Issues surrounding self testing. ' Small'sample'size' Truly'informed'consent'(with'no'pressure'to'par;cipate)' Objec;vity'of'risks,'and'results' ''

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1 UnabletomakehiscaseinstudieswithlabmicebecauseH.#pylori#affectsonlyprimates) andprohibitedfromexperimen;ngonpeople,marshallgrewdesperate.finallyheran anexperimentontheonlyhumanpa;enthecouldethicallyrecruit:himself. BBfromtoday sreading IdidntquiteexplaintomybosswhatIwasdoing.Hewaspassingtheendoscopeon meandiwaslyingtheregaggingaway,hesays,"barry,imnotsurewhyyouasked metodothistestonyou,andidontwantyoutotellme."itwasdontask,donttell. Iwrotetheexperimentupinthethirdperson,becauseitwasverydisreputabletobe doingaselfbexperimentofoneandthenwri;ngitup,andtheeditorofthemedical journalofaustraliastuckhisneckoutandpublishedit.amerwardacoupleofpeople figuredoutthatitwasreallyaselfbexperimentonme,butididntownuptoit straightaway. BBBarryMarshall Smallsamplesize Trulyinformedconsentwithnopressuretopar;cipate) Objec;vityofrisks,andresults Issues surrounding self testing Whatwewouldliketodo,hopefullywithfundingfromNIH,islaunchbig,longBterm programs.youwouldenteryourbabyintoatrialthedayheisborn.wewouldhavehis genomedecoded.we dsurveyyourmicrobiome[allthemicroorganismsinthebodyand theirdna]andmaybeyourhusband smicrobiome,andallthatwouldgoinadatabase. Thenwewouldcomealongandtakeafecesculturefromyourbabyeachmonth.Andif everhegotafever,wewouldswabhischeekandsavethat. Wewoulddo10,000kidslikethis.Then,in20years ;me,wewouldfindthat30ofthem developedcoli;s,andwewouldgoback.ifwecouldgetallofthatmaterialoutofthe deepfreezeandrunitthroughthesequencingmachine,wewouldfindtheanswer.

2 LawrenceDavid&EricAlm LawrenceDavid&EricAlm h]p:// faculty/_images/lawrence_david.jpg h]p://cee.mit.edu/sites/default/files/alm.jpg h]p://genomebiology.com/2014/15/7/r89 h]p://genomebiology.com/2014/15/7/r89 LawrenceDavid&EricAlm Whatwereyouthinking?Wasthatjustawayofbypassingthehuman studiesreviewboardprocess? BBfromthereporterintheBarryMarshallreading Weobtainedwri]eninformedconsentfrombothsubjectsenrolledinthestudy.Thisstudy wasapprovedbythemitcommi]eeontheuseofhumansasexperimentalsubjectsstudy # )andcompliedwiththeHelsinkiDeclara;on. h]p:// faculty/_images/lawrence_david.jpg h]p://cee.mit.edu/sites/default/files/alm.jpg h]p://genomebiology.com/2014/15/7/r89

3 LawrenceDavid&EricAlm FunFactsaboutBacteria Therearemorethan1030bacteriaonearth&fewerthan1010humans) Earthcontainsmorebacteriathanallotherscombined Broadspectruman;bio;cs willhavetogivewaytonarrow spectrum,targetedtherapies. BBtoday sreading Bacteriainhabitdeserts,ice,hydrothermalvents,hotsprings,etc Thenumberofbacterialspeciesises;matedat>1billion 10%ofourowndrybodyweightconsistsofbacteria Thereare10;mesthe#ofbacterialcellsinahumanthanhumancells h]p:// h]p:// Various uses of bacteria Producingmedicines Various uses of bacteria Makingfood Conver:ngNitrogen forplants Biodegrada:on h]p:// h]p://oregonstate.edu/dept/foodsci/dairy/dairy_products.jpg Insec:cides Diges:on h]p:// h]p:// h]p:// h]p://teachnetblab.org/santab2003/tnetarchive/hamner/karen_hamner_body_sys/dig.gif

4 These bacteria are called Vibrio fischeri Bacteria have symbiotic relationships with many organisms h]p:// h]p://bricker.tcnj.edu/micro/le9/vibrio_fischeri.jpg h]p:// h]p://microbiology.unh.edu/faculty/whistler/images/image3.jpg Twowaystomakephylogene:ctrees: 1.Usingphysicalcharacteris:cs Twowaystomakephylogene:ctrees: 1.Usingphysicalcharacteris:cs

5 Twowaystomakephylogene:ctrees: 1.Usingphysicalcharacteris:cs How do we identify these bacteria? Physically: Growingbacterialculturesonsolidmedia Growingbacterialculturesinliquidmedia Microscopy rat mouse frog Growing bacterial cultures on solid media Bacterial colonies come in many shapes and sizes What is the plate made of? What do we call one clump of cells? How many genetically identical cells are in each clump? Where did that clump of cells come from? h]p:// h]p:// h]p://

6 Growing bacterial cultures in liquid media Growing bacterial cultures in liquid media Pickacolony Growaliquidculture h]p://2013.igem.org/wiki/images/thumb/e/ea/igem_bielefeld_2013_device.jpg/400pxbigem_bielefeld_2013_device.jpg h]p://eshop.eppendorfna.com/upload/productbig/m1352b0000_e24%20shaker.jpg Performing microscopy on bacterial cells Phase Contrast Fluorescence DNA) EM Whydoculturing&stainingnotworkfeasibly foriden:fyingmanybacteria? h]p://2013.igem.org/wiki/images/0/06/barecillus_hbsubrfp_dapi.jpg h]p://

7 Whydoculturing&stainingnotworkfeasibly foriden:fyingmanybacteria? Thephylogene:ctreeoflifeonEarth Certainspeciesarerarebutares;llcri;caltothestabilityanddiversity ofacommunity. Anoverviewofthehumanmicrobiome LawrenceDavid&EricAlm smicrobiome :mecourse h]p://genomebiology.com/2014/15/7/r89