FISO Seminar – May 3, 2017
Towards In Situ Sequencing for Life Detection
Christopher E. Carr Research Scientist, MIT Research Fellow, MGH Science PI, Search for Extra-Terrestrial Genomes (SETG)
[email protected] | setg.mit.edu | @carr_lab Image: Jenny Mo-ar/NASA
Search for Extra-Terrestrial Genomes (SETG) Team
Not pictured: Levon Avakian, John Cashion, SETG Alumni 5/3/17
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“I believe we are going to have strong indica@ons of life beyond Earth in the next decade and defini@ve evidence in the next 10 to 20 years” – Ellen Stofan, (then) Chief Scien3st (NASA) April 7, 2015
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Today • • • •
What is life? Where should we search for it? How should we detect it? What comes next?
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Today • • • •
What is life? Where should we search for it? How should we detect it? What comes next?
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Life As We Know It DNA RNA Proteins
Proper@es EvoluHon Growth ReproducHon Metabolism 5/3/17
Poten@al Features InformaHonal polymers Cell and populaHon growth Cell division Metabolites
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“RNA World”
NASA “A self-sustaining chemical system capable of Darwinian evoluHon” 6
Origin(s) of Life Astrochemistry
ArHficial Life
Volcanism
UV-driven synthesis
Hydrothermal Vents Mural at NASA Ames Research Center 5/3/17
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Requirements for Life (as we know it) • • • • •
CHNOPS elements Liquid water / water activity > 0.61 Redox gradient (energy flux) Moderate temperatures pH, salinity, pressure, etc.
What environments meet the requirements? NAP h-ps://goo.gl/110XN5
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Today • • • •
What is life? Where should we search for it? How should we detect it? What comes next?
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Searching for Life Beyond Earth Other Ocean Worlds…
Exoplanets
Mars
A direct search for life
Enceladus
James Webb Space Telescope
Europa
Credits: NASA/JPL-Caltech/SETI 5/3/17
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Is Carbon Based Life Universal? “Weak Panspermia” Sugars (Ribose)
Nucleobases
Comet (simulated) Meteorite(s)
ESA/Rose-a/NAVCAM, CC BY-SA IGO 3.0
CC BY-SA 3.0 h-ps://goo.gl/SGBkXz
Synthesis of prebio3c molecules in early solar nebula (Nuevo et al. 2009, 2012; Ciesla & Sandford, 2012), ribose and other sugars in late solar nebula (Meinert et al. 2016); Meteori3c amino acids & nucleobases (Engel et al. 1997; Mar3ns et al. 2008; SchmiL-Kopplin et al. 2010; Cooper et al. 2011; Callahan et al. 2011)
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Shared Ancestry? ~4 billion years ago … “Lithopanspermia”
Calcula3on/Simula3on (Gladman & Burns, 1996; Gladman et al. 1996; Gladman et al. 1997; Mileikowsky et al. 2000); Low temperature meteori3c transfer (Weiss et al. 2000); Microbes survive ejec3on shock (Burchell et al. 2004; Stöffler et al. 2007; Horneck et al. 2008; Meyer et al. 2011) Credit: ESO/M. Kornmesser CC 4.0 h-ps://goo.gl/7Vz5eS 5/3/17
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Potential Refugia for Life on Mars Poten@al Near-Surface Zones of Extant Life
Low Exposure Age Regions
Recurring Slope Lineae (RSLs) - Liquid Brines?
Fresh Impact Craters
Water Ice Fog / AcHve Water Cycle?
HRSC/MEX/ESA
HiRISE NASA/JPL/ASU/MSSS
Subsurface Regions
Extensive overlap between Mars and Earth of zones habitable for life as we know it (Jones et al., 2011) 5/3/17
Mars Odyssey / Mars Global Surveyor / NASA/JPL/ASU
Example: Subsurface environments offer UV and radiaHon shielding, heat, moisture
HiRISE NASA/JPL/ASU/MSSS
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Lava Tube
h-p://goo.gl/GupK1H
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How universal is biochemistry? 4.6 Ga Gya
4.1
ets
Com
Venus Earth Mars
Complex organics form, mix in the solar nebula
•
Me
teo r
ites
3.8
Titan Europa Enceladus
Late Heavy Bombardment: Meteoritic transfer between Earth and Mars (and Venus?)
3.5
Extant life?
Isotopic evidence of life on Earth Start of transition from wet to dry on Mars Fossil evidence of life on Earth
Mars: Enceladus: Related life? 2nd genesis? Shadow biosphere on Earth?
Weak Panspermia: Common building blocks of life – Synthesis of prebiotic molecules in early solar nebula (Nuevo et al. 2009, 2012; Ciesla & Sandford, 2012), ribose and other sugars in late solar nebula (Meinert et al. 2016) – Meteoritic amino acids & nucleobases (Engel et al. 1997; Martins et al. 2008; SchmittKopplin et al. 2010; Cooper et al. 2011; Callahan et al. 2011)
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Lithopanspermia: Shared ancestry between Earth and Mars?
– Calculation/Simulation (Gladman & Burns, 1996; Gladman et al. 1996; Gladman et al. 1997; Mileikowsky et al. 2000) – Low temperature meteoritic transfer (Weiss et al. 2000) – Microbes survive ejection shock (Burchell et al. 2004; Stöffler et al. 2007; Horneck et al. 2008; Meyer et al. 2011)
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Today • • • •
What is life? Where should we search for it? How should we detect it? What comes next?
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Searching for Life Beyond Earth Proper@es of Life • Metabolism • Growth • ReproducHon • EvoluHon
e.g., Klein 1978; Klein 1979
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Biomarkers • Biofabrics • BiomineralizaHon • Body fossils • SpaHal chemical pa-erns • Biogenic gases (methane) e.g. Grotzinger et al. 2012 • Isotope raHos • Future missions: Biogenic organic molecules (amino acids, lipids, nucleic acids) • Need definiHve biomarkers! Charged linear informa7onal polymers likely universal for aqueous-based life. 18
Priority: Biogenic Organic Molecules
On icy moons: biogenic organic molecules even more important, because some biosignatures are not present or are inaccessible.
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Why nucleic acids?
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Survival Time of DNA Model of DNA Hydrolysis
Survival of the coldest adapted from Millar & Lambert, 2013
Mars
Mars temperature preserves DNA on longer 3mescales versus Earth 5/3/17
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Search for Extra-Terrestrial Genomes (SETG) Data Processing
Rover Icy Moon Orbiter
Ocean Explorer
Sequence Analysis
Proteobacteria Firmicutes
DNA/RNA XNA extraction
Biologically -based Nanopore Sequencing
Archaea Bacteroidetes Chloroflexi
Current TRL 4
ValidaHon using hard to lyse spores (Bacillus sub3lis)
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Non-standard bases (Inosine nucleoside)
RadiaHon Resistant Memory (CBRAM)
Neural Network-based Data Processing
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Extraction Modules (4)
Volume-accurate Pre-TRL6 SETG Model: • 4 extracHon modules • 2 sequencers
Sequencing (internal) Data Processing (internal) Fluidics
9.5 cm
22 cm 14cm
Current Best Estimate
Average Contingency
Allocation
System Volume
2.7 L
28%
3.4 L
System Mass
3.7 kg
28%
4.8 kg
130 W-hr
31%
170 W-hr
Budget
Energy (Per Sample)
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Carr et al. 2017 IEEE Aerospace (In Press)
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System Margin
Specification 4.3 L
25%
6.0 kg 210 W-hr
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Abundance & Sensitivity 1
10
102
103
104
105
106
107
108
109 Cell Density (#/g)
Europa Ocean energetic upper limit?
2.5 · 105 Low-moisture a
1 ppb
terrestrial analogs of Mars (Atacama)
Saturated bacterial culture DNA (mass/mass)
10-15 10-14 10-12 10-11 10-10
10-9
10-8
TRL6 Target Carr et al. (2017) AbSciCon Abstract #3395 5/3/17
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10-7
10-6
10-5 B. subtilis ATCC 6633 spores
500 ng DNA for 50 mg sample 25
Subsystem Requirements Sample Delivery
Extraction
Sequencing
1 ml/50 mg after any concentration
Current Best
104 spores 40 pg DNA
5% Yield
Achieved: B. subtilis spores in Mars analog soils
Forward Contamination? Putative (Mars) Life?
OmniLyse ®
Target
Analysis
0.06% Yield
0.0001% (typical) 0.0025% (optimal)
>1M bases called
Detection of known Earth organism with
