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 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 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

-19 30 10 /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 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 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: Cold­active enzyme architecture confers flexibility and thermolability (fewer charged amino acids, less α­helices) Do 9A proteins have fewer charged amino acids and α­helices?

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