Oral Biology: Molecular Techniques and Applications

522 Pages·2022·18.724 MB·English

by  Gregory J. Seymour, Mary P. Cullinan, Nicholas C.K. Heng, Paul R. Cooper

Methods in
Molecular Biology 2588
Gregory J. Seymour
Mary P. Cullinan
Nicholas C.K. Heng
Paul R. Cooper Editors
Oral Biology
Molecular Techniques
and Applications
Third Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
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School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Oral Biology
Molecular Techniques and Applications
Third Edition
Edited by
Gregory J. Seymour and Mary P. Cullinan
School of Dentistry, The University of Queensland, Herston, QLD, Australia
Nicholas C. K. Heng and Paul R. Cooper
Faculty of Dentistry, University of Otago, Dunedin, New Zealand
Editors
GregoryJ.Seymour MaryP.Cullinan
SchoolofDentistry SchoolofDentistry
TheUniversityofQueensland TheUniversityofQueensland
Herston,QLD,Australia Herston,QLD,Australia
NicholasC.K.Heng PaulR.Cooper
FacultyofDentistry FacultyofDentistry
UniversityofOtago UniversityofOtago
Dunedin,NewZealand Dunedin,NewZealand
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2779-2 ISBN978-1-0716-2780-8 (eBook)
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Preface
Thebiologicalandphysicalsciencesremaintheresearchbasethatunderpinsadvancesinthe
prevention and treatment of oral diseases, and it is in this context that this third edition
continues the theme of the very successful previous editions of Oral Biology: Molecular
TechniquesandApplications.Asinpreviouseditions,itisrecognizedthatitisnotpossibleto
include all possible techniques in a single volume. Nevertheless, many of the techniques
covered in the previous editions remain valid and have been extensively updated and
included in this edition together with 14 new chapters. In recent years, there have been
majoradvancesinthefieldofregenerativebiologysuchthattwoofthenewchapterscover
3D printing and cell seeding of 3D scaffolds. Chapters on gene editing and the use of
CRISPRinoralbiology,andhistoneacetylationanddeacetylationtechniquesarealsointhis
edition, further reflecting advances in the application of molecular techniques to oral
biology. In presenting a selection of up-to-date molecular methods applicable to the study
of oral health and disease, it is hoped that this third edition of Oral Biology: Molecular
TechniquesandApplicationswillcontinuetobeabasicresourcenotonlyfornewresearchers
butalsoforexperiencedscientistswishingtoexpandtheirresearchplatformintonewareas
oforalbiology.
Herston,QLD,Australia GregoryJ.Seymour
MaryP.Cullinan
Dunedin,NewZealand NicholasC.K.Heng
PaulR.Cooper
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I SALIVA AND OTHER ORAL FLUIDS
1 RNASequencingAnalysisofSalivaexRNA.......... ........ ....... ........ 3
KarolinaElz˙bietaKaczor-UrbanowiczandDavidT.W.Wong
2 ProteomeAnalysisofOralBiofluidsinPeriodontalHealthandDisease
UsingMassSpectrometry........... ....... ....... ........ ....... ........ 13
NagihanBostanciandKaiBao
3 SalivaDiagnosisUsingSmallExtracellularVesiclesandSalivaomics ........... 25
PingpingHan,XiangLi,WeiWei,andSaˇsoIvanovski
4 AntioxidantMicronutrientsandOxidativeStressBiomarkers......... ........ 41
IrundikaH.K.Dias,HelenR.Griffiths,MikeR.Milward,
MartinR.Ling,IainL.C.Chapple,andMelissaM.Grant
PART II MOLECULAR BIOSCIENCES
5 TheOralMicrobiotainHealthandDisease:AnOverview
ofMolecularFindings ...... ........ ....... ....... ........ ....... ........ 61
Jose´F.SiqueiraJr.andIsabelaN.Roˆc¸as
6 TheLongandShortofGenomeSequencing:UsingaHybridSequencing
StrategytoSequenceOralMicrobialGenomes ...... ........ ....... ........ 75
NicholasC.K.HengandJo-AnnL.Stanton
7 MicrobialCommunityProfilingUsingTerminalRestrictionFragment
LengthPolymorphism(T-RFLP)andDenaturingGradient
GelElectrophoresis(DGGE)........ ....... ....... ........ ....... ....... . 91
Jose´F.SiqueiraJr,MitsuoSakamoto,andAlexandreS.Rosado
8 BioinformaticApproachesforDescribingtheOralMicrobiota........ ........ 105
KristiBiswas,MichaelW.Taylor,andDavidT.J.Broderick
9 AdhesionofYeastandBacteriatoOralSurfaces ..... ........ ....... ........ 131
RichardD.Cannon,KarlM.Lyons,KennethChong,
KathrynNewsham-West,KyokoNiimi,andAnnR.Holmes
10 QuantitativeAnalysisofPeriodontalPathogensUsingReal-Time
PolymeraseChainReaction(PCR).......... ....... ........ ....... ........ 157
Mª.Jose´Marin,ElenaFiguero,DavidHerrera,andMarianoSanz
11 MethodstoStudyAntagonisticActivitiesAmongOralBacteria....... ........ 171
FengxiaQiandJensKreth
12 GenerationofMultispeciesOralBacteriaBiofilmModels.. .. ........ ........ 187
JasonL.Brown,MarkC.Butcher,ChandraLekhaRamalingamVeena,
SafaChogule,WilliamJohnston,andGordonRamage
vii
viii Contents
13 MarkerlessGenomeEditinginCompetentStreptococci...... ....... ........ 201
RogerJunges,RabiaKhan,YaninaTovpeko,HeidiA.Åmdal,
FernandaC.Petersen,andDonaldA.Morrison
14 AProtocoltoProduceGeneticallyEditedPrimaryOralKeratinocytes
UsingtheCRISPR-Cas9System..... ....... ....... ........ ....... ........ 217
SvenE.NiklanderandKeithD.Hunter
15 Size-BasedMethodforEnrichmentofCirculatingTumorCells
fromBloodofColorectalCancerPatients.... ....... ........ ....... ........ 231
SaiShyamVasantharajan,EdwardBarnett,ElinS.Gray,
EuanJ.Rodger,MichaelR.Eccles,SharonPattison,
FranMunro,andAniruddhaChatterjee
16 StrategyforRNA-SeqExperimentalDesignandDataAnalysis ....... ........ 249
GregoryGimenez,PeterA.Stockwell,EuanJ.Rodger,
andAniruddhaChatterjee
17 CharacterizationoftheExpressionandRoleofHistoneAcetylation
andDeacetylationinDentalPulpCells...... ....... ........ ....... ........ 279
YukakoYamauchiandHenryF.Duncan
18 Genome-WideAnalysisofPeriodontalandPeri-implant
CellsandTissues.... ....... ........ ....... ....... ........ ....... ........ 295
MoritzKebschull,AnnikaThereseKroeger,
andPanosN.Papapanou
19 DifferentialExpression,FunctionalandMachineLearningAnalysis
ofHigh-Throughput–OmicsDataUsingOpen-SourceTools........ ........ 317
MoritzKebschull,AnnikaThereseKroeger,
andPanosN.Papapanou
20 Micro-RNAProfilinginDentalPulpCellCultures..... ...... ..... .. ........ 353
MichaelaKearneyandHenryF.Duncan
PART III CELLS AND TISSUES
21 OralEpithelialCellCultureModelforStudyingthePathogenesis
ofChronicInflammatoryDisease.... ....... ....... ........ ....... ........ 371
MikeR.Milward,MartinR.Ling,MelissaM.Grant,
JoannaBatt,andIainL.C.Chapple
22 ACellCultureMethodfor theIsolationandStudyofPrimaryHuman
DentalPulpCells.......... ........ ....... ....... ........ ....... ........ 393
ShellyArora,BenedictSeo,LaraFriedlander,
andHaizalMohdHussaini
23 CulturingAdipose-DerivedStemCellsUnderSerum-FreeConditions ........ 407
DiogoGodoyZanicotti,TrudyJ.Milne,andDawnE.Coates
24 QuantitativeReal-TimeGeneProfilingofHumanAlveolarOsteoblasts
UsingaOne-StepSystem........... ....... ....... ........ ....... ........ 417
DawnE.Coates,SobiaZafar,andTrudyJ.Milne
Contents ix
25 FabricationandCharacterizationofDecellularizedPeriodontalLigament
CellSheetConstructs ...... ........ ....... ....... ........ ....... ........ 429
Amro Farag,CedryckVaquette,DietmarW.Hutmacher,
P.MarkBartold,andSaˇsoIvanovski
26 ImmunohistochemistryandImmunofluorescence.... ........ ....... ........ 439
HaizalMohdHussaini,BenedictSeo,andAlisonM.Rich
27 Characterization,Quantification,andVisualizationofNeutrophil
ExtracellularTraps ......... ........ ....... ....... ........ .. ..... ...... .. 451
JosefineHirschfeld,IlariaJ.Chicca,CarolynG.J.Moonen,
PhillipaC.White,MartinR.Ling,HelenJ.Wright,
PaulR.Cooper,MikeR.Milward,andIainL.C.Chapple
28 CellSeedingon3DScaffoldsforTissueEngineeringandDisease
ModelingApplications ..... ........ ....... ....... ........ ....... ........ 473
FannyBlaudez,CedryckVaquette,andSaˇsoIvanovski
29 WorkflowforFabricating3D-PrintedResorbablePersonalizedPorous
ScaffoldsforOrofacialBoneRegeneration.......... ........ ....... ........ 485
CedryckVaquette,DaniloCarluccio,MartinBatstone,
andSaˇsoIvanovski
30 MethacrylatedGelatinasanOn-DemandInjectableVehicle
forDrugDeliveryinDentistry ...... ....... ....... ..... ... ....... ........ 493
W.BentonSwanson,AbdelHameedMahmoud,SethWoodbury,
andMarcoC.Bottino
31 InVitroBiologicalTestingofDentalMaterials...... ........ ....... ........ 505
JithendraRatnayake,JosetteCamilleri,
T.NethminiHaththotuwa,andJeffreyHuang
Index ...................................................................... 525
Contributors
HEIDIA.ÅMDAL • DepartmentofOralBiology,FacultyofDentistry,UniversityofOslo,Oslo,
Norway
SHELLYARORA • SirJohnWalshResearchInstitute,FacultyofDentistry,UniversityofOtago,
Dunedin,NewZealand
KAIBAO • SectionofOralHealthandPeriodontology,DivisionofOralDiseases,Department
ofDentalMedicine,KarolinskaInstitutet,Stockholm,Sweden
EDWARDBARNETT • DepartmentofPathology,DunedinSchoolofMedicine,Universityof
Otago,Dunedin,NewZealand
P.MARKBARTOLD • ColgateAustralianClinicalDentalResearchCentre,DentalSchool,
UniversityofAdelaide,Adelaide,Australia
MARTINBATSTONE • HerstonBiofabricationInstitute,MetroNorthHospitalandHealth
Service,Brisbane,QLD,Australia
JOANNABATT • TheSchoolofDentistry,UniversityofBirmingham,Birmingham,UK
KRISTIBISWAS • DepartmentofSurgery,FacultyofMedicalandHealthSciences,University
ofAuckland,Auckland,NewZealand
FANNYBLAUDEZ • SchoolofDentistry,TheUniversityofQueensland,Brisbane,Australia
NAGIHANBOSTANCI • SectionofOralHealthandPeriodontology,DivisionofOralDiseases,
DepartmentofDentalMedicine,KarolinskaInstitutet,Stockholm,Sweden
MARCOC.BOTTINO • DepartmentofCariology,RestorativeSciences,andEndodontics,
UniversityofMichiganSchoolofDentistry,AnnArbor,MI,USA;Departmentof
BiomedicalEngineering,CollegeofEngineering,UniversityofMichigan,AnnArbor,MI,
USA
DAVIDT.J.BRODERICK • DepartmentofSurgery,FacultyofMedicalandHealthSciences,
UniversityofAuckland,Auckland,NewZealand;SchoolofBiologicalSciences,University
ofAuckland,Auckland,NewZealand
JASON L.BROWN • OralSciencesResearchGroup,CollegeofMedical,VeterinaryandLife
Sciences,GlasgowUniversity,Glasgow,UK;GlasgowBiofilmResearchNetwork,Glasgow,
UK
MARKC.BUTCHER • OralSciencesResearchGroup,CollegeofMedical,VeterinaryandLife
Sciences,GlasgowUniversity,Glasgow,UK;GlasgowBiofilmResearchNetwork,Glasgow,
UK
JOSETTECAMILLERI • SchoolofDentistry,InstituteofClinicalSciences,CollegeofDentaland
MedicalSciences,UniversityofBirmingham,Birmingham,UK
RICHARDD.CANNON • SirJohnWalshResearchInstitute,FacultyofDentistry,Universityof
Otago,Dunedin,NewZealand
DANILOCARLUCCIO • HerstonBiofabricationInstitute,MetroNorthHospitalandHealth
Service,Brisbane,QLD,Australia
IAINL.C.CHAPPLE • TheSchoolofDentistry,UniversityofBirmingham,Birmingham,UK;
DepartmentofPeriodontology,BirminghamDentalSchoolandHospital,Universityof
Birmingham,Birmingham,UK
ANIRUDDHACHATTERJEE • DepartmentofPathology,DunedinSchoolofMedicine,University
ofOtago,Dunedin,NewZealand;SchoolofHealthSciences,UPESUniversity,Dehradun,
India
xi