Former Lab Members

Former Lab Members.

Diane Rico

Graduate Student
Email: dianer4 at u.washington.edu
Office: 206-685-4118

Education:
M.S. in Biology, California State University, Los Angeles (2012)
B.A. in Biology, University of California, Santa Cruz (2000)

Research Interests:
Two ecotypes of the diatom Ditylum brightwellii have been isolated from Puget Sound water samples. One of the ecotypes is globally distributed and blooms in Puget Sound in early spring. The second ecotype has only been identified in Puget Sound, where it blooms later in the year. Blooms of the two ecotypes correlate with distinct silicic acid concentrations and solar irradiance levels (Rynearson, Newton, & Armbrust, 2006). Since the second ecotype has approximately twice the DNA as the global ecotype, it is likely to have diverged as a result of a genome duplication event. I am interested in comparing gene sequences expressed by the two ecotypes to identify those genes responsible for the adaptive success of the second ecotype in Puget Sound.

Publications:
In Preparation:
Stauffer, BA, AG Gellene, D Rico, C Sur, DA Caron. Growth of the heterotrophic dinoflagellate Noctiluca scintillans on red tide-forming dinoflagellates and raphidophytes.

Tony Chiang

Postdoctoral Research Fellow

How does the environment impact biodiversity? Specifically, how do differing oceanic regions affect the genotype - and potentially phenotype - of members of a given species.

My research focuses primarily on the mathematical and statistical modeling of polymorphic regions for seven separate oceanic strains of Thalassiosira pseudonana. Using data derived from next-generation sequencing technologies, I use simple statistical methods to model areas of significantly high or low variability such as single nucleotide polymorphisms (SNPs) or large-scale insertions or deletions. The ability to estimate regions of high variability gives clues to the adaptation mechanisms of the species for differing environments. Conversely, estimating regions of low to no variability across strains helps us determine essential genomic sequences.

I am also broadly interested in the role of theoretical computer science in biology. As data becomes larger and more abundant, it will be much more necessary to find efficient ways to store, query, and share data. My preliminary work in this area uses a graph theoretic framework to represent metagenomes. My collaborators and I are building a novel data structure for metagenomes so that we might be able to generalize the notion of comparative genomics.

Research Interests:

  • Computational Biology
  • Graphical Models
  • Learning Algorithms
  • Application of mathematics, statistics, and computer science to biologically driven problems
  • Consequences of climate change on marine ecologies

Broader Interests:

  • Politics of climate change
  • Public health policy  
  • Sustainability
  • Social Justice
  • Science Education

Positions Held:
Postdoctoral Research Fellow, School of Oceanography, University of Washington, 2011-Present
Affiliate Postdoctoral Fellow, Computer Science & Engineering, University of Washington, 2011-Present
Graduate Research Fellow - Computational Statistics, University of Cambridge, 2006-2010
Graduate Research Assistant - Pure Mathematics, University of California at Berkeley, 2001-2005

Education:
Doctor of Philosophy - King's College, University of Cambridge
Bachelor of Science - Massachusetts Institute of Technology

Honours:

  • King's College Studentship, King's College, University of Cambridge, 2008 - 2010
  • Overseas Research Studentship Fellow, University of Cambridge, 2008 - 2010
  • Ferris Fund Bursury, King's College, University of Cambridge, 2008
  • NSF EMSW21 (DMS-0354321) under Mark D. Haiman, University of California, Berkeley, 2004
  • NDSEG Graduate Student Fellowship Finalist, 2001
  • NSF Graduate Student Fellowship Honourable Mention, 2001
  • Paul Grey Fellowship Award for Undergraduate Research, MIT, 2001
  • Nankai University International Fellowship, Center for Combinatorics, Nankai University, 1999
  • Massachusetts Institute of Technology Jack C Tang Scholarship, 1997-2001

Publications:

  1. Tony Chiang, Denise Scholtens. A General Pipeline for the Quality and Statistical Assessment of Protein Interaction Data Using R and Bioconductor. Nature Protocols, 2009.
  2. Denise Scholtens, Tony Chiang, Wolfgang Huber, Robert Gentleman. Estimating Node Degree in Bait-Prey Networks. Bioinformatics, 2008.
  3. Tony Chiang, Nianhua Li, Sandra Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, Wolfgang Huber. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics, 2007.
  4. Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber. Coverage and Error Models on Protein-Protein Interaction Data by a Directed Graph Analysis. Genome Biology, 2007.
  5. Tony Chiang. On the Cayley Graph of Finitely Generated Abelian Groups. Journal of Undergraduate Research, June 2001, MIT PRESS.

Contact:
phone: +1.206.685.4196
email: surname@ocean.washington.edu

My primary affiliation is within the Oceanography department; I have a secondary affiliation with the Computer Science and Engineering group. I am co-mentored by Ginger Armbrust and Larry Ruzzo of Oceans and CSE respectively.

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Gwenn M. Miller Hennon

gwennm@uw.edu

Research Interests and Current Projects:

Phytoplankton are responsible for producing half of the oxygen we breathe everyday. They also fix carbon into organic matter, which not only drives the food chain for all marine life, but it also sinks into the deep in a process called the biological pump. The biological pump helps to shape the earth's response to increasing CO2 and warming climate. In order to understand what the future holds for earth's ecosystems we need to understand what factors drive the phytoplankton productivity and the biological pump and how these factors will change in the future.

Physiology and Gene expression of a Model Diatom acclimated to elevated CO2:

I am interested in how increasing carbon dioxide levels in the atmosphere will affect the physiology and gene expression of diatoms and the biological pump. Phytoplankton, including diatoms, have evolved to cope with relatively low CO2 by developing carbon concentrating mechanisms (CCMs). Now as CO2 levels are rising rapidly, these CCMs may down regulated, changing the fluxes of energy and carbon in diatom cells. I am interested in how diatoms will acclimate to higher CO2 levels and if there will be significant physiological changes that could effect the biological pump and ocean ecology.

I just published in Nature Climate Change on culturing experiments with the diatom Thalassiosira pseudonana under low, medium and high CO2 and nitrate limitation. Using gene expression data we found co-regulated CCM and photorespiration genes that are regulated by cyclic-AMP giving us insights into how diatoms acclimate to rising CO2 (http://www.nature.com/nclimate/journal/vaop/ncurrent/full/nclimate2683.html).

Gradients in Microbial Ecology and the Biological pump across the Western Tropical Atlantic:

It is thought that with increasing global temperature, the oceans will become more strongly stratified, resulting in changes in phytoplankton communities. Smaller phytoplankton might out-compete larger phytoplankton resulting in a shift in the ecosystem as well as the size of organic particles and the efficiency of the biological pump.

Using the SeaFlow underway flow cytometer I collected continuous data along the DeepDOM 2013 cruise to investigate gradients in phytoplankton community composition and growth rate. In collaboration with Evan Howard and Rachel Stanley of Woods Hole Oceanographic Institution as well as Francois Ribalet, I'm preparing a manuscript to on the apparent differences in inorganic nitrogen limitation between Prochlorococcus ecotypes in different biogeochemical provinces.

Education:

Ph. D. in Oceanography, University of Washington (2015)

M. S. in Oceanography, University of Washington (2012)

B. S. in Chemistry, Massachusetts Institute of Technology (2009)

Honors:

Dean A. McManus Excellence in Teaching Award (2013)

NOAA Earnest F. Hollings Scholarship (2007-2009)

Presentations and Publications:

Hennon, G. M. M. ; Howard, E.; Stanley, R.; Ribalet, F..; Armbrust, E. V. . “In situ division rates of Prochlorococcus reveal different nitrogen-utilizing ecotypes across the tropical Atlantic” (in prep)

Hennon, G. M. M. ; Ashworth J.; Groussman, R.D.; Berthiaume, C.; Morales, R. L.; Baliga, N.S.; Orellana, M.V.; Armbrust, E. V. . “Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression” (2015) Nature Climate Change

Hennon, G. M. M. ; Quay, P.; Morales, R. L.; Swanson, L. M.; Armbrust, E. V. . “Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate-limited chemostat” (2014) Journal of Phycology

Hennon, G. M. ; Armbrust, E. V.; “Acclimated Physiology and Gene Expression of the Diatom Thalassiosira pseudonana under Elevated CO2” (2013) ASLO Aquatic Sciences Meeting, New Orleans, LA, USA

Hennon, G.M.; Armbrust, E.V.; Ashworth, J.; Lee, A.; Orellana, M.V.; Baliga, N.S.; “Acclimated Physiology of the Diatom Thalassiosira pseudonana under Pre-Industrial and Future Levels of CO2: Implications for Carbon Sequestration” (2011) PSA annual meeting. Seattle, WA, USA

Bowman, J; Chan, K. Y.; Durkin, C.; Hennon, G.; Smith, D.; Sullivan, B. “Is Diversity Related to Service Provision Across an Ecosystem?” (2011) World Conference on Marine Biodiversity, Aberdeen, Scotland

Wood, M; Strutton, PG; Eberhart, B; Foley, DG; Forster, Z; Hunter, M; McKibben, SM; Miller, G; O’Higgins, L; Peterson, WT; Peterson, TD; Trainer, V; Smith, D; Tweddle, JF; White, AE. (2010) “MOCHA: Monitoring Oregon Coastal Harmful Algae”, Ocean Sciences Meeting

McKibben, SM; Strutton, PG; Wood, M; Miller, G; Eberhart, B; Trainer, V. “Development of a Predictive Model for In Situ Domoic Acid Concentrations off the Oregon Coast”. (2010) Ocean Sciences Meeting

Miller, GM. “Investigating Humpback Whale (Megaptera novaeangliae) diets using fatty acid trophic markers”, NOAA Hollings Scholar Presentation Week, Silver Spring MD, July 2008

Antos, J.M.; Miller, G.M.; Grotenbreg, G.M.; Ploegh, H.L.. Lipid Modification of Proteins through Sortase-Catalyzed Transpeptidation. JACS. 2008

Jeffrey W. Turner

Contact Information
Jeffrey W. Turner
Postdoctoral Scientist
jeff.turner@noaa.gov
jturner8@u.washington.edu
206.860.3420 office
206.860.3467 fax

Education
Ph.D., University of Georgia, Odum School of Ecology, 2010. Thesis adviser: Erin K. Lipp. Thesis title: Environmental factors and reservoir shifts contribute to the seasonality of pathogenic Vibrio species.

B.S., Mercer University, Chemistry, 1998.

Research Interests
If you've eaten raw seafood, especially bivalve mollusks such as oysters, or dipped a toe into the ocean, you've likely encountered Vibrio parahaemolyticus (Vp). Vp is a Gram-stain negative bacterium indigenous to coastal marine waters and the leading cause of seafood-borne bacterial gastroenteritis worldwide. Central to safeguarding the public from Vp is the ability to distinguish between virulent and avirulent strains of this bacterium. This distinction is based on the presence or absence of genes and or genetic elements, which are known to be associated with virulence. Seemingly straightforward, the control and prevention of this Vp is largely based on the screening of water and seafood for the presence or absence of a single virulence factor – the thermostable direct hemolysin (TDH). Unfortunately, not all clinical isolates elaborate TDH and additional virulence-associated factors, such as the thermostable related hemolysin (TRH) and proteins related to the type III secretion system (T3SS), can also contribute to pathogenesis.

In the Pacific Northwest (USA), traditional Vp virulence markers, such as TDH, are especially poor determinants of virulence. In a unique collaboration between Ginger Armbrust (UW’s Center for Environmental Genomics) and Mark Strom [NOAA’s West Coast Center for Oceans and Human Health (WCCOHH) at NOAA’s Northwest Fisheries Science Center], I am using sequencing by oligonucleotide ligation and detection (SOLiD) to sequence the genomes of 20 Vp strains. These strains originate from the Pacific Northwest and represent a diversity of environmental sources and include several clinical isolates. Genome – genome comparisons will aid in the identification of genes and genetic elements unique to pathogenic strains, which are locally endemic to the PNW. Once genetic features of pathogenesis are determined, future work can focus on the development of gene-specific assays to identify potentially virulent strains in environmental samples. These improved virulence assays will then be deployed onboard a marine biosensor (Environmental Sampling Processor, ESP), which will be integrated within a network of tools focused on the realization of a Vibrio early warning system.


Electron scanning microscopy of V. parahaemolyticus cells attached
to the shell of a crab. Photo courtesy of Carla Ster and Rohinee Paranjpye.


Environmental Sampling Processor (ESP) (minus instrument housing) for environmental monitoring of microbial pathogens and harmful algal blooms (HABs). The ESP was developed by the Monterey Bay Aquarium Research Institute (MBARI) and manufactured by SpyGlass Biosecurity.

Collaborations
Please follow these links below to learn more about NOAA's West Coast Center for Oceans and Human Health (WCCOHH) and NOAA's Oceans and Human Health Initiative (OHHI).

Funding
This research is funded by NOAA's Oceans and Human Health Initiative's (OHHI) Postdoctoral Traineeship, the National Research Council's (NRC) Research Associateship Program and NOAA's Marine Biosensor Program (see NOAA's Integrated Ocean Observing System, IOOS).

Publications
Turner, J. W., L. Malayil, D. Guadognoli, D. C. Cole and E. K. Lipp (2013). Detection of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae with respect to seasonal fluctuations in temperature and plankton abundance. Environmental Microbiology doi:10.1111/1462-2920.12246.

Turner, J. W., R. N. Paranjpye, E. Landis, N. Gonzales-Escalona, W. B. Nilsson, S. V. Biryukov and M. S. Strom (2013). Population Structure of Clinical and Environmental Vibrio parahaemolyticus from the Pacific Northwest Coast of the United States. PLoS ONE 8 (2): e55726. doi:10.1371/journal.pone.0055726.

Strom, M. S., R. N. Paranjpye, W. B. Nilsson, J. W. Turner, and G. K. Yanagida (2013). Pathogen update: Vibrio species. In Advances in Microbial Food Safety. 1: 97-113. J Sofos (ed), Woodhead publishink, Cambridge, U.K.

Xu, J., J. W. Turner, M. Idso, S. V. Biryukov, L. Rognstad, H. Gong, M. S. Strom and Q. Yu (2013). In situ strain level distinction of Vibrio parahaemolyticus using surface enhanced Raman spectroscopy. Analytical Chemistry 85 (5): 2630–2637.

Mote, B. L., J. W. Turner and E. K. Lipp (2012). Persistence and growth of the fecal indicator bacteria, enterococci, in detritus and natural estuarine plankton communities. Applied and Environmental Microbiology 78: 2569-2577.

Malayil, L., J. W. Turner, B. L. Mote, K. Howe and E. K. Lipp (2011). Evaluation of enrichment media for improved detection of V. cholerae and V. vulnificus from estuarine water and plankton. Journal of Applied Microbiology 110 (6): 1470-1475.

Sutherland, K. P., J. W. Porter, J. W. Turner, M. K. Meyers, M. L. Griffith, J. C. Futch and E. K. Lipp (2010). Human sewage identified as likely source of white pox disease of the threatened Caribbean elkhorn coral, Acropora palmata. Environmental Microbiology 12 (3): 112-1131

Turner, J. W., B. Good, D. Cole and E. K. Lipp (2009). Plankton composition and environmental factors contribute to Vibrio seasonality. International Society of Microbial Ecology 3:1082-1092.

Tobin-D’Angelo, M., S. Thomas, D. Cole and J. W. Turner (2007). Vibrio in Georgia. Georgia Epidemiology Report 23: 1-4.

Research Background
My diversity of research interests is unified by a central concept in that the status and health of our oceans is inextricably connected to human health. This central concept allows me to integrate my education as a chemist and an ecologist and work experience as an aquatic toxicologist with my research as a microbial ecologist. A common objective of my work has been to characterize the ecology of microorganisms in the marine environment, which adversely affect human health. Pathogenic species of the Vibrio genus, such as V. cholerae, V. parahaemolyticus and V. vulnificus, are often the focus of my research; however, my experience includes work with microbial indicators (Escherichia coli and Enterococcus faecalis) and microbial pathogens of corals (Serratia marcescens).

My dissertation research was primarily focused on describing how fluctuations in environmental factors (such as temperature and salinity) and shifts in the composition of the plankton reservoir affect the prevalence and seasonality of pathogenic Vibrio species. Results show that fluctuations in environmental factors alone were unable to account for the seasonal variation encountered in our field studies. Shifts in the abundance of plankton taxa were strong Vibrio drivers. In particular, seasonal variation in the abundance of diatoms, copepods and decapods appear to play a temperature-independent role in the observed Vibrio seasonality. In sum, this research suggests that future Vibrio predictive models could be improved through characterizing Vibrio prevalence in the context of environmental factors as well as bloom formation and shifts in the abundance and life history of specific plankton taxa.

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Julie Koester

Post-doctoral Researcher

The focus of my research is to find connections between genes, phenotypes and the environmental forces of natural selection. Diatoms are my test-organisms of choice.

Two populations of the planktonic diatom Ditylum brightwellii co-occur in Puget Sound, but are differentiated by genome size (Koester et al. 2010); they are hypothesized to be cryptic species. Species Dbr2 has a 2-folder larger genome size than Dbr1, and likely arose from Dbr1 via whole genome duplication because its distribution is restriction to the northeastern Pacific Ocean, whereas Dbr1 has a circum-global distribution. Duplicated genes tend to accumulate mutations that are masked by working copies. These mutations may be selected for and sweep through a population providing adaptive benefit.

Seven percent of the protein coding genes in Thalassiosira pseudonana were determined to be positively selected (i.e. adaptively beneficial) by comparing homologous genes from seven strains of T. pseudonana. These genes disproportionately code for transcriptional regulators and protein-binding proteins. In addition, five positively selected genes that are putatively associated with the cell wall are up-regulated under iron and silicate limitation (Koester et al. in prep).

 

Left to right 1-3: 1) Two gametic valves and one large valve from a sexual clone of Ditylum brightwellii from the Gulf of Maine, 2-3) Ditylum brightwellii: a large clone from Puget Sound and small clone from New Zealand.

 

Education

Ph.D. University of Washington, 2012

M.S., University of Maine, 2005

B.Sc. Honours, University of British Columbia, 1991

 

Publications

  • Koester, J.A., Swanson, W.J., Armbrust, V.E. (submitted) Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation
  • Koester, J.A., Brawley, S.H.B., Karp-Boss, L. and Mann, D. 2007. Sexual reproduction in the marine centric diatom Ditylum brightwellii (Bacillariophyta). European Journal of Phycology. 42(4):351-366
  • Koester, J.A., Swalwell, J.E., von Dassow, P., Armbrust, V.E. 2010. Genome size differentiates co-occurring poplations of the planktonic diatom Ditylum brightwellii (Bacillariophyta).  BMC Evolutionary Biology. 10:1 doi:10.1186/1471-2148-10-1

Shady A. Amin

Microbial interactions are likely as old as life itself and will continue to play an integral role in shaping microbial diversity. Can we use a combination of culturing and molecular techniques (e.g. next-gen sequencing) to understand how these interactions evolved, how important are they today, and how will they respond to climate change?

Postdoctoral Fellow
Email: shadyam at u.washington.edu
Office: 206-685-4196

Education:
Ph.D. in Bioinorganic Chemistry, University of California, San Diego/San Diego State University (2010)
M.A. in Inorganic Chemistry, San Diego State University (2005)
B.Sc. in Biochemistry, University of California, Santa Barbara (2003)

Research Interests:
I'm interested in how marine microbes talk to each other. These types of interactions are mostly uncharacterized yet they play a critical role in the physiology of interacting organisms, which leads to a change in the chemical environment surrounding those cells and subsequently to the whole ecosystem. Because diatoms are among the most important primary producers in the oceans, I am investigating inter-species interactions between diatoms (photosynthetic eukaryotes) and the two other domains of life (heterotrophic prokaryotes): 1) bacteria and 2) archaea.


1) Diatom-bacterial interactions are common in the oceans and can be beneficial or lethal. Only a small number of these interactions have been described. One possible mechanism for a diatom to detect and respond to beneficial or "pathogenic" bacteria is through detection of a molecule the bacteria produce. Many marine bacteria use hydrophobic signals to communicate with each other (i.e. quorum sensing). Similar to some plants, diatoms maybe able to detect beneficial vs lethal bacteria by differentiating between their excreted molecular signals. Currently, I'm using whole transcriptome analysis and metabolomics to study interactions between diatoms and their bacterial microflora. So far, evidence suggests there are an array of complex interactions that take place between the diatom and its many bacterial partners.
(Fig. 1: Diatom-associated bacteria are confined to two phyla and a limited number of genera as illustrated by the maximum likelihood phylogenetic tree of the bacterial domain.

2) Archaea have been typically associated with extreme environments such as hydrothermal vents. However, we now know that marine archaea dominate many parts of the marine environment and influence global biogeochemical cycles. For example, Ammonia-oxidizing Archaea (AOA) play an important role in the nitrogen cycle by oxidizing ammonia to nitrite. Their dominance in many marine habitats and presence in the upper water column (e.g. chlorophyll a maxima where phytoplankton thrive) suggest that they are likely to interact with other microbes including diatoms. Currently, I'm studying trace metal limitation of the only cultured marine AOA isolate with wider implications to diatom metal availability. Recently published results from this study show that AOA may be strongly limited by Cu availability in many parts of the marine environment. Many oceanic diatoms also require a high Cu demand, suggesting that both taxa may be interacting/competing for Cu particularly in the open ocean.


(Fig. 2: This figure shows the effect of free cupric ion concentrations on ammonia oxidation of the only representative marine AOA available in culture. Based on this data, AOA are expected to be Cu-limited below 10-13 M. This value is in excess of free cupric ion concentrations measured in many parts of the oceans.

Publications:
1) Qin, W.; Amin, S.A.; Martens-Habbena, W.; Urakawa, H.; Devol, A.H.; Moffett, J.W.; Armbrust, E.V.; Ingalls, A.E.; Stahl, D.A. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. Proc. Natl. Acad. Sci. U.S.A., Early Access.

2) Jacquot, J.; Horak, R.E.; Amin, S.A.; Devol, A.; Ingalls, A.E.; Armbrust, E.V.; Stahl, D.A.; Moffett, J.W. Assessment of the potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary. Marine Chemistry, 162, 37-49.

3) Amin, S.A.; Moffett, J.W.; Martens-Habbena, W.; Jacquot, J.; Han, Y.; Devol, A.; Ingalls, A.; Stahl, D.A.; Armbrust, E.V. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications to nitrification in the marine environment. Limnology and Oceanography, 2013, 58, 2037-2045.

4) Weerasinghe, A.;Amin, S.A.; Barker, R.; Othman, T.; Romano, A.; Siburt, C.P.; Tisnado, J.; Lambert, L.A.; Huxford, T.; Carrano, C.J.; Crumbliss, A.L. Borate as a synergistic anion for Marinobacter algicola ferric binding protein, FbpA: A role for boron in iron transport in marine life Journal of the American Chemical Society, 2013, 135, 14504-14507.

5) Gärdes, A.; Triana, C.; Amin, S.A.; Green, D.H.; Trimble, L.; Romano, A.; Carrano, C.J. Detection of a Photoactive Siderophore Biosynthetic Genes in the Marine Environment. BioMetals, 2013, 26, 507-516.

6) Romano, A.; Trimble, L.; Hobusch, A.; Schroeder, K.; Amin, S.A.; ; Hartnett, A.; Barker, R.A.; Crumbliss, A.; Carrano, C.J. Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893. Metallomics 2013, 5, 1025-1030.

7) Amin, S.A.; Parker, M.S.; Armbrust, E.V. Interactions between diatoms and bacteria. Microbiology and Molecular Biology Reviews 2012, 76, 667-684. Journal Cover

8) Amin, S.A.; Green, D.H.; Gardes, A.; Romano, A.; Trimble, L.; Carrano, C.J. Siderophore-mediated iron uptake in two clades of Marinobacter spp. associated with phytoplankton: The role of light. BioMetals 2012, 25, 181-192.

9) Amin, S.A.; Green, D.H.; Al-Waheeb, D.; Gardes, A.; Carrano, C.J. Iron transport in the genus Marinobacter. BioMetals 2012,25,135-147.

10) Amin, S.A.; Green, D.H.; Kuepper, F.C.; Sunda, W.G.; Carrano, C.J. Photolysis of iron siderophore chelates promotes bacterial-algal mutualism. Proceedings of the National Academy of Sciences of the U.S.A. 2009, 106, 17071-17076.

11) Amin, S.A.; Green, D.H.; Kuepper, F.C.; Carrano, C.J. Vibrioferrin, an unusual marine siderophore: Iron binding, photochemistry and biological implications. Inorganic Chemistry 2009, 48, 11451-11458.

12) Zhang, G; Amin, S.A.; Kuepper, F.C.; Holt, P.D.; Carrano, C.J.; Butler, A. Ferric stability constants of representative marine siderophores: Marinobactins, Aquachelins, and Petrobactin. Inorganic Chemistry 2009, 48, 11466-11473.

13) Carrano, C.J.; Schellenberg, S.; Amin, S.A.; Green, D.H.; Kuepper, F.C. Boron and marine life: A new look at an enigmatic bioelement. Marine Biotechnology, 2009, 11, 431-440.

14) Harris, W.R.; Amin, S.A.; Kuepper, F.C.; Green, D.H.; Carrano, C.J. Borate binding to siderophores: Structure and stability. Journal of the American Chemical Society 2007, 129, 12263-12271.

15) Amin, S.A.; Kuepper, F.C.; Green, D.H.; Harris, W.R.; Carrano, C.J. Boron binding by a siderophore isolated from marine bacteria associated with the toxid dinoflagellate Gymnodinium catenatum. Journal of the American Chemical Society 2007, 129, 478-479.

 

Kate Hubbard

Extensive diversity has been detected in phytoplankton communities, and while some organisms appear to be ubiquitously distributed throughout the marine environment, other organisms appear to be constrained to particular places or environments. I am interested in the connection between diversity and distribution across different environments, and more specifically, how physiology, dispersal, and (physical and chemical) environment may structure marine diatom communities. For my graduate studies, I am surveying genetic diversity in the harmful alga, Pseudo-nitzschia. Most of my research takes place in the coastal and estuarine waters of British Columbia and Washington, although I am interested in the global distribution of Pseudo-nitzschia (and welcome potential sampling collaborations). This research is being conducted as part of the Pacific Northwest Center for Human Health and Ocean Studies, a multi-disciplinary investigation to understand how harmful algae blooms are initiated in the marine environment, and the impacts they have on shellfish and humans (and vice versa). The genus Pseudo-nitzschia is comprised of some 30 species, and is perhaps best known because many species are able to produce the neurotoxin domoic acid. Diatoms in this genus also exhibit a cosmopolitan distribution, with species detected in all oceans including polar regions. Individual species, however, can be notoriously difficult to identify. For my master's research, I designed genus specific primers and developed a Pseudo-nitzschia Automated Intergenic Spacer Analysis (ARISA) to easily and accurately identify species in environmental samples (Hubbard et al. 2008). ARISA can be used in tandem with environmental clone libraries to identify diversity at the species and sub-species levels. For my PhD research, I am using these approaches to identify population structure (in toxic and non-toxic blooms), across coastal and estuarine environmental gradients (e.g. salinity). Ecological investigations of distribution patterns, coupled with circulation models, will be used to make predictions about the impact of physiology and physical oceanography on dispersal, which will be tested using Pseudo-nitzschia isolates in laboratory experiments. Education: M.S. in Oceanography, University of Washington, 2005. B.A. in Biology, New College of Florida, 2002. Recent publications: Hubbard, K.A., Rocap, G., and Armbrust, E.V. 2008. Inter- and intra-specific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae). J. Phycol. 44 (3) 637-649. Marchetti, A., Lundholm, N., Kotaki, Y., Hubbard, K.A., Armbrust, E.V., and Harrison, P.J. 2007. Identification and assessment of domoic acid production in oceanic Pseudo-nitzschia (Bacillariophyceae) from iron-limited waters in the northeast subarctic Pacific. J. Phycol. 44 (3) 650-661.

Hood Canal in February, 2008

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Sara J. Bender


Recent Graduate

Education
Ph.D., Biological Oceanography. University of Washington (2013).
M.Sc., Oceanography. University of Washington (2009).
B.A. summa cum laude, Biological Sciences. Rutgers University (2005).

Research Overview
My research is motivated by the overarching question, How does nitrogen availability affect diatom physiology and in turn, how does diatom physiology impact the marine environment through the drawdown of nitrogen?

During my graduate school tenure, I have worked in the laboratory on individual diatom species, as well as embarked on several research cruises off of central California, Oregon, Washington and Vancouver Island to interrogate diatom nitrogen metabolism in diverse nitrogen regimes. My goal has been to identify and quantify transcript abundances for molecular markers of diatom N metabolism, including responses to different nitrogen sources and responses to different degrees of nitrogen availability.  Ultimately, these molecular markers will be used as part of larger metatranscriptomic datasets to monitor changes in diatom N uptake and N assimilation in the field.

Project 1: The role of the urea cycle in the model marine diatom Thalassiosira pseudonana

This work improves our understanding of diatom intracellular processes by incorporating the urea cycle into the bigger picture of N metabolism in a model diatom and by examining the effect of nitrogen sources on these metabolic pathways.
(Shown left: Simplified schematic of diatom nitrogen metabolism. Protist 2012)

Project 2: Comparative diatom transcriptomics in response to the onset of nitrate starvation.

This project is motivated by the need to better understand diatom-shared traits of N metabolism during growth on low nitrogen, and to determine whether assumptions about a "uniform diatom response" to changes in nitrogen availability, are relevant given the diversity of the diatom group.
(Shown right: Cultures of Fragilariopsis cylindrus growing in the lab.)

Project 3: Using in situ markers of diatom metabolism coupled to metatranscriptomes to determine the nitrogen response of diatom field communities to changing nitrogen regimes.

Several research cruises steaming from the coast to the open ocean have allowed us to conduct onboard, deck incubations of the ambient phytoplankton community, as well as to collect large-scale filtrations for metatranscriptomic sequencing. This includes a recent collaboration between our lab group and GEOTRACES to couple 'omics sampling to trace ocean elements. Analyses of all of this work will provide a snapshot of diatom metabolism in the field, told from the cell's perspective.
(Shown left: Colleen wrestling with incubator tubing onboard the R/V Wecoma.)


Publications
Durkin, C.A., Bender, S.J., Chan, K.Y.K., Gaessner, K., Grunbaum, D., and Armbrust, E.V. (2013). Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography. 58(5):1707-1726.

Bender, S.J., Parker, M.S. and Armbrust, E.V. (2012). The coupled effects of light and nitrogen source on the urea cycle and nitrogen metabolism over a diel cycle in the marine diatom Thalassiosira pseudonana. Protist. 163: 232-51.  

Durkin, C.A., Marchetti, A., Bender, S.J., Truong, T., Morales, R., Mock, T. and Armbrust, E.V. (2012). Frustule-related gene transcription and the influence of diatom community composition on silica precipitation in an iron-limited environment. Limnology and Oceanography. 57(6): 1619-1633.

Bidle, K.D. and Bender, S.J. (2008). Iron starvation and culture age activate metacaspases and programmed cell death in the marine diatom, Thalassiosira pseudonana. Eukaryotic Cell. 223-46.


Claire Ellis

As a research technician in Ginger Armbrust's lab I am fortunate to be involved in a range of diverse projects.  I help graduate students and post-docs investigate questions on marine phytoplankton dynamics and participate in cruises to collect samples that are used for many projects in the lab. 

I began working in the Armbrust lab as a sophomore undergraduate student at UW and am still working on research that began as my senior project on the molecular analysis of Pseudo-nitzschia species.  The project is part of an ongoing collaboration with the Woods Hole Oceanographic Institute to examine the diversity and distribution of Pseudo-nitzschia species along the East Coast of the United States.  Pseudo-nitzschia is a potentially harmful diatom species that has the ability to produce the biotoxin domoic acid during harmful algae bloom events.  The overall objective of this project is to better understand the occurrence of domoic acid.  Because species of Pseudo-nitzschia are difficult to identfy by microscopy and morphology, we used a DNA fingerprinting technique (ARISA) developed by Kate Hubbard (a former graduate student in our lab) to distinguish between species and strains.  By examining Pseudo-nitzschia communities in samples collected from Georges Bank and the Gulf of Maine during May, June, and July of 2008 we are hoping to provide further insight to different water parameters necessary for Pseudo-nitzschia species distributions and the processes that are likely important in the occurrence of domoic acid and harmful algae blooms. 

One of my current projects includes testing culture samples for the presence of domoic acid by using surface plasmon resonance (SPR).  This innovative approach analyzes binding of domoic acid to antibodies immobilized on sensor chips coated with gold surfaces.  The Soelberg lab has developed a compact portable SPR machine that allows us to test samples in the lab and at sea on research cruises. 

I will be continuing my investigative research experience by attending graduate school at UW in the fall. The outstanding mentoring and guidance I received while working in the Armbrust lab contributed to my interest in research, and my training and experiences will contribute to my success as a graduate student.

Micaela S. Parker

I am a research scientist in the School of Oceanography at the University of Washington. I combine molecular tools and bioinformatics with physiology experiments for the study of marine diatoms. Diatoms are some of the most dominant and important organisms for global carbon cycling in the world’s oceans. They are responsible for about 40% of marine primary production and play a critical role in global climate. Through photosynthesis, diatoms capture the greenhouse gas carbon dioxide and produce oxygen. Annually, diatoms generate one fifth of the oxygen we breathe.

I am specifically interested in the diatom genus Pseudo-nitzschia because many of these species can produce a potent neurotoxin called domoic acid (DA). DA can accumulate in filter feeders such as clams, mussels and oysters. When humans consume shellfish contaminated with DA, they can become very sick. The condition is known as amnesic shellfish poisoning because symptoms include memory loss. DA is also associated with illness and mortality in marine mammals and other vertebrates such as sea birds. I am using comparative transcriptomics (gene expression) to understand the genes that are differentially expressed in Pseudo-nitzschia species when the cells are producing the toxin. The goal is to uncover genes involved in toxin production and develop these as markers for assessing toxin production in field samples. In collaboration with the Joint Genome Institute, we have a draft genome of Pseudo-nitzschia multiseries, in addition to several RNASeq libraries which we are currently analyzing.

I have several other projects that I collaborate on with current and former members in our lab at the Center for Environmental Genomics. These include: the discovery of an iron storage protein called ferritin in Pseudo-nitzschia, which may help explain their success in open ocean iron-poor environments, as well as a metatranscriptome of an iron-addition experiment at Ocean Station Papa (see Adrian Marchetti's website for more information on these projects). Currently, I am also using comparative genomics to investigate strain level diversity within the species Thalassiosira pseudonana (with a lot of help from Chris, Dave and Rhonda in our lab). We have used a SOLiD Analyzer to re-sequence six additional strains (for a total of 7 genomes) and have run light treatment experiments with two of these strains for a whole transcriptome level comparison. I am also collaborating with one of our graduate students, Sara Bender, to investigate the role of the urea cycle in diatoms (see Sara's page for more information). 

 For my Ph.D. thesis research, I investigated the expression of genes involved in the cycling of carbon and nitrogen within a diatom cell during photorespiration. 

 For more information on the Center for Human Health and Ocean Studies, please see our website. For more information on my previous research projects, please see my CV.

Education

  • Ph.D. in Oceanography, University of Washington, 2004.
  • M.S. in Oceanography, University of Washington, 1999.
  • coursework in Plant Pathology, Cornell University, 1994-1995.
  • B.S. summa cum laude in Biology, minor in German, University of Massachusetts, 1994.

 

Publications

  • Port, J.A., M.S. Parker, R.B. Kodner, J.C. Wallace, E.V. Armbrust, E.M. Faustman. (2013). Identification of G protein-coupled receptor signaling pathway proteins in marine diatoms using comparative genomics. BMC Genomics. 14(1):503. doi:10.1186/1471-2164-14-503
  • Read, B.A., et al. (2013). Emiliania’s pan genome drives the phytoplankton’s global distribution. Nature. 499:209–213. doi:10.1038/nature12221
  • Amin, S.A., M.S. Parker, E. V. Armbrust. (2012) Interactions between diatoms and bacteria. Microbiol. Mol. Biol. Rev. 76, 667-684. Journal Cover
  • Marchetti A., D. Schruth, C.A. Durkin, M.S. Parker, R. Kodner, C. T. Berthiaume, R. Morales, Allen, A. E., and E. V. Armbrust. (2012). Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proceedings National Academy of Science Plus, USA doi: 10.1073/pnas.1118408109.
  • Bender, S. J., M.S. Parker, E. V. Armbrust. (2011). The coupled effects of light and nitrogen source on the urea cycle and nitrogen metabolism over a diel cycle in the marine diatom Thalassiosira pseudonana. Protist doi:10.1016/j.protis.2011.07.008.
  • Maheswari, U., K. Jabbari, A. E. Allen, J.-P. Cadoret, A. De Martino, M. Heijde, M. Katinka, J. La Roche, P. J. Lopez, V. Martin–Jézéquel, T. Mock, J.-L. Petit, B. M. Porcel, M. S. Parker, A. Vardi, E. V. Armbrust, J. Weissenbach and C. Bowler. (2010). Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology 11:doi:10.1186/gb-2010-11-8-r85.
  • *Marchetti, A., M.S. *Parker, L.P. Moccia, E.O. Lin, A.L. Arrieta, F. Ribalet, M.E.P. Murphy, M.T. Maldonado, and E. V. Armbrust. (2009). A novel ferritin identified in bloom-forming marine pennate diatoms. Nature 457: 467-470. doi:10.1038/nature07539. *These authors contributed equally to this work.
  • Worden, A. et al. (2009). Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324 (5924): 268 – 272
  • Parker, M.S., T. Mock, and E.V. Armbrust. (2008). Genomic Insights Into Marine Microalgae. Annual Review of Genetics 42:619–45.
  • Bowler, C. et al. (2008). The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature 456:239-244.
  • Erdner, D.L., Dyble, J., Parsons, M.L., Stevens, R.C., Hubbard, K.A., Wrabel, M.L., Moore, S.K., Lefebvre, K.A., Anderson, D.M., Bienfang, P., Bidigare, R.R., Parker, M.S., Moeller, P., Brand, L.E., Trainer, V.L. (2008) Centers for Oceans and Human Health: a unified approach to the challenge of harmful algal blooms. Environmental Health 7(Suppl 2):S2 doi:10.1186/1476-069X-7-S2-S2
  •  Moore, S.K., V.L. Trainer, N.J. Mantua, M.S. Parker, E.A. Laws, L.C. Backer and L.E. Fleming. (2008). Impacts of climate variability and future climate change on harmful algal blooms and human health. Environmental Health 7:(Suppl 2):S4
  • *Kroth, P. G., A. Chiovitti*, A. Gruber*, V. Martin-Jezequel*, T. Mock*, M. S. Parker*, M. S. Stanley*, A. Kaplan, L. Caron, T. Weber, U. Maheswari, E. V. Armbrust, and C. Bowler. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. (2008) PLoS ONE 3:e1426. Full Text Link *These authors contributed equally to this work.
  • Montsant, A. A. E. Allen, S. Coesel, A. De Martino, A. Falciatore, M. Heijde, K. Jabbari, U. Maheswari, M. Mangogna, E. Rayko, M. Siaut, A. Vardi, K. E. Apt, J. A. Berges, A. Chiovitti, A. K. Davis, M. Z. Hadi, T. W. Lane, J. C. Lippmeier, D.Martinez, M. S. Parker, G. J. Pazour, M. A. Saito, K. Thamatrakoln, D. S. Rokhsar, E. V. Armbrust, C. Bowler. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43:585-604.
  • Parker, M.S. and E.V. Armbrust. (2005). Synergistic effects of light, temperature and nitrogen source on transcription of genes for carbon and nitrogen metabolism in the centric diatom Thalassiosira pseudonana (Bacillariophyceae). Journal of Phycology 41:1142-1153. Full Text Link N.B. This paper was highlighted in the following review: Allen, A.E. (2005). Defining the molecular basis for energy balance in marine diatoms under fluctuating environmental conditions. Journal of Phycology 41: 1073–1076.
  • Armbrust, E. Virginia, John A Berges, Chris Bowler, Beverley R. Green, Diego Martinez, Nicholas H. Putnam, Shiguo Zhou, Andrew E. Allen, Kirk E. Apt, Michael Bechner, Mark A. Brzezinski, Balbir K. Chaal, Anthony Chiovitti, Aubrey K.Davis, Mark S. Demarest, J. Chris Detter, Tijana Glavina, David Goodstein, Masood Z. Hadi, Uffe Hellsten, Mark Hildebrand, Bethany D. Jenkins, Jerzy Jurka, Vladimir V. Kapitonov, N. Kröger, Winnie W.Y. Lau, Todd W. Lane, Frank W. Larimer, J. Casey Lippmeier, Susan Lucas, Mónica Medina, Anton Montsant, Miroslav Obornik, Micaela Schnitzler Parker, B. Palenik, Gregory J. Pazour, Paul M. Richardson, Tatiana A. Rynearson, Mak A. Saito, David C. Schwartz, Kimberlee Thamatrakoln, Klaus Valentin, Assaf Vardi, Frances P. Wilkerson, and D. S. Rokhsar. (2004). The genome of the diatom Thalassiosira pseudonana: Ecology, evolution and metabolism. Science 306: 79-86. Full Text Link
  • Parker, M.S., E.V. Armbrust, J. Piovia-Scott and R G. Keil. (2004). Light regulation of a photorespiratory gene (glycine decarboxylase) in the centric diatom Thalassiosira weissflogii (Bacillariophyceae). Journal of Phycology 40:557-567. Full Text Link
  • Parker, M.S., P.A. Jumars and L. L. LeClair.(2002). Population genetics of two bivalve species (Protothaca staminea and Macoma balthica) in Puget Sound , Washington. Journal of Shellfish Research. 22(3): 681-688.
  • Weir, A.M.; Schnitzler*, M.A.; Tattar, T.A.; Klekowski, E.J. Jr. ; Stern, A.I. (1996). Wound periderm development in red mangrove, Rhizophora mangle (L.). Intl. J. Plant Sci. 157(1): 63-70.
  • Schnitzler*, M.A. (1994). The anatomy of fungal resistance mechanisms in Rhizophora mangle (L.), red mangrove. Undergraduate Honors Thesis. University of Massachusetts, Honors Program.

* maiden name = Schnitzler

 

 

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Robin Kodner

 

rkodner at u.washington.edu

Affiliations:

UW Center for Environmental Genomics

UW Friday Harbor Labs

Beam Reach Marine Science and Sustainability School

 

Education

Harvard University PhD, Biology, 2007
Department of Organismic and Evolutionary Biology
Thesis Advisor: Dr. Andrew Knoll


University of Wisconsin-Madison Bachelors of Science, 2000
Majors: Paleobiology with honors and History
Academic Advisor: Dr. Linda E. Graham

 

Research Background

I have my training as a geobiologist and have experience working with molecular biology, organic geochemistry and fossils.    I integrate methods from a variety of fields to best address the questions that most interst me . My past work has focused on recognizing and interpreting evidence of life in the geologic record and using it to understand the past contribution of marine organism to global carbon sinks. I used modern organisms as a platform for exploring the past recorded in microfossils and organic geochemical signatures. Thus, my thesis work combined comparative biochemistry, phylogenetics, genomics, micropaleonotolgy, SEM/TEM and microchemical techniques.

My current research is focusing on modern marine phytoplankton and using targeted metagenomics to study phytoplankton communities response to environmental change. I am investigating the sources and sinks of organic carbon from marine phytoplankton communities by studying environmental genomes and transcriptomes.  I am working on a number of datasets in collaboration with the Armbrust lab, including one from my field site is the San Juan Islands (WA) where I am a resident scientist at the Friday Harbor Labs  (http://depts.washington.edu/fhl/) and Faculty for the Beam Reach Marine Science and Sustainabitly School (http://www.beamreach.org/). This work will contribute to the growing effort to understand the biological feedback in the global carbon cycle.

Overview of Research Interests

I'm interested in phytoplankton communitiy dynamics and their role in biogeochemistry at multiple scales - from seasonal, to geologic time scales.  I use metagenomics, metatrancriptomics, and comparative genomics to study these microbial eukaryotic communities. The foundations of my work bring together ideas from evolutionary biology, geology, and biological oceanography to study the co-evolution of the biosphere and the geosphere. My focus is the evolutionary history and functional ecology of photosynthetic eukaryotes in past and present environments.  In particular I am interested in the role of phytoplankton in the global carbon cycle and linking genomic data with geological and environmental data.   Though eukaryotic phytoplankton are quantitatively highly influential in the global carbon cycle, they have generally been understudied in the field of genomics and have only recently become the subjects of metagenomic and metatrancriptomic studies. In my work I seek to increase our knowledge of microbial eukaryotic genomics and ecology in the context of the changing Earth system.   

 

My current research focus is developing in three areas: (1) developing bioinformatic tools and pipelines for gene identification  in metagenomes and metatranscriptomes using phylogenetic methods (2) analyzing a variety of metagenomic and metatrancriptomic projects (3) synthesizing environmental, biochemical, and genomic data, with specific emphasis on the carbon cycle.  In addition, I have begun to apply these research directions to two applied projects: investigating harmful algal blooms and algae-based biofuel.

 

(1)  I have been collaborating with Frederick Matsen, a mathematical and computational biologist at University of California – Berkeley on a new, phylogenetics based gene identification program called pplacer (Matsen, Kodner, and Armbrust, in prep). Identification of sequences via phylogenetic analysis is preferable to similarity searches like BLAST, because it provides evolutionary information about each sequence and allows for identification of yet unidentified groups.  Look for info on pplacer here http://matsen.fhcrc.org/pplacer/.

 

(2) I am currently working on one metagenome project in collaboration with Alex Worden's group at MBARI.  This project is looking at eukaryotic phytoplankton functional diversity thought a transect from the coast of Montery Bay, CA to to the off shore waters.  I am also collaborating on two metatranscriptome projects, one in collaboration with other folks in the Armbrust lab, looking at sample from Station P in the subarctic North Pacific and the other in collaboration with Jon Zehr's group at UC Santa Cruz, looking at a transect through the Amazon River plume.

 

(3) I am working on sequencing samples from Eastsound, WA, where I sampled thorough a toxic diatom bloom in June, 2009, 2010 and 2011.  I've also been advising work on mixed community cultures for algal biofuel for Bodega Algae in Cambrige, MA.

 

I'm also interested in experiential education and community based science education, outreach, and citizen science.  I'm working on developing a citizen science phytoplankon monitoring program in the San Juans to help build a base-line for understanding changes in phytoplankton communitiies on various time scales. I'm currently teaching field-based courses out of the Friday Harbor labs and working with many boat-based partners in the San Juans who are out and about collecting planton for me.  Stay tuned or more info!

 

 

Dissertation Research

I worked on a number of projects during my PhD work at Harvard University in Andy Knoll's lab (http://www.fas.harvard.edu/%7Eknollgrp/index.htm), and with Roger Summons (MIT, Department of Earth, Atmospheric, and Planetary Sciences) and Ann Pearson (Department of Earth and Planetary Sciences, Harvard University).

  • Sterols in Choanoflagellates and the evolution of sterol biosynthesis in eukaryotes
One of the pioneering areas of my research is using genomic data to identify genes for biomarker biosynthesis, in order to investigate taxonomic specificity and evolution of these molecules. I defined the biosynthetic potential of an organism to produce sterol biomarkers using genes from a complete genome sequence. I use this approach in a study with choanoflagellates, marine microorganisms with a sequenced genome and that hold an important phylogenetic position with respect to the origin of metazoans. The origin of metazoans is putatively marked in the geologic record by a sterol-derived biomarker, believe to be specific to demosponges. I investigated the potential of choanoflagellates to make this biomarker using genomic information. The genomic approached allowed a new way to determine the potential of biomarker production and to investigate the evolution of the biosynthetic pathway of a biomarker using phylogenomics (Kodner, et. al, PNAS, July 22, 2008).
  • Sterols in the Plantae (green and red algae): distribution, phylogeny, and relevance for interpreting geologic steranes
I created a database of sterol lipids, the progenitor of one of the most common classes of lipid biomarkers, from algal groups in the kingdom Plantae. These lipids (characterized with GC-MS) were again placed within a phylogenetic framework to describe the distribution and evolutionary history of these molecules within a diverse monophyletic lineage. This analysis aids in interpreting the Paleozoic sterane record, and is currently used as evidence that green algae were dominant primary producers in ancient oceans (Kodner, et al., in press, Geobiology, August 2008).
  • Distribution of algaenan (aliphatic biopolymer) in algal groups
I characterized a biopolymer thought to be a green algal biomarker (algaenan) from a diverse group of algae using pyrolysis GC-MS and put it in a phylogenetic context. This work helped to establish that algaenan, found in great abundance in the geologic record, actually has a very limited distribution among modern green algae and is not likely to be the source of the common geopolymer (Kodner, et al. in prep).
  • Biology, ultrastructure and chemical analysis of phycomate prasinophytes: a modern analog for organic walled microfossils
I study a unique marine green algal phytoplankton from the genus Halosphaera, which is a phycomate prasinophyte. The phycoma, a green algal reproductive structure presented as the best modern analog for the most ancient eukaryotic organic microfossils. The phycoma has long been thought to have substantial preservation potential and superficially resembles many ancient spheroidal microfossils. By this association, much of the organic walled microfossil record has been described as remains of phytoplankton. This project involved locating and field sampling this elusive structure, which remains unculturable. My SEM, TEM, and chemical analyses show limited support for the relation of spheroidal microfossils and phycoma, and support some new fossil ultrastructure data that suggest a greater diversity of organisms produce spheroidal microfossils than previously thought (Cohen, Kodner, and Knoll, in prep). This work has also called into question long standing ideas about microfossil preservation. In addition, I am describing the species I work on in Washington as a new species Halosphaera. 

 

Publications

Kodner, R. B., Matsen, F.A., Hoffman, N., Berthiaume, C., Armbrust, E. V., A fast, phylogenetic based pipeline for shotgun environmental sequences analysis. In prep

Marchetti, A, Schruth D., Durkin C., Berthiaume C. ,Morales, R., Parker M.S., Kodner, R.B. Armbrust, E.V.  Taxonomic and metabolic shifts in an iron-stimulated eukaryotic marine plankton community from the NE Pacific Ocean revealed through comparative metatranscriptomics. submitted

Matsen, F.A., Kodner, R. B, and Armbrust, E. V., pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of metagenomic sequences on a reference tree. 2010. BMC Bioinformatics, 11:538 (30 October 2010)

Phoebe A. Cohen, Knoll, A.H., and Kodner, R.B.  Large spinose microfossils in Ediacaran rocks as resting stages of early animals. Proceedings of the National Academy of Sciences.  2009.: Issue 106:6519-6524 

Kodner, R. B., Summons, R.E., Knoll, A. H. Phylogenetic Investigation of the Aliphatic, Non-hydrolyzable Biopolymer Algaenan, with a Focus on the Green Algae. Organic Geochemistry, 2009

Kodner, R. B., Summons, R.E., Pearson, A., King, N., and Knoll A. H. Sterols in a unicellular relative to the metazoans. 2008. Proceedings of the National Academy of Sciences, 105: 9897-9902

Kodner, R. B., Summons, R.E. Pearson, A., and Knoll, A. H. A quantitative investigation of sterols in the red and green algae from a phylogenetic perspective: Relevance for the interpretation of geologic steranes. 2008. Geobiology, 6(4):411-20

Graham, L. E., R. B. Kodner, M. M. Fisher, J. M. Graham, L. W. Wilcox, J. M. Hackney, J. Obst, P. C. Bilkey, D. T. Hanson, M. E. Cook. 2003. Early land plant adaptations to stress: a focus on phenolics. In The Evolution of Plant Physiology, A. R. Hemsley and I. Poole [eds.], Academic Press, London. pp. 155–170.
Redecker D, R. Kodner, L.E. Graham. 2002. Palaeoglomus grayi from the Ordovician. Mycotaxon 84: 33-37

Kodner R. B.
and L.E. Graham. 2001. High-temperature, acid-hydrolyzed remains of Polytrichum (Musci, Polytrichaceae) resemble enigmatic Silurian-Devonian tubular microfossils. American Journal of Botany 88 (3): 462-466

Redecker D, R. Kodner, L.E. Graham. 2000. Glomalean fungi from the Ordovician.
Science 289: 1920-1921

 




 

Colleen Durkin

email: cdurkin@u.washington.edu
webpage: students.washington.edu/cdurkin

     Two characteristics of diatoms that influence biogeochemical cycles are their high productivity and their unique silica cell walls.  As a result, diatoms control the silicon cycle in the ocean and couple the carbon and silicon cycles.  The largest particle export in the ocean is associated with sinking diatoms, which sequesters carbon into the deep ocean.  My research is motivated by the complicated factors that influence whether diatoms bloom, how much silica they incorporate into their cells, and their tendency to sink.  I am identifying which genes are involved in cell wall formation and how they respond to different nutrient conditions.  This involves comparing gene content among diatom genomes, measuring gene expression in controlled lab experiments, and correlating changes in gene expression with changes in cell wall physiology.  I am also applying what we learn about these genes in lab experiments to understanding natural populations.  My goal is to use these genes to directly measure how diatoms in the ocean are responding in a particular environment.  This will help us to identify which diatoms are responding, how they are changing their physiology, and under what conditions.  Ultimately, this type of information will help us understand the conditions, timing, and community composition that most influence biogeochemical cycles.

Publications:

Durkin, C.A., T. Mock, E.V. Armbrust. 2009. Chitin in diatoms and its association with the cell wall. Eukaryotic Cell 8:1038-1050
link

Current Research:

1.  Identifying shared genes among diverse diatoms that are likely associated with the cell wall, and measuring gene expression in different nutrient limiting conditions.  Genes found among diverse lab diatoms will be easier to find in diverse field populations.

Franzika Lutz and Tiffany Truong and two undergrads helping with this project.

2. Measuring diatom cell wall changes along the Line P transect in the subarctic North Pacific using both a silica stain (PDMPO) and gene expression.

Adrian Marchetti and Rhonda Morales collecting water from the CTD on the JP Tully in June 2008

3.  Measuring community responses to different silicic acid concentrations along the Washington and Oregon Coasts with the CMOP program.

Sara Bender and Jarred Swalwell deploying a CTD in rough seas aboard the RV New Horizon in May 2009.

Ellen O. Lin

I am a technician in the lab of Dr. Ginger Armbrust. My research revolves around the many various projects Dr. Armbrust and the post-docs in the lab are currently working on. I also deal with many of the collaborative projects that come through including our current collaborations with the Joint Genome Institute to sequence the genomes of Pseudonitzschia multiseries and Fragilariopsis under the direction of Dr. Micaela Parker and Dr. Thomas Mock respectively. I am also involved with the development of several EST libraries with the Joint Genome Institute at the level of RNA extraction. I have in the past been involved with generating several subtraction libraries for the organism Pseudonitzschia australis to analyze what genes are turned on when it starts to produce the chemical domoic acid, a marine toxin. Domoic acid is a dangerous toxin that can contaminate the shellfish population and eventually work it's way up the food chain where it can cause permanent short term memory loss in humans, and in the worst cases it can be fatal. It is our hope that we can better understand on a molecular level some of the chemical pathways and triggers for why these diatoms go toxic. I also participate with Dr. Micaela Parker and Dr. Adrian Marchetti in the study of iron and the genes used to regulate it. My studies revolve around trying to pull the gene ferritin, a gene discovered in the previously mentioned subtraction libraries, out of different types of phytoplankton using specially designed code-hop primers. I am also currently the Megabace technician for our facility. I am involved in running and maintaining our Megabace 1000 sequence analyzer whom we have affectionately named “Sofia”. The sequencing facility supports the sequencing efforts of faculty, students, and researchers from various labs in the larger University of Washington's scientific community as well as our own smaller marine molecular community.

Irina Oleinikov

Research Scientist
Phone: (206)685-6883
Email: irinao at uw.edu

As a research scientist in the Armbrust lab, I am responsible for maintaining our extensive culture collection and am the lab's diatom culturing guru. I also assist the graduate students and postdoctoral fellows in implementing their experiments and enjoy working in such a collaborative environment.

Adrian Marchetti

Adrian has moved to the University of North Carolina at Chapel Hill.  Visit his website here.

Thomas Mock

 

Thomas is currently a faculty member at the University of East Anglia (UEA) in Norwich.

 

Before I came to the University of Washington, I obtained my Dr. rerum naturalis from the University of Bremen (Germany) at the Alfred Wegener Institute for Polar and Marine Research (AWI) in 2003 after graduating (Diploma) from the Kiel University (Germany) with a degree in Biological Oceanography in 1998. I have subsequently done postdoctoral work for 2 years at the AWI. My research topics are acclimation and adaptation of marine and particularly polar sea ice diatoms to their extreme environmental conditions (link). My postdoctoral work here at the Department of Oceanography in the group of Ginger Armbrust is related to genome wide expression analysis with the marine diatom Thalassiosira pseudonana. We are intent to construct the first Microarrays for this diatom in order to identify transcription units, which are related to important environmental conditions such as excess light intensity, carbon dioxide limitation or iron limitation. Publications

  • Mock T, Hoch N (in press) Long-term temperature acclimation of photosynthesis in steady-state cultures of the polar diatom Fragilariopsis cylindrus. Photosyn. Res.
  • Mock T, Thomas DN (2005) Recent advances in sea-ice microbiology. Environ. Microbiol. 7(5) 605-619.
  • Thomas DN, Mock T (2005) Life in frozen veins - coping with the cold. The Biochemist 27(1) 12-16.
  • John U, Mock T, Valentin K, Cembella AD, Medlin LK (2005) The dinoflagellates come from outerspace but haptophytes and diatoms do not. Harmful Algae 2002. Proceedings of the X. International conference on harmful algae. Steidinger KA, Landsberg JH, Tomas CR & Vargo GA (Eds.) Florida Fish and Wildlife Conservation Comission and Intergovermental Oceanographic Comission of UNESCO.
  • Mock T, Valentin K (2004) Photosynthesis and cold acclimation - molecular evidence from a polar diatom. J Phycol. 40 732-741.
  • Mock T, Kruse M, Dieckmann GS (2003) A new microcosm to investigate oxygen dynamics at the sea-ice water interface. Aquat. Microb. Ecol. 30 197-205.
  • Biele J, Ulamec S, Garry J, Sheridan S, Morse AD, Barber S, Wright I, Tueg H, Mock T (2002) Melting probes at Lake Vostok and Europa. ESA Proceedings SP-518 115-118.
  • Mock T, Dieckmann GS, Haas C, Krell A, Tison JL, Belem Al, Papadimitriou S, Thomas DN (2002) Micro-optodes in sea ice: a new approach to investigate oxygen dynamics during sea ice formation. Aquat. Microb. Ecol. 29 297-306.
  • Mock T, Kroon BMA (2002) Photosynthetic energy conversion under extreme conditions: I Important role of lipids as structural modulators and energy sink under N-limited growth in Antarctic sea ice diatoms. Phytochem. 61 41-51.
  • Mock T, Kroon BMA (2002) Photosynthetic energy conversion under extreme conditions: II The significance of lipids at low temperature and low irradiance in Antarctic sea ice diatoms. Phytochem. 61 53-60.
  • Mock T (2002) In situ primary production in young Antarctic sea ice. Hydrobiol. 470 127-132
  • Dieckmann GS, Thomas DN, Mock T (2002) Life in sea ice. Scientific American (German edition), Dossier: Life in Space, p 13-15.
  • Krembs C, Mock T, Gradinger R (2001) A mesocosm study of physical-biological interactions in artificial sea ice: effects of brine channel surface evolution and brine movement on algal biomass. Polar Biol. 24 356-364.
  • Mock T, Gradinger R (2000) Changes in photosynthetic carbon allocation in algal assemblages of Arctic sea ice with decreasing nutrient concentrations and irradiance. Mar. Ecol. Prog. Ser. 202 1-11.
  • Mock T, Gradinger R (1999) Determination of Arctic ice algal production with a new in situ incubation technique. Mar. Ecol. Prog. Ser. 177 15-26.
  • Mock T, Meiners KM, Giesenhagen HC (1997) Bacteria in sea ice and underlying brackish water at 54 26'55''N (Baltic Sea, Kiel Bight) Mar. Ecol. Prog. Ser. 158 23-40.

Patents

  • Mock T, Valentin K (2004) Delta12-desaturase sequence from Fragilariopsis cylindrus. PCT/DE03/03180
  • Mock T, Valentin K (2004) Calpain7-protease sequence from Fragilariopsis cylindrus. PCT/DE03/02401

 

Mikelle L. Nuwer

I hold both a B.S and M.S. in Biological Oceanography from the University of Washington.  I am currently pursing a PhD. in Biological Oceanography.  The topic of my dissertation research is the spatial and temporal patterns of molecular genetic variation in a group of planktonic calanoid copepods.  I employ DNA sequence variation in mitochondrial genes to determine phylogenetic relationships, examine geographic variation, and make inferences about the population structure of species in the Calanus helgolandicus clade.  This work is a necessary first step for understanding speciation, ecology and community dynamics of the crustacean zooplankton.

Peter von Dassow

Peter von Dassow

Ann Riddle

Ann Riddle

Tatiana Rynearson

Tatiana Rynearson is currently a faculty member at the Graduate School of Oceanography, University of Rhode Island.

http://www.gso.uri.edu/users/rynearson