Flow Cytometry for Student Research at Friday Harbor Laboratories
Microplankton, tiny plants, animals and other microbes, are key components of our ocean ecosystems. Photosynthetic phytoplankton are the major primary producers, drawing down atmospheric carbon and “fixing” it in a form that can be consumed by other organisms. Zooplankton (larvae and other tiny animals) rely on phytoplankton as their primary food source, as do many larger animals that filter the microalgae out of suspension (e.g. mussels, barnacles, sponges, tunicates). Some microplankton proliferate and produce toxins, and these “Harmful Algal Blooms” pose threats to populations of invertebrates, fish, and humans. Despite these and many other compelling reasons for students to conduct basic and applied research on microplankton at Friday Harbor Laboratories, their ability to do so is currently limited. This proposal aims to fill this pressing need by requesting funds for a new state-of-the-art flow cytometer. Flow cytometry is a versatile and widely used tool in all biological sciences, and can be used to enumerate and characterize types and cell properties of plankton in the field and in lab experiments. The availability of a flow cytometer at FHL would greatly expand the possible research projects for students and importantly, would also provide students with the skills and conceptual underpinning to use and apply this important tool in their future careers.
STF Category - Machinery and Research
This proposal requests the purchase of "equipment specific to scientific inquiry" needed by students at FHL when conducting their research projects.
The University of Washington’s Friday Harbor Laboratories (FHL) (http://depts.washington.edu/fhl) is a world-renowned field station for education and research in marine sciences. Each year, over 1100 students spend time here—taking courses, attending workshops, participating in field trips, and performing research. Our facilities, located on a forested campus on San Juan Island, include accommodations and a dining hall that can support over 100 students at any one time. Students live, eat, and work on the lab grounds, in an immersive learning experience that’s often unparalleled during their college careers.
FHL offers over 20 classes per year, not only in foundation subjects like Marine Botany, Invertebrate Biology and Marine Birds and Mammals, but also in more advanced, cutting-edge topics like Marine Infectious Diseases, Ocean Acidification and Marine Genomics. Committed to providing students with a truly interdisciplinary education, we even offer marine-themed Creative Writing and Literature classes. Each year, FHL selects leaders in their fields to teach this broad range of subjects, with more than 3/4 of instructors coming from other campuses. For our 2015 courses, we’ve recruited our faculty from eight UW schools and departments as well as institutions in nine other states and five other countries.
FHL classes are taught in spring, summer, and autumn quarters. During spring and autumn, undergraduates attend quarter-long classes for a total of 15-16 credits per quarter. In the summer (two terms), undergraduates and graduates take 5-week-long, 9-credit classes. Most classes include lectures, extensive hands-on experience in the field and lab, and student research projects related to course content. Several courses each year are devoted exclusively to research, providing undergraduates the opportunity to work on projects they choose under the guidance of world-class scientists.
In addition to offering its own classes, FHL hosts courses, workshops, and field trips from other campuses. During the winter, spring, and fall quarters of 2014, more than 20 such groups (over 500 students) visited the labs—not only from UW Seattle, UW Tacoma, and other campuses in Washington state, but also from universities in Massachusetts, Virginia, Maryland, and Colorado. Also in 2014, over 400 students came to the labs to participate in conferences, and tens of others stayed here to work on independent research projects (often for PhD dissertations).
The impact of an FHL experience is best expressed with students’ own words, as written on 2014 course evaluations: “The overarching theme of getting your hands dirty in the field and through doing and observing was a way better way to learn than reading about it.” “I learned so much about where I want my career to go, while learning valuable tools for becoming a professional in science.” “This experience is so immersive. I felt like I really got to know my professors this quarter.” “The instructors were the best I’ve ever had at UW.” “It was awesome to live and work closely with passionate experts in the field that they are teaching about.” “It made me learn.” “Best college quarter yet.”
Much of the success of our classes stems from the hands-on experience that our students gain while working on research projects associated with their course work. For undergraduates in particular, this experience is rare and very gratifying. Students usually design a project, collect data in the lab or in the field, and then analyze and present the results of their study.
Many of these student projects require counting small organisms such as phytoplankton, bacteria and other microbes. Too small to see with the naked eye, these planktonic communities form the base of our ocean’s food webs and are critical components to the healthy functioning of all marine ecosystems. Some students are interested in the organisms themselves, while others ask questions about their relationship to other organisms within their community. For example, a marine botany student would need to count the number of cells in a phytoplankton culture and compare those data to a phytoplankton grown in different culture conditions. Oceanography students collect water samples in the field at various locations and return to the laboratory to identify and count the plankton in the samples. They repeat these measurements at numerous locations and over many months to characterize how the plankton abundances change over time and place. Students studying marine disease would need to probe water or other samples for specific pathogens. Finally, invertebrate biologists interested in growth rates of plankton feeders would use a cytometer to quantify the rate at which animals remove microorganisms from the surrounding water. In all cases, the process of identifying and counting small cells is greatly enhanced with a flow cytometer.
Our current capability for counting and identifying cells in small samples from the field or laboratory experiments is rudimentary- done by eye with a microscope, one cell at a time. This is slow and tedious work. The flow cytometer, which is presently unavailable to students at FHL, is faster, more accurate and better able to detect rare cell types in low abundance. This modern technology will greatly expand the scope of projects available to students and ensure they are of the highest quality. Moreover, this instrument will give students hands-on experience with the sorts of tools used in cutting-edge research. The end result will be more engaged students, more accurate data, and increased breadth and depth of student inquiry at FHL.
Benefits to Students and the University
The requested equipment will enhance the breadth, depth and quality of our student research projects and laboratory experiences by allowing for rapid, accurate enumeration of marine microorganisms in the laboratory. It is expected that over 100 students will benefit from this state-of-the-art flow cytometer each year, and this equipment should remain functional for at least 10 years.
Many graduate students will use this equipment extensively for their thesis work, while other students in courses would be introduced to the equipment via shorter term research projects or class exercises. It is not uncommon for the results of a student research project conducted at Friday Harbor Labs to be re-worked into a scientific publication after the student's departure. In other cases an FHL student project becomes the seed of their future research (e.g. capstone or graduate study). Thus, the student research experience stimulates further investigation and may open entirely new avenues of interest. The results benefit the academic record of our students as well as the reputation of the University of Washington.
From the FHL Director:
"FHL research capacity for students would be greatly enhanced with a table top flow cytometer. We have many courses that allow research experiences for undergraduate students and we have funded 15-20 graduate student summer research projects for the past five years with FHL resources. A table top flow cytometer would be used by those studying algae, bacteria and other micro-organisms as well as different blood types in invertebrates and vertebrates. The University of Washington's Friday Harbor Laboratories has continued our world-class research apprenticeship program for undergraduates, with a new endowment for student support. This intense training program includes major reliance upon state-of-the-art research tools to permit undergraduate students to learn how to plan, conduct and present scientific research.
FHL's undergraduate educational efforts have also been supported generously by the Howard Hughes Medical Institute, Microsoft, Mary Gates Endowment, Washington Research Foundation, and others. In addition, the National Science Foundation (NSF) has awarded FHL for the past six years to carry out an undergraduate REU summer Program, which has been combined with our existing Blinks endowment and money from BEACON to support 15-18 undergraduates conducting research at FHL each summer. Many of our other undergraduate classes, in fall spring and summer, also include research projects by the students.
FHL is continuously working to provide increased financial support to all its programs, including explicitly, instructional and research training efforts, from non-State of Washington sources (private foundations, individuals, and federal sources). This initiative has resulted in development of support up to about 75% of the apprenticeship program from non-UW sources. However, this also requires, as a crucial prerequisite, stable support for our physical plant and supplemental support for student technology tools. Thus STF support of this kind continues to be fundamentally important leverage.
Therefore, I strongly support this initiative by FHL faculty Emily Carrington and Evelyn Lessard, and urge its support by the STF. Many thanks for considering this proposal!"
-Billie J. Swalla, Director, Friday Harbor Laboratories
"This instrument will give students hands-on experience with the sorts of tools used in cutting-edge research. Using a flow cytometer, students will be able to take a census of the very small. By automatically naming and counting the microbes in a water sample, students will be able to distill the vast diversity of marine life into a more comprehensible list of which microbes are present and which are most important. This capability, which is presently unavailable to students at FHL, will open the door to a huge range of more sophisticated and exciting student projects than are currently possible."
-Alex Gagnon, Assistant Professor Oceanography
“Several graduate and undergraduate research projects in the coming years will require counting plankton, in order to 1) quantify feeding rates of bivalves like mussels and oysters or 2) explore the spatiotemporal variation in plankton abundance in the Salish Sea (Puget Sound) . This flow cytometer will bring us out of the dark ages of counting cells on a microscope slide (slow and tedious) to the cutting-edge technology of automated cell counters. The result will be more engaged students, more accurate data, and increased breadth and depth of student inquiry.”
-Emily Carrington, Professor of Biology
“Flow cytometry is a versatile and widely used tool in biological sciences today. In
marine plankton studies, it is used routinely to enumerate and characterize
types and cell properties of plankton in the field and in lab experiments. A flow
cytometer would be an essential tool for students in the Marine Protist Ecology course
that I plan to teach at FHL next summer. The availability of a flow cytometer at FHL would
greatly expand the possible research projects for students in this class, but importantly,
would also provide students with the skills and conceptual underpinning to use and apply
this important tool in their future careers.”
-Evelyn Lessard, Professor, Oceanography
“Several of my graduate students have investigated suspension feeding in benthic invertebrates, and one of my beginning graduate students will definitely be doing so this summer. This instrument will allow them to quantify the food available to suspension feeders in both field and laboratory situations, and to examine which components of the plankton are being consumed. Undergraduates working with me in the Marine Ecology Research Experience will also make use of the flow cytometer to examine the feeding behavior and particle selectivity of marine invertebrates. I would also like to design a new laboratory exercise around this instrument for Biology 356 “Foundations of Ecology” , at FHL, to explore electivity in an experimental setting.”
-Kenneth P Sebens, Professor, Dept. of Biology and School of Aquatic and Fishery Sciences
“Students doing research projects as part of our Fall and Spring Research Experience courses periodically want to count plankton, and this has either been impossible or very tediously - and inaccurately - done on a compound microscope. For example, a student one year wanted to compare feeding rates of different filter feeders -- this is done by seeing how fast they 'clear' the water of plankton, and these kinds of data could be very rapidly obtained using a flow cytometer. Instead she had to use relatively inaccurate and very slow chlorophyll measurements.”
-Megan Dethier, Associate Director for Academics and the Environment, Friday Harbor Laboratories
“As a teacher and mentor in biological oceanography for undergraduate and graduate students at UWS and FHL and in the Blinks program for URM science students, I believe a new cytometer to quantify plankton populations in the water column would fill a pressing need for students interested in both basic and applied research. For example, many of my students focus on marine larvae; they need to know the food, predators and pathogens in which larvae must survive and develop. Many other students are interested in Harmful Algal Blooms; they need to know where, when and why small populations of toxic cells erupt to cause negative ecological impacts. Students interested in diverse aspects of OA and other environmental chance need to know how the base of the food web responds to physical factors and other biota to regulate productivity and diversity. All these students would obtain essential data from the proposed instrument.”
-Daniel Grunbaum, Professor, School of Oceanography and FHL
“I would envision the students in phycology courses being able to utilize this equipment to: 1) be able to do much more detailed and accurate studies of phytoplankton population ecology; 2) study the biomechanics, dispersal, and predation of algal spores; 3) look at the production of detrital material from kelp and other macrophytes, its uptake and utilization and 4) use it to study unicellular algal growth rates in response to light, nutrients, pathogens, etc.
- Tom Mumford, Professor, Friday Harbor Laboratories
Upon approval and funding, the flow cytometer will be purchased and installed. Training is provided on-site at the same time the equipment is delivered and installed.
Resources Provided by Department
Note that our Laboratories are located on San Juan Island, isolated from the main Seattle campus of the University. Thus, there are no "nearby" resources from other universities or departments.
The FHL Stockroom contains a large collection of research equipment and supplies available to students and researchers. Reusable equipment is available at no charge, and is checked out via computer database. The equipment in the stockroom is maintained, repaired, or replaced by our Stockroom staff.
In addition to these resources, the instructors of our various classes often bring some equipment from their UW home departments (e.g., Applied Physics Lab) or from outside institutions for the use by their students. For example, our European instructors for the Fish Swimming class bring a limited amount of high speed video equipment, but the logistics are often prohibitive. All students rely heavily on the equipment on hand at FHL.
Students will receive training in the use of the flow cytometer initially by trained FHL Staff and faculty (see Item #3 for on-site training provided upon delivery of the flow cytometer). It is anticipated that over time expert users (e.g., grad students and faculty) will add to this pool of personnel who can train new, less-experienced users.
Our IT staff also gives a computer orientation to all arriving students, explaining the use of storage space on our file server and how to transfer their data output from the flow cytometer software. Students have access to our Student Computer Lab 24/7, using a keycode for after-hours. This lab provides 16 iMac computers (half booted in Windows) 2 printers, and 2 scanners. Smaller computing areas (with 4 or 5 common-use computers) are available in the Fernald Bldg and the Lecture Hall.
Our department provides students with a wireless network in all lab buildings and student housing. We contract with NoaNet and K20 for our connection to the Internet.
Please see the statement (Departmental Endorsements) from Director Billie Swalla regarding other student support provided by our department.
Access Restrictions (if any)
The flow cytometer will be housed in a dry laboratory (one with no seawater tables) on the FHL campus. Students will be made aware of the flow cytometer and its capabilities. Interested users will have access to the equipment, including keycode access for after hours. A logbook will be used to track usage.
"Having a bench top flow cytometer for use at FHL would be of great benefit to students, especially those involved in research courses. Several Nearshore Ecology Research Experience students in recent years have had projects that involved quantifying plankton communities temporally or based on tidal cycles. Having access to a user-friendly flow cytometer would allow students to increase their sample sizes and collect more robust data."
-Katie Dobkowski, Graduate Student in Biology
“I develop novel Harmful Algal Bloom sensors, and as such regularly need to validate my results against standard methods like manual microscope counts and automated flow cytometers. In the near future (this year and next year), I will be doing field validation trials, including trials at FHL, for which a flow cytometer would vitally useful.”
-Owen Coyle, Graduate Student in Oceanography
“Having a flow cytometer at FHL would be useful for my graduate research. My research will likely involve modeling the bioenergetics of barnacles on San Juan Island. Since barnacles feed on plankton, parameterizing the energetics models will require counting plankton in water samples. I would benefit from using a flow cytometer by being able to efficiently count plankton. This benchtop model appears more user-friendly than a larger flow cytometer that I worked with at another marine station.”
-William King, Graduate Student in Biology
“Having a flow cytometer would be extremely helpful for counting algae cells for feeding, ensuring that oysters are receiving the proper cell density. For larval experiments the flow cytometer would allow us to count the number of larvae that are released.”
-Bryanda Wippel, Graduate Student in SAFS
“A flow cytometer would be useful for my graduate research in bioenergetics modeling. I am currently learning how to use mechanistic modeling to study how food, temperature influence mussel growth, and I plan to expand on this to also look at how these factors interact to influence mussel biomaterials for my graduate research. Mussel food availability and injestion affects not only normal growth and reproductive responses, but could be a physiological buffer for response to stressors such as low pH, high temperature, and changes in salinity. I would use the cytometer to count phytoplankton in water samples, and also use it to determine size classes most readily ingested by mussels. This flow cytometer also has the capability of running many samples at once via a 96 well plate. Some flow cytometers can be difficult to work with, but this model is said to be easy to use which will help make it more accessible to students like me interested in quantifying phytoplankton conditions.”
-Molly Roberts, Graduate Student in Biology
“My research on crossbreeding in oysters involves the spawning and rearing of millions of oyster larvae from different genetic lines. Getting accurate larval counts seems trivial, but it is no small feat. Having an efficient means of counting early-stage larvae, not to mention the algae upon which they rely, would be an enormous asset.”
-Dan Gillon, Graduate Student in SAFS
“A flow cytometer would be a great addition to the equipment available for student use at FHL. With this equipment, I will be able to better study mussel feeding in my ocean acidification experiments. The easy-to use model makes it easy to involve undergraduates I work with in these assays.”
-Laura Newcomb, Graduate Student in Biology
“A flow cytometer would be incredibly beneficial to marine algae students at Friday Harbor Labs. It is often impossible to tell whether certain algal species are gametophytes or sporophytes based on morphology, and so, little is known about the gametophyte to sporophyte ratios of seaweed communities. This is important because the gametophyte to sporophyte population ratios can greatly impact seaweed fertilization, reproduction and dispersal. Flow cytometry can be used to determine whether propagules produced by seaweed are a gametophyte or a sporophyte, and this instrument would incredibly useful in investigating the population makeup of many seaweed communities by students at Friday Harbor Laboratories.”
-Rebecca Guenther, Graduate Student at Friday Harbor Laboratories
“One of the best things about being a UW Biology graduate student based at Friday Harbor Laboratories is the full support of the FHL faculty and staff and the incredible research resources available at the lab, despite being removed from the main campus in Seattle. Although a trip down to Seattle is always welcome, being able to have all the services of a large university right here in Friday Harbor has greatly improved my ability to be successful in my program of study. My advisor conducts long term ecological research throughout the Salish Sea region and we have recently discussed adding in phytoplankton and zooplankton surveys to our existing benthic community dataset and the addition of the Guava Easycyte flow cytometer would make this and other sampling possible. I know this resource would also enhance the teaching capabilities of many of the courses here, including the Pelagic Ecosystem Function course I have been a Teaching Assistant for in the past.”
-Derek Smith, Graduate Student in Biology
guava® easyCyte™ 6HT/2L Base System.
Guava easyCyte 6HT/2L, Base System. Includes: Laptop computer (1), User's manual (1), Guavasoft CD (1), Flow Cell (2), Flow Cell Removal Tool (1), 96-well microplates (5), 1.5mL microcentrifuge tubes (25), 0.5 mL microcentrifuge tubes (25),Guava easyCheck Kit (50 tests), Guava ICF (Instrument Cleaning Fluid) (100mL), 12 month warranty. Note 9.6% sales tax is included and there is no shipping charge (all included with on-site training).
GuavaSoft Software Package for Guava easyCyte HT Systems; Includes InCyte, Express Pro and guavaSuite Modules. For more
Software required to run Guava easyCyte Base system. 9.6% sales tax included.
Advanced On-site Guava Training, Full Day (up to 3 trainees)Justification
Training for FHL staff on use and
Total requested: $64,856.00
Total funded: $64,856.00
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