FIRST UAEU SYMPOSIUM ON BIOLOGICAL SCIENCES

“GENOMICS & BIOINFORMATICS”

November 13-15, 2016

IT Building United Arab Emirates University

Al Ain, United Arab Emirates

2

3

Organized by

Department of Biology, College of Science & Khalifa Center for Genetic Engineering and Biotechnology

United Arab Emirates University

Supported by

Sponsored by

4

OrganizingCommitteeDrKhaledAmiri(Chairman),DepartmentofBiology,UAEUniversityDrRanjitVijayan(DeputyChairman&Secretary),DepartmentofBiology,UAEUniversityProfAmrAmin,DepartmentofBiology,UAEUniversityProfEduardoBlumwald,DepartmentofPlantSciences,UniversityofCalifornia,DavisDrRabahIratni,DepartmentofBiology,UAEUniversityDrSynanAbuQamar,DepartmentofBiology,UAEUniversityDrRamziBelkhodja,KhalifaCenterforGeneticEngineeringandBiotechnologyDrYusraAlDhaheri,DepartmentofBiology,UAEUniversityDrMohamedLotfy,DepartmentofBiology,UAEUniversityDrMohamedEnan,DepartmentofBiology,UAEUniversityDrMohamedTaher,DepartmentofBiology,UAEUniversityMrNoushadKaruvantevida,DepartmentofBiology,UAEUniversityMsRajaAlMeskari,DepartmentofBiology,UAEUniversityMsHalimaAlMeqbaali,DepartmentofBiology,UAEUniversityMsSamiraAlDashti,DepartmentofBiology,UAEUniversityMsAsmaaAbuObaid,DepartmentofBiology,UAEUniversityMsSalwaSultan,DepartmentofBiology,UAEUniversityMsAsmaAlBloushi,KhalifaCenterforGeneticEngineeringandBiotechnology

5

Program

6

DAY 1: SUNDAY, NOVEMBER 13, 2016 Location: Hilton Al Ain

5:00 pm – 6:00 pm REGISTRATION

6:00 pm – 6:15 pm WELCOME ADDRESS Dr Khaled Amiri Chairman, Organizing Committee

6:15 pm – 6:30 pm OPENING ADDRESS Prof Mohamed Albaili Vice Chancellor, UAE University

6:30 pm – 7:30 pm PLENARY LECTURE Prof Eduardo Blumwald University of California, Davis, USA

7:30 pm – 9:30 pm DINNER

7

DAY 2: MONDAY, NOVEMBER 14, 2016

Location: IT Building, United Arab Emirates University

SESSION 1: GENOMICS Chairs: Dr Khaled Hazzouri & Dr Pere Arús

9:00 am – 9:50 am KEYNOTE LECTURE K1. Disruptive technologies for understanding and improving disease resistance in crop plants Prof Richard Michelmore University of California, Davis, USA

9:50 am – 10:20 am INVITED TALK I1. New genomics-based approaches for perennial crop breeding: peach as an example Dr Pere Arús Center for Research in Agricultural Genomics, Barcelona, Spain

10:20 am – 10:40 am COFFEE BREAK

10:40 am – 11:10 am INVITED TALK I2. Building genomic tools for plant breeding: Our experiences improving red clover, ryegrass, and Bracharia Dr José de Vega-Bartol The Genome Analysis Center, Norwich, UK

11:10 am – 11:40 am INVITED TALK I3. Redox strategies for crop improvement Dr Pavel Kerchev Ghent University, Ghent, Belgium

11:40 am – 11:55 am O1. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop Dr Khaled Hazzouri New York University, Abu Dhabi, UAE

11:55 am – 12:10 pm O2. Genomics and transcriptomic profiles of imatinib resistance in gastrointestinal stromal tumor Dr Asmaa Elzawahry National Cancer Center, Japan

12:10 pm – 1:40 pm LUNCH & POSTER PRESENTATIONS

8

SESSION 2: TRANSCRIPTOMICS

Chairs: Dr Synan AbuQamar & Dr R. Manimekalai

1:40 pm –2:30 pm KEYNOTE LECTURE K2. Genetic characterization of salinity tolerance traits to increase salinity tolerance of crops Prof Mark Tester King Abdullah University of Science and Technology, Saudi Arabia

2:30 pm – 3:00 pm INVITED TALK I4. Alternative splicing in FMR1 premutation carrier Prof Flora Tassone University of California, Davis, USA

3:00 pm – 3:30 pm INVITED TALK I5. Transcriptomics to unravel functional markers for crop improvement Dr R. Manimekalai Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India

3:30 pm – 4:00 pm COFFEE BREAK

4:00 pm – 4:15 pm O3. A genome-wide identification of the miRNAome and transcriptome in response to salinity stress in the date palm tree (Phoenix dactylifera L.) Dr Mahmoud Yaish Sultan Qaboos University, Oman

4:15 pm – 4:30 pm O4. De novo transcriptome analysis of non-model plant Andrographis paniculata using mRNA-Seq data for gene discovery and marker identification Mr Vivek Chadramohan Siddaganga Institute of Technology, India

4:30 pm – 4:45 pm O5. Identification of genes involved in responses to environmental stress using reverse genetic approaches Dr Synan AbuQamar United Arab Emirates University, UAE

4:45 pm – 6:30 pm WORKSHOP (Selected participants only due to space limitations) W1. From FASTQ to BAM: accurate alignment of short reads and references Dr José de Vega-Bartol The Genome Analysis Center, Norwich Research Park, Norwich, UK

9

DAY 3: TUESDAY, NOVEMBER 15, 2016

Location: IT Building, United Arab Emirates University

SESSION 3: SYSTEMS BIOLOGY Chairs: Dr Ghada Al-Kafaji & Dr Roderic Guigó

9:00 am – 9:50am KEYNOTE LECTURE K3. Unraveling metabolic pathways regulating fruit ripening Prof Eduardo Blumwald University of California, Davis, USA

9:50 am – 10:20 am INVITED TALK I6. The human transcriptome across tissues and individuals Dr Roderic Guigó Center for Genomic Regulation, Barcelona, Spain

10:20 am – 10:40 am COFFEE BREAK

10:40 am – 11:10 am INVITED TALK I7. Cross-talk between intragenic epigenetic modifications and exon usage across developmental stages of human cells Dr Siba Shanak The Arab American University, Jenin, Palestine

11:10 am – 11:25 am O6. Circulating microRNA-126 in peripheral whole blood as a potential biomarker for type 2 diabetes-related vascular complications Dr Ghada Al-Kafaji Arabian Gulf University, Bahrain

11:25 am – 11:40 am O7. Rice root germin-like protein 2 gene promoter (OsRGLP2) is responsive to different plant signaling molecules in potato Dr Tariq Mahmood Quaid-i-Azam University, Islamabad, Pakistan

11:40 am – 11:55 am O8. From dissecting complex networks in Arabidopsis to revealing new developmental mechanisms and adaptive strategies in date palm Dr Ikram Blilou Wageningen University, Netherlands

12:00 pm – 1:30 pm LUNCH & POSTER PRESENTATIONS

10

SESSION 4: BIOINFORMATICS/PROTEOMICS

Chairs: Dr Rabah Iratni & Dr Marek Mutwill

1:30 pm – 2:20 pm KEYNOTE LECTURE K4. Strategies for building and annotating high quality genome sequences Dr Ivo Gut Centro Nacional de Análisis Genómico, Barcelona, Spain

2:20 pm – 2:50 pm INVITED TALK I8. Gene module multiplication drives pathway expansion in plants Dr Marek Mutwill Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany

2:50 pm – 3:20 pm INVITED TALK I9. Dissection of climacteric fruit ripening using genetic and genomic resources in melon Dr Jordi Garcia-Mas Center for Research in Agricultural Genomics, Barcelona, Spain

3:20 pm – 3:40 pm COFFEE BREAK

3:40 pm – 4:10 pm INVITED TALK I10. The 1000 Arab Genome: Characterizing the genome of ethnic groups in UAE. Dr Habiba Alsafar Khalifa University Center for Biotechnology, Abu Dhabi, UAE

4:10 pm – 4:25 pm O9. Integrated genomic analysis of the human mitochondrial transcriptome Dr Youssef Idaghdour New York University, Abu Dhabi, UAE

4:25 pm – 4:40 pm O10. Anti-breast cancer activity of carnosol in vivo and in vitro and in silico analysis of its target interactions Dr Rabah Iratni United Arab Emirates University, UAE

4:40 pm – 6:15 pm WORKSHOP W2. Current and upcoming DNA sequencing technologies Prof Richard Michelmore University of California, Davis, USA

6:15 pm – 6:30 pm CLOSING ADDRESS Dr Khaled Amiri Chairman, Organizing Committee

11

PostersP1. Usingofwholegenomebisulfitesequencing(WGBS)toidentifygeneexpressionprofile

regulatedbycytosinemethylationundersalinitystressindatepalmMissIbtisamRashidSaidAlHarrasiSultanQaboosUniversity,Oman

P2. ComparativegenomicsstudyforAcidithiobacillusferrooxidansDrRajeshPatelHemchandracharyaNorthGujaratUniversity,India

P3. AnalysisofMendelianrandomizationstudiesofbiomarkersandtype2diabetes:observationsfromanalysisDrNadiaHussainAlAinUniversityofScienceandTechnology,UAE

P4. IdentificationofArabidopsiscandidategenesinresponsetobioticandabioticstressesusingcomparativemicroarrays.MrArjunShamUnitedArabEmiratesUniversity,UAE

P5. ExpressionprofilingofArabidopsisWRKY33mutantsinresponsetoBotrytiscinereaMsShammaAl-ShamsiUnitedArabEmiratesUniversity,UAE

P6. CRELD1genemaypredisposetheriskofatrioventricularseptaldefectsinDownSyndromepatientsofNorthIndianoriginMsAmbreenAsimSanjayGandhiPostGraduateInstituteofMedicalSciences,India

P7. IdentificationofpremutationandgrayzoneFMR1carrierstatusinreproductiveagewomenbyTP-PCRMrsDeepikaDelsaDeanSanjayGandhiPostGraduateInstituteofMedicalSciences,India

P8. NovelNR1I2mutationsasprobablecauseofintellectualdisabilityDrInushaPanigrahiPGIMER,India

P9. GeneticcharacterizationofEpinephelusmarginatusintheMediterraneanSea:ContributionofmicrosatellitemarkersMissAzizaElgidINSTM,Tunisia

P10. NovelmutationinfamilywithWNT1-relatedosteoporosisDrSiyaramDidelPGIMER,India

P11. AnalysisofCGGrepeatstatusatFMR1geneinprematureovarianinsufficiencycases:AstudyfromSGPGIMS,LucknowDrSaritaAgarwalSanjayGandhiPostGraduateInstituteofMedicalSciences,India

P12. MetagenomicAnalysisofSoilMicrobesandRiskAssessmentofTransgenicCottoninNorthernKarnataka,IndiausingDGGEandARDRAtechniquesDrDevarajanThangaduraiKarnatakUniversity,India

12

P13. BS-SeqanalysispipelinefortargetednextgenerationsequencingdataMrPSandeepMallyaManipalUniversity,Manipal,India

P14. PredictionoftranscriptionfactorbindingsitesindifferentiallyexpressedgenesforwaterstressinricemediatedbyPseudomonasfluorescensMrsAbidaP.S.KeralaAgriculturalUniversity,India

P15. Identifyingavoveldeletionmutationinexon3ofphenylalaninehydroxylase(PAH)geneinphenylketonuria(PKU)patientsofUAEpopulation.DrMuhammadShahidNazirUniversityofModernSciences,UAE

P16. Genome-wideanalysisrevealedthatDNAmethylationisadynamicregulatorofsaltandosmoticstressinriceDrFiazAhmadBahauddinZakariyaUniversity,Pakistan

P17. IdentificationofsuperiorbuffalobullsforincreasingmilkproductionthroughgenomeanalysesMissSaherIslamUniversityofVeterinary&AnimalSciences,Lahore,Pakistan

P18. Morphology,physiologyandmicroenvironmentdeterminethemorphogeneticpotentialofcelltypesofleafcallusofpearlmilletcultivars.DrT.V.R.LakshmiUniversityofModernSciences,UAE

P19. Wholegenomesequencingandgeneannotationofalmond(Prunusdulcis)MsSumishaHabeebUAEUniversity,UAE

P20. Evaluationofsuitablereferencegenesindatepalm(PhoenixdactyliferaL.)underdroughtandsalinitystressforquantitativereal-timePCRMrHimanshuVishwasPatankarSultanQaboosUniversity,Oman

P21. Overexpression,purification&antimicrobialactivityofrecombinanthumanßdefensin3DrZaighamAbbasUniversityofPunjab,Pakistan

P22. Construction,expressionandpurificationofthymosinα1-Azu28fusionproteinfortargetedcancertherapyMrMuhammadShahbazAslamUniversityofPunjab,Pakistan

P23. TestimonyofrbcLandmatKlociforeightUnitedArabEmiratesnativeplantspeciesDrAlagappanKumarappanUniversityofModernSciences,UAE

P24. UsingnovelremotesensingapproachesandcarbonisotopediscriminationtopredictdroughttoleranceinIPTtransgeniccreepingbentgrassinthefieldDrRamziBelkhodjaKhalifaCenterforGeneticEngineeringandBiotechnology,UAE

P25. Anti-malarialdrugdiscoveryusingintegrativebiologyandsystemsbiologyDrVishalMevadaHemchandracharyaNorthGujaratUniversity,India

13

P26. In-silicodesignofinhibitorsforCyclinDependentKinase2moleculeinBreastCancer:acomputationalapproachMrsSreejishaP.S.UnitedArabEmiratesUniversity,UAE

P27. SynthesizednovelFmoc-2-aminothiozole:protectiveagainstcadmiuminducedapoptosis,teratogeniceffectonzebrafish(Daniorerio)embryosandmoleculardockingstudiesMsVaishnaviMSiddagangaInstituteofTechnology,India

P28. Structuralinsightsintothepolypharmacologicalactivityofdietaryflavonolsonserine/threoninekinasesMsBincyBabyUAEUniversity,UAE

P29. Inhibitingnon-receptortyrosinekinasesassociatedwithprostatecancerusingpolypharmacologicalnaturalcompoundsMsPriyaAntonyUAEUniversity,UAE

P30. BioinformaticmethodologiesrevealmetagenomicDepictionofIndianhotsprings’microbialcommunityDrPravinDudhagaraVeerNarmadSouthGujaratUniversity,India

P31. AdvancedStatisticalMethodsinGeneticAssociationstudiesDrSureshKumarSharmaPanjabUniversity,Chandigarh,India

P32. eHealthapplicationsforclinicalgeneticsDrMuhammadJawadHashimUnitedArabEmiratesUniversity,UAE

P33. Artificialintelligence(AI),genomicsandpersonalizedmedicineMrShaheenNShahGenomicsCentral,India

14

15

KeynoteSpeakers

Prof.RichardW.Michelmore

After studying Natural Sciences at Cambridge, RichardMichelmore joined thefacultyoftheUniversityofCaliforniaatDavisin1982.RichardwasthefoundingDirectoroftheGenomeCenteratUCDavisin2003;sincethenhehasoverseenthe recruitment of over sixteen genomics and bioinformatics faculty and thedevelopmentoffiveservicecores.HeiscurrentlyaDistinguishedProfessorintheDepartments of Plant Sciences, Molecular and Cellular Biology, and MedicalMicrobiologyandImmunology.Richardhaspublishedover160scientificpapers.His multidisciplinary research utilizes a synthesis of molecular, genetic andevolutionaryapproaches(http://michelmorelab.ucdavis.edu).His interestsspanbasic research into the molecular basis of specificity in plant-pathogen

interactions to translational plant genetics and crop improvement. His research is focused oncomparative and functional genomics with an emphasis on plant disease resistance and pathogenvariability. In addition, his program coordinates and hosts the bioinformatics component of theCompositae Genome Project. Richard’s interests also include applications of next-generation DNAsequencingapproachestoallareasofbiologyanditsimminentimpactonsocietyingeneral.Inparticular,heaimstoexploitsuchapproachesforinformation-drivendeploymentofresistancegenesinplantstoprovidedurablediseaseresistance.Inaddition,heisinterestedinfosteringresearchtoenhancefoodsecurityinternationally.

Prof.EduardoBlumwald

Dr.EduardoBlumwald,Ph.D.servesasaDistinguishedProfessorofcellbiologyatthe University of California, Davis and as a Faculty at the Lawrence BerkeleyNational Laboratory. Dr. Blumwald's research program is multidisciplinary innature, combining physiology, biochemistry,molecular biology and omics. Thegeneral objectives of his work are: (i) the study of the cellular andmolecularmechanisms that regulate ion homeostasis in plants; (ii) to characterize theresponsesofplantstoenvironmentalstress(e.g.,salt,drought,andheat)andtoengineertransgenicstress-tolerantcrops; (iii) thestudyof thebiochemicalandmolecularbasesofsugarandacidaccumulationinfruitsand(iv)thedevelopment

of genomic resources for the improvement of fruit quality. Dr. Blumwald serves as a Editorial BoardMemberandAssociateEditorofseveralscientificjournalsandastheEditor-in-ChiefofPlantScience.

16

Prof.MarkTesterMarkTesterisProfessorofBioscienceatKingAbdullahUniversityofScienceandTechnology(KAUST),SaudiArabia.HewaspreviouslyinAdelaide,wherehewasaResearchProfessorintheAustralianCentreforPlantFunctionalGenomicsandDirectoroftheAustralianPlantPhenomicsFacility.Markledtheestablishmentofthis Facility, a $55m organisation that develops and delivers state-of-the-artphenotypingfacilities,includingThePlantAccelerator,aninnovativeplantgrowthandanalysisfacility.Henowleadsaresearchgroupinwhichforwardandreversegeneticapproachesareusedtounderstandandmanipulatetraitsthatcontributetosalinitytoleranceandimprovethisincropssuchasbarleyandtomatoes.His

aspirationistounlockseawater,bydevelopinganeweconomicallyviableagriculturalsystemwheresalt-tolerantcropsareirrigatedwithpartiallydesalinisedseawaterorbrackishgroundwater.ProfessorTesterobtainedhisBachelor’sdegreeinbotanyfromtheUniversityofAdelaidein1984,andhis PhD in biophysics from theUniversity of Cambridge in 1988. Hewas awarded a Junior ResearchFellowshipfromChurchillCollege,Cambridgein1988,aBBSRC(UK)ResearchDevelopmentFellowshipin2001,andanAustralianResearchCouncilFederationFellowshipin2004.HemovedtoSaudiArabiain2013.

Dr.IvoGut

Ivo Gut is a Director of the Centro Nacional de Análisis Genómico (CNAG) inBarcelona,oneofthelargestEuropeangenomesequencingoperations,whichheestablishedin2010.His research interests are genomics, genetics, high-throughput nucleic acidanalysis methods, proteomics, implementation of –omics methods, omicstechnologies, automation bioinformatics, data analysis, disease geneidentification, cancer genomics, agrogenomics. He has more than 20 yearsexperienceinhigh-throughputnucleicanalysis(genotypingandsequencingDNA,RNAandDNAmethylation),technologydevelopmentinnucleicacidandprotein

analysis. HewasHeadofTechnologyDevelopmentandAssociateDirectorat theCentreNationaldeGénotypage(CNG)–CEA(1999-2009),whereheestablishedthehighestthroughputgenotypingplatforminEuropeandexecutedmanygenome-wideassociationstudies,heinitiatedandwasthecoordinatoroftheEU-fundedProjectREADNAinwhich2nd,3rdand4thgenerationnucleicacidanalysistechnologieswere developed. READNA Consortium was awarded with “Stars of Europe” Prize from the FrenchMinistryofHigherEducationandResearchin2013.HereceivedhisPhDinPhysicalChemistryfromtheUniversityofBaselin1990.AfterhisappointmentsasResearchFellowatHarvardMedicalSchoolandImperial Cancer Research Foundation of London, he led a group in the Department for VertebrateGenomicsatMax-Planck-InstituteforMolecularGenetics.Heisauthorofmorethan300researchpapers,11reviewsand12bookchapters,citedover21000times,inventorof25patentsorpatentapplications,founderof4biotechstart-ups,andservesonnumerousinternationaladvisoryboards.

17

Abstracts:OralPresentations

18

KEYNOTELECTURESK1.DisruptivetechnologiesforunderstandingandimprovingdiseaseresistanceincropplantsProf.RichardMichelmoreTheGenomeCenter&DepartmentofPlantSciences,UniversityofCalifornia,Davis.

Althoughmoreremainstobelearnt,greatstrideshaverecentlybeenmadeintheunderstandingofthemolecularandgeneticbasisofdiseaseresistanceinplants.Itisnowtimetodeploythisknowledgeto provide more durable disease resistance. Much of these advances have been enabled byimprovements in analytical technologies and further advances are anticipated. In particular, highthroughputDNAsequencingenablesdetailedanalysisofcropsandtheirpathogens.Itisnowpossibletocharacterize variable pathogen populations and use this information for the rational deployment ofresistancegenessoastomaximizetheevolutionaryhurdleforthepathogentobecomevirulent.

Muchofourworkoverthepastthirtyyearshasfocusedonresistancetodownymildewinlettuce.Lettuce(Lactucasativa)isoneofthemostvaluablevegetablecropsanddownymildew,causedbyBremialactucae,isthemostimportantfoliardiseaseoflettuceworldwide.Theuseofresistantvarietiesisthemosteffectivemethod forcontrolling thisdisease;however,pathogenvariabilityhas led to therapiddefeatofindividualresistancegenes.Over50resistancegeneshavebeenidentifiedandlettucedownymildewisoneofthebestgeneticallycharacterizedplantdiseases.Wholegenomesequencingofmultiplegenotypeshasallowedtheidentificationofcandidateresistancegenesinthehostandvirulencefactorsinthepathogen.Knowledge-drivendeploymentofeffectiveresistancegenesasgenepyramidsprovidestheopportunityformoredurableresistancetoB.lactucae.Genestackingusinggenomeeditinghasthepotentialmakingthisprocessmoreefficient.Inaddition,host-inducedgenesilencingofvitalpathogengenespresentspotentiallyinsurmountableevolutionaryhurdlesforthepathogentoovercomeinordertobecomevirulent.

K2.GeneticcharacterizationofsalinitytolerancetraitstoincreasesalinitytoleranceofcropsProf.MarkTesterKingAbdullahUniversityofScience&Technology,SaudiArabia

Fortypercentoftheworld’sfoodisproducedunderirrigation,andthisisdirectlythreatenedbyover-exploitationofwaterresourcesandchangesintheglobalenvironment.Inthistalk,thefocuswillbeontheuseofforwardgeneticapproachesfordiscoveryofgenesrelatedtosalinitytoleranceinbarley,riceandtomatoes.Ratherthanstudyingsalinitytoleranceasatraitinitself,wedissectsalinitytoleranceintoaseriesofcomponentsthatarehypothesisedtocontributetooverallsalinitytolerance.

Forbarley,twoconsecutiveyearsoffieldtrialswereconductedattheInternationalCenterforBiosalineAgriculture,asitewithsandysoilandverylowprecipitation.Dripirrigationsystemsallowedthecontrolofsalinitybysupplyingplotswithlow(1dS/m)andhighsalinitywater(17dS/m).AbarleyNestedAssociationMapping(NAM)populationdevelopedbyKlausPillenhasbeenusedtodissectphysiologicallyandgeneticallycomplextraitsinresponsetosaltstress.Tentraitsrelatedtoyieldandyieldcomponents(e.g.daystoflowering,harvestindex,100seedmass)wererecordedandfivestress-indiceswerederivedfromeachofthesemeasurements.Wehaveidentifiedtwosignificantlocilocatedonthelongarmsofchromosomes1Hand5H,whicharebothassociatedwithseveraltraitscontributingtosalinitytolerance,namelydaystoflowering,daystomaturity,harvestindexandyield.

For tomatoes, the focus is on genetics of tolerance in wild tomatoes, specifically Solanumgalapagense,SolanumcheesmaniaeandSolanumpimpinellifolium.Anassociationgeneticapproach isbeing taken. High quality genome sequences have been made, and genotyping-by-sequencingundertaken.TomatoeshavebeenphenotypedinThePlantAcceleratorandinthefield,andanalysesarecurrentlyinprogress.

19

Theapplicationofthisapproachprovidesopportunitiestosignificantlyincreaseabioticstresstoleranceofcrops,andthuscontributetoincreasingagriculturalproductioninmanyregions.K3.UnravelingmetabolicpathwaysregulatingfruitripeningProf.EduardoBlumwaldDepartmentofPlantSciences,UniversityofCalifornia,Davis,USA Ripening is aprocess regulatedbya largenumberof genes that control theprogressive fruitmaturation. During ripening, fruits undergo several physiological and biochemical modifications thatinfluence properties associatedwith fruit quality, such as texture (fruit softening), color (chlorophylldegradation and accumulation of non-photosynthetic pigments), aroma (production of volatilecompounds)andtaste(increaseinsugarsanddeclineinorganicacids).Traditionally,fruitripeninghasbeen defined as either climacteric or non-climacteric. Increased levels of autocatalytic ethyleneproduction and high respiration rates during ripening characterize climacteric fruits. Non-climactericfruitsshownoincreaseorautocatalyticethyleneproductionorrespirationratesduringripening. Wecharacterizedandcomparedtwoplumcultivars(PrunussalicinaLindl.cvSantaRosa[SM]anditsbud-sportmutantcv.SweetMiriam[SM]).AlthoughSRandSMsharethesamegeneticbackground,theydisplaycontrastingripeningbehavior,i.e.climacteric(SR)andnon-climacteric(SM).Weintegratedtranscriptomics, proteomics, metabolomics, enzymatics and physiology to assess thebiochemical/molecular regulation of ethylene-dependent and ethylene-independent biosyntheticpathwaysthatareassociatedwithfruitripeningineachcultivar.RNAseqanalysesidentifiedover5,000genesdisplayingdifferential expressionbetween the cultivars.Weightedgene co-expressionnetworkanalysis allowed the identification of several gene modules associated with hormone and sugarhomeostasis.Furthermore,severalhubgeneswereidentifiedbasedonintra-moduleconnectionsoftheco-expressionnetworks,amongtheseweregenesencodinganumberoftranscriptionfactorsandkeyregulators of hormone and carbohydrate metabolism. Targeted analyses of some of these genesfacilitatedthedetectionofalteredbiosyntheticpathwaysinbothplumvarieties.Forexample,intermsofsugarhomeostasis,theclimactericvariety(SR)displayeda“sucrose-associated”metabolismwhilethenon-climacteric variety (SM) showed a “sorbitol-associated” metabolism. Differences in transcriptaccumulation of key enzymes regulating the synthesis/degradation of sucrose or sorbitol revealedvariety-specific metabolic interactions directly associated with the observed changes in sugarhomeostasis.

This experimental system provides a unique tool to study metabolic pathways underlyingcontrasting fruit ripening behavior. Understanding the steps associated with the regulation ofsorbitol/sucrosehomeostasisandtheincreasedproductionofsugaralcoholswillenhancedfruitqualityandcontributetothedevelopmentoffruitswitha lowglycemic index(highsorbitol, lessglucoseandfructose),addingtothehealthbenefitsoffruitconsumption.

K4.StrategiesforbuildingandannotatinghighqualitygenomesequencesDr.IvoGutCentroNacionaldeAnálisisGenómico(CNAG-CRG),Barcelona,Spain

AttheCNAGwehavecarriedoutdenovogenomeassemblyandannotationformanydifferentspecies(e.g.Iberianlynx,turbot,cedaraphid,almond,wasp,olive).Theobjectiveofeachdenovoassemblyistoprovidehighcontiguityandscaffoldingwithcorrectorderandorientationofcontigssothatdownstreamannotationhasthebestpossiblechancetorecoverthegenesandgenestructurescorrectly.Overtheyearswehave refined thesequencingstrategies thatweapply tooptimizecontiguityandscaffoldingwhilereducingtheoverallcostofadenovoassemble.Ourbasicstrategiesusepaired-endwholegenomeshotgunsequencingtogetherwithmatepairanalysis,fosmidpoolshotgunsequencingandfosmidend

20

sequencinginpoolsthatareallrunonIlluminasequencingsystems.Computationalassemblystrategiesstart with de novo assembly of fosmid pools, followed by error correction with the whole genomeshotgundata.Scaffolding isrefinedwithmatepairandfosmidendsequences.Throughoutweapplyacontigbreakingandre-assemblystrategy.Weareconstantlyexploringdatatypesfromdifferenttypesofsequencerstooptimizethequalityofanassemblyandthecostofbuildinganewgenomesequence.Inparticular, these are the inclusion of fosmid pool sequencing using Pacific Biosciences and OxfordNanopore Technologies MinIon systems and optical mapping strategies with the Iris system fromBioNanoGenomics.AfterassemblyannotationisdoneusingacombinationofcomputationaltoolsandRNA sequencing of mRNA from several different tissues of the species we are sequencing. In thispresentationwewilldiscussthestrategiesandpipelinesthatwehavedevelopedtoachievehighqualityreferencegenomesandannotationsforthedifferentdenovoprojectscarriedoutattheCNAG.

21

SESSION1:GENOMICSI1.Newgenomics-basedapproachesforperennialcropbreeding:peachasanexempleDr.PereArúsIRTA,CenterforResearchinAgriculturalGenomicsCSIC-IRTA-UAB-UB,Spain

Perennialcrops,includingmostsweetfruit,palms,grapes,olives,coffee,mostornamentals,etc.areanimportantsourcegastronomicoraestheticpleasureandprovideforvitamins,fiber,antioxidantsandotherhealth-relatedproducts thatcomplementthecaloriesprovidedbycerealsandotherstaplefoods. They often have long intergeneration periods and are clonally propagated. Their cultivationextends foraround1/8of theworld’s total food-producingsurfaceandrepresentsmorethan60%ofworld’s patents and breeder’s rights titles. Conventional breeding methods consist of phenotypicselectionfromprogenyofcrossesbetweentwohighlyheterozygousparents.Theselectedplantsarethenclonallypropagatedand tested foryieldandquality.This scheme is fastandsimple,but ithasmajordrawbacks:recombinationisusedtoaverylimitedextentandtraitintrogressionfromexoticsourcesispracticallyimpossible.Weproposethreeapproachesbasedontheselectionofthewholegenomewithmolecularmarkers,andapplythemtopeach(Prunuspersica):a)marker-assistedintrogression,wherenew genes of interest from other Prunus species compatible with peach are identified, and peachindividualswithasingleexoticintrogressionarerecoveredinonlytwobackcrossgenerations.Anexampleisprovidedbasedonalmond×peachhybrids;b) “resynthesis”,where it ispossible identifying in theselfedprogenyofahigh-valuecultivar:a)genotypeswiththesamegeneticcompositionastheoriginalcultivar,exceptforoneorfewchromosomalregions,andb)twocomplementaryhomozygous(ornearly-homozygous) individuals that crossedwill produce hybrids with a nearly-identical genotype that theoriginal cultivar, and c) VORIS (varieties obtained by resynthesis and introgression), using the twoprevious concepts to obtainwith a lownumberof generations a cultivar, nearly-identical to a highlyperformingone,withageneincorporatedfromanexoticsource.

I2.BuildingGenomictoolsforplantbreeding:Ourexperiencesimprovingredclover,ryegrass,andBrachariaDr.JosédeVega-BartolTheGenomeAnalysisCenter,NorwichResearchPark,Norwich,UK

Advances in NGS and assembly techniques allow to generate high quality genomes of

heterozygousandcomplexplantsthatwerepreviouslyinaccessible.Thesegenomesareausefultoolforbreedingandplantresearch.Theycanbeexploredbycomparativegenomics,usedtoassetthediversityofnaturalandsyntheticpopulations,or identifythecausal lociofcomplexagronomictraits.Wehaveproducedchromosome-scalegenomesofredclover,ryegrassandthetropicalforageBracharia.WehavesequencedplantsofredcloverfromaroundEuropetocharacterizeitsdiversityanddomestication,andlaterusedthisdatatoidentifyusefulelitegenotypestoenrichthebreedingprogram.WearealsousinggenomicapproachestocharacterizetheprogenyintheredcloverandBrachiariabreedingprograms,andtoidentifythekeyregulatorsbehindcomplextraits,liketolerancetoacidsoilsandpersistency.

22

I3.RedoxstrategiesforcropimprovementDr.PavelKerchevDepartmentofPlantSystemsBiology,VIB,BelgiumDepartmentofPlantBiotechnologyandBioinformatics,GhentUniversity,Belgium

Theincreasedawarenessthatreactiveoxygenspecies(ROS)canactassignalingmoleculeshasopenednewavenuestoexploitredoxbiologyforcropimprovement.Understandinghydrogenperoxide(H2O2)signalingisparticularlyimportantduetoitsrelativelylonghalf-lifeandmajorproductionduringnormalphysiologicalprocesssuchasphotorespiration.Toanalyzemolecularmechanismsthatregulatethe response to increased H2O2 levels, we have been using Arabidopsis thaliana mutants lackingperoxisomal catalase activity (cat2-2) needed for H2O2 decomposition. By screening for second-sitemutationsthatattenuatethephotorespiratoryphenotypeofcat2-2,weisolatedanumberofmutationsthatrescuedthecelldeathofcat2-2plantsunderphotorespiration-promotingconditions.Usingasimilarapproach,weprobedtheabilityof10000chemicalstoalleviatethecelldeathphenotypeofcat2-2plantsand identified 34 hit molecules. I will discuss the functional roles of two confirmed mutations andhighlighttheoutcomesofthechemicalscreen.Thisstrategyhasthepotentialtodeliverstress-protectiveagrochemicalsandcandidateleadgenesthatcanformthebasisofbetterperformingcrops.

O1. Whole genome re-sequencing of date palms yields insights intodiversificationofafruittreecropDr.KhaledHazzouriNewYorkUniversity,AbuDhabi,UAECo-authors:KhaledM.Hazzouri,JonathanM.Flowers,HendrikJ.Visser,HussamS.M.Khierallah,Ulises

Rosas,GinaM.Pham,RachelS.Meyer,CarynK. Johansen,ZoeA. Fresque,KhaledMasmoudi,Nadia

Haider,NabilaElKadri,YoussefIdaghdour,JoelA.Malek,DeborahThirkhill,GhulamS.Markhand,Robert

R.Krueger,AbdelouahhabZaid&MichaelD.Puarugganan

Datepalms (Phoenixdactylifera)are themostsignificantperennialcrop inaridregionsof theMiddle East and North Africa. Here, we present a comprehensive catalogue of approximately sevenmillion single nucleotide polymorphisms in date palms based on whole genome re-sequencing of acollectionof62cultivars.PopulationstructureanalysisindicatesamajorgeneticdividebetweenNorthAfricaandtheMiddleEast/SouthAsiandatepalms,withevidenceofadmixtureincultivarsfromEgyptand Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated withselective sweeps that may underlie geographic adaptation.We report candidate mutations for traitvariation, including nonsense polymorphisms and presence/absence variation in gene content inpathwaysforkeyagronomictraits.Wealsoidentifyacopia-likeretrotransposoninsertionpolymorphismintheR2R3myb-likeorthologueoftheoilpalmvirescensgeneassociatedwithfruitcolourvariation.Thisanalysisdocumentspatternsofpost-domesticationdiversificationandprovidesagenomicresourceforthiseconomicallyimportantperennialtreecrop.

23

O2. Genomics and transcriptomic profiles of imatinib resistance ingastrointestinalstromaltumorDr.AsmaaElzawahryNationalCancerCenter,JapanCo-authors: Asmaa Elzawahry, Tsuyoshi Takahashi, Sachiyo Mimaki, Katsuya Tsuchihara, ToshirouNishida,andMamoruKato

Background The gastrointestinal stromal tumor (GIST) is the most common frequentmesenchymaltumorofthedigestivetract.GISTproliferationisdrivenbygain-of-functionmutationsinKIT. These characteristics have facilitated the targeted therapies development that based on withtyrosine kinase inhibitors, such as imatinib. Although many clinical studies have demonstratedrevolutionizedeffectsofimatinib,morethan80%ofpatientslastlydevelopdiseaseprogressiondrivenbysecondaryresistancemutations inKITkinasedomains.However,thefullspectrumofgenomicandtranscriptomicchangesbehind the resistance remainsunknown.ResultsThis studyanalyzedgenomicandtranscriptomicchangesindrug-sensitiveand-resistantcelllinesagainstimatinib.Wealsolookedatan“intermediate”cell-linebeforereachingthefull resistance.We identifiedSNVsandCNAsfromthenext-generation sequencing and also the transcriptome from microarrays. For clinical insights, weconductedexomesequencingfortwoclinicalsampleswiththeresistance.Notably,thecelllinebrieflyexposedtoimatinibexhibiteddrastictranscriptionalchanges,butfewgenomicchanges.ConclusionWesuggest thatpre-existingcelldeath-resistantsubpopulationsarethemaincause for full resistanceviasecondary KIT mutations. The combination of chemotherapy with imatinib and apoptosis pathway-targetingdrugs,couldlimittheemergenceofdrug-resistantcancer.

24

SESSION2:TRANSCRIPTOMICSI4.AlternativesplicinginFMR1premutationcarriersProf.FloraTassoneUniversityofCaliforniaDavis,USA

Over 40% ofmales and ~16% of female carriers of a FMR1 premutation allele (55-200 CGGrepeats)areatriskfordevelopingFragileX-associatedTremor/AtaxiaSyndrome(FXTAS),anadultonsetneurodegenerativedisorderwhile,about20%offemalecarrierswilldevelopFragileX-associatedPrimaryOvarian Insufficiency(FXPOI), inadditiontoanumberofneurodevelopmentalandadult-onsetclinicalproblems(FMR1associateddisorders).MarkedelevationinFMR1mRNAlevelshavebeenobservedwithpremutationallelesandtheresultingRNAtoxicity isbelievedtobethe leadingmolecularmechanismproposed for these disorders. The FMR1 gene, as many housekeeping genes, undergoes alternativesplicing. Using Single molecule real time sequencing (SMRT) (SMRT) and qRT-PCR we have recentlyreportedthat,althoughtherelativeabundanceofallFMR1mRNAisoformsissignificantlyincreasedinthepremutationgroupcomparedtocontrols,thereisadisproportionateincrease,relativetotheoverallincreaseinmRNA,intheabundanceofisoformssplicedatbothexons12and14.Intotal,weconfirmedtheexistenceof16outof24predictedisoformsinoursamples.However,itisunknown,whichisoforms,whenoverexpressed,maycontributetothepremutationpathology.Toaddressthisquestionwehavefurther defined the transcriptional FMR1 isoforms distribution pattern in different tissues, includingheart, muscle, brain and testis derived from FXTAS premutation carriers and age-matched controls.PreliminarydataindicatesthepresenceofatranscriptionalsignatureoftheFMR1gene,whichclustersmoreby individual thanbytissuetype.We identifiedadditional isoformsthanthe16reported inourpreviousstudy,includingagroupwithparticularsplicepatternsthatwereobservedonlyinpremutationsbutnot incontrols.OurfindingssuggestthatthecharacterizationofexpressionlevelsofthedifferentFMR1 isoforms is fundamental for understanding the regulation of the FMR1 gene as well as forelucidatingthemechanism(s)bywhich“toxicgainof function”oftheFMR1mRNAmayplayarole inFXTAS and/or in the other FMR1-associated conditions. In addition to the elevated levels of FMR1isoforms,thealteredabundance/ratioofthecorrespondingFMRPisomers,orgenemethylation,couldaffecttheoverallfunctionofFMRPinpremutations.I5.TranscriptomicstounravelfunctionalmarkersforcropimprovementDr.R.ManimekalaiICAR–SugarcaneBreedingInstitute,India

Agriculturalcropsareputintovariousbiotic/abioticstressfactorsduringtheirgrowthphases.Thevagariesofclimaticconditionsandtherebythechangesinthescenarioofpest/pathogengreatlyaffecttheproductionandproductivityofcrops.Thisabstractperceivesthepotentialoftranscriptomicsindecipheringtheinteractionbetweencropsandstressfactorstodevelopfunctionalmarkersforcropimprovement.Inparticular,wholegenometranscriptomesequenceinformationutilizedtounderstandtheassociationbetweenthecropandbiotic/abioticstressfactors.Transcriptomics-basedanalysisofphytoplasma (plant pathogen) associated coconut root wilt diseases highlighted the differentiallyexpressedgenesinvolvedinphysiologicalresponseofthediseasepalms.Thegenesimplicatedinwaterstress, response to ethylene, cell wall biosynthesis were largely up-regulated and genes related tophotosynthesisandplantdefencesuchaschitinase,LRRdomain,glucosidase,pathogenesisrelated(PR)weredown-regulated indiseasedpalms.However, thesamepathogen inarecanutpalm isassociatedwithyellowleafdiseaseexhibitsadifferentscenario.Thegenesinvolvedinplant-pathogeninteractionpathwayswere differentially expressed, specifically, genes such as, LLR family protein and apoptosisinducing factor were up-regulated and RUBPcase andmost of the chloroplast related (plastocyanin,thioredxoin)genesweredownregulatedindiseasedcondition.Thetranscriptomeofsugarcaneunderoxidative stress showed thedifferential expressionof zinc ionbindingproteinsunder stress. There issignificantdifferenceinmiRNAprofilesofcultivatedvarietyandwildspeciesofsugarcaneunderoxidative

25

stress. The co regulatedmiRNAand transcripts inparticular conditionhelps to identify thepositivelyregulatedgenesforfurtherimprovementofcropsthroughtransformation/MAS.Transcriptomeisanalternative to genome sequence especially for complex polyploid crops for developingmarkers. Thewhole transcriptomecanbeused todevelopexpressedQTL (eQTL) and it ispossible tomapon toasegregatingpopulationfordevelopmentoffunctionalmarkersandwouldaidapplyinggenomicselectionstrategiesinplantbreeding.O3. A genome-wide Identification of the miRNAome and transcriptome inresponsetosalinitystressinthedatepalmtree(PhoenixdactyliferaL.)Dr.MahmoudYaishSultanQaboosUniversity,Oman

Datepalm isan important tree inaridandsemiaridregionshowever; in therecentyears thisplantexperiencesanenormouschallengeduetoexcessivesoilsalinitywhichcausesasignificantyieldloses.Despite theexistenceof a certain levelof salt adaptation capability, themolecularmechanismbehind this tolerance is completely unknown in this plant. This mechanism likely encompasses theinvolvementofepigeneticfactorssuchassmallnon-codingRNA(sRNA)moleculesknownasmiRNAwhichusually play a role in the post-translational modifications when plants exposed to abiotic stressesincludingsalinitystress.Inthisproject,fourlibrariesofsRNAswereconstructedandahigh-throughputSolexasequencingapproachhasbeenemployedtogenerateagenome-wideassessmentofmiRNAomeinresponsetosalinityofdatepalmseedlings.Atotalof251millionrawreadswereobtainedfromNaCl-treatedanduntreatedleavesandrootslibrariesincludinga153uniqueconserved,89nonconservedanda 180 putative novel uniquemiRNA/miRNA* sequences allwere encodedby appropriate precursors.Sequence analysis showed some predicted miRNA gene targets have a potential function in saltadaptation mechanism. While global differential miRNAome expression analysis showed that mostmiRNAs repressed in roots upon exposure to salinity, the same analysis showed that the miRNAexpressioninleavesisslightlydownregulatedunderthesameconditions.TheexpressionlevelofsomemiRNAwasexperimentallytestedusingqRT-PCRsuggestingthatthesemiRNAsmightplayaroleingeneexpression regulation in date palm. The miRNAome discovered in this study provided insights intomolecularaspectsofmiRNA-mediatedgeneexpressionandthereforetheseresultswouldprovideabasisforfurtherunravellingthemechanismonhowmiRNAscancontrolsalinityadaptationmechanismindatepalm.O4.Denovotranscriptomeanalysisofnon-modelplantAndrographispaniculatausingmRNA-SeqdataforgenediscoveryandmarkeridentificationMr.VivekChadramohanSiddagangaInstituteofTechnology,IndiaCo-authors:VivekChandramohan,AnubhavKaphle,SindhuGangarudraiah,MohitJhunjhunwala

AndrographispaniculataNees,knownas‘Kalamegha’inSanskrit,isanherbaceousplantinthefamily Acanthacea and is known to have a broad range of pharmacological potential. However,Andrographis being a non-modal plant, genomic analysis is limited by very small quantity of publiclyavailableannotated sequencedata.Our research, thus, focusesonemploying transcriptomicanalysisbasedonNGStogeneratetranscript informationabouttheplantandcharacterizemetabolicpathwayrelatedtoditerpenoidsbiosynthesis.Paired-endreadsweredownloadedfromtheNCBISRAdatabaseofIDSRR1292497andwerequality-checkedandtrimmedtoproducecleanreads.Weassembledintotalof197,537,498readsdenovousingTrinityassembler,andCLCGenomicsWorkbench(CLC)usingvariousk-mer values to optimize the assembly. Trinity outputs a total of 86,215 transcripts and 64,488 trinity‘genes’withaveragelengthof1156.63andN50of2111.%GCcontentwascalculatedtobearound42.56.RSEMwasusedtocalculaterelativeabundanceofisoformsintheexperimentpoolofmRNA.ThecontigswereextractedandusedasqueriesinBLASTxagainsttheRef-Seqproteindatabase(plantdivision).The

26

majorityofcontigsproducedsignificanthitswithexpectationvaluesunder1.0E-5andshowedsimilaritywithVitisviniferaandSesamumindicum.Blast2GOtoolwasusedtofunctional-annotatetheobtainedtranscriptsequence.Inaddition,weidentifiedsimplesequencerepeatmotifsintranscriptsusingMISAtool. We used KASS online annotation from KEGG to elucidate the genes involved in di-terpenoidbiosynthesis.Thetranscriptssetgeneratedhereprovidearesourceforgenediscoveryanddevelopmentoffunctionalmolecularmarkers. Inaddition,thestrategyfordenovoassemblyoftranscriptomedatapresentedherewillbehelpfulinothersimilartranscriptomestudies.O5.IdentificationofgenesinvolvedinresponsestoenvironmentalstressusingreversegeneticapproachesDr.SynanF.AbuQamarDepartmentofBiology,UnitedArabEmiratesUniversity,UAE

Transcriptionalreprogrammingformsamajorpartofaplant’sresponsetoenvironmentalstress.WeinvestigatedtheeffectsofcombinationsofbioticandabioticstressesonthetranscriptomelevelofArabidopsisgenomeusingcomparativemicroarrays.Weshowedauniqueprogramofgeneexpressionwasactivatedinresponsetoeachbioticandabioticstress.Inaddition,abioticstress-inducedgeneswerecommonlyregulatedwithBotrytiscinerea infection.TheArabidopsiscellwallexpansin-likeA2(EXLA2)genewasidentifiedbasedonitsdown-regulationinresponsetoinfectionbythenecrotrophicpathogenB.cinerea,andonthereducedsusceptibilityofitsmutantstothesamepathogen.Theexla2mutantsalsoenhanced tolerance to the phytoprostane-A1 (PPA1). Our results suggest that the absence or down-regulationofEXLA2 leadsto increasedresistancetoB.cinerea inaCOI1-dependentmanner,andthisdown-regulationcanbeachievedbyPPA1treatment.TheEXLA2issignificantlyinducedbysalinityandcold,andexogenousapplicationofAbscisicacid(ABA).Theexla2mutantalsoshowedhypersensitivitytowards increasedsaltandcold,andthishypersensitivityrequiredafunctionalABApathway.Overall,EXLA2appearstobeimportantinresponsetoenvironmentalstress,particularlyinthepathogenesisofnecrotrophicpathogensandtolerancetoabioticstress.Futuredirectionstofurtheranalyzethefunctionsofcommonlyexpressedgenesinresponsetoenvironmentalstresswillincreaseourunderstandingoftheplantstressresponse.

27

SESSION3:SYSTEMBIOLOGY

I6.ThehumantranscriptomeacrosstissuesandindividualsDr.RodericGuigó CenterforGenomicRegulations,UniversitatPompeuFabra,Spain

Thepilotphaseof theGenotype-TissueExpression (GTEx)projecthasproducedRNASeqfrom1,641samplesoriginatedfromupto43tissuesfrom175post-mortemdonors,andconstitutesauniqueresourceto investigatethehumantranscriptomeacrosstissuesand individuals.Clusteringofsamplesbased on gene expression recapitulates tissue types, separating solid from not solid tissues, whileclustering based on splicing separates neural from non-neural tissues, suggesting that post-transcriptionalregulationplaysacomparativelyimportantroleinthedefinitionofneuraltissues.About47%ofthevariationingeneexpressioncanbeexplainedbyvariationofacrosstissues,whileonly4%byvariationacross individuals.Wefind that therelativecontributionof individualvariation is similar forlncRNAsandforproteincodinggenes.However,wefindthatgenesthatvarywithethnicityareenrichedin lncRNAs,whereasgenesthatvarywithagearemostlyproteincoding.Amonggenesthatvarywithgender,wefindnovelcandidatesbothtoparticipateandtoescapeX-inactivation.Inaddition,bymerginginformationonGWASweareableto identifyspecificcandidategenesthatmayexplaindifferences insusceptibilitytocardiovasculardiseasesbetweenmalesandfemalesanddifferentethnicgroups.Wefindthatgenes thatdecreasewithageare involved inneurodegenerativediseases suchasParkinsonandAlzheimerand identifynovel candidates thatcouldbe involved in thesediseases. Incontrast togeneexpression, splicing varies similarly among tissuesand individuals, andexhibits a largerproportionofresidualunexplainedvariance.Thismayreflectthatthatstochastic,non-functional fluctuationsoftherelative abundances of splice isoforms may be more common than random fluctuations of geneexpression.BycomparingthevariationoftheabundanceofindividualisoformsacrossallGTExsamples,wefindthatalargefractionofthisvariationbetweentissues(84%)canbesimplyexplainedbyvariationinbulkgeneexpression,withsplicingvariationcontributingcomparativelylittle.Thisstronglysuggeststhatregulationattheprimarytranscriptionlevelisthemaindriveroftissuespecificity.Althoughbloodisthemost transcriptionallydistinctof the surveyed tissues,RNA levelsmonitored inbloodmay retainclinicallyrelevantinformationthatcanbeusedtohelpassessmedicalorbiologicalconditions.I7.Cross-talkbetweenintragenicepigeneticmodificationsandexonusageacrossdevelopmentalstagesofhumancellsDr.SibaShanakZentrumfürBioinformatik,UniversitätdesSaarlandes,GermanyArabAmericanUniversity-Jenin,Palestine

Differentialexonusagehasbeenreportedtoaffectthelargemajorityofgenesinmammaliangenomes. It has been shown that different splice forms sometimes have distinctly different proteinfunctions. Here, we present an analysis of the Human Epigenome Atlas (version 8) to connect thedifferential usage of exons in various developmental stages of human cells/tissues to differentialepigeneticmodificationsattheexonlevel.WefoundthatthedifferentialincidenceofproteinisoformsacrossdevelopmentalstagesisoftenassociatedwithchangesinhistonemarksaswellaschangesinDNAmethylationinthegenebodyorthepromoterregion.Manyofthegenesthataredifferentiallyregulatedattheexonlevelwerefoundtobeassociatedwithdevelopmentandmetabolism.

Differentialexonusageisamechanismusedbycomplexorganismstoincreasetheusabilityofthegene-codingregions,sothatseveraldifferentproteinsareexpressedfromthesamechromosomalposition. Epigenetics studies inherited modifications to genes that do not belong to the raw DNAsequence,butneverthelessmodulategeneexpression. Epigenetics iswell-associatedwithalternativesplicinginthegenebody,buttheconnectiontodistinctdevelopmentalstageshasnotbeenaddressed

28

sofar.Hereweshowthatasizeablenumberofgenesthatareessentialfordevelopmentshowstrongassociationsbetweendifferentialexonusageandepigeneticmodifications.O6.CirculatingmicroRNA-126inperipheralwholebloodasapotentialbiomarkerfortype2diabetes-relatedvascularcomplicationsDr.GhadaAl-KafajiArabianGulfUniversity,Bahrain

Patientswith type 2 diabetesmellitus (T2D) develop serious complications that reduce theirqualityof life and life expectancy.Biomarkers for earlydetectionof thediseaseand identificationofindividualsatriskofdevelopingcomplicationswouldbeclini¬callysignificanttoimprovethecareofthesepatients.Smallnon-codingRNAscalledmicroRNAs(miRNAs)regulategeneexpressionandparticipateindiverse cellular processes such as metabolism, inflammation responses, and angiogenesis; and theirdysregulation has been associated with various diseases including T2D and its related vascularcomplications.Recently,miRNAshavebeenshowntobestalelypresent in thecirculationandcanbeusedasbiomarkersfordiseasediagnosisorprognosis.MiR-126ishighlyenrichedinendothelialcellsandaltereditscirculatinglevelshasbeenreportedinthebloodofT2Dpatients.TheaimofthisstudywastoinvestigatetheexpressionofcirculatingmiR-126andtoassessitspotentialasablood-basedbiomarkerfordiabeticnephropathy(DN)andcoronaryarterydisease(CAD)inT2Dpatients.TheexpressionofmiR-126wasevaluatedinperipheralwholebloodusingTaqMan-basedquantitativerealtimePCRfromfourgroups:T2Dpatientswithoutmicrovascularormacrovascularcomplications(n=52),DNpatients(n=50;29withmicroalbuminuriaand21withmacroalbuminuria),CADpatients(n=50)andnon-diabetichealthycontrols(n=50).TheexpressionlevelsofcirculatingmiR-126weresignificantlydecreasedinT2Dpatientsand further decreased in DN patients and CAD patients compared to non-diabetic healthy controls(P<0.05).MultivariatelogisticregressionanalysisconfirmedtheindependentassociationoflowermiR-126 levels with T2D, DN and CAD (P<0.05). In the group of patients with DN, circulating miR-126negatively correlatedwith albuminuria andpositivelywith glomerular filtration rate, and in addition,negativelycorrelatedwithfastingglucose(FG),glycatedhemoglobin(HbA1c),triglycerideandlowdensitylipoprotein(LDL)(P<0.05).Moreover,stepwisemultipleregressionanalysis identifiedalbuminuriaasasignificantpredictorofmiR-126(P<0.05),andreceiveroperatingcharacteristic(ROC)analysisrevealedasignificantabilityofbloodmiR-126todifferentiatebetweenT2Dpatients,DNpatients,andnon-diabetichealthycontrols(P<0.05).InthegroupofpatientswithCAD,circulatingmiR-126negativelycorrelatedwithFG,HbA1candLDL(P<0.05).Furthermore,ROCanalysisshowedthatmiR-126inperipheralbloodwasablediscriminatebetweenT2Dpatients,CADpatients,andnon-diabetichealthycontrols(P<0.01).Ourdata suggest thatdecreasedexpressionofmiR-126 is associationwithdiabetic renal andcardiacdefect,andthatcirculatingmiR-126maybeapromisingblood-basedbiomarkerforidentificationofT2DpatientsatriskofdevelopingDNandCAD.O7.Ricerootgermin-likeprotein2genepromoter(OsRGLP2)isresponsivetodifferentplantsignalingmoleculesinpotatoDr.TariqMahmoodQuaid-i-AzamUniversity,Islamabad,PakistanCo-authors:TariqMahmood,FaizaMunir

Germins and germin-like proteins (GLPs) signify a vital plant proteins family taking part innumerous stress linked and developmental activities. In plants under stress situations the signalingcascadesaregenerated,initiatingvariousphysiologicalchangesthateventuallystimulatetheexpressionof particular gene batteries conferring tolerance in response to stress conditions. In present study,regulationof theOryzasativarootexpressedgermin-likeprotein2genepromoter (~1100-bp) ligatedupstreamtotoareportergene(GUS)wasascertainedinresponsetodifferentplantsignalingmoleculesin transgenic potato plants. Fourmajor signalingmolecules i.e. jasmonic acid (JA), salicylic acid (SA),abscisicacid(ABA)andhydrogenperoxide(H2O2)wereexogenouslyapplied,inresponsetowhichthe

29

OsRGLP2promoteractivitywasfoundtobedifferentlystimulated.Asrevealedthroughquantitativerealtime PCR analysis. The finding suggested involvement of JA, SA, ABA andH2O2 dependent signalingpathwaysinstimulationofOsRGLP2promoter.Thisworkisavaluableadditiontotheinformationbeinggathered about themechanisms through which the GLPs are stimulated and exert their role duringexposureofplantstovariousstresses.O8.FromdissectingcomplexnetworksinArabidopsistorevealingnewdevelopmentalmechanismsandadaptivestrategiesindatepalmDr.IkramBlilouWageningenUniversityResearch,Netherlands

Transcription factors function as cell fate determinants. In the Arabidopsis roots, thetranscriptionfactorsSHORT-ROOT,SCARECROWandtheBIRDproteinscontrolasymmetriccelldivisionand endodermal specification through a complex network involving protein complex formation andtranscriptional regulation. Here we report the spatial distribution of these complexes using Försterresonance energy transfer measured by fluorescence lifetimemicroscopy, we show that differentialtranscription factor conformation and promoter specific distribution in living roots imply a complexspatial regulatory network at the level of cell-specific transcription factor interactions. In Date palm,Phoenixdactylifera,weidentifiedcomponentsofthedescribednetworkandmappedtheirexpressionatthecellularresolutionandwearecurrentlystudyingtheirfunctioninbothArabidopsisanddatepalm.Datepalmareamongthefewplantsadaptedtodroughtandtohighlevelsofsoilsalinity,however,themolecular mechanisms conferring date palm tolerance to these conditions remain largely unknown.Recently,wehave shown that selecteddatepalm rootbacterial endophytesalleviatedrought stress.UsingthemodelplantArabidopsis,wereportthatdatepalmbacteriapromoterootgrowthandincreasesystemarchitecturethroughmodulatingtheplanthormoneauxin.WealsoshowthatthesebacteriaactthroughtheepidermallayerandpromoteroottolerancetosalinityanddroughtinArabidopsisanddatepalm plants. Our experimental data combined with mathematical models strongly suggest that thisincreasedtoleranceismediatedbychangesinauxindistributionandtransport.Thesedataprovideanewentryinusingdatepalmgrowthpromotingbacteriaasabiotechnologicalapproachtopromotetolerancetodroughtandsalinityincrops.Inaddition,understandingdevelopmentalprocessindatepalmandusingomics approacheswill be very instructive towards understanding strategies for adaptation to desertconditions.

30

SESSION4:BIOINFORMATICS/PROTEOMICS

I8.GenemodulemultiplicationdrivespathwayexpansioninplantsDr.MarekMutwilMaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,Germany

The survival of species depends on their ability to adapt to new environments. Adaptiveinnovationsrequiregeneticmaterial,mainlyprovidedbygeneduplications,whichcan leadtoneworalternative pathways. However, the principles behind the emergence of such pathways are notunderstood.Here,weshowthatapproximatelyonethirdofthegenesofaplant’sgenomeparticipateinhundreds of alternative pathways, which were primarily generated by single gene duplications. Wedetermined the copy number of alternative pathways by searching for sets of genes, termed genemodules,thatoccurmultipletimesingeneco-functionnetworksofeightplantspecies.Wefoundthatplantsemployageneticcopy-and-pasteprincipletoincreasethenumberanddiversityofgenemodules.Our findings demonstrate that gene module multiplication has provided the capacity for plants toincreasetheirrepertoireofcellularfunctions.I9.DissectionofclimactericfruitripeningusinggeneticandgenomicresourcesinmelonDr.JordiGarcia-MasCenterforResearchinAgriculturalGenomics,Barcelona,Spain

Melon(CucumismeloL.)isacucurbitofhigheconomicvalueandaninterestingmodelsystemtostudyfruitripening,asbothclimactericandnon-climactericvarietiesexistinthisspecies.Theavailabilityofthegenomesequenceandre-sequencingofseveralmelonaccessionsprovidepowerfultoolstohelpcharacterizinggenesinvolvedinclimactericfruitripening.Anintrogressionline(IL)populationinthePieldeSapo(PS,non-climacteric)backgroundcontainingintrogressionsfromPI161375(SC,non-climacteric)hasbeenused tocharacterize twoQTLs,eth6.3andeth3.5,whichprovideclimacteric ripening toPS.eth6.3hasbeencloned,andeth3.5hasbeenmappedinashortgenomicinterval.AnewRILpopulationobtainedaftercrossingPSwith theVédrantais (Ved)climactericmelon type revealed thatclimactericripening is a complex trait. The combination of these genetic resourceswith genomic toolswill helpdissectingthemechanismsthatcontrolclimactericripeninginmelon.

I10.The1000ArabGenome:CharacterizingthegenomeofethnicgroupsinUAE.Dr.HabibaAlsafarKhalifaUniversityCenterforBiotechnology,AbuDhabi,UAE

There is an intolerable gap in the human genome landscape. Human Genome Organisation(HUGO),HaplotypeMap(HapMap)andotherinternationalconsortiahaveallneglectedtoincludeethnicgroupsoftheArab-speakingworldintheirsequencingefforts.ThegenomicorganizationofethnicgroupswithinArabiaispoorlydefineddespitetheregionbeingthecrossroadofhumanmigrationoutofAfricasome50,000to85,000yearsagoaswellasbeingthehubofbidirectionalflowbetweentradersfrom3continents in more contemporary history. There are many examples where lack of information ishinderingtheprovisionofadequateclinicalservices.ThisprojectisaboldsteptoaddressthedeficiencyingenomicdataonpopulationsoftheMiddleEast.Serendipitously,therecentadvancementsinDNAsequencing technology have coincidedwith the need to improve our understanding of the genomicorganizationintheArabianpopulation.

31

O10.IntegratedgenomicanalysisofthehumanmitochondrialtranscriptomeDr.YoussefIdaghdourNewYorkUniversity,AbuDhabi,UAE

Mitochondria are vitally important for basic cellular function. Sequence variation inmitochondrial DNA has been associated with a large number of diseases, as well as fundamentalprocesses suchas aging.However, little is knownabout theextent andnatureof transcriptomic andepigeneticvariationinmitochondrialRNAanditsdownstreameffects.UsingdeepRNAsequencingfromlargenumberofhumansamplesandanelegantbioinformaticapproach,wedocumentmitochondrialRNA sequence variation andquantify the levels RNAprocessing andmodification in population-scaledata.Wefindremarkable levelsofheteroplasmyandvariationacross individuals,aswellassitesthatshowconsistentsignaturesofepigeneticmodification.Mostinterestingly,wefindextensivevariabilityatspecific mitochondrial tRNA positions and report nuclear genetic and gene expression variationassociatedwith it. Theobserved large-scale variationobservedat these sites couldhavea significanteffectonmitochondrialfunction.O11.Anti-breastcanceractivityofcarnosolinvivoandinvitroandinsilicoanalysisofitstargetinteractions.Dr.RabahIratniDepartmentofBiology,CollegeofScience,UnitedArabEmiratesUniversity,UAE

We have previously demonstrated that carnosol, a natural compound, inhibited in vitro cellviability and colony growth, and induced cell cycle arrest, autophagy and apoptosis in humanbreastcancer cells. In the present study, we evaluated the ability of carnosol to inhibit tumor growth andmetastasis invivo.Usingchickembryotumorgrowthassay,weshowedthatcarnosolsignificantlyandmarkedly suppressed tumor growth andmetastasis of breast cancer.Moreover,we found that non-cytotoxicconcentrationsofcarnosoldecreasedthemigrationanddownregulatedtheexpressionandtheactivityofMMP-9 in the triplenegativebreast cancer (TNBC)MDA-MB-231cells.Mechanistically,wedemonstratedthatcarnosolpromotedproteasome-dependentdegradationofp300inallthepanelofbreastcancercellsanalyzed.Furthermore,inadditiontopromotingp300degradation,carnosolinhibitedtheacetyltransferaseactivityofrecombinantp300.Insilicodockinganalysisindicatedthatcarnosolmightinhibitp300HATactivitybyblockingtheentryofacetyl-CoAbindingpocketofthecatalyticdomain.Thisstudyfurtherconfirmscarnosolasapromisinganti-breastcancertherapeuticcompound,andidentifiesitasanewinhibitorofp300tobeaddedtothepanelofinhibitorsidentifiedsofar.

32

33

Abstracts:PosterPresentations

34

POSTERABSTRACTSP1. Using of Whole Genome Bisulfite Sequencing (WGBS) to identify geneexpressionprofileregulatedbycytosinemethylationundersalinitystressindatepalmIbtisamRashidSaidAlHarrasiSultanQaboosUniversity,OmanCo-authors:IbtisamAlHarrasi,MahmoudW.Yaish

Date palm (Phoenix dactylifera L.) is the most important domesticated tree in the arid andsemiarid countriesof theMiddleEastandNorthAfrica. In recentdecades, soil salinityhasbecomeaglobalproblemespeciallyinagriculturallandsofaridandsemi-aridregions.ThereisgrowingevidencethatDNAmethylationplaysanimportantroleinregulatinggeneexpressioninresponsetoabioticstress.Therefore,thisstudyaimstoinvestigatedifferentialDNAmethylationstatusofthreesequencecontexts(mCG,mCHG,mCHH,whereH = A, C or T) that occur in date palmunder salinity stress and controlconditions using cytosine methylome sequencing (methylC-seq) technology. The study also aims toidentify salinity stress-responsive genes regulated by DNAmethylation based onmetylome and RNAsequencing analysis. Pooled DNA and RNA samples from the control and salinity treatments wereanalyzed.Theanalysiscoveredupto324,987,795and317,056,091totalreadsofthecontrolandsalinity-treatedsamples,respectively.Amongthese,19,209,086(5.9%)fromthecontroland19,185,920(6.0%)fromthesalinity-treatedsamplewerealignedtouniquepositionsofmCGsandcovered40%and41%ofthetotalgenomiccytosine(s)withanaveragereaddepth0f17foldcoverageperDNAstrandforbothwithabisulfiteconversionratesof99%and98%forthecontrolandtreatedDNApools,respectively.Theclusteranalysisoftop100differentiallymethylatedsites(DMSs)ofmCG,mCHGandmCHHshowedthatthemajorityofthemCHHsiteswerehypermethylatedinthegenomeofplantsgrownunderthecontrolcondition. RNA sequencing revealed the presence of around 6,000 differentially regulated genes inresponsetosalinityhowever,therelationshipbetweenDNAmethylationandtranscriptomeabundanceisyettobedetermined.Thisworkprovidesanewinsightondatepalmepigeneticregulationmechanismsinresponsetosalinitystress.P2.ComparativegenomicsstudyforAcidithiobacillusferrooxidansRajeshPatelDepartmentofLifeSciencesHemchandracharyaNorthGujaratUniversity,Patan.IndiaCo-authors:RajeshPatel,VishalMevada,RajeshChaudhariandGhelaniAnjana

Acidithiobacillusisthemostimportantgenusofchemolithotrophsthatmetabolizesulfur.Theycanbeisolatedfromrivers,canals,acidifiedsulfatesoils,minedrainageeffluentsandotherminingareas.AcidithiobacillusareadaptedtowidevariationsoftemperatureandpHandcanbereadilyisolatedandmoreenriched.Thegenushasemergedasaneconomicallysignificantbacteriuminthefieldofleachingofsulfideores.InpresentworkanattempthasbeencarriedouttocomparethegenomicinformationofAcidithiobacillus sp. GGI-221 strain of Indian origin with two well-studied genome AcidithiobacillusferrooxidansATCC53993andAcidithiobacillusferrooxidansATCC23270.ATCC23270strainwashavingthehighestgenomesizeof2982,397bpfollowedby2,885,038bpand2,284,565bprespectivelyforATCC53993andGGI221strain.Maximum3086codingsequenceswerereportedforATCC23270followedby2953and2694codingsequencesrespectivelyreportedforATCC53993andGGI221strain.Maximum83RNAsgenewerereportedforATCC23270followedby52and41RNAsforATCC53993andGGI221strainrespectively.Total27subsystembasedannotationwasresultedfromtheRASTbasedannotationprocess.OnlythreesubsystemPhotosynthesis,MotilityChemotaxisandSecondaryMetabolismwereabsentinallthe three strain. Subsystem for Dormancy and Sporulation was similar for all the three strain. For

35

subsystem Potassium Metabolism, Iron acquisition and metabolism, Phosphorus Metabolism andCarbohydratessubsystemcategoryhighersubsystemfeaturecountwasreportedforGGI221strainwithcomparison to other strain. For remaining 19 subsystem category less subsystem feature countwasobtainedforGGI221strainwithrespecttoATCC23270followedbyATCC53993.IncomparisonwithGGI221andATCC23270total1362proteinwerereportedoutofwhich1090werecommonwhile18proteinswerepresent.ThecomparativegenomicsanalysiswasbaseduponRapidAnnotationusingSubsystemTechnology (RAST) comparison andwhole genomealignment approach to findout the similarity anddifferenceinthestrainforunderstandingmolecularevolutionprocessandtheirapplicationregardstoeffectivebiotechnologicalapplicationofstrain.

P3.AnalysisofMendelianrandomizationstudiesofbiomarkersandtype2diabetes:observationsfromanalysisNadiaHussainAlAinUniversityofScienceandTechnology,UAE

Inepidemiology,manybiomarkersarenotedtobeassociatedwithtype2diabetes(T2D)risk.

TheaimofthisstudywastoidentifyandsummarizecurrentevidenceforcausaleffectsofbiomarkersonT2D.

AsystematicliteraturesearchinPubMedandEMBASE(untilOctober2015)wasdonetoidentifyMendelian randomization studies that examinedpotential causal effectsof biomarkersonT2D.Datafromtwolarge-scalegenome-wideassociationstudies(GWAS)wereused:theMeta-AnalysesofGlucoseandInsulin-relatedtraitsConsortium(MAGIC)forglycemictraitsandDiabetesGeneticsReplicationandMeta-analysis (DIAGRAMv3) for T2D. GWAS summary statisticswere extracted for the same geneticvariants,whichwereusedintheoriginalMendelianrandomizationstudies.Twelveoutof21biomarkers(from32studies)havebeenreportedtobecausallyassociatedwithT2DinMendelianrandomization.Most biomarkers that were investigated were from a single cohort study or population. Of the 12identifiedbiomarkers,nominallysignificantassociationswithT2Dorglycemictraitswereachievedforthose genetic variants related to bilirubin, pro-B-type natriuretic peptide, Delta-6 desaturase anddimethylglycine.SeveralMendelianrandomizationstudieshaveinvestigatedthenatureofassociationsofbiomarkerswithT2D.However,therewereonlyfewbiomarkersthatmayhavecausaleffectsonT2D.FurtherresearchisrequiredtoevaluatethecausaleffectsofmultiplebiomarkersonT2Dandglycemictraitsusingdatafromlarge-scalecohorts.

P4.IdentificationofArabidopsiscandidategenesinresponsetobioticandabioticstressesusingcomparativemicroarraysArjunShamUnitedArabEmiratesUniversity,UAECo-authors:ArjunSham,KhaledMoustafa,SalmaAl-Ameri,AhmedAl-Azzawi,RabahIratni,SynanAbuQamar

Plantshaveevolvedwithintricatemechanismstocopewithmultipleenvironmentalstresses.Toadaptwith biotic and abiotic stresses, plant responses involve changes at the cellular andmolecularlevels.Weinvestigatedtheroleofcyclopentenonesinmediatingplantresponsestoenvironmentalstressthrough TGA (TGACG motif-binding factor) transcription factor, independently from jasmonic acid.Candidategeneswere identifiedbycomparingplants inoculatedwithBotrytiscinereaortreatedwithheat,saltorosmoticstresswithnon-inoculatedornon-treatedtissues.About2.5%heat-,19%salinity-and41%osmoticstress-inducedgeneswerecommonlyupregulatedbyB.cinerea-treatment;and7.6%,19%and48%ofgeneswerecommonlydownregulatedbyB.cinerea-treatment,respectively.

Ourresultsindicatethatplantresponsestobioticandabioticstressesaremediatedbyseveralcommonregulatorygenes.ComparisonsbetweentranscriptomedatafromArabidopsisstressed-plants

36

supportourhypothesisthatsomemolecularandbiologicalprocessesinvolvedinbioticandabioticstressresponseareconserved.Thirteenof thecommonregulatedgenes toabioticandbiotic stresseswerestudiedindetailtodeterminetheirroleinplantresistancetoB.cinerea.Moreover,aT-DNAinsertionmutant of the Responsive to Dehydration gene (rd20), encoding for amember of the caleosin (lipidsurface protein) family, showed an enhanced sensitivity to B. cinerea infection and drought. Futureresearchdirections towards a better dissectionof thepotential crosstalk betweenB. cinerea, abioticstress,andoxylipinsignalingareofourparticularinterest.P5.ExpressionprofilingofArabidopsisWRKY33mutantsinresponsetoBotrytiscinereaShammaAl-ShamsiUnitedArabEmiratesUniversity,UAECo-authors:ShammaAl-Shamsi,SynanF.AbuQamar,ArjunSham

Botrytiscinereaisanecrotrophicfungusthatcausesplantdiseasesonawiderangeofcrops.TheWRKY33 transcription factor was reported for resistance to B. cinerea. We compared ArabidopsisWRKY33overexpressinglinesandwrky33mutantthatshowedalteredsusceptibilitytoB.cinereawiththeircorrespondingwildtype(WT)plantsusingthehigh-throughputmicroarraygeneexpressionanalysis.InWT, about 1660 genes (7% of the transcriptome) were up regulated and 1054 genes (5% of thetranscriptome) were down-regulated at least twofold at early stages of inoculation with B. cinerea,confirmingpreviousdataofthecontributionofthesegenesinB.cinerearesistance.TheexpressionsofB.cinerea-regulatedgenes,encodingforproteinsandmetabolitesinvolvedinpathogendefenseandnon-defenseresponses,seemtobedependentonafunctionalWRKY33gene.TheexpressionprofileofOPDA-andPPA1-treatedArabidopsisplantsinresponsetoB.cinerearevealedthatcyclopentenonescanalsomodulate WRKY33 regulation upon inoculation with B. cinerea. These results support the role ofelectrophilicoxylipinsinmediatingplantresponsestoB.cinereainfectionthroughtheTGAtranscriptionfactor.FurtherinvestigationstoelucidatethefunctionandmechanismofcyclopentenonemetabolismduringB.cinereaandothernecrotrophicpathogensinfectionsareunderway.P6.CRELD1genemaypredisposetheriskofAtrioventricularseptaldefectsinDownSyndromepatientsofNorthIndianOriginAmbreenAsimSanjayGandhiPostGraduateInstituteofMedicalSciences,IndiaCo-authors:AmbreenAsim,RohiniSharma,SaritaAgarwal1,InushaPanigrahi

Downsyndrome(DS),alsocalledastrisomy21,isoneofthemostleadingcauseofintellectualdisability. DS is associated with number of phenotypes including Congenital Heart Disease (CHD),Leukemia,Alzheimer’sdisease,Hirschsprung’sdiseasesandothers.DSaffectsabout1in700livebirths.Objectives:ToexploretheroleofCRELD1variantsoncongenitalheartdefects,wesequencedtheexon4,9,10 of CRELD1in the samples from North India. Sixty participants were included in the geneticassociationstudyandtheywerestratifiedasDSwithatrioventricularseptaldefect(AVSD),DSwithoutAVSDandAVSDwithoutDScases.AsignificantassociationwasfoundbetweenDShavingAVSDandsevenpolymorphismswhichincludesrs7699000959(c.368G>A),rs73118372(c.1136T>C,presentat10thexon-intron junction), rs3774207 (c.1119C>T, present at 10th exon-intron junction), rs9878047 (c.1049-129T>C), two deletions of A at positions 9891 and 10281 and g.9768T>A, rs377654613 (c.447 G>A,present at exon 4). Mutation Taster software (http://mutationtaster.org/) and NCBI blast(http://blast.ncbi.nlm.nih.gov/Blast.cgi)wasusedtopredictthevariant.Sincethesevariantsare,presentonlyDShavingAVSDgroup,sowehypothesizethatthesevariantsmayincreasetheriskofAVSDinDSpatients.

37

P7.IdentificationofpremutationandgrayzoneFmr1carrierstatusinreproductiveagewomenbyTP-PCRDeepikaDelsaDeanSanjayGandhiPostGraduateInstituteofMedicalSciences,IndiaCo-authors:DeepikaDelsaDean,SrinivasnMuthuswamy,SaritaAgarwal

FragileXSyndrome(FXS),thesecondmostcommontypeofXlinkedmentalretardationiscausedduetosilencingofFMR1geneduetohyperexpansionandhypermethylationofCGGrepeatatits5’UTR.ExistingdefinitionsdescribethenormalrangeofFMR1CGGrepeatsas6–44,theGrayzone(GZ)rangeas45–54repeats,permutation(PM)rangeas55–200repeatsandFXSpositivefullmutation(FM)caseswith>200repeats.Thoughasymptomatic,PMandGZcarrierfemaleareatahighriskoftransmittingexpandedalleleinthesubsequentgeneration.Owingtohighprevalenceoftheseallelesinthegeneralpopulation(1 PM in 113–259 females and 1 GZ in 66 females), screening of women of reproductive age foridentification of PM andGZ carrier is of great clinical utility. As there is no cure for FXS thus timelyidentificationofcarrierswillopendoorsforgeneticcounsellingandoptionofanti-nataldiagnosisforatriskwomenand thereby reduce the incidenceof FXS in the society. This Paper focusesondoing themolecularcharacterizationofCGGrepeatsequenceatFMR1geneinwomenofreproductiveagebyusingindigenouslydevelopedTP-PCRmethodforidentificationofcarriers.GenomicDNAwasextractedfrom150reproductiveagewomen(17yearsto40years).TP-PCRamplificationforFMR1alleleisconductedandtheampliconsgeneratedweresubjectedtofragmentanalysesandresultsweredocumented.TP-PCRanalysisof150samplesofreproductiveagewomenidentified1.3%(2of150)subjectswithallelesintheGZregion,49and50CGGrepeats,whilerest98.7%(148of150)subjectswithallelesinthenormalrange (29 to 42 repeats). No PM carrier was identified among the studied cohort. Knowledge ofpremutation allele frequency in the general populationwill establish an estimate of FXS burden andofferingpriorgeneticcounsellingmayimprovethequalityoflife,bothmentallyandfinancially.Howeverinspiteofclinicalsignificanceofconductingscreeningprogramforidentificationofthecarrierstatusofreproductive agewomen, such objective had greatly suffered due to unavailability of accurate, costeffectiveandrapidmoleculartechniques.TheindigenouslydevelopedTP-PCRinourstudyischeaperandincomparisontoavailablecommercialkitsandthusithasprovedtobeeconomicallymorefeasibletobeusedinscreeningprogram.

P8.NovelNR1I2mutationsasprobablecauseofintellectualdisabilityInushaPanigrahiPGIMER,IndiaCo-authors:InushaPanigrahi,SiyaramDidel,HoneyReddi,NanditaMullapudi

HumanNR1I2orPXRservesasakeytranscriptionalregulatoroftheCYP3A4gene.Itisinvolved

in transport through the blood brain barrier, and interacts with P-glycoprotein or Abcb1. TheseinteractionshavebeenexploredindevelopingtreatmentforAlzheimer’sdisease.Mentalretardationhasbeen linked to mutations in the HSD17B10 gene, which alters the neuronal steroid and isoleucinemetabolism.WefoundhomozygousNR1I2mutationsinachildwithunexplainedintellectualdisability.Thescreeningformalformationsthroughradiologicalandimagingtechniqueswasnegative.Karyotypingdoneruledoutanyaneuploidies.Targetednextgensequencing(NGS)revealedmutationsintheNR1I2gene-c.242G>Ainexon2inhomozygousstate.Thisvariantisrareinpopulationdatabasesandpredictedtobedamagingoninsilicoanalysis(Polyphen).Theparentswerenonconsanguineousbutcarriersforthesamemutation.Wehypothesize thatNr1I2mutationsmightbecausing thephenotype-microcephaly,andintellectualdisabilityinthechildbyalteringtheneuronalsteroidmetabolism.Keywords:bloodbrainbarrier,pregnaneXreceptor,mentalretardation,microcephaly,steroidmetabolism.

38

P9.GeneticcharacterizationofEpinephelusmarginatusintheMediterraneanSea:ContributionofmicrosatellitemarkersAzizaElglidINSTM,TunisiaCo-authors: AElgid,B.Crouau-Roy,M.N.Bradai

In this study, we used seven microsatellite markers to analyze the diversity and geneticdifferentiation of populations of grouper Epinephelus marginatus from the Mediterranean Central(Tunisia and Libya). Themean number of alleles per locus and the proportion of polymorphic locusshowed the existence of high variability. The two populations analyzed have the same rate ofheterozygosity(He=0.5±0.35),thesevaluesaresimilartothoseobservedinothermarinefish.AnappliedtestonthetwosamplesshowedsignificantdeparturefromHardy-Weinbergequilibrium(FIS=0.177;P<0.001)andFSTvalue (0.024;p<0.05). TheGAG45andGAG007 lociwere responsibleof theobservedheterozygotedeficit.P10.NovelmutationinfamilywithWNT1-relatedosteoporosisSiyaramDidelPGIMERCHANDIGARH,IndiaCo-authors:InushaPanigrahi,SiyaramDidel,VimleshSoni,HaritaKhipal,SujanDhar,NanditaMullapudi

Osteogenesisimperfecta(OI)isaninheriteddisorderwithosteoporosisandrecurrentfractures.

Childrenpresentingwithrecurrentfracturesandbowingoflimbshavesevereformofthedisorder.WNT-1homozygouspatienthavemorefrequentfractureswhileheterozygouscarriersofthemutationinWNT-1genearealsofoundtohaveearlyonsetosteoporosis.WeidentifiedafamilywithWNT-1mutationoutofcohortof30patientsofOIunderfollowupinthegeneticclinic.Theindexcase,a6-montholdshowed41bp deletion in splice region following exon 1 of WNT-1 gene in homozygous state on Sangersequencing. The mutation was reported as likely pathogenic on bioinformatic analysis. To furthercharacterizethesignificanceofthemutationwestudiedhismotherwhois30yearoldwithbluesclerabutnofracture.HerDEXAscanoflumberspineshowedosteoporosisandshewasheterozygousforthemutation.Nextgenerationsequencing(NGS)done for thechilddidn’t showanysignificantvariation inotherOIgenesincludingCOL1A1,COL1A2,SERPINH1,CRTAP,LEPRE1,PP1B,1F1TM5andBMP1genes.Fatheralsohadhistoryofbackachebutwasnotavailableforevaluation.ThusweconcludethatthisnovelvariantidentifiedinthechildwithOIislikelycauseforthedisease.P11.AnalysisofCGGrepeatstatusatFmr1geneinprematureovarianinsufficiencycases:AstudyfromSGPGIMS,LucknowSaritaAgarwalSanjayGandhiPostGraduateInstituteofMedicalSciences,India

FragileXSyndrome(FXS),thesecondmostcommontypeofXlinkedmentalretardationiscausedduetosilencingofFMR1geneduetohyperexpansionandhypermethylationofCGGrepeatatits5’UTR.CurrentdefinitionsdescribethenormalrangeofFMR1CGGrepeatsas6–44,theintermediaterangeas45–54repeats,andthepremutationrangeas55–200repeats.ThoseaffectedbyFXShave>200repeats(fullmutation).PMallelesarehighlyunstableandgetexpandedtoFMwhenmaternallytransmittedin50%oftheoffspring.PMisoftenassociatedwithPrimaryovarianinsufficiency(POI).Inspiteofovariandysfunction5-10%ofPOIwomencanstillconceiveandhaveaviablepregnancywitha50%chanceofgivingbirth toaFXSpositiveoffspring.This studyaims to testFMR1PMstatusbyusing indigenouslydevelopedTP-PCR,forallwomenpresentingwithPOIinordertoruleoutthechanceofbeingPMpositiveasacauseofovarianinsufficiencyandtoavoidtheloadofthisdisorderinthesociety.GenomicDNAwas

39

extracted from 79 POIwomenwith average age of 30.02+5.94 years (17years to 40 years). TP- PCRamplification for FMR1allele is conducted and the amplicons generatedwere subjected to fragmentanalysesandresultsweredocumented.Molecularscreeningof79POIsubjectsresultedinidentificationof2PMpositive(2.5%)subjectswith80and67CGGrepeatnumber.Theremaining77POIsubjectshadCGGrepeatsintherangeof29to40repeats,normalrange.ExtendedfamilyscreeningofPMpositivePOIsubjectsrevealedmaternaltransmissioninoneofthesubjectwhileothersubjectwasfoundtohavea familyhistoryofFXSwithhernephewbeingFMpositive.Conclusions:ScreeningofPOIwomen foridentificationofPMallelesisofgreatclinicalutilityduetotheinherentriskoftheseallelestoexpandFM.As the indigenously developed TP-PCR in our study is cheaper and rapid in comparison to availablecommercialkitandthuscanmeethighdiagnosticoutputrequirement,ithasprovedtobeeconomicallymorefeasibletobeusedinscreeningprogram.TheidentificationofPMcarrierstatusamongthePOI/POFsubjectswill servedual purposeof identifying the cause for ovariandysfunction aswell as providingprenatal diagnosis to prevent the birth of FM male child (Fragile X syndrome). We at SGPGI haveestablishedthistechniqueindigenouslyandareprovidingnationwideserviceforroutinediagnosisandscreeningforFXS.

P12.MetagenomicanalysisofsoilmicrobesandriskassessmentoftransgeniccottoninNorthernKarnataka,IndiausingDGGEandARDRAtechniquesDevarajanThangaduraiDepartmentofBotany,KarnatakUniversity,Dharwad,Karnataka,IndiaCo-authors:DevarajanThangadurai,JeyabalanSangeetha,MuniswamyDavid

Metagenomics,thestudyofgenomesfrommicrobialcommunitiesthanindividualspeciesisthe

novelapproachtodealwith99%ofmicroorganismsthatareunculturableandexistsinseveralextremeenvironments. This approach has the potential to reveal genetic diversity, population structure andfunctionalecosystemsofdiversemicroorganisms.Withtheadventofmolecularandgenomictoolssuchas polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) and amplifiedribosomalDNArestrictionanalysis(ARDRA),itispossibletorevealandunderstandthemicrobialdiversitypatternsfromdiverseecologicalniches.Inthecurrentstudy,theriskassessmentoftransgeniccottononsoil microbial community was carried out using DGGE and ARDRA techniques. Transgenic and non-transgeniccottoncultivatedsoilsampleswerecollectedfromthreedistrictsofNorthernKarnataka inIndia (Dharwad, Belgaum and Bagalkot). Metagenomic DNA was isolated from transgenic and non-transgeniccottoncultivatedsoilsamplesandthesamehasbeensubjectedforPCR,DGGEandARDRAanalysis using several microbial species specific universal primers to analyze the possible effect oftransgeniccottononsoilmicrobialcommunities.P13.BS-SeqanalysispipelinefortargetednextgenerationsequencingdataPSandeepMallyaSchoolofLifeSciences,IndiaCo-authors: SandeepMallya, Pradyumna Jayaram, Smitha Bhat, Shama Prasada Kabekkodu, SanjibanChakrabartyandKapaettuSatyamoorthy

DNAmethylation is thephenomenonof theadditionofamethylgroupespeciallyat the fifthpositionofcytosineinthecontextofCGdinucleotidesthathasthepotentialtoaltergeneexpression.BisulfitetreatmentoftheDNA,convertsthecytosineresiduestouracilleaving5-methylcytosineresidueintact is one of the most persuasive technique to study DNAmethylation. This technique has beenroutinelyusedinSangermethodofsequencingtodeterminethemethylationlevelsattheindividualCGsites.Presently,next-generationsequencingtechniquessuchasBS-Seq(bisulfitesequencing)areusedtodeterminetheextentofmethylationatagenomiclevel.Thisstrategyissuitableforresearcherslookingatregionsofinterestwhomaynothavetheresourceforgenomewidesequencing.TargetedBS-Seq,mayhelpresearchersworkingonselectiveregionsfromlargenumberofsamples,wherespecifictargetsare

40

amplified and sequenced. Currently, most of the analytical techniques and the available tools aredesigned forwholegenomebisulfitesequencingandareunable toefficientlyquantifymethylation intargetedsequencing.Here,wepresentapipelinetoefficientlyanalyzeandquantifymethylationdatageneratedfromsingleendsequencingoftargetedregions.Targetedbisulfitesequencingreadsinfastqformat ispreprocessedtocheck forqualityandcorrected.Thisdata is thenmappedtothereferencesequenceusingabisulfitespecificmapper,andtheresultantdataisquantifiedusingBi-QanalyserHT.The entire workflow is automated using shell scripts and hosted online to make it user-friendly forresearcherstoanalyzeandvisualizetargetedbisulfitesequencedata.

P14. Predictionof transcription factorbinding sites indifferentially expressedgenesforwaterstressinricemediatedbyPseudomonasfluorescensAbidaP.SKeralaAgriculturalUniversity,IndiaCo-authors: Manjesh.S,P.SAbida,P.A.Valsala,RoseMaryFranciesandP.SSreejisha

Theregulationofvariousbiologicalprocesses in theplantsystems,especiallyduringdifferentadverseclimaticconditionsarebroughtaboutbythechangeintheexpressionofdifferentgeneswhichinturnistheresultofthebindingofspecifictranscriptionfactorsintheirrespectivetranscriptionfactorbindingsites(TFBSs).Inthisstudy,anin-silicoanalysisofthedataofdifferentiallyexpressedgenesofriceunderwaterstressmediatedbyPseudomonasfluorescenswasperformedtofindouttheTFBSs.TheAGIcodesofdifferentiallyexpressedgeneswereutilizedforthepredictionofTFBSsbyperformingorthologuesearchagainstArabidopsisgenomeinRGAP(RiceGenomeAnnotationProject)database.Further,TFBSswereidentifiedbyAthaMapdatabase,agenome-widemapofTFBSsinArabidopsisthaliana,andSTIFDB2(StressResponsiveTranscriptionFactorDatabaseV2.0)databasewhichisacomprehensivecollectionofbioticandabioticstress responsivegenes inArabidopsisandOryzasativaL.TheMatrixscore≥10andThreshold≥5wereselectedaspotentialTFBSsusing“Search”toolinAthaMapandZ-scorewithabove1.5were indicated as potential TFBSs in STIFDB2. The significant TFBSswere analyzed based on theparametersprovidedbydatabasesandwerecrossvalidated.TheresultsrevealedthattheWRKY,MYB,HSF, bZIP, ARF, AP2/EREBP, bHLH, Trihelixand ABI3/VP1 TF families and their respective TFBSswerepredicted as functionally significant. These predicted TFBSs would be responsible for the change inexpressionofgenesunderwaterstress.Keywords:Waterstress,rice,TFBSs,AthaMap,STIFDB2.

P15. Identifying a novel deletion mutation in exon 3 of phenylalaninehydroxylase(PAH)geneinphenylketonuria(PKU)patientsofUAEpopulationMuhammadShahidNazirUniversityofModernSciences,UnitedArabEmiratesCo-authors:MuhammadNazir,AhmadElShafey,SheikhaSanqoor,AmalBarnawe

Phenylketonuria(PKU)isaninheritedautosomalrecessivedisorderthatincreasesthelevelsofanaminoacidphenylalanineintheblood.Aliver-specificphenylalanine-4-hydroxylaseenzymeinstructedbyphenylalaninehydroxylase(PAH)genecatalyzesthehydroxylationofphenylalaninetotyrosine.ThemutationsinthePAHgenereducestheactivityofphenylalanine-4-hydroxylaseenzymewhichleadstothe accumulation of phenylalanine in the tissues and plasma of PKUpatients and causes intellectualdisabilityandotherserioushealthproblems.InthepresentstudygeneticmutationsinthePAHgenewereidentifiedinthePKUpatientsofUAEpopulation.Afterobtaininginformedconsent,46Bloodsampleswerecollectedfromeightfamiliesincluding13PKUpatients.DNAextraction,PCRamplificationandDNAsequencingwasperformedtofindthegeneticmutationpresentinPAHgene.Amajordeletionofabout100bpwasobservedinexon3ofPAHgeneofPKUpatientsstudied.Theresultsobtainedinthisstudywerealsocomparedwithpublishedresearchwork.Itwasobservedthatthisnoveldeletionmutationis

41

presentonly inPKUpatientsofUAEpopulation. The futureworkwill include theDNAsequencingofremaining PKU patients, and to measure the oxidative stress using various parameters such asGlutathione/glutathionedisulfide(GSH/GSSG)usingGSSG/GSHQuantificationkitandMalondialdehyde(MDA)byusingthiobarbituricacidAssayintheplasmafromUAEpatientssufferingfromphenylketonuria.This researchworkwill be helpful to find a specificmutations andoxidative stress parameters as anindicative of PKU disease which will ultimately lead to develop a better diagnostic and preventivemeasuresagainstPKUdisease.

P16. Genome-wide analysis revealed that DNA methylation is a dynamicregulatorofsaltandosmoticstressinriceFiazAhmadInstituteofPureandAppliedBiology,PakistanCo-authors:FiazAhmad,JiHuang,Hong-ShengZhang

Genome-wideMeDIP-seqwasperformedtoanalyzetheepigeneticroleofDNAmethylationforsaltandosmoticstressregulationinrice.Overall,weobservedagreatvariationinmethylationofthetargetgenesthatcausedtheirdifferentialexpressionandfinallyregulatedthetargetstress.BycomparingthemethylationlevelofCKvs.NaCltreatmentandCKvs.PEGtreatmentitwasfoundthatcontrolhasmoremethylationquantitythantwostressedsamples.Atthegenelevel,thereadswerealsoquantifiedindifferentgenicregionsincludingCpGislands,upstream2k,five-UTR,CDS,intron,three-UTRandfinallyinvestigated in downstream2k. This analysis revealed that upstream2k (promoter) is highly involved(about43.14% inCK,42.35% inNaCland43.81% inPEG) regionand theothers significantly involvedregionsweredownstream2kandcodingsequences(CDS).ThroughMeDIP-on-chiphybridization33,009different regulatory expressed genes were isolated, and there was a negative correlation betweenMeDIP-seqdata andmRNAdata throughout genome. Similarly, fourmodified formsof geneson thebehalfofpromoterandgenebodymethylationwereobservedthroughoutthegenome.Basedonthesignalintensitiesofgenechipmicroarrays,theexpressedgenesweredividedintofivegroups:lower,low,medium,highandhigheranddifferent levelofmethylationforeachgroupwasanalyzed.RT-PCRandqRT-PCR was performed to confirm the expression patterns of targeted genes for stress regulation.Keywords:MeDIP-on-genechip;DNAmethylation/demethylation;abioticstresses;Oryzasativa.

P17. Identification of superior buffalo bulls for increasing milk productionthroughgenomeanalysesSaherIslamUniversityofVeterinary&AnimalSciencesLahore,PakistanCo-authors:SaherIslamAmnaArshadBajwaWasimShehzadMuhammadAbdullahMuhammadYasirZahoor

Milkproductionenhancementholdspromise for theprosperityandprogressofPakistan.Bullselection is important as compared todamdue to its statusofhalf herd.A superiorbuffalobull hascapabilitytoproducemanythousandoffspringinhislifespanascomparedtodamwhoproducesonly5-6.Tilltodate,thebestprocedureforbullselectionwasestimatedbreedingvalues(EBVs)usingbestavailablecomputersoftware.Theseevaluatingmethodhavetheirownmeritsanddemeritsbutduetoavailabilityofnon-authenticateddata,theirreliabilityhasbeenquestionable.Toresolvethisproblem,bullselectionwillbeproceedexploitingGenotypingbysequencing(GBS)approach.Itisflexible,novel,sufficientlyhigh-throughputandcapableofprovidingacceptablegeneticmarkersforgenomicselectionand genome wide association studies (GWAS). The GBS is simple and highly multiplexed system toconstructlibrariesfornextgenerationsequencing(NGS).Itisexpectedthatsuchselectionwillbemorereliable and help to promote dairy industry when the semen of such superior bulls distributed to

42

Governmentandprivatebreeders.So,Identificationofsuperiorbuffalobullsthroughgenomeanalysesmaybeusefulapproachto increasemilkproduction insubsequentgeneration.Bloodsampleswillbecollected from physically healthy buffalo bulls. Then DNA will be extracted followed by restrictiondigestionofwholegenome.Genotyping-by-sequencing (GBS)willdesigned forefficientgenotypingoflargenumbersofsamplesusingNGSplatform.Genomecomplexitywillreducewithmethylation-sensitiverestrictionenzymedigestion.Theendsofsmallrestrictionfragmentsaresequencedat96-to384-plexlevels per flow channel on the Illumina HiSeq instrument. GBS allows simultaneous discovery andgenotypingofthousandsofSNPs.Thengenomeanalysiswillbeperformedtoidentifythesuperiorbuffalobullsforincreasingmilkproduction.Thisstudywillhelptoidentifythesuperiorbuffalobulls.Genomeanalysesofselectedanimalswillhelptoincreasemilkproductionandalsohelptoimproveeconomyandhealthstatus.

P18. Morphology, physiology and microenvironment determine themorphogeneticpotentialofcelltypesofleafcallusofpearlmilletcultivarsT.V.R.LakshmiUniversityofModernsciences,UnitedArabEmiratesCo-authors:Jawad-Salehi,M.KrishnaRao,T.V.R.Lakshmi.

Plantregenerationisaprerequisiteforgenetictransformationexperiments.Pearlmilletbeinganopenpollinatedcrop,micropropagationismandatorytoobtainpurelinesofadesiredgenotype,towardsthisendeavor,leafexplantsof3cultivarsofpearlmilletIP8182,ICP501andVg272werechosenforthepresentstudy.LeafexplantsoffieldgrownplantsfailedtocallusinMSorN6mediumsupplementedwith2,4-D(1-5.0mg/L)orNAA(5.0mg/L),whilethoseofinvitrogrownseedlingsofallcultivarscallusedinthesamemedia.Leafbladeandleafsheathcallusedin2weeks,leafsheathrespondedearlierthantheblade.Callusinitiatedfromthecutendsorfromtheinjuredregionsofthebladewhichisnotincontactwiththemedium.Explantsfromyoungerleavescallusedbetterthanthoseofolderleaves.AllcultivarsrespondedbesttoMSmediumcontaining5.0mg/L2,4-Dforcallusinduction,withdifferentPercentofsuccess.FourmonthsoldembryogeniccalliofcvIP8182andofVg272differentiatedtoplantletsinMSbasalmediuminamonth;thoseofICP501failedtodifferentiateinthesamemedia.Theplantletsweretransferredto½strengthMSmediumandwerehardenedinHoagland’nutrientcompositionsfor2weeksbeforetheyweretransferredtoautoclavedsoil.Genotypicdifferenceswereobservedamongthethreecultivarswithrespecttocallusingandplantletformation.Thechronologicalseriesofcallusmorphologicaldatastudiedat microscope revealed three distinct types: 1.Multicellular globules, containing bipolar somaticembryoids,2.Long,multicellular,one-cellthickfilamentsand3.Large,club-shapedcells,hostingintra-cellularembryoidlikestructuresinallthreecultivars.Differentcelltypesoftheleafexplantofpearlmilletresponddifferentlytothesamecultureconditions,afeaturesharedamongthethreecultivars.Themicro-environmentand thephysiological conditionof cellsappear tobe responsible for themorphogeneticpotentialofmesophyllcells.

P19.Wholegenomesequencingandgeneannotationofalmond(Prunusdulcis)SumishaHabeebUAEUniversity,UAECo-authors:SumishaHabeeb,AvinashDhar,ShemiRamesh,VivekChandramohan

Prunusdulcis (Almond)isasmalldeciduoustreesbelongingtotheRosaceaefamily.ThestudyfocusesonpresentingthedraftgenomeofP.dulcisalongwithSNPidentification.Therawdata,paired-endsequencelibrariesgeneratedusingIlluminaGenomeAnalyzer IandII (BioprojectaccessionSRP).Thequalityofthereadswascheckedforlow-qualitybases,adaptersandunwantednucleotides.Allthelow-quality readswere trimmedoff thusgivingbetter reads.A totalof+12.19GbptrimmeddatawassubjectedtoDeNovoassemblyusingDDBJpipelineandvelvetforLinuxforvariousK-mervalues.The

43

optimumK-mervalueforP.dulciswasfoundtobe39withthetotalnumberofcontigsandoptimumN50valueas541874and1235respectively.TheassembledsequencewascomparedwithreferencegenomePrunusmumeforgenepredictionandanalysisalongwithSNPdetection.Hereby,thedraftgenomeofP.dulciswascompletedalongwith significantSNPs identification.TheP.dulcisgenome isexpected toprovideinformationonRosaceaeevolutionandalsocanprovideimportantdatawhichcanbeusedfortheimprovementoffruittreeswithmuchmorenutritionalandmedicinalvalue.

P20.Evaluationofsuitablereferencegenesindatepalm(PhoenixdactyliferaL.)underdroughtandsalinitystressforquantitativereal-timePCRHimanshuVishwasPatankarSultanQaboosUniversity,OmanCo-authors: Himanshu V. Patankar, Dekoum. V.M. Assaha, Rashid Al-Yahyai, Ramanjulu Sunkar, andMahmoudW.Yaish

Date palm is a socio-economically important crop plant in the arid and semi-arid regions,supportinghumanpopulationintheMiddleEastandNorthAfrica.Theseareashavebeenlargelyaffectedby drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is arelativelysalt-anddrought-tolerantplant,inwhicheffortshavebeendirectedtoidentifyinggenesandpathwaysthatconferitsstresstolerance.Quantitativereal-timePCR(qPCR)isapromisingtechniquefortheanalysisofstress-induceddifferentialgeneexpression,which involves theuseofstable referencegenesfornormalizinggeneexpression.Inanattempttofindthebestreferencegenesfordatepalm’sdroughtandsalinityresearch,weevaluatedthestabilityof12mostcommonlyusedreferencegenes,usingRefFinderwhichintegratesgeNorm,NormFinder,BestKeeperandComparative∆CTmethods.ThecomprehensiveresultsfromtheseanalysesrevealedthatHEATSHOCKPROTEIN(HSP),UBIQUITIN(UBQ)andYTHdomain-containingfamilyprotein(YT521)weremorestableindrought-stressedleaves,whereasGLYCERALDEHYDE-3-PHOSPHATEDEHYDROGENASE(GAPDH),ACTINandTUBULINweremorestableindrought-stressed roots. On the other hand, SMALL SUBUNIT RIBOSOMAL RNA (25S), YT521, 18SRIBOSOMALRNA(18S);andUBQ,ACTIN,ELONGATIONFACTOR1-ALPHA(eEF1a)weremorestable inleavesandroots,respectively,undersaltstress.Thestabilityofthesereferencegeneswasverifiedbyusingtheabioticstress-responsiveCYTOSOLICCu/ZnSUPEROXIDEDISMUTASE(Cyt-Cu/ZnSOD),ABSCISICACIDRECEPTOR(ABA),andthePROLINETRANSPORTER2(PRO)genes.Thesestablereferencegeneswillfacilitatestudiesongeneexpressionanalysisandfunctionalcharacterizationofgenesassociatedwithdroughtandsalinitytoleranceindatepalm.Keywords:datepalm,drought,salinity,quantitativereal-timePCR,housekeepinggenes,differentialgeneexpression.

P21.Overexpression,purification&antimicrobialactivityofrecombinanthumanßdefensin3ZaighamAbbasUniversityofThePunjab,Lahore,PakistanCo-authors:ZaighamAbbas,ShahbazAslam

Humanßdefensin3(hBD-3)isanovelmemberofdefensinfamilythathasabroadspectrumofantimicrobialactivity.hBD-3alsoexhibitscytotoxicandchemotacticactivitiesunlikeotherdefensins.ThehBD3gene(accessionnumberAJ237673)wassynthesizedfromIntegratedDNATechnology(IDT®).ThegenewasclonedinE.coliDH5αusingpTZ57R/TvectorandrestrictionsitesingeneterminalendswereaddedbyPCR.TheclonedhBD-3genewassubclonedinpET28a(+)expressionvectortotransformBL21(DE3) cells for expression of recombinant hBD-3. The optimum conditions for the expression werefollowing:LBmedia,theinductionwith0.5mMIPTGandincubationat37°Cfor6hours.ThemolecularweightofrecombinanthBD-3is15kDa.RecombinanthBD-3waspurifiedbyelectroelutionandnickel

44

affinitychromatography.AntimicrobialactivityofhBD-3wasdeterminedbydiscdiffusionmethodagainstBacillusthuringiensis,Bacillussimplex,Bacillusmurallis,PsychrobacteralimentariusandStaphylococcusaureus.hBD-3was foundhighlyactiveagainstBacillusmurallisand lessactiveagainstStaphylococcusaureus. Recombinant hBD-3 itsels or in combination with other antibiotics could be treat multidrugresistantpathogens.P22. Construction, expression and purification of thymosin α1-Azu28 fusionproteinfortargetedcancertherapyMuhammadShahbazAslamUniversityofThePunjab,Lahore,PakistanCo-authors: Muhammad Shahbaz Aslam, Arifa Arshad, Aftab Ahmed, Iram Gull, Zaigham Abbas,MuhammadAminAthar

Thymosinα1(Tα1)haswidevarietyoftherapeuticapplicationsandiscurrentlybeingusedeitheralone or in combination therapy for the treatment of several diseases such as cancer. It induce theproductionanddifferentiationoflymphocytesthroughincreasingCD3+,CD4+andCD8+cellproliferation,stimulatingtheproductionofdifferentcytokines,increasingtheexpressionofIL-2receptors,recruitingtheprenaturalkillercellsandincreasingtheproductionofantibodies.AzurinisacuperodoxinproteinofPseudomonasaeruginosawhosepeptidefragmentfromaminoacids50-77(Azu28)actsasapotentialcellpenetratingpeptideandpreferentiallypenetratescancerouscells, stabilizesp53 inside the tumorcellsandinducesapoptosisthroughBaxmediatedcytochromecreleasefrommitochondria.Inthisstudy,geneencodingAzu28wasfusedwithTα1genetoenhancetheanti-cancereffectofTα1andtargetingTα1tocanceroustissues.OverlapextensionPCRwasusedtofuseTα1geneandAzu28geneandfusedgenewasclonedintopTZ57/Rvector.TransformedcloneswerescreenedbycolonyPCRandrestrictionanalysis.Fusiongenewassub-clonedintopET28a(+)andrecombinantfusionproteinwasexpressedinE.coliBL21(DE3)after4hourinductionwith1mMIPTGat370C.TheFusionproteinwaspurifiedNickelchromatography using 150mM imidazole and characterizedwithwestern blot and immune dot blotassays.It isconcludedthatsynergiceffectofTα1andAzu28willnotonlymakeitmoreeffectiveanti-cancerdrugbuttumorpenetratingabilityofAzu28willmakeittargetedtherapeutictoolforsafeandsecuretreatmentofpatients.P23.TestimonyofrbcLandmatKlociforeightUnitedArabEmiratesnativeplantspeciesAlagappanKumarappanCollegeofBiotechnology,UniversityofModernSciences,UnitedArabEmiratesCo-authors:AlagappanKumarappan,LinaMaloukh,HoussamAlWakil,MohammedHJarrar,VenkataTRajyalakshmi

Plant DNA barcoding is a tool for rapid species identification that consists of a short DNAsequenceuniquetoeachspeciesontheplanet.AninternationalbodyofthePlantWorkingGroup(PWG)oftheConsortiumfortheBarcodingofLife(CBOL)studiedandvalidatedafewgeneloci;recommendedtwo candidate-plastid sequences (rbcL andmatK) for species identification. The flora of United ArabEmirates(UAE)isidentifiedbasedontheirmorphologyandnobarcodeisavailableforanyoftheplantspecies so far. An attempt is made to develop barcode for a small group of 8 native plants (2monocotyledons and6dicotyledons)with rbcL andmatKplastid gene sequences.GenomicDNAwasisolatedfromthe8plantspecies,therespectiveDNAwasamplifiedwithrbcLand/ormatKprimersetsfollowingthestandardprotocols;theamplifiedPCRproducts(querysequences)werematchedwiththeclosestmatchintheNationalCenterforBiotechnologyInformation(NCBI).MEGA5softwarewasusedtoconstructphylogenetictreeanalysisbyusingneighbor joining(NJ)method.Theresolvingpowerof

45

rbcLwasaccurateamongall8plantswhilethediscriminatorypowerofmatKmatchedfor6outof8plantspecies.WeconcludethatforthetestedgroupofplantstherbcLregioniswellconservedthanmatK,atentativepossibilitytobeverifiedforalargersampleofplantspecies.Furtherworkinthisdirectionwillenableconformationofmorphological.P24.UsingnovelremotesensingapproachesandstableisotopetopredictdroughttoleranceinIPTtransgeniccreepingbentgrassinthefieldRamziBelkhodjaKhalifaCenterforGeneticEngineeringandBiotechnology,UAEUniversity,AlAinCo-authors:RamziBelkhodja,MartinKottakcal,SalimaAlSenaaniandKhaledAmiri

Water availability is a significant challenge to plant production in United Arab Emirates andincreasedroughttoleranceofplantsisoneofthenationalpriorityandstrategyforthecountry.Inthelast20years,genomicsfordroughtresistance,includinggenediscoveryandfunctionalgenomics,havebeen increasing exponentially. Since then, many transgenic plants harboring genes that encode fordroughtresistancehavebeenproducedinmanymodelandcropsplants.Inthiswork,wehaveevaluateddifferenttransgeniccreepingbentgrasslineswithIsopentenyltransferase(IPT)gene(underthecontrolofdrought inducedpromoterPSARK)thatencodesarate limitingenzymeincytokininbiosynthesisthatinduceadelayinleafsenescenceunderdroughtstress.Theexperimentwascarriedoutinthefieldwith3transgeniclinesandwildtype(nontransformed)ascontrol.Fortheassessmentofthegreenbiomass,we have used a novel affordable and easy-use methods based on vegetation indices derived fromconventionalcamera.Ourmeasurementsconfirmthatoneofthetransgeniclines(IPT-9),keepagreenbiomassduringtheperiodofdroughttreatments.TheseresultswerecorroboratedwithRT-PCRanalysisand Carbon Isotope discrimination. These preliminary data have to be confirmed by other lines indifferentenvironmentsandanalyzetheGxEinteractionandgeneexpression.P25.Anti-malarialdrugdiscoveryusingintegrativebiologyandsystemsbiologyVishalMevadaDepartmentofLifeSciencesHemchandracharyaNorthGujaratUniversity,Patan,IndiaCo-authors:VishalMevada,RajeshChaudhari,PravinDhudhagara,RajeshPatel

Therewereanestimated198millioncasesofmalariaworldwide(range124–283million)in2013andanestimated584000deaths(range367000–755000).90%ofallmalariadeathsoccur inAfrica.Emergingparasite resistance toantimalarialmedicinesandmosquito resistance to insecticides, if leftunaddressed, could render some of the current tools ineffective and trigger a rise in globalmalariamortality. The P. falciparum, Anopheles gambiae and Homo sapiens genome sequences have beencompletedinthebetween2000-2002andrepresentnewstartingpointsinthecenturies-longsearchforsolutionstothemalariaproblem.Inthepastfewyears,therehavebeenstrongdemandstogenerateandintegratemolecular,functionalandpharmacologicaldataintoacommonmalaria-relatedchemogenomicknowledgespace.Inthepresentwork,wehaveexperimentedtheintegrativeapproachofusinginsilicostudyfortargetfindingandmoleculardocking,pharmacophorebasedscreeningincombinationwithinvitro study for screening novel drug candidate against P. falciparum. The Research Database wasdevelopedfromthegenomics,literatureandligandinformation.Genomedatawereincorporatedintopathologics software and embedded further with current literature information and made availableoffline andonline for researcher. Search for novel anti P. falciparumwas done from theHeterobasedatabase library comprisingmore than 3000 compounds reported from the Ph. D thesis available inGujarat state University Library. The consecutive in silico and in vitro screening resulted in 27 leadcompoundswithpotentialantiP.falciparumactivity.Theleadcompoundscanbeexploredeventuallyasdrug candidate for antimalarial drug discovery. The consensusmatrix analysis formolecular docking,Structure-basedpharmacophoreand ligand-basedpharmacophorebasedwaseffective to reduce the

46

shortlisted compounds from individual screening to consensus lead compound with augmentedassurance.ThemajorstudywasconcenteredonthePlasmepsintargetfromtheP.falciparumandthetopcompoundrecordedfrominsilicoscreeningwas3001.Consequentlycompound3001andsimilarcompoundswereexploredwithinvitrostudyanddispalyedcomparabletrendinactivity.However,theactiveleadcompoundsofinvitrostudywere3004,3007and3010againstbothP.falciparumandP.vivax.Asineithercasecompound3007havethemostversatileabilitytobindwiththemultipletargetsincludingmulti-drugresistanttargets.Substantially,compound3007wasappearedasthebestleadcompoundofthepresentstudy.Theinsilicoscreeningresultsproposedtheneedoffurtherstudyoncompound3007forantiP.vivax.andanti-HIVdrugdiscovery.PolypharmacologyinsilicoscreeningagainstseventargetsforP.falciparumextracted22compoundswithexceptionalpotential.Furthermore,thecompound518(4-(2-chloro-6,8-dimethylquinolin-3-yl)-6-(3-nitrophenyl)-3,3a,4,5-tetrahydro-2H-indazol-3-one) wasobtainedastheoutstandingcompoundfordualtargetingtheHIVandP.falciparuminthecurrentstudy.Thiscanbefurtherexploredwithinvitrotesting.

P26.In-silicodesignofinhibitorsforcyclindependentkinase2moleculeinbreastcancer:acomputationalapproachSreejishaP.S.UnitedArabEmiratesUniversity,UnitedArabEmiratesCo-authors: P.SSreejisha,S.Achuthsankar,AburawiElhadiH,EmeraldStarling,P.SAbida

InBreastcancerdisease,thecellsinthebreastbegintogrowoutofcontrolandmetastasizetoinvadenearbytissuesandevenusuallyspreadthroughthebody.Insignalcascademechanisms,includingphosphorylation regulateactivitieswithin the cell.A change in the levelofphosphorylation canhavesignificanteffectsoncellularactivity.Cyclin-dependentkinase2(CDK-2) isoneofthosekinaseswhichplayscentralrolesinregulationofcellcycleprogression,transcriptionandmetabolism.DeregulationofCDKsduetoamplification,overexpressionormutationcontributestoproliferationofcancercells.Thesekinases therefore constitute biomarkers of proliferation and attractive pharmacological targets fordevelopmentof anticancer compounds.HenceCDK-2wasusedas apotential targetmolecule in thiscomputer aided drug designing. The in-silico study was used to identify the inhibitors, using threedimensional structures for Breast cancer susceptibility protein CDK-2 structure using Bioinformaticssoftware. Several bioinformatics tools and softwarewereused todetermine thepropertiesof targetmoleculeandtodevelopnewandimprovedleadcompounds.3DstructureofCDK-2wasobtainedfromProteindatabank.ThestructurewasvalidatedbyRamachandranplotanalysisandtheactivesiteofthetargetmoleculewasfoundoutusingCASTpserver.Variouschemicallibrariescontainingthe3Dstructureofapproximatelyfivehundredmoleculeswerevirtuallyscreenedagainstitemployingmoleculardocking.The computational experiments undertaken resulted in the identification of three molecules, whichdockedwellintotheactivesiteofthetarget.ThesethreemoleculesobeyedLipinski’sruleoffivewhichhavebeenidentifiedaspotentialanti-canceragentsinthisin-silicostudy.

47

P27.SynthesizednovelFmoc-2-aminothiozole:protectiveagainstcadmiuminducedapoptosis,teratogeniceffectonzebrafish(Daniorerio)embryosandmoleculardockingstudiesVaishnaviMSiddagangaInstituteofTechnology,IndiaCo-authors:VaishnaviM,HSLalithamba,MohankumarThangavelVivekChandramohan

The1,3Thiozoleisaninterestingbuildingblockinnaturalandsyntheticcompoundwhichhavebeenstudiedasavariouspeptidebasedcompound.Duetohealthaspectsof thiozole,weselectivelysynthesized Fmoc-2-aminothiozole-2-phenylalanine and Fmoc-2-aminothiozole-2-trptophan based onHantzach’s protocol via mixed anhydride reaction forming the intermediates diazomethyl ketone,bromomethylketoneandundersonicationthiozoleswas formed.WefoundprotectivemechanismofFmoc-2-aminothiozole-2-phenylalanine and Fmoc-2-aminothiozole-2-trptophan against cadmiumintoxicated zebrafish embryos (Danio rerio). Embryos exposed to cadmium exhibited significantlyreducedsurvival,delayedhatching,increasedcardiacfunctionandphenotypicabnormalitiesat24,48,72and96hpf.Finally,weevaluatedinordertocheckthedruglikenessofthesynthesisedcompoundmoleculardockingwasdoneagainsttheproteininvolvedincontrolofvarietyofcellularprocesses.The3Dx-raycrystallographyproteinstructurewasretrievedfromtheproteindatabank(PDB)PDBID:1BX6andminimizationwascarriedout.SynthesisedcompoundsweredesignedandcheckedforLipinskiruleof 5,ADMETproperties to find thedruk likeliness. These compoundswere allowed todockwith theproteinfor200defaultiterationsandtheinteractionsofthecompoundsandproteinwasanalysedandalsotheHydrogenbondinteractionswasalsoobtainedbythemolecules,selectedleadcompoundsweresubjectedintomoleculardynamicstounderstandthestructurestability.Ourresultsshownlesstoxicitycomparestandardcompounds.

P28.Structuralinsightsintothepolypharmacologicalactivityofdietaryflavonolsonserine/threoninekinasesBincyBabyUAEUniversity,UnitedArabEmiratesCo-authors:BincyBaby,PriyaAntony,WalaaAlHalabi,ZahrahAlHomedi,RanjitVijayan

Discoveringordesigningdrugmoleculesthatcansimultaneouslyinteractwithmultipletargetsisgaininginterestincontemporarydrugdiscovery.Serine/threoninekinasesareattractivetargetsamongprotein kinases for therapeutic intervention in oncology due to the altered expression in cellularphosphorylation.Quercetin,anaturallyoccurringflavonol,hasattractedattentionforitsabilitytoinhibitvariouscancercelllines.Thebiologicalactivityofquercetinglycosideshasalsoreceivedsomeattentionduetotheirhighbioavailabilityandactivityagainstvariousdiseasesincludingcancerbuthasbeenstudiedto a lesser extent. This study explored the structural insights of themultitarget inhibitory activity ofquercetin and its glycoside derivative, isoquercitrin on serine/threonine kinases using molecularmodeling. Structural analysis showed that both quercetin and isoquercitrin exhibited good bindingenergiesandinteractedwiththekeyaspartateresidueinthehighlyconservedAsp–Phe–Glymotif.Theresults indicate that isoquercitrin could be a more potent inhibitor of several members of theserine/threoninekinasefamily.Thus,thisstudyprovidesastructuralpictureofthemultitargetinhibitorypropertyofquercetinanditspotentialtobeachemicalplatformforoncologicalpolypharmacology.

48

P29. Inhibiting non-receptor tyrosine kinases associatedwith prostate cancerusingpolypharmacologicalnaturalcompoundsPriyaAntonyUAEUniversity,UnitedArabEmiratesCo-authors:PriyaAntony,BincyBaby,ZahrahAlHomedi,WalaaAlHalabi,RanjitVijayan

Prostate cancer is one of the most frequently diagnosed forms of cancer with high globalincidenceandmortalityrate.Proteinkinasesareattractivetherapeutictargetsagainstprostatecancerduetotheirvitalroleinregulatingvariouscellularprocesses.Overexpressionofseveralnon-receptortyrosinekinases(NRTKs)havebeenwidelyobservedinprostatecancer.Inthisstudy,alargecollectionofnaturalcompoundsfromtheInterBioScreenlibrarywasvirtuallyscreenedagainstthreemajorkinases-Bruton's tyrosine kinase (BTK), focal adhesion kinase (FAK) and Src kinase to identify novelpolypharmacological molecules that could inhibit the activity of these proteins. Molecular dockinganalysis revealed that four natural compounds that are structurally similar, possessedpolypharmacologicalpropertiesbyinteractingwiththesethreeNRTKsinasimilarmannerbyorientingone end towards the hinge region and the other towards the activation loop. Binding score andinteractionsof thesenatural compoundswerebetter than currently available kinase inhibitors. Thus,thesenaturalmoleculescouldbeaframeworkfordevelopingnovelkinaseinhibitorsforthetreatmentofprostatecancer.

P30.Bioinformaticmethodologiesrevealmetagenomicdepictionof Indianhotsprings’microbialcommunityPravinDudhagaraDepartmentofBiosciences,VeerNarmadSouthGujaratUniversity,Surat,IndiaCo-authors:PravinDudhagara,AmitMangrola,AnjanaGhelani,RajeshPatel

High-throughput sequencing allows quick and inexpensive analysis of econiches andrevolutionizingmicrobialecologystudiesofextremeenvironments.However, theeffectiveanalysisofthe huge biological data is a key challenge of computational biology. In this study, we analysed 9metagenomes of Indian hot springs and their comparative studies were conducted using MG-RAST.Furthermore,thephylogeneticandfunctionalcharacterizationsofthemicrobialcommunitieshotspringswereperformedtodecodethehiddenmicrobialecosystem.Allhotspringswerefoundtodominatedbybacteria and viruseswith a significant presenceof unassigned sequences. Thedominating Firmicutesphylainmostofthehotspringwasreportedduetotheirthermo-tolerancenature.However,Taptapani,Arti, and Unkeshwar hot springs dominated by Bacteriodetes, Cyanobacteria, and Actinobacteriarespectively indicated the geographic variation play the significant role in a distribution ofmicroorganisms.Deinococcus-Thermusgroupin5hostspringcanbesignificantlyusedasametagenomicbiomarker to identifies the radioactive substances. The co-occurrence association between complexmicrobialcommunitiesattaxonomicandfunctional levelwerealsosignificant.Thedetectionofstressresponse genes in hot springmetagenomes reveals the secrets hold by thermophiles for survival atelevatedtemperature.Uncharacterizedgenesdetectioninallmetagenomesisthekeyinventiontowardsthehiddenunculturablemicrobes.Thediversityofunculturablebacteriainallhotspringsdemonstratesavastgenepoolforbiotechnologicalexplorationandcreatesamajorfaceformicrobiologiststoknowthe phylogenetic correlation and ecological implication of habitats. The result also enlightens theabundance,diversity,distributionandcoexistenceofmicroorganisms.

49

P31.AdvancedstatisticalmethodsingeneticassociationstudiesSureshKumarSharmaPanjabUniversity,Chandigarh,India

Duringthelasttwodecades,manystatisticaltestshavebeenproposedforgeneticassociationsaswellasfornextgenerationsequencing.Thesetestsareusefultoanalyzegenotypeandnextgenerationsequencingdataand todetect genetic variations thatmaybe responsible fordiseaseprogression. Inassociationstudies,standardapproachistoconsideronephenotypeatatimebutthenewapproachesduringthelastfewyearshavefocusedonmultiplecorrelatedphenotypesandgenotypesjointly.Manygenetic associations are observed through phenotypes and genotypes and it could be affected bycovariates like age, sex etc. Variables included in genetic studies are measured on different scales.Recognizingthesescalesisanimportantpartofanyresearch.Identificationofoutliersinunivariateandmultivariateanalysisisalsoanimportantaspect.SequentialKernelAssociationTest(SKAT)forrareandcommonvariantsiscomputationallyefficientregressionmethodtotestforassociationbetweengeneticvariants(commonandrare)inaregionandacontinuousordichotomoustraitwhileeasilyadjustingforcovariates. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation inexpression levels ofmRNAs. eQTLs thatmap to the approximate location of their gene-of-origin arereferredtoaslocaleQTLs.Incontrast,thosethatmapfarfromthelocationoftheirgeneoforigin,oftenondifferentchromosomes,arereferredtoasdistanteQTLs.Often,thesetwotypesofeQTLsarereferredtoascisandtrans.Inthistalk,Iwillbecoveringsomepartofresearchmethodology,identificationofoutliers,differentmeasuresofassociationusefulingeneticstudiesandsomepartofeQTLanalysis.

P32.EHealthapplicationsforclinicalgeneticsMuhammadJawadHashimUnitedArabEmiratesUniversity,UAE

The field of genetics is advancing at an accelerated pace. Clinical genetics is the practicalimplementation of genomics and bioinformatics for guiding medical decisions in patient care.Applications(orinformally‘apps’)formobileelectronicdevicessuchastheiPadandAndroidtabletsandsmartphoneshavethepotentialtoassistgeneticistsatthepointofcare.Inthisstudy,currentlyavailablemobileapplications(‘apps’)werereviewedforgeneticcounsellingbyfamilyphysiciansandotherhealthprofessionalsprovidingcaretofamilieswithinheritabledisorders.MethodsGeneticsappsweresearchedthroughMEDLINEviaPubMedusingtheterm“geneticmobileapp”,withoutrestrictiononlanguageordateofpublication.AconcurrentsearchwasconductedoniTunes[AppleInc.]andtheGooglePlayStore[https://play.google.com/store/]forappsontheseplatforms.Appswerereviewedfromthepublisher’sdescriptionsanduser’s comments. Functionalitywasassessed for appsbasedon typical clinicalworkenvironmentbasedonthefollowingcriteria(1)applicabilitytoclinicalgenetics,(2)usabilitydefinedasintuitivenessandease-of-use,and(3)contentvalidity.TheMEDLINEsearchyielded86totalarticles,oftheseonly3wererelevanttothestudy.Selectedarticles includedreviewsofgeneticsappsaswellasguidelines for development. A survey of 166 people on use ofmobile apps for personswith geneticdisorders such as Down's syndrome, Williams' syndrome, and 22q11 deletion syndrome found anencouragingattitude.Unfortunately,veryfewstudiesevaluatedtheclinicaleffectivenessoftheseappsin improvingpatientoutcomes.Oneexceptionwasan iPhoneapp thatassistedpatientswith familialdysautonomiaforbalanceandgaittraining.Wefoundnoappsthatpromiseddirect-to-consumergenetictestingathomebasedonsinglenucleotidepolymorphisms(SNPs).Fewappsmetourcriteriaforusability,specificallyforchildrenwithgeneticdisorders.Asmallrangeofmobiledevice/smartphoneapplications(‘apps’)existforclinicalgenetics.Mostoftheseappshavenotbeenvalidatedforclinicaleffectiveness.Whilepromisingasusefultoolsforimprovingcareofpersonswithgeneticdisorders,theseappsneedfurtherrefinement.

50

P33.ArtificialIntelligence(AI),GenomicsandPersonalizedMedicineShaheenNShahGenomicsCentral,IndiaCo-authors:ShaheenNShah,SafaShaheen

Theconceptofpersonalizedmedicinehasevolvedwithcurrent trends ingenomicsgiving theextrabitofpersonalization,intheoryatleast.Whileclassicalgenomics(withoutusingMl/AI)stillisyearsaway from delivering tailored personalizedmedicine and we are yet to fully explore the solutions -modern&alternates,andthesolutionsthatcurrentlybeingspecializedismajorlyinmodernmedicine.From the recent nature article 0 speaks of fairly direct natural extract for cancer treatment, thenatural/alternateformsdofindtractionintheIndiansubcontinent,andhavehadselectiverelativeimpactintreatingvariousailments,thoughdisputableinsomecircles.InplacesliketheMiddleEasthavehadtheUnaniformaswell,thefocusherebeingdifferent"bodytypes"respondingdifferentlytowaysofmedicine, with renowned hospitals like the Amrita 1 giving IntegratedMedical treatment. AI basedtreatmentslikeAIM2iscurrentlysettomodernmethodologyoftreatmentbasedoftheircases'databasederived frommodernmedical techniques only. Herewe face two fronts A. the AI partwhere in theMachineLearningneedstobeorientedinclusiveoftheproven/documentedsuccesscasesinAlternativeformsbeinAyurveda,Unaniand/Homoepathy,encompassingagreater&morechallengingdeviationsB.TheGenomicspartwhereinactiveeffortstoseehowthe isolatedmetaboliteworksatthe"omics"levels:Middleeastern/GCCCountriesliketheUAEhavingasizeableexpatpopulationcanplayhosttothemyriadofphenotypespresentintheirmixedpopulation-ArabEuropeanAsianmix3.AsforthelocalUAE population studies, cue can be taken from the Qatar genome 4 where in some families (likeSuawaidis)shareancestryacrosstheborders.Inmattersoftranscontinentaldiversityandwellaseaseofaccesstothe“local”Indiansubcontinentpopulation(ofIndiaPakistanNepalandSrilanka)effortsintheUAEintheabovedirectionincollaborationwithparentscountrieswouldbearconsiderablefruit.Hereweareinaraceagainsttime,atimewhereinevercomplexcancerleadstheworldsdeathcases5Weareat a unique juncture in history wherein highly efficient machine learning is being deeply genomicscrunchingbigdata,pacingpersonalizationofmedicine-onlyintegratingmedicineofallprovenformscandojusticetotheterm“personal”.

51

INDEXOFPARTICIPANTSZaighamAbbas,UniversityofThePunjab,Lahore,PakistanSynanF.AbuQamar,UnitedArabEmiratesUniversity,UAESaritaAgarwal,SanjayGandhiPostGraduateInstituteofMedicalSciences,IndiaFiazAhmad,InstituteofPureandAppliedBiology,PakistanIbtisamRashidSaidAlHarrasi,SultanQaboosUniversity,OmanGhadaAl-Kafaji,ArabianGulfUniversity,BahrainHabibaAlsafar,KhalifaUniversityCenterforBiotechnology,AbuDhabi,UAEShammaAl-Shamsi,UnitedArabEmiratesUniversity,UAEPriyaAntony,UAEUniversity,UAEPereArús,IRTA,CenterforResearchinAgriculturalGenomicsCSIC-IRTA-UAB-UB,SpainAmbreenAsim,SanjayGandhiPostGraduateInstituteofMedicalSciences,IndiaMuhammadShahbazAslam,UniversityofThePunjab,Lahore,PakistanBincyBaby,UAEUniversity,UAERamziBelkhodja,KhalifaCenterforGeneticEngineeringandBiotechnology,UAEUniversity,UAEIkramBlilou,WageningenUniversityResearch,NetherlandsEduardoBlumwald,UniversityofCalifornia,Davis,USAVivekChadramohan,SiddagangaInstituteofTechnology,IndiaJosédeVega-Bartol,TheGenomeAnalysisCenter,NorwichResearchPark,Norwich,UKDeepikaDelsaDean,SanjayGandhiPostGraduateInstituteofMedicalSciences,IndiaSiyaramDidel,PGIMERChandigarh,IndiaPravinDudhagara,VeerNarmadSouthGujaratUniversity,Surat,IndiaAzizaElglid,INSTM,TunisiaAsmaaElzawahry,NationalCancerCenter,JapanJordiGarcia-Mas,CenterforResearchinAgriculturalGenomics,Barcelona,SpainIvoGlynneGut,CentroNacionaldeAnálisisGenómico(CNAG-CRG),Barcelona,SpainRodericGuigó,CenterforGenomicRegulations,UniversitatPompeuFabra,SpainSumishaHabeeb,UAEUniversity,UAEMuhammadJawadHashim,UnitedArabEmiratesUniversity,UAEKhaledHazzouri,NewYorkUniversity,AbuDhabi,UAENadiaHussain,AlAinUniversityofScienceandTechnology,UAEYoussefIdaghdour,NewYorkUniversity,AbuDhabi,UAERabahIratni,UnitedArabEmiratesUniversity,UAESaherIslam,UniversityofVeterinary&AnimalSciencesLahore,PakistanParamjitKaur,PanjabUniversity,Chandigarh,IndiaPavelKerchev,DepartmentofPlantSystemsBiology,VIB,BelgiumAlagappanKumarappan,UniversityofModernSciences,UnitedArabEmiratesT.V.R.Lakshmi,UniversityofModernsciences,UAEVaishnaviM.,SiddagangaInstituteofTechnology,IndiaTariqMahmood,Quaid-i-AzamUniversity,Islamabad,PakistanSalmaAMahmoud,KingFaisalSpecialistHospital&ResearchCentre,SaudiArabiaPSandeepMallya,SchoolofLifeSciences,IndiaR.Manimekalai,ICAR–SugarcaneBreedingInstitute,IndiaVishalMevada,HemchandracharyaNorthGujaratUniversity,Patan,IndiaRichardMichelmore,UniversityofCalifornia,Davis,USAMarekMutwil,MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,Germany

52

MuhammadShahidNazir,UniversityofModernSciences,UAEInushaPanigrahi,PGIMER,IndiaRajeshPatel,HemchandracharyaNorthGujaratUniversity,Patan.IndiaHimanshuVishwasPatankar,SultanQaboosUniversity,OmanAbidaP.S.,KeralaAgriculturalUniversity,IndiaSreejishaP.S.,UnitedArabEmiratesUniversity,UAEShaheenNShah,GenomicsCentral,IndiaArjunSham,UnitedArabEmiratesUniversity,UAESibaShanak,ZentrumfürBioinformatik,UniversitätdesSaarlandes,GermanySureshKumarSharma,PanjabUniversity,Chandigarh,IndiaFloraTassone,UniversityofCaliforniaDavis,USAMarkTester,KingAbdullahUniversityofScienceandTechnology,SaudiArabiaDevarajanThangadurai,KarnatakUniversity,Dharwad,Karnataka,IndiaMahmoudYaish,SultanQaboosUniversity,Oman

53

NOTES

54

NOTES

55

56

Organized by Department of Biology, College of Science &

Khalifa Center for Genetic Engineering and Biotechnology United Arab Emirates University

Supported by

Sponsored by