BacteriaArchaeaEucaryaAnimalsGreennonsulfurSlimeEntamoebaebacteriaMoldsMitochondrionFungiMethanosarcinaGramPlantsExtremePurpleMethanobacteriumpositiveHalophilesbacteriaThermobacteriaMethano-CiliatesChloroplastproteuscoccusThemoPyrodictiumcoccUCyanobacteriaFlagellatesFavobacteriaTrichomonadsThermotogaAquifexMicrosporidiaDiplomonadsCommonAncestor(s)(Giardia)
PCRamplificationofany16SgeneonEarthuniversal Primer515 GTGCCAGCMG CCGCGGTAAHUMANGGCAAGTCTG GTGCCAGCAG CCGCGGTAAT TCCAGCTCCA...1 Kb...CTAGAGGAAGTAAAAGTCGTAACAAGGTTT CCGTAGGTGAARCHAEAGGCAAGACCG GTGCCAGCCG CCGCGGTAAT ACCGGCAGTC...1Kb..CGCAAGGGGG ATTAAGTCGT AACAAGGTAG CCGTAGGGGABACTERIAGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGG..1 kb.GATGATTGGG GTGAAGTCGT AACAAGGTAG CCGTATCGGATTCAGCA TTGTTCCAWYGGCATuniversal primer1391OnedoublestrandedDNAmoleculefromabacterium ina slurryofsoil...GATGATTGGG GTGAAGTCGT AACAAGGTAG CCGTATCGGAtopGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGG..1 KbCCGATTGATG CACGGTCGTC GGCGCCATTA TGCATCCACC..1 KP..CTACTAACCCCACTTCAGCATTGTTCCATC GGCATAGCCTbottomMeltthatoneDNAmoleculeinasonicatedslurryofsoilat95°C,andadd1012copiesofbothuniversal16sprimersTheprimersfindtheircomplementaryregionontheDNA,andanewcopyofthe16SgeneisnowmadebyaddedDNApolymeraseenzyme.GGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGG..1Kb...GATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAtopTTCAGCATTGTTCCAWYGGCAT Primer1391primer515GTGCCAGCMG CCGCGGTAAuniversalGGCGCCATTA TGCATCCACC...1 Kb...CTACTAACCC CACTTCAGCA TTGTTCCATC GGCATAGCCTbottomCCGATTGATGCACGGTCGTC30cyclesof95°C,55°c,75°c(2minpercycle)1kilobaseamplified230=109foldandfluorescent
PCR amplification of any 16S gene on Earth universal primer515 GTGCCAGCMG CCGCGGTAA HUMAN GGCAAGTCTG GTGCCAGCAG CCGCGGTAAT TCCAGCTCCA.1 kb. CTAGAGGAAG TAAAAGTCGT AACAAGGTTT CCGTAGGTGA ARCHAEA GGCAAGACCG GTGCCAGCCG CCGCGGTAAT ACCGGCAGTC.1 kb. CGCAAGGGGG ATTAAGTCGT AACAAGGTAG CCGTAGGGGA BACTERIA GGCTAACTAC GTGCCAGCAG CCGCGGTAAT ACGTAGGTGG.1 kb. GATGATTGGG GTGAAGTCGT AACAAGGTAG CCGTATCGGA TTCAGCA TTGTTCCAWY GGCAT universal primer 1391 One double stranded DNA molecule from a bacterium in a slurry of soil top GGCTAACTAC GTGCCAGCAG CCGCGGTAAT ACGTAGGTGG .1 kb.GATGATTGGG GTGAAGTCGT AACAAGGTAG CCGTATCGGA bottom CCGATTGATG CACGGTCGTC GGCGCCATTA TGCATCCACC.1 kb.CTACTAACCC CACTTCAGCA TTGTTCCATC GGCATAGCCT Melt that one DNA molecule in a sonicated slurry of soil at 95°C, and add 1012 copies of both universal 16S primers The primers find their complementary region on the DNA, and a new copy of the 16S gene is now made by added DNA polymerase enzyme. top GGCTAACTAC GTGCCAGCAG CCGCGGTAAT ACGTAGGTGG .1 kb.GATGATTGGG GTGAAGTCGT AACAAGGTAG CCGTATCGGA - TTCAGCA TTGTTCCAWY GGCAT primer1391 universal primer515 GTGCCAGCMG CCGCGGTAA - bottom CCGATTGATG CACGGTCGTC GGCGCCATTA TGCATCCACC.1 kb.CTACTAACCC CACTTCAGCA TTGTTCCATC GGCATAGCCT 30 cycles of 95°C, 55°C, 75°C (2 min per cycle) 1 kilobase amplified 230=109 fold and fluorescent
16SPCRisthestandardmethodforEarthlifedetection1359papersusingsearchterms:16Sandmicrobialcommunity9papers inMay06ForexampleIsolation and Characterization ofaNewClostridium sp.That Performs EffectiveCellulosic WasteDigestion in aThermophilic Methanogenic Bioreactor.Appl Environ Microbiol.2006May;72(5):3702-9.Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat.Appl Environ Microbiol.2006 May;72(5):3685-95.RNA-Based StableIsotopeProbingandIsolation of AnaerobicBenzene-DegradingBacteriafromGasolineContaminatedGroundwater.Appl Environ Microbiol. 2006 May;72(5):3586-92Dynamics ofa Pig Slurry Microbial CommunityduringAnaerobic Storage and Management.Appl Environ Microbiol.2006May;72(5):3578-85
16S PCR is the standard method for Earth life detection 1359 papers using search terms: 16S and microbial community 9 papers in May 06 For example Isolation and Characterization of a New Clostridium sp. That Performs Effective Cellulosic Waste Digestion in a Thermophilic Methanogenic Bioreactor. Appl Environ Microbiol. 2006 May;72(5):3702-9. Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat. Appl Environ Microbiol. 2006 May;72(5):3685-95. RNA-Based Stable Isotope Probing and Isolation of Anaerobic Benzene-Degrading Bacteria from GasolineContaminated Groundwater. Appl Environ Microbiol. 2006 May;72(5):3586-92. Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management. Appl Environ Microbiol. 2006 May;72(5):3578-85
SETG,aSearchforExtraterrestrialGenomesAPcRDetectorForLifeonMarsAncestrallyRelatedtoLifeonEarthGaryRuvkun,ProfessorofGenetics,HarvardMichaelFinney,FormerChiefScientificOfficerandPrincipal,MJResearchMariaZuber,ProfessorofGeophysicsandPlanetaryScience,MITGeorgeChurch,Director,CenterforComputationalGenetics,HarvardSteveQuake,ProfessorofAppliedPhysics,StanfordWalterGilbert,UniversityProfessor,HarvardWilliamMayer,AssociateDirector,CenterforSpaceResearch,MiTPostdoctoralFellowsChristopherCarr,PostdoctoralFellow,MiTDeptofEarthandPlanetarySciencesandMGHDept.ofMolecularBiologyTomIsenbarger,PostdoctoralFellow,UnivofWisconsinGraduateStudentsSarahJohnson,MITDeptofEarthandPlanetarySciencesSupportedbyaNASAASTIDGrantNRA-01-01-ASTID-02006/01/05-5/31/08GaryRuvkunandMariaZuber,CoPls.SETG,SearchforExtraterrestrialGenomes:AninsituPCRDetectorForLifeonMarsAncestrallyRelatedtoLifeonEarth
SETG, a Search for Extraterrestrial Genomes A PCR Detector For Life on Mars Ancestrally Related to Life on Earth Gary Ruvkun, Professor of Genetics, Harvard Michael Finney, Former Chief Scientific Officer and Principal, MJ Research Maria Zuber, Professor of Geophysics and Planetary Science, MIT George Church, Director, Center for Computational Genetics, Harvard Steve Quake, Professor of Applied Physics, Stanford Walter Gilbert, University Professor, Harvard William Mayer, Associate Director, Center for Space Research, MIT Postdoctoral Fellows Christopher Carr, Postdoctoral Fellow, MIT Dept of Earth and Planetary Sciences and MGH Dept. of Molecular Biology Tom Isenbarger, Postdoctoral Fellow, Univ of Wisconsin Graduate Students Sarah Johnson, MIT Dept of Earth and Planetary Sciences Supported by a NASA ASTID Grant NRA-01-01-ASTID-020 06/01/05-5/31/08 Gary Ruvkun and Maria Zuber, Co PIs. SETG, Search for Extraterrestrial Genomes: An in situ PCR Detector For Life on Mars Ancestrally Related to Life on Earth
UniversalPrimersDNAPrepDiluteReleaseConcentrateAmplifySoilDNADNADNAMixtureCBDWaterWasteAmplifySequencingDNAbySynthesisEPrimersDNADetection/ClassificationCurrentProjectsDNA Extractionfromsoil:MicrofluidicTestbedMicrobial CommunityLimitstosensitivityAnalysis:Rio TintoCurrentVersionConceptDNA sizePlanEvolutiondistribution
Current Version Evolution Microfluidic Testbed Concept DNA size distribution DNA Extraction from soil: Limits to sensitivity Plan Microbial Community Analysis: Rio Tinto Current Projects Release DNA Concentrate DNA Soil Water Universal Primers Amplify DNA Dilute Mixture Waste Amplify DNA Sequencing by Synthesis Primers DNA Detection/Classification DNA Prep A B C D E F