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Astrobiology Virology Astrobiology Virology 100nm ...and other things related to my PhD ANU Planetary Science June 2011 Abstract Astrobiology is fundamentally concerned with the understanding of the origin, evolution and distribution of life in our universe. The study of viruses and other controversially biotic entities has broadened our perspective of what we classically consider to be life and what we might overlook with our Terran blinders on. I'll address virology as relevant to the field of Astrobiology and the evolution (and definition!) of life, my projects on viral molecular dynamics in cold environments, and attempt to justify what I am doing at ANU in a geochemistry group. ANU Planetary Science June 2011 Outline i. virology as relevant to the field of Astrobiology ii. viral molecular dynamics in cold environments iii. what I am doing at ANU ANU Planetary Science June 2011 Research Experience Cornell University 2002-4 Boyce Thompson Research Institute 2003 Cornell 2001-2 2000-1 Stony Brook/ Columbia Cornell 2004-6 2007-8 Seattle BioMed UW Astrobiology/Oceanography Deming Catling Meadows Buick Sullivan ANU Planetary Science June 2011 Astrobiology NASA: “the study of the origins, distribution, evolution and future of life in the universe” How does life begin and develop? What is life’s future on Earth and beyond? Does life exist elsewhere? ANU Planetary Science June 2011 Astrovirology I don't know how to define life; but I know know it when I see it (cit) Ken Stedman Baruch Blumberg Portland State University Fox Chase Cancer Center NASA Ames etc. NAI Virus Focus Group inaugural meeting, October 2002 ...how viruses may have influenced the origin and evolution of life here on Earth, and perhaps elsewhere in the Solar System Virology research that addresses questions pertinent to astrobiology ANU Planetary Science June 2011 Astrovirology What's a virus? -virus is a small infectious agent that can replicate only inside the living cells of organisms TMV Rickettsia sp. Trypanosoma cruzi Prion -Obligate intracellular parasites cannot reproduce outside their host cell, meaning that the parasite's reproduction is entirely reliant on intracellular resources (perhaps worth figuring out some definition, because they appear to be everywhere...) ANU Planetary Science June 2011 Astrovirology Viruses are both everywhere... and are incredibly diverse 106/ml 30 10-19/ml 10 /global ocean Angly et al. 2006 V P B 9 1032 nm= 1020km; Milky Way =1018 km 10 unique genes expected ANU Planetary Science June 2011 Astrovirology Viruses have enormous impact on microbial life I. They kill lots of cells 1029 infections per day nutrient recycling (virus shunt to microbial loop) 'Kill the winner' release 108 tons of carbon virus infection debris from space! Suttle 2005 Wilson et al. 1999 ANU Planetary Science June 2011 Astrovirology Viruses have enormous impact on microbial life Viruses and horizontal gene transfer II. They move genes between organisms (= transduction) How viruses can mess with this: Generalized Specialized The way Darwin saw it: Anderson 2010 Kill the winner; move genes-> promote biodiversity ANU Planetary Science June 2011 Astrovirology Origins of viruses i. parastic bacteria that lost ability to function independently ii. escaped genes iii. simultaneous origin with cells (or prebiotic systems) Koonin et al 2006 Prangishvili et al 2005 ANU Planetary Science June 2011 Astrovirology Giant viruses, virophage and virocells Lascola et al. 2008 Mimivirus 1.2Mb 0.2um >1000 genes Sputnik/Mamavirus deformed Mamavirus Raoult and Forterre 2008 Virion ≠ life ≠ virus ≈acorn 'a capsid-encoding organism, composed of proteins and nucleic acids, that self-assembles in a nucleocapsid and uses a ribosome-encoding organism for the completion of its life cycle' ANU Planetary Science June 2011 Astrobiology Rotation Summary (part I) - viruses are difficult to define, and challenge our perceptions of what life is - viruses are hugely abundant and morphologically and genetically diverse - viruses are responsible for cellular mortality and maintenance of diversityViruses and horizontal gene transfer How viruses can mess with this: The way Darwin saw it: - viruses contribute to genomic evolution now and may have as early as the diversification of domains - viruses may have been responsible for biological innovations such as DNA and the nucleus ergo... - virology research can inform astrobiological questions (=astrovirology?) virus diversity is very poorly explored ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A most cold active PHS characterized Virus-like particle production at -12 C 9A cells or phage x107/ml Cp34H Wells and Deming 2006 more psychrophilic? ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A Are there elements of the 9A genome that may confer cold-activity? PROTEIN: Cold-active enzyme architecture confers flexibility and thermolability (fewer charged amino acids, less α-helices) Do 9A proteins have fewer charged amino acids and α-helices? Are there elements of the 9A genome that indicate additional range or function? GENOME COMPARISONS: Are there C. psychrerythraea genes in 9A? Are there other bacterial/archaeal/viral genes? OPPORTUNISITC GENE EVALUATION: What other range/function information can be gleaned from 9A genes? ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A NGCC Radisson Cp34H .txt ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A -most cold active phage host system -first to have both the host and phage genomes sequenced genome is comprised of four modules; GC contents suggestive of mosaic origins ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A characterized as a Siphoviridae -bacteriophage -linear -dsDNA, -noncontractile tail 9A characters do not group with any single Siphoviridae genera gene exchange? ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Colwelliaphage 9A ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs = subsurface brine layers within permafrost -Mars analog site? -extreme microbial environment How did this thing form? What is the biological component? Do viruses play are role in this ecosystem? ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Cryopegs Can viromes serve as proxies for microbial metabolism in permafrost? ANU Planetary Science June 2011 Viral Dynamics- Cold Environments Arctic sea ice metavirome (Ever wonder why a PhD takes 7 years in the US?) ANU Planetary Science June 2011 Astrobiology Rotation ... names to consider for the sort of project you might be interested in are xx, yy, zz, aa, bb, cc and Jochen Brocks. Of them... Jochen is by far your best bet. ANU Planetary Science June 2011 Astrobiology Rotation Brocks Lab Ancient microbial system reconstruction Biomarker contamination control Prokaryotic succession Jochen Brocks Bird Watching PI Janet Hope sample preparation organic extraction HPLC- GC-MS Lab Manager Amber Jarrett Nur Gueneli Bennie Bruistein Marita Smith Danielle Gruen Marine RedOx N-isotopes Biomarker SST Catagenetic preservation reconstruction India rocks ANU Planetary Science June 2011 Astrobiology Rotation Molecular Fossils -confer taxonomic information Oldest DNA ~1Ma -resistant to degradation Permafrost Willerslev et al. 2004 biomolecules : nucleic acids, lipids, carbohydrates, proteins Lipids Oldest proteins: 80Ma Dinosaur bones -most stable Schweitzer et al. 2009 -still subject to chemical and biological degradation -preservation aided by absence of air/biology Kerogens -poorly characterized Oldest carbs: age -highly heterogeneous -amorphous -insoluble -polymeric over 80% of the organic molecules found in the fossil record [cit] Oldest lipids: 2-3Ga ANU Planetary Science June 2011 Astrobiology Rotation Isotope fractionation partial separation of light isotopes from heavy isotopes during chemical reactions Kinetic- separates isotopes by mass during unidirectional processes (i.e. evaporation of seawater to form clouds -> rainwater 'lighter' than seawater) difference in mass between 1H and 2H is almost 100% ANU Planetary Science June 2011 Project Overview Is evaporitic H-fractionation reflected in n-alkane biomarkers from ancient evaporitic deposits? - δH shift with increasing evaporation in basin? - anhydrite deposits have extreme δH values? - H-isotopes influenced by thermal maturity? H-istopes and salinity if rate evap. > rate precip. then increase δD of basin Sachse and Sachs, 2008 [Change steroid to Fig D. Nelson n-alkane in diagam] Astrobiology Rotation Amadeus Basin Mt. Charlotte-1 drillcore -inland seas -tenuous marine connection -deposition of dolomite, -test the stratigraphy/structure of the gypsum and halite Mount Charlotte Anticline depth: 2115 m Sea water: 3.5ppt Precipitates composition: Dolomite: 7ppt Gypsum: 17.5ppt 649 m mid-Neoproterozoic Halite: 35ppt Bitter Springs Formation 487 m late-Neoproterozoic Pertatataka Formation 800Ma Neoproterozoic Biomarkers 69 m Early Cambrian Chandler Limestone - n-alkanes abundant, 249 m Mid-Late Cambrian increase with dolomite Jay Creek Limestone - oldest evidence: hypersaline microorganisms haloarchaea biologically-mediated dolomite precipitation ANU Planetary Science June 2011 Astrobiology Rotation Experimental Design XRD Anhydrite:Dolomite Interior/Exterior Sample Ratio Separation- collection Contamination ASE Control Column GC-IRMS Chromatography GC-MS/MS Zeolite Molecular Sieve Separation ANU Planetary Science June 2011 .
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