MED499UndergraduateResearchProjectDescription

IparticipatedinundergraduateresearchunderDr.Bomsztyk,MD,whoisaProfessorof
MedicineandanAdjunctProfessorofPharmacology.Dr.Bomsztykslabstudiestheepigenetic
andchromatinmodificationsthatresultinthealteredgeneexpressionthatcharacterizesmany
majorhumandiseases,notablycancer,diabetes,andillnessassociatedwithinflammationand
infection.Oneofthecurrentchallengesinthisfieldisidentifyingtheproteinprotein
interactionsresultingfromepigeneticmodifications.Toaddressthis,Dr.Bomsztykslabworks
indevelopinghighthroughputandsensitivityepigenetictrackingmethods,andprogramsfor
computationalanalysis.Particularly,thedevelopmentoftheMatrixChromatin
Immunoprecipitation(MatrixChIP)assaytosimultaneouslymeasureDNAmethylationand
manyothergenomiceventswithgreaterspecificity,lessnonspecificbinding,andinmuchless
time,opensopportunitiesforunderstandingthecomplexgeneticmodificationsandinteractions
ofmanydiseases.MorecanbereadinDr.Bomsztyks2011paper,YuJ,FengQ,RuanY,
KomersR,KiviatN,BomsztykK.MicroplatebasedplatformforcombinedchromatinandDNA
methylationimmunoprecipitationassays.2011.BMCMolecularBiology.2011Nov18;12:49.
Iworkedapproximately9hoursperweek(3credits)fortwoquarters,WinterandSpring
of2013,foratotalof6creditsinMED499,thatIwishtohavecounttowardsmybiologylab
requirements.Atthetimeofmyinternship,thelabwasfocusedparticularlyonepigenetic
changesinacutekidneyinjury(BomsztykK,DenisenkoO.EpigeneticalterationsinAcute
KidneyInjury.SeminarsinNephrology.2013Jul;33(4):32740.)Theresearchquestion
addressedwas,wasistheroleofepigeneticchangeandchromatinremodelinginthe
pathogenesisofkidneydiseasefollowingacutekidneyinjury?AsIwasnewtothelab,Iwas
onlyassistinginthisproject.Myprimaryrolewasgaininganacademicunderstandingof,and
physicalexpertiseintheexperimentaltechniquesthelabhadspecificallydevelopedfortheir
epigeneticinvestigations.Uponshowingproficiencyinthetechniqueswithcontrolantibodies
andDNAsamples,Iwastoaidinrunningassaystoclassifyepigeneticmarker(suchas
phosphorylation)associationswithdifferentantibodies,andinterprettheresultsonacomputer
program.
Specifically,IfirstlearnedhowtodoPCRonmicrochipplates,andlater,Ilearnedthemore
detailedMatrixChIPprotocol,whichassaysepigeneticinteractionsbyattachingantibodiesto
thewallsofa96wellplate,washingwithchromatin,degradingunboundchromatin,andfinally
doingPCRontheresultingantibodyboundDNA.ThePCRamplificationresultsarethen
analyzedbyacomputerprogramthatIlearnedhowtooperate,todisplaychromatinantibody
associationsinaclearway.Thebenefitsofthismethodarethatmultipleantibodiescanbe
crosstestedonasingleplate,andmanyroundsofPCRcanbeperformedfromoneMatrixChIP
plate,whichisespeciallyusefulgiventhecomplexnatureofepigeneticalterations.
Thisresearchprojectwillgreatlyenhancemyunderstandingofmolecular,cellularand
developmentalbiology(mymajor)asgeneticsisatthebasisofallbiology,andepigeneticsisa
youngandrapidlygrowingfieldofstudythathasalreadyfundamentallyalteredour
understandingofhowbiologicaldiversityisgeneratedandpassedon.Thisisparticularly
relevanttounderstandinghumandisease,which,asapremedbiologymajor,isofspecial
interesttome.AsIalreadycompletedthisproject,Icansaythattheunderstandingoflab

techniquesandtheresearchprocessthatIgainedhasdirectlyhelpedmeinunderstandingmany
ofmyupperlevelbiologyclasses.