Bacteriophages: Methods and Protocols, Volume IV

220 Pages·2019·4.664 MB·English

by  Martha R. J. Clokie, Andrew Kropinski, Rob Lavigne

Methods in
Molecular Biology 1898
Martha R. J. Clokie
Andrew Kropinski
Rob Lavigne Editors
Bacteriophages
Methods and Protocols
Volume IV
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Bacteriophages
Methods and Protocols, Volume IV
Edited by
Martha R. J. Clokie
Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
Andrew Kropinski
Departments of Food Science, and Pathobiology, University of Guelph, Guelph, ON, Canada
Rob Lavigne
Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
Editors
MarthaR.J.Clokie AndrewKropinski
DepartmentofGeneticsandGenomeBiology DepartmentsofFoodScience,andPathobiology
UniversityofLeicester,UniversityRoad UniversityofGuelph
Leicester,UK Guelph,ON,Canada
RobLavigne
LaboratoryofGeneTechnology
KULeuven
Leuven,Belgium
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8939-3 ISBN978-1-4939-8940-9 (eBook)
https://doi.org/10.1007/978-1-4939-8940-9
LibraryofCongressControlNumber:2017932425
©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction
onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
andthereforefreeforgeneraluse.
Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC, part of
SpringerNature.
Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A.
Preface
In2015wecelebratedthecentenaryofthefirstdescriptionofbacteriophagesbyFrederick
Twortand thenin2017byFelixd’He´rellewho independentlydiscoveredthem. Onemay
wonderhowthey,orindeedotherbacteriophagescientificiconsoflatergenerations,suchas
EmeryEllisandMaxDelbru¨ck,GiuseppeBertaniorMarthaChase,wouldviewthecurrent
status of “their” research field. Fortunately, this (American) Phage Group laid the founda-
tion of molecular biology and bacterial genetics by focusing on a defined set of phage and
host strains. By focusing on just a few phages, significant progress was made in our
understanding at a mechanistic level, and work carried out by this group and others in the
1950sandonwardsstillservesasabedrockinour understandingofphagebiology.
High-throughput sequencing of both phages and phage metagenomes is increasingly
revealingthemassivephagediversityinouroceansandsoilsandprovidingunparalleledclues
abouttheecologicalimpactphageshaveataglobalscale.Onemayarguethattheavailability
of advanced technology is defining today’s research, generating vast amounts of data, and
enablingustopaintamuchbroaderpicturethanwaspreviouslypossible.However,perhaps
ourdistinguishedpredecessorswouldwarnusaboutnotlosingcreativityanddepth.Ifthis
werethecase,wearetakingheedofthesewarningsinthisbook,Bacteriophages:Methodsand
Protocols,Volume4,asseveralchaptersfocusonthefunctionalelucidationofphageandtheir
proteins.
A second discernable trend within bacteriophage biology is the drive toward
application-driven research, often involving partnerships with industry. The needs for
novel therapeutics and diagnostics are driving biotechnology companies, to embrace both
phagetherapy,designerphage,andphage-derivedproducts.Partnershipisakeywordhere,
as cautionary words from our predecessors both early and from the later scientists/entre-
preneurs who sought to commercialize phages would likely warn against industrial work
leadingtosecrecyandadvocateperformingresearchinanopenandcommunicativemanner.
It is this drive for application-driven research and the partnerships with industry that are
leading toward new innovations reflected here by the chapters dedicated to various novel
phage therapy models. It has never been a more exciting and possible time to develop
bacteriophagesfor manyapplications.Thegenetictoolsarehereto manipulatephages;we
havesystemsformanybacterialgroups,andoursequencingcapacitytohelpusunravelthe
mechanicsofphagebiologyhasneverbeenaspowerful.
v
vi Preface
As a final note, we would like to thank the contributing authors for their work and
patience for the completion of this volume. And, in the end, we are all indebted to the
scientists who came before us for their example, creativity, and knowledge. We hope this
bookcaninturninspireanextgenerationofphagebiologists.
Leicester,UK MarthaR.J.Clokie
Guelph,ON,Canada AndrewKropinski
Leuven,Belgium RobLavigne
Contents
Preface ..................................................................... v
Contributors................................................................. xi
1 PhageFISHforMonitoringPhageInfectionsatSingleCellLevel............. 1
JimenaBarrero-CanosaandCristinaMoraru
2 FluoromycobacteriophagesforDrugSusceptibilityTesting(DST)
ofMycobacteria......................................................... 27
MarianaPiuriandGrahamF.Hatfull
3 EngineeringBacteriophage-BasedBiosensors............................... 37
DanielBrownell,JohnKing,BrianCaliando,LadaSycheva,
andMichaelKoeris
4 IntroductionofPhageGenomeintoEscherichiacolibyElectroporation ....... 51
NikaJanezˇ,SaˇsaHaberlMeglicˇ,KarelFlisar,DamijanMiklavcˇicˇ,
andMatjazˇ Peterka
5 Site-SpecificMutagenesisofBacillussubtilisPhageSPO1.................... 57
CharlesR.Stewart
6 GeneticManipulationofLyticBacteriophageswithBRED:
BacteriophageRecombineeringofElectroporatedDNA..................... 69
LauraJ.Marinelli,MarianaPiuri,andGrahamF.Hatfull
7 IsolationofCompetitivePhageDisplay-ModifiedBacteriophage
T4withAffinityChromatography......................................... 81
KrystynaDa˛browska
8 ImmobilizationofIntactPhageandPhage-DerivedProteins
forDetectionandBiocontrolPurposes .................................... 89
HanyAnany,LubaY.Brovko,DenisArutyunov,NilufarPoshtiban,
AmitSingh,UpasanaSingh,MichaelBrook,ChristineSzymanski,
StephaneEvoy,andManselW.Griffiths
9 PeptidoglycanHydrolyticActivityofBacteriophageLyticProteins
inZymogramAnalysis................................................... 107
LorenaRodrı´guez-Rubio,DavidM.Donovan,BeatrizMartı´nez,
AnaRodrı´guez,andPilarGarcı´a
10 AnalyzingPhage–HostProtein–ProteinInteractions
®
UsingStrep-tag IIPurifications.......................................... 117
JeroenDeSmet,HanneHendrix,andAnVandenBossche
11 TechniquestoAssessPhage–BiofilmInteraction............................ 137
DianaVilasBoas,CarinaAlmeida,NunoAzevedo,
SannaSillankorva,andJoanaAzeredo
12 ScreeningforGrowth-InhibitoryORFansinPseudomonas
aeruginosa-InfectingBacteriophages ...................................... 147
HanneHendrix,InesStaes,AbramAertsen,andJeroenWagemans
vii
viii Contents
13 UseofGreaterWaxMothLarvae(Galleriamellonella)
asanAlternativeAnimalInfectionModelforAnalysis
ofBacterialPathogenesis................................................. 163
FatimaKamal,DanielleL.Peters,JaclynG.McCutcheon,
GaryB.Dunphy,andJonathanJ.Dennis
14 UseofaSilkworm LarvaModelinPhageTherapyExperiments .............. 173
JumpeiUchiyama,IyoTakemura-Uchiyama,andShigenobuMatsuzaki
15 ExploitationofDrosophilaInfectionModelstoEvaluate
AntibacterialEfficacyofPhages........................................... 183
Hye-JeongJang,Hee-WonBae,andYou-HeeCho
16 Duckweed(Lemnaminor)andAlfalfa(Medicagosativa)
asBacterialInfectionModelSystems...................................... 191
FatimaKamal,AlinaRadziwon,CarlyM.Davis,
andJonathanJ.Dennis
17 UseofaChickenEmbryoLethalityAssaytoAssesstheEfficacy
ofPhageTherapy....................................................... 199
Ange´linaTrotereauandCatherineSchouler
18 QuantitatingPhageEfficacyinReady-To-EatMeats ........................ 207
AndrewChibeuandSampathkumarBalamurugan
Index ...................................................................... 215
Contributors
ABRAM AERTSEN (cid:1) LaboratoryofFoodMicrobiology,KULeuven,Leuven,Belgium
CARINAALMEIDA (cid:1) Laborat(cid:1)oriodeInvestigac¸a˜oemBiofilmesRosa´rioOliveira(LIBRO),
CentreofBiologicalEngineering(CEB),UniversityofMinho,Braga,Portugal;Instituto
NacionaldeInvestigac¸a˜oAgra´riaeVeterina´ria,Vaira˜o,Portugal
HANYANANY (cid:1) AgricultureandAgri-FoodCanada,GuelphResearchandDevelopment
Center,Guelph,ON,Canada;FoodScienceDepartment,CanadianResearchInstitutefor
FoodSafety,UniversityofGuelph,Guelph,ON,Canada
DENISARUTYUNOV (cid:1) DepartmentofBiologicalSciences,AlbertaGlycomicsCentre,University
ofAlberta,Edmonton,AB,Canada
JOANA AZEREDO (cid:1) Laborat(cid:1)oriodeInvestigac¸a˜oemBiofilmesRosa´rioOliveira(LIBRO),
CentreofBiologicalEngineering(CEB),UniversityofMinho,Braga,Portugal
NUNOAZEVEDO (cid:1) Laborat(cid:1)oriodeEngenhariadeProcessos,Ambiente,Biotecnologia
eEnergia,FaculdadedeEngenhariadaUniversidadedoPorto,UniversidadedoPorto,
Porto,Portugal
HEE-WONBAE (cid:1) DepartmentofPharmacy,CollegeofPharmacyandInstituteof
PharmaceuticalSciences,CHAUniversity,Gyeonggi-do,SouthKorea
SAMPATHKUMARBALAMURUGAN (cid:1) GuelphResearchandDevelopmentCentre,Agricultureand
Agri-FoodCanada,Guelph,ON,Canada
JIMENABARRERO-CANOSA (cid:1) DepartmentofEnvironmentalTechnology,Technische
Universita€tBerlin,Berlin,Germany
DIANAVILASBOAS (cid:1) Laborat(cid:1)oriodeInvestigac¸a˜oemBiofilmesRosa´rioOliveira(LIBRO),
CentreofBiologicalEngineering(CEB),UniversityofMinho,Braga,Portugal
MICHAELBROOK (cid:1) DepartmentofChemistryandChemicalBiology,McMasterUniversity,
Hamilton,ON,Canada
LUBAY.BROVKO (cid:1) FoodScienceDepartment,CanadianResearchInstituteforFoodSafety,
UniversityofGuelph,Guelph,ON,Canada
DANIELBROWNELL (cid:1) Sample6Technologies,Woburn,MA,USA
BRIAN CALIANDO (cid:1) Sample6Technologies,Woburn,MA,USA
ANDREWCHIBEU (cid:1) GuelphResearchandDevelopmentCentre,AgricultureandAgri-Food
Canada,Guelph,ON,Canada;ParmalatCanada,London,ON,Canada
YOU-HEECHO (cid:1) DepartmentofPharmacy,CollegeofPharmacyandInstituteof
PharmaceuticalSciences,CHAUniversity,Gyeonggi-do,SouthKorea
KRYSTYNADA˛BROWSKA (cid:1) BacteriophageLaboratory,InstituteofImmunologyand
ExperimentalTherapy,PolishAcademyofSciences,Wrocław,Poland
CARLYM.DAVIS (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,Edmonton,
AB,Canada
JEROENDESMET (cid:1) Lab4Food,KULeuven,Geel,Belgium
JONATHANJ.DENNIS (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,
Edmonton,AB,Canada
DAVIDM.DONOVAN (cid:1) AnimalBiosciencesandBiotechnologyLaboratory,BeltsvilleArea
ResearchCenter,ARS,NEA,USDA,Beltsville,MD,USA
GARYB.DUNPHY (cid:1) NaturalResourceSciences,FacultyofAgriculturalandEnvironmental
Sciences,McGillUniversity,Montreal,QC,Canada
ix
x Contributors
STEPHANEEVOY (cid:1) DepartmentofElectricalandComputerEngineering,Universityof
Alberta,Edmonton,AB,Canada
KARELFLISAR (cid:1) LaboratoryofBiokibernetics,DepartmentofBiomedicalEngineering,Faculty
ofElectricalEngineering,UniversityofLjubljana,Ljubljana,Slovenia
PILARGARCI´A (cid:1) DairySafeGroup,DepartmentofTechnologyandBiotechnologyofDairy
Products,InstitutodeProductosLa´cteosdeAsturias(IPLA-CSIC),Asturias,Spain
MANSELW.GRIFFITHS (cid:1) FoodScienceDepartment,CanadianResearchInstituteforFood
Safety,UniversityofGuelph,Guelph,ON,Canada
GRAHAMF.HATFULL (cid:1) DepartmentofBiologicalSciences,PittsburghBacteriophageInstitute,
UniversityofPittsburgh,Pittsburgh,PA,USA
HANNEHENDRIX (cid:1) LaboratoryofGeneTechnology,KULeuven,Leuven,Belgium
NIKAJANEZˇ (cid:1) CentreofExcellenceforBiosensors,InstrumentationandProcessControl,
CentreforBiotechnology,Ajdovscina,Slovenia
HYE-JEONGJANG (cid:1) DepartmentofPharmacy,CollegeofPharmacyandInstituteof
PharmaceuticalSciences,CHAUniversity,Gyeonggi-do,SouthKorea
FATIMAKAMAL (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,Edmonton,AB,
Canada
JOHNKING (cid:1) Sample6Technologies,Woburn,MA,USA
MICHAELKOERIS (cid:1) Sample6Technologies,Woburn,MA,USA
LAURA J.MARINELLI (cid:1) DivisionofDermatology,DepartmentofMedicine,DavidGeffen
SchoolofMedicine,UniversityofCalifornia,LosAngeles,LosAngeles,CA,USA
BEATRIZMARTI´NEZ (cid:1) DairySafeGroup,DepartmentofTechnologyandBiotechnologyofDairy
Products,InstitutodeProductosLa´cteosdeAsturias(IPLA-CSIC),Asturias,Spain
SHIGENOBU MATSUZAKI (cid:1) DepartmentofMicrobiologyandInfection,KochiMedicalSchool,
KochiUniversity,Kochi,Japan
JACLYNG.MCCUTCHEON (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,
Edmonton,AB,Canada
SASˇAHABERLMEGLICˇ (cid:1) LaboratoryofBiokibernetics,DepartmentofBiomedicalEngineering,
FacultyofElectricalEngineering,UniversityofLjubljana,Ljubljana,Slovenia
DAMIJANMIKLAVCˇICˇ (cid:1) LaboratoryofBiokibernetics,DepartmentofBiomedicalEngineering,
FacultyofElectricalEngineering,UniversityofLjubljana,Ljubljana,Slovenia
CRISTINAMORARU (cid:1) InstituteforChemistryandBiologyoftheMarineEnvironment,
Oldenburg,Germany
MATJAZˇ PETERKA (cid:1) CentreofExcellenceforBiosensors,InstrumentationandProcessControl,
CentreforBiotechnology,Ajdovscina,Slovenia
DANIELLEL.PETERS (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,
Edmonton,AB,Canada
MARIANA PIURI (cid:1) DepartamentodeQuı´micaBiol(cid:1)ogica,FacultaddeCienciasExactasy
Naturales,UniversidaddeBuenosAires,IQUIBICEN-CONICET,BuenosAires,
Argentina;Laboratorio“Bacteri(cid:1)ofagosyAplicacionesBiotecnol(cid:1)ogicas”,Departamentode
Quı´micaBiol(cid:1)ogica,FCEyN,UBA,CiudadUniversitaria,CiudadAut(cid:1)onomadeBuenos
Aires,Argentina
NILUFARPOSHTIBAN (cid:1) DepartmentofElectricalandComputerEngineering,Universityof
Alberta,Edmonton,AB,Canada
ALINARADZIWON (cid:1) FacultyofScience,BiologicalSciences,UniversityofAlberta,Edmonton,
AB,Canada
ANARODRI´GUEZ (cid:1) DairySafeGroup,DepartmentofTechnologyandBiotechnologyofDairy
Products,InstitutodeProductosLa´cteosdeAsturias(IPLA-CSIC),Asturias,Spain