astrobiology and bioinformatics: past, present, and future · movile cave, romania hutchens et al....

Astrobiology and Bioinformatics:Past, Present, and Future

R. Eric Collins22 July 2010

McGill University

Definitions: Astrobiology

● “The study of the origin, evolution, distribution, and future of life in the universe”

● Basic Questions from the Astrobiology Roadmap:

● How does life begin and evolve?● Does life exist elsewhere in the universe?● What is the future of life on Earth and beyond?

Definitions: Astrobiology

● Nature and distribution of habitable environments in the universe

● Planetary Analogues, Exoplanets

● Habitable environments and life in the Solar System

● Extremophiles and Cryomicrobiology

● Astrobiology Instrument and Technology Development

● The emergence of life

● How Early life on Earth interacted and evolved with the environment

● Evolutionary mechanisms and environmental limits of life

● The principles that will shape life in the future

● Signatures of life on other worlds and on early Earth

● Biosignatures

10 Great Findings in Astrobiology

● Three Domains of Life

● ALH84001

● Amino acids in meteorites

● 51 Peg

● Planetary formation models

● Sulfur MIF & the Great Oxidation Event

● Lipid biomarkers from Archaean rocks

● Atmospheric chemistry models

● Subsurface ocean on Europa

● Everything about Titan

Definitions: Bioinformatics

● “The application of statistics and computer science to the field of molecular biology”

● Common applications of Bioinformatics:

● Sequence analysis● Genome annotation and comparative genomics● Computational evolutionary biology● Analysis of gene expression and regulation● Prediction of protein structure and protein

expression● Modeling complex ecological systems

The Era of Molecular Genetics and Exobiology

● 1924: Alexander Oparin writes “The Origin of Life”

● 1947, 1952: Joshua Lederberg founded modern bacterial genetics and gene manipulation

● 1954: “The Origins of Life” by JBS Haldane, geneticist

● 1960: Lederberg writes “Exobiology: Approaches to Life Beyond Earth”

● 1965: Linus Pauling founded the use of “Molecules as Documents of Evolutionary History”

● 1977, 1990: Carl Woese identified Archaea as the Third Domain of Life

The Rise of Computers

● NASA Ames Center for Bioinformatics (1996 to 2001)

● NASA Center for Astrobioinformatics (December 2003 to Feb 2004)

● NASA Center for Computational Astrobiology (2000 to 2008)

The PCR Revolution:Culture Independence

● Applications● Ribosomal RNA gene sequencing● Fluorescence in situ hybridization (FISH)● Functional gene sequencing (amoA, dsrAB, etc.)● Community fingerprinting (TRFLP, ARISA, DGGE)● Stable isotope probing (SIP) of DNA, RNA, lipids

● Essential resources● RDP: Ribosomal Database Project● SILVA & arb● Greengenes

Beaufort Sea, NWTCollins et al. 2010

Eel River Basin, CaliforniaOrphan et al. 2001

Geothermal Hot SpringsZhang et al. 2008

Shark Bay, Western AustraliaLeuko et al. 2006

Beaufort Sea, NWTCollins et al. 2010

Movile Cave, RomaniaHutchens et al. 2003

The Sequencing Revolution:Comparative Genomics

● Technology

● Sanger sequencing: $7000/Mb, 96 x 700bp reads● Microarrays: $100-$1000 per slide, ~10,000 probes● Mass spectrometer, ~$500 per experiment

● Applications

● Genomics● Transcriptomics● Proteomics

● Essential resources

● DOE JGI IMG: Integrated Microbial Genomes

– 1911 Bacteria, 84 Archaea, 76 Eukarya● NCBI Genomes

Antarctic water, Siberian PermafrostMedigue et al. 2005

Ayala-del-Rio et al. 2010

Anaerobic/Thermophilic Bacteria/Archaea

The Sequencing Revolution (2.0):Metagenomics

● Next Generation Sequencing technology

● 454: $30/Mb, 1 million x 400bp reads, 12 hours● Illumina: $6/Mb, 15 million x 2 x 100bp reads, 5 days● SOLiD: $3/Mb, 200 million x 2 x 25bp reads, 5 days● PacBio, Ion Torrent, Helicos, ...

● Applications

● Metagenomics: whole community sequencing● Deep Sequencing: hypervariable tag sequencing● Transcriptomics: whole transcriptome sequencing● ????

● Essential resources

● IMG/m (217 metagenomes), CAMERA

High Performance Computing in Canada

● Réseau québécois de calcul de haute performance● https://rqchp.ca

● SHARCnet● http://sharcnet.ca

● WestGrid● http://westgrid.ca

Diffuse Hydrothermal VentsSogin et al. 2006

Lost City, Mid-Atlantic RidgeBrazelton et al. 2009

World Ocean viromesAngly et al. 2006

Cuatro Ciénegas, MexicoBreitbart et al. 2008