People

The Armbrust Lab

E. Virginia Armbrust

Ginger Armbrust Principal Investigator armbrust at u.washington.edu

 

Phytoplankton are the main focus of research in our lab. These organisms are responsible for about 40% of the total amount of photosynthesis that occurs on our planet. They play a critical role in the global carbon cycle and ultimately in global climate. Because much of the organic carbon generated by phytoplankton is used by bacteria, we also study bacterial/phytoplankton interactions.

Education

Positions Held

Publications

Sara Bender

 

Graduate Student

Phone: (206)685-4118

Email: sbender@u.washington.edu

Education
B.A. summa cum laude, Biological Sciences. Rutgers University (2005).
M.S., Oceanography. University of Washington (2009).
Graduate Student, Biological Oceanography. University of Washington (2006-Present).

Research Background
In the marine environment, diatom blooms occur in regions where nitrogen (N) concentrations are elevated, associating these organisms with high N budgets. Although inorganic N sources (such as ammonium, NH4+; nitrate, NO3-) are considered to be the main form of diatom nutrition, recent work has promoted the importance of dissolved organic N (DON) in phytoplankton growth. DON is an often overlooked component of marine N-sources and can account for up to 83% of the N pool composition. A better understanding of the effects of N-source on diatom physiology will improve both estimates of total carbon fixation in coastal environments and the effects of increased DON inputs into marine waters.

Research Interests
My research interests include the study of diatom molecular ecology in both the laboratory and the field. More specifically, my research seeks to understand the role of the urea cycle, a recently identified pathway involved in N metabolism in marine diatoms using gene expression studies, flow cytometry, field incubations, and metatranscriptomics. Typically, the urea cycle is found in heterotrophic organisms, and it provides a way for cells to detoxify NH4+. Recently, a complete urea cycle was identified in the photoautotroph Thalassiosira pseudonana, and it is hypothesized to connect N metabolism with several other vital cellular pathways.  For my Master's research project, my driving research questions were:
  • What role does the urea cycle play in cellular metabolism in diatoms, and does this cycle affect the balance of energy within the cell?
  • How does temperature and light intensity affect the urea cycle?
  • What are the connections between N source and photosynthesis in diatoms?
Publications
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. 7(2): 223-46.

Chris Berthiaume

As the lab's system administrator I'm responsible for making sure that our computer resources are running smoothly. We have three major pieces of computer equipment:

The focus of my work is adminstering these clusters and porting needed biology applications to a parallel computing environment. This can either be a road well-travelled in the case of bioinformatics applications on a beowulf cluster, or less-travelled in the case of interactive data visualization on a tiled-display cluster.

Colleen Durkin

I am interested in the mechanisms used by phytoplankton to survive in different environments and their interactions with other organisms. I am excited to combine genome sequence information with lab and field experiments to further understand these processes. For my Master's work I am investigating the role of chitin in diatom ecology. Chitin is the most abundant polymer in the marine environment and several diatom genera are known to produce long chitin fibers. This chitin can make up 18% of their cellular nitrogen and 30% of their biomass. These extensions can also alter their interactions with zooplankton. Diatom genome sequencing has revealed a complicated array of chitin related genes for synthesis, binding, and breaking down chitin. I would like to use these genes to figure out how, when, and why chitin is important to diatom survival. Because chitin synthesis requires nitrogen and iron, the role of chitin producing organisms might change in different nutrient environments. The reasons for chitin use might be directly related to the diatom cell (for increased drag or structural support), or related to interactions with other organisms. Chitin spines change the effective size of a diatom cell, altering the trophic level of its predators. Also, the enzymes used to degrade chitin might be used as a defense mechanism against fungal parasites whose cell walls are composed of chitin. I hope to clarify the role of chitin in diatoms by studying gene expression under a variety of lab conditions. I also hope to apply these molecular methods to environmental samples taken along the equatorial Pacific.

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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Vaughn Iverson

Vaughn Iverson Pre-doctoral Research Associate 206-685-4127 vsi at u.washington.edu

Research Interests

Microorganisms in the marine environment are always found living in association with one another. In particular, wherever there is a natural population of phytoplankton, associated heterotrophic bacteria will also be present. Traditionally in the laboratory, we go to great lengths to maintain pure cell cultures—a very unnatural act—so that we may study phytoplankton in isolation from all other types of organisms. This reductionist approach has been a valuable tool to shed light on the roles these organisms individually play in the environment; but the behaviors observed as cells adjust to a sterile lab environment are skewed, and simplified, by the absence of interaction with members of the natural communities these organisms have co-evolved with over many millions of years. I am interested in measuring and modeling the complex biochemical interactions within communities of marine microorganisms, as one would find in virtually any water sample taken from the environment. My strategy is to achieve this through the development and deployment of automated biological sensors capable of observing microbial communities in the field, and directly measuring their behaviors and interactions by quantifying specific proteins or nucleic acids of interest. Such instruments will take quite some time to develop and perfect, but my research aims to take definite steps in this direction. Biological research has been forever changed in the past 25 years by the sequencing of whole genomes for many organisms. Much of biological oceanography is being similarly transformed by the flood of genomic data now available for a wide variety of marine prokaryotic and eukaryotic organisms, with much more on the way. Using this information, I am developing ‘model systems’—relatively simple communities of organisms with sequenced genomes, living together—to study community behaviors and symbioses that are absent from pure cultures. Looking longer-term, well studied model systems such as these will facilitate the development and automation of molecular techniques and instruments targeting mixed populations; first in the lab and ultimately with natural communities in the field. My first model systems are diatom-bacteria communities designed specifically to investigate the mechanisms and potentially mutualistic behaviors leading to the exchange of B-vitamins between phytoplankton and heterotrophic bacteria. In addition, I am very interested in the study of whole genomes of sequenced marine diatoms to look for evidence of selective sweeps and skewed mutation rates through the detailed examination of patterns in the occurrence of single nucleotide polymorphisms (SNPs). This work may lead to new insights about genetic diversity, population dynamics and the role of sexual reproduction in these fascinating and globally important organisms.

Background & Bio

I grew up near Tacoma, WA and graduated from Gig Harbor High School in 1985. From there I went to Washington State University in Pullman (Go Cougs!), earning a B.S. in Computer Science and Chemistry in 1989. After a year working for Weyerhauser Corp. in 1990 designing and building some of the first computer networks and e-mail systems at the company, I attended the University of Washington in Seattle (Go Dawgs!) where I did research on artificial intelligence, computer graphics, signal processing and data compression, earning a M.S. in Computer Science and Engineering in 1993. After a short stint at IBM Corp. in Boca Raton, FL, I joined Intel Corp. in Hillsboro, OR, spending nearly 12 years there as a research scientist, inventor and engineering manager working on the development of high performance video compression algorithms and other media related graphics and signal processing technologies. During this time, I was also the lead editor of the ISO/IEC MPEG-21 (21000-2) international multimedia standard, which meant that I spent a disproportionate amount of my time in airplanes, airports and hotel conference rooms around the world. In 2002 I moved back to Seattle, working at the Intel Research lab near the University of Washington. I left Intel in early 2005 for a year of travel and time for exploration of what I might want to do next. As I followed my interests, one thing led to another and I ended up meeting Ginger Armbrust, volunteering in her lab during the summer of 2005 working with Micaela Parker on a diatom bioinformatics project, and becoming generally excited about finding a way to bring together my long-term interests in engineering, biochemistry, and the marine environment. Continuing my explorations, I spent Autumn of 2005 at the UW Friday Harbor Laboratories - Center for Cell Dynamics, studying cytoskeletal protein dynamics during cytokinesis in GFP transformed C. elegans embryos using laser confocal microscopy and computer simulations. I joined the Armbrust lab at UW Oceanography as a Ph.D. student in January 2006.

Education

 

Publications

 

U.S. Patents (20)

 

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Vaughn's book montage

In Defense of Food: An Eater's Manifesto
Water for Elephants
Power, Sex, Suicide: Mitochondria and the Meaning of Life
The Beautiful Cigar Girl: Mary Rogers, Edgar Allan Poe, and the Invention of Murder
Freakonomics Rev Ed: A Rogue Economist Explores the Hidden Side of Everything
Dancing Naked in the Mind Field
The End of the Alphabet


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Robin Kodner

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Postdoctoral Fellow - UW Friday Harbor Labs

rkodner at u.washington.edu


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


Overview of Research Interests

I use metagenomics, metatrancriptomics, and comparative genomics to study 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.  I've also been advising work on mixed community cultures for algal biofuel for Bodega Algae in Cambrige, MA.

 

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 work focuses on lipid biomarkers. Biomarkers are molecules preserved independently in the environment, thereby providing a record of organisms that may not be otherwise recognizable. These molecules can be used to describe ancient organisms and ecosystems independent of a traditional fossil record when analyzed from rocks, and can be used to track biomass in water and sediment in modern environments and the recent past. Yet biomarkers only work when restricted to a defined group of organisms. I have worked to characterize the taxonomic specificity of common biomarkers.

My current research is focusing on modern marine phytoplankton and using targeted metagenomics to study community production of lipid biomarkers in the environment to expand on the culture based studies I conduted for my dissertation. I am investigating the sources and sinks of organic carbon from marine phytoplankton communities by studying genes for biomarker biosynthesis in in metagenomes and characterizing lipids in the same samples.  am focusing on phytoplankton in Puget Sound and my field area is the San Juan Islands (WA) where I am a Friday Harbor Labs Postdoctoral Fellow (http://depts.washington.edu/fhl/). This work will contribute to the growing effort to understand the biological feedback in the global carbon cycle.


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).

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).
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).
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).
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. 
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Publications

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. 2009. in prep

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


Julie Koester

When are new species formed, and how do we recognize them?  The ocean appears to be a well mixed habitat, yet new, cryptic species of phytoplankton are identified each year. I am interested in how populations of organisms in the ocean differentiate from one another such that they are reproductively isolated. I am currently investigating the role that polyploidy plays in speciation of diatoms and the opportunities that polyploidy provides for gene differentiation.  Duplicated genes may be released from selection pressures and mutate freely.  When environmental conditions change, the resultant gene diversity may provide a favorable allele that is selected for in the new environment.  Polyploid species tend to have larger cell sizes than their diploid relatives, therefore altering the physiology of each cell. Ultimately, I would like to tie genetic differences back to observable physiological differences between sister species with different genome sizes.

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.

 

Publications

Adrian Marchetti

Research Scientist

Phone: 206-685-4196

e-mail: amarchetti-at-ocean.washington.edu

Education:

B.Sc. Biology, McGill Univeristy, Montreal PQ (1998)

Ph.D. Botany, University of British Columbia, Vancouver BC (2005)

Research Interests:

My primary research focus is biogeochemical evolution of phytoplankton in marine environments. Biogeochemical evolution is defined as the changes in the genomes of organisms and in the chemistry of their environment, as they influence each other over time. I combine laboratory-based and field-based studies to answer fundamental questions on factors influencing phytoplankton distributions and abundance, and to advance our understanding of how these organisms interact with their environment and influence ocean biogeochemistry. I am interested in studying trace metals, such as iron, that are essential for the nutrition of phytoplankton and how future climate changes will influence phytoplankton growth and ecology. For example, we have discovered that pennate diatoms such as Pseudo-nitzschia contain the gene to encode for ferritin, which is a highly specialized iron concentrating protein. The acquisition of ferritin by certain diatoms may contribute to their success in low-iron environments where new inputs of iron are primarily confined to pulse events through atmospheric dust deposition. More details about this study may be found here.  I also study how growing phytoplankton impact ocean nutrient inventories by measuring biological rate processes. Several approaches are taken to my investigations. First, I work with marine isolates of diatoms in the laboratory, which allows for refined studies to determine the molecular biology and physiology of a specific group of phytoplankton. Second, I participate on research cruises to investigate natural phytoplankton assemblages, as this provides for a more ecologically relevant context to assess how these organisms acclimate and adapt to different environments and how their nutrient requirements will influence marine biogeochemistry.

Publications:

Rhonda Marohl

As a Research Engineer in the Armbrust Lab, I get to participate in many different projects, and work with virtually everyone in the lab. Currently, I’m working with Adrian to try and find the ferritin gene in Nitzschia species, which could help explain why pennate diatoms are often the dominant species that bloom during iron fertilization experiments. I’m also helping Adrian create clone libraries from samples taken during these iron fertilization experiments to see how diverse the community is, and also if they contain certain genes of interest. One big part of my job is to run our newest piece of equipment, the flow cytometer (affectionately called Leo). A flow cytometer records the size and fluorescence (chlorophyll, DNA, etc.) of sample particles below 70µm in size, and sorts the particles according to these parameters. It does this by creating a very thin stream of water and injecting sample particles into the middle of this stream. As the individual particles flow through the stream, they are hit with different wavelengths of laser light. This light is interrupted, or scattered, by the particles, and a computer records this scatter displaying the information in real time. Thus, you can see the size and fluorescence of your particles as they are going through the machine! Because the flow cytometer records data in real time, it is possible to select certain particles according to the parameters of your choice and sort them into 96 well plates, test tubes, or microscope slides. This is very useful for trying to make cultures axenic, isolating a certain population of interest to look at under the microscope (or culture), and “seeing” particles that are too small for the microscope to detect. We have also taken the flow cytometer out to sea to collect real time data looking at microscopic phytoplankton and bacteria in the field. I’m working with two grad students, Sara and Colleen, to try and expand the uses of the flow cytometer. Sara is interested in using the flow cytometer to look at how pico-eukaryotic and bacterial populations change throughout the year in Hood Canal. Colleen is interested in the uses of chitin in diatoms, and we’ve been optimizing the machine to detect certain chitin stains. It is our hope that we will continue to find new and exciting uses for the machine to further understand the biology of the small size classes in the ocean.

Irina Oleinikov

Micaela S. Parker

I am a research scientist and coordinator for the Pacific Northwest Center for Human Health and Ocean Studies. I use molecular techniques to understand the biochemistry of cellular processes in marine phytoplankton. 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 using two diatom species (Thalassiosira weissflogii and Thalassiosira pseudonana). For my work with the Center for Human Health and Ocean Studies, I am using comparative genomics and expression libraries to understand the genes that are differentially expressed in Pseudo-nitzschia australis and Pseudo-nitzschia multiseries cells when they produce the toxin domoic acid. The goal is to uncover genes involved in toxin production and develop these as markers for assessing toxin production in field samples. I also collaborate with other members in our lab on various projects, including the discovery of ferritin in Pseudo-nitzschia species (for more information on this project, see Adrian Marchetti's webpage). 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

 

Publications

* maiden name = Schnitzler

 

 

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Rita Peterson

Rita

I am the assistant to Dr. Armbrust. I work behind the scenes to facilitate administrative operations of our busy and dynamic lab. My role casts a wide net: From budget forecasting and scheduling to meeting coordination, purchasing and hospitality, it is all in an ever-changing day’s work. I also plan the quarterly seminar series jointly sponsored by the University of Washington and NOAA and their Centers for Oceans and Human Health. This series promotes dialogue among scientists, students and others who seek to understand the diverse and complex interactions of oceans and human health. In this age of global warming, I am privileged be part of this important research setting. It gives me joy to be a supportive presence to a wonderful group of talented, hard-working techs, students and scientists, known affectionately as the “Armbrusters.”

Francois Ribalet

Last update January 2010

Postdoctoral fellow, ribalet at u.washington.edu

Research interests

My current research interests lie predominately in the area of physiology and ecology of marine phytoplankton and their role in the carbon cycle. My long-term goal is to understand how physical and chemical factors regulate phytoplankton productivity and community structure in the oceans. Currently, I am studying how steep physical and chemical gradients, by creating important ecological niche partioning, affect phytoplankton productivity. We have recently discovered hidden blooms of various small-celled phytoplankton in a narrow region confined between open-ocean and coastal waters in the North Pacific. Invisible to satellite images, these small cells greatly enhance uptake of atmospheric CO2 into the sea and likely flourish in comparably specialized regions throughout the world’s ocean.

Traditional sampling methods typically average across large temporal or spatial scales and make it difficult to study these localized biological hotspots. I am using a new generation of flow cytometer (Seaflow, developed by Jarred Swalwell at the University of Washington) that performs continuous underway measurements of phytoplankton abundance and composition, to study the small-scale structure of phytoplankton in these confined environments. This instrument analyzes thousands of cells per second, continuously, and for several weeks, which makes the data analysis a significant challenge. With the assistance of David Schruth and Chris Fox (UW undergraduate student), I am developing new analytical tools for SeaFlow data analysis, such as an advanced model-based clustering algorithm to automate the identification of phytoplankton populations, and and a web-based software for data visualization.

Education

Publications

Patent

David M. Schruth

As the Informatics Research Consultant for the Lab, I'm responsible for the design, development, and maintenance of the lab's databases, web interfaces, and analysis pipelines. I also employ my plotting and statistical skills to assist the lab's researchers in preparing reports, publications & presentations. Since joining the lab I've had the privilege to work on several exciting projects:

Former Lab Members

Former Lab Members.

Peter von Dassow

Peter von Dassow

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

 

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

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.

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.