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, my focus is creating DNA and RNA libraries to run on our high throughput sequencing machine, the SOLiD. The SOLiD is pretty amazing in that it can sequence a whole diatom genome in one run! This is done by breaking up the DNA or RNA into millions of short fragments, attaching these fragments to tiny beads, and attaching the beads to a microscope slide. The slide is put in the SOLiD sequencer where random fluorescent probes are washed over the DNA or RNA that is attached to the beads. These probes code for two bases, and when a certain probe finds its match in the sample, it attaches itself to the DNA/RNA. The SOLiD then takes a picture using certain light filters to determine which probe is sitting where and on what bead. This process happens over and over until the whole fragment is sequenced. Right now, the SOLiD generates about 700 million 50 -100 base-pair reads per run which is about 35-70 billion bases of data! Putting all of the bases in order, aligning them to a reference genome, and/or assembling the reads is extremely computationally intensive. We have a team of bioinformaticians (see the pages of Vaughn, Chris, and Dave) who develop tools and pipelines that aid in data analysis of SOLiD reads. We are using the SOLiD technology in our lab for a variety of different applications including genome re-sequencing, de-novo genome sequencing, environmental metagenomics, and experimental and environmental transcriptomics.
Another aspect of my job is to run 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 (Check out the pages of Jarred and Francois for information about a cool underway flow cytometer called the SeaFlow!).
- Koester, J. A., C. Berhtiaume, N. Hiranuma, M. S. Parker, V. Iverson, R. Morales, A. Sarwate, W. L. Ruzzo, E. V. Armbrust. 2018. Sexual ancestors generate an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana. Scientific Reports 8, Article number: 10492.
- Hamilton, M., G. M. M. Hennon, J. Needoba, R. Morales, T. D. Peterson, M. Schatz, J. Swalwell, E. V. Armbrust, F. Ribalet. 2017. Dynamics of Teleaulax-like cryptophyes during the decline of a red water bloom in the Columbia River Estuary. Journal of Plankton Research doi.org/10.1093/plankt/fbx029.
- Turner, Jeffry W., Chris Berthiaume, Rhonda Morales, E. Virginia Armbrust, Mark S. Strom. 2016. Genomic evidence of adaptive evolution in emergent Vibrio parahaemolyticus ecotypes. Elementa: Science of the Anthroprocene DOI 10.12952/journal.elementa.000117.
- Hennon, G. M. M., Justin Ashworth, Ryan D. Groussman, Chris Berthiaume, Rhonda L. Morales, Nitin Baliga, Monica Orellana, E. V. Armbrust. 2015. Diatom acclimation to elevated CO2 via cAMP signaling and coordinated gene expression. Nature Climate Change 5:761-765.
- Amin, S.A., L. R. Hmelo, H. van Tol, B. Durham, L. Truxal, K. Heal, R. Morales, C. Berthiaume, B. Djunaedi, M. A. Moran, A. Ingalls, M. Parsek, and E.V. Armbrust. 2015. Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria. Nature 522:98-101.
- Hennon, Gwenn M. M., Paul Quay, Rhonda L. Morales, Lyndsey M. Sandwick, E. Virginia Armbrust. 2014. Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate-limited chemostat. Journal of Phycology 50:243-253.
- Bender, S.J., C.A. Durkin, C. Berthiaume, R. Morales, and E.V. Armbrust. 2014. Transcriptional responses of three model diatoms to nitrate limitation. Frontiers in Marine Science: Aquatic Microbiology doi: 10.3389/fmars.2014.00003.
- Durkin, C.A., A. Marchetii, S. J. Bender, T. Truong, R. Morales, T. Mock, and E. V. Armbrust. 2012. The influence of frustule-related gene transcription and diatom community composition on silica precipitation in an iron-limited environment. Limnology and Oceanography 57:1619-1633.
- Vaughn Iverson, Robert M. Morris, Christian D. Frazar, Chris T. Berthiaume, Rhonda L. Morales, and E. Virginia Armbrust, Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota, Science, Vol. 335 no. 6068 pp. 587-590, February 3rd, 2012 [Link at Science]
- 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.
- Ribalet, F., Marchetti, A., Hubbard, K.A., Brown, K., Durkin, C.A., Morales, R., Robert, M., Swalwell, J.E, Tortell, P.D., and Armbrust, E.V. 2010. Unveiling a phytoplankton hotspot at a narrow boundary between coastal and oceanic waters. Proceedings of the National Academy of Sciences USA [107:16571-16576]