesastherapeutics 49 5.1 Introduction 71
3.6.2 Chimericantigenreceptor 49 5.2 Methodofde-novoandreference-based
3.6.3 Syntheticgenomesandvaccinedesign DNAsequencing 71
(SARS-CoV-2andotherviruses) 49 5.3 GenerationofDNAreads 72
3.7 Livingtherapies—engineeringmicrobesand 5.4 Qualityassessmentofreads 73
bacteriophagetotreatdisease 50 5.5 TrimmingofDNAreads 74
3.7.1 Engineeredbacteria(suchas 5.6 MappingofDNAreads 74
Salmonella)todelivervaccines 50 5.7 Assembly 75
3.7.2 Understandingdiseasemechanism 50 5.8 AnalysisofDNAsequencesfor
3.7.3 Syntheticbiology-basedpathway marker-basedsurveillanceofdiseases 75
engineeringforpharmaceutical 5.9 Phylomedicineofgeneticdiseases 76
production 50 5.10 Methodofde-novoandreference-based
3.7.4 Constructingbiosyntheticpathways 50 RNAsequencing 76
3.7.5 Optimizingpathwayflux 51 5.11 GenerationofshortRNAreadsand
3.7.6 Programmingnovelfunctionalityand qualityassessment 77
materials 51 5.12 TrimmingofRNAreads 77
3.7.7 Chemicalretrosynthesisanditsfuture 5.13 MappingofRNAreads 77
applicationsinhealthcare 51 5.14 AssemblyofRNAreads 77
3.8 Futurechallengesandconclusions 51 5.15 Analysisofdifferentialexpressionof
Acknowledgment 52 genesindiseasesstatesandinprognosis
References 52 ofdisease 78
Contents ix
5.16 Analysisofalternativesplicingofgenes 6.4.3 Featureselectionwithdecisiontrees 92
andgenefusionindiseasestates 78 6.4.4 Featureselectionbyanalysis 94
5.17 AnalysisoflongnoncodingRNAandits 6.4.5 AnalysiswithedgeRorDESeq2 94
relevancetodisease 78 6.4.6 Pickupmachinelearningmodels 96
5.18 Genecoexpressionanalysisand 6.4.7 Evaluatemachinelearningmodel 96
annotationofTF-TFBSandgene 6.4.8 Workflowforprocessingreadingsin
regulatorynetwork 79 RNA-seq 98
5.19 MethodofDAP-sequencingand 6.5 BIGDATA 100
genome-wideannotationofcistrome 79 Acknowledgments 101
5.20 AnalysisofDAPsequencesandits References 101
applicationinhealthcare 81
5.21 Genome-widemappingofTF-TFBSand
visualizationofgene-regulatorynetwork 81 7. Omics applications in reproductive
References 81 medicine 103
Rabajdova´ Miroslava,Sˇolty´sKatarı´na,
Sˇpakova´ IvanaandUrdzı´kPeter
6. Innovative technologies in precision
healthcare 83 7.1 Genetictestingandmolecularmethodsof
femaleinfertility 103
Sˇolty´sKatarı´na,KlˇocMarek,Rabajdova´ Miroslava
7.1.1 Molecularmethodsoftranscriptome
andMarekova´ Ma´ria
analysisinfemaleinfertility 103
6.1 Definingprecisionandpersonalized 7.1.2 Methodsofmetabolomicsanalysis
medicine 83 offemaleinfertility 104
6.1.1 Assessingemergingtechnologiesfor 7.1.3 Methodsofproteomicsanalysisof
personalizedprecisionmedicines’ femaleinfertility 106
clinicaltrials 83 7.1.4 Molecularmethodsofmicrobial
6.1.2 Biosensorsinpersonalizedmedicine 84 analysisoffemaleinfertility 107
6.1.3 Omicsinprecisionhealthcare 84 7.1.5 Molecularmethodsofgenomic
6.1.4 Engineeringprecisionmedicine analysisoffemaleinfertility 108
technologyandplatforms 84 7.2 Genetictestingandmolecularmethods
6.2 Databasesapplicationsinprecision ofmaleinfertility 109
healthcare 85 7.2.1 Molecularmethodsoftranscriptome
6.2.1 Microbiomedatabases 85 analysisofmaleinfertility 110
6.2.2 Databasesforprotein-codinggenes 86 7.2.2 Methodsofmetabolomicsanalysisof
6.2.3 Databasesfornoncodinggenes 86 maleinfertility 111
6.2.4 Databasesusedforannotationof 7.2.3 Molecularmethodsofproteomic
humangeneticvariantsand analysisofmaleinfertility 111
rearrangements 86 7.2.4 Molecularmethodsofmicrobial
6.2.5 Predictionofgenefunction 87 analysisofmaleinfertility 112
6.3 Bioengineering,machinelearningfor 7.2.5 Molecularmethodsofgenomic
personalizedmedicine 87 analysisofmaleinfertility 113
6.3.1 Principleofmachinelearning 87 7.3 Genetictestingandmolecularmethods
6.3.2 Whymachinelearning? 88 ofembryonicanalysisandmonitoring
6.3.3 Supervisedmachinelearning 89 duringtheinvitrofertilizationprocess 115
6.3.4 Unsupervisedmachinelearning 89 7.3.1 Invasivepreimplantationgenetic
6.3.5 Reinforcementlearning 89 testingoftheembryointheinvitro
6.3.6 Onlinelearning 90 fertilizationprocess 115
6.3.7 Recommendationsinmachine 7.3.2 Noninvasivegenetictestingofembryo
learning 90 qualityfortheinvitrofertilization
6.3.8 Testingandverification 90 processfromthespentblastocyst
6.4 Applicationofbioinformaticsmachine medium 115
learningandin-depthdataanalysis 90 7.3.3 Transcriptomicanalysesinspent
6.4.1 Getthedata 91 culturemedium 116
6.4.2 Exploreandpreparedata 91 7.4 Omicsmethodsofinfertility 118
