Blinks - NSF REU - BEACON Internship Program
Research Experiences for Undergraduates
Integrative Biology and Ecology of Marine Organisms
Application deadline: February 15, 2017
Program dates: June 12 to August 5, 2017 (8 weeks)
Friday Harbor Laboratories' Blinks - NSF REU - BEACON Summer Internship Program seeks to link undergraduate students with scientist-mentors as collaborators in marine science research projects. The program takes advantage of the pristine environment, remarkable biodiversity, and the scientific and technical resources at University of Washington's marine science research facility. We have combined the NSF REU program with the Blinks Research Fellowship program, which targets groups who are historically underrepresented in the marine sciences, with the NSF-funded BEACON Program. In cooperation with the the Andrew W. Mellon Foundation, the National Science Foundation and the Anne Hof Blinks Memorial Fellowship, the Blinks-REU-BEACON Program offers a full immersion research experience for motivated undergraduates, post-baccalaureates and graduate students. In keeping with the University of Washington's policy of encouraging diversity in its student body including underrepresented groups, the program seeks 10-15 students of diverse backgrounds and interests to participate in a eight week summer research project in the marine sciences. By linking fellows with marine scientists in a 1:1 research experience, fellows learn both the process and the substance of scientific research. As the research progresses, fellows will be encouraged to become semi-independent collaborators. The experience will expose fellows to the life and work of a marine science research laboratory. The program will incorporate workshops, seminars and training sessions in addition to hands-on research.
The mentors and projects vary from year to year according to the developing research interests of faculty and students. Research projects are designed by the scientists to be achievable projects which dovetail with their research plans. Project descriptions are posted below. Fellows will work semi-independently with mentor supervision for approximately 40 hours per week.
As participants in the FHL community, students will participate actively in FHL community activities, e.g. attend the weekly seminars, eat in the Dining Hall and live in the student dormitory. Early in the summer session, there will be a meeting of student participants with graduate students and mentors to share perspectives on graduate programs and participation in academic life, with a brief description of ongoing projects, and a question/answer session. At the end of their internship, fellows will present their research in a short powerpoint talk. Fellows will also write a scientific paper describing their work, and revise it based upon feedback from the mentor.
Friday Harbor Labs is University of Washington's marine science field research station. Located north of Puget Sound in the San Juan Islands, FHL takes advantage of a remarkable diversity of marine habitats and organisms. FHL hosts 15-20 courses per year and approximately 100 independent researchers during the year. The 484 acre campus is the site for thirteen lab buildings, a dining hall, 3 dorms and other housing units.
Research at FHL emphasizes marine invertebrate zoology, phycology, fisheries science, conservation biology, cell and molecular biology, biomedical sciences, oceanography and other scientific disciplines. Investigators and students use diversified field resources as well as modern analytical technologies such as a CT scanner, nucleotide sequencer, scanning laser confocal microscopes, centrifuges, HPLC, TEM, SEM and other equipment. Friday Harbor Labs is equipped with a 58' research vessel, numerous smaller boats, cold rooms, and an extensive seawater system serving numerous lab buildings. The facility includes a computer lab, networked research labs, wi-fi connectivity, a well equipped stockroom, a 17,000 volume library, and SCUBA facilities.
Participants will be provided with financial support to meet costs of room, board and round trip travel, plus a stipend (amount to be determined).
The NSF REU Site grant supports U.S. citizens or permanent residents during their undergraduate careers. The Blinks Endowment supports students who bring diversity to the FHL student body in any phase of their undergraduate or graduate career.
1. Fill out the FHL REU Application form to apply for participation in a specific research projects. We recommend applying for up to three projects given the stiff competition for admission to the program. In the ethnicity field, please be sure to indicate if you're from an underrepresented group.
2. Apply to work with a specific mentor by writing a one-page application statement which describes your background, your interest in this project, and how this specific research project will help you achieve your career goals. Please submit up to three application statements, one for each project to which you'd like to apply, and send them to email@example.com. The statements should be sent as separate files in .doc, .docx or .pdf format.
3. Request unofficial copies of your transcript to be sent to firstname.lastname@example.org. Transcripts can be either official or unofficial, and either electronic or on paper. Electronic transcripts are preferred. If your school prepares only paper transcripts, please send them to Mark Tetrick at the address below.
4. Request two letters of recommendation from faculty members who are familiar with your work. Letters should be emailed from faculty directly to email@example.com.
Questions may be directed to firstname.lastname@example.org
Students who are selected will be notified in late March.
REU Research Projects for 2017
- Dr. Sophie George. The effects of food patches on the behavior of seastar larvae in haloclines, and protein expression by larvae exposed to fluctuating salinity.
- Dr. Vikram Iyengar. Sexual selection on the seashore: Mating systems of marine arthropods.
- Dr. Christopher Kenaley An Integrative Study of the Skin Material Properties in Sculpins.
- Dr. Matt Kolmann Why so many fishes? Morphological diversification across the marine to freshwater transition in temperate and tropical fishes
- Dr. Tony Pires. Ocean acidification in the life history of a gastropod
- Dr. Billie Swalla. BEACON Program internships.
The effects of phytoplankton patches and fluctuating salinity on protein expression and the behavior of echinoderm larvae in haloclines
A regular occurring event in the coastal waters of the Pacific Northwest is a decrease in salinity to less than 15‰ in some areas, as a result of increased precipitation and ice melts during the spring and summer months. George and Walker (2007) and Pia, Johnson, and George (2012) observed salinity-induced morphological changes for Dendraster excentricus (top right) and Pisaster ochraceus larvae (bottom left). For example, Pisaster larvae reared at 20‰ were shorter and wider while those reared at 32‰ were longer and slender. The development to metamorphosis and the production of juveniles by larvae exposed to 20‰ (bottom right, juvenile P. ochraceus) in of itself is intriguing given that these species cannot regulate the osmolarity and ion content of their internal fluids. These studies indicate that the timing, magnitude and duration of ice melts and rainfall in the Pacific Northwest could alter larval morphology, larval feeding and swimming, and possibly the quality of new P. ochraceus recruits into the intertidal zone in the Puget Sound. During the summer of 2016, research will continue looking at larval behavior of P. ochraceus in haloclines with and without food. Students will also investigate the effect of multiple low salinity events on protein expression in P. ocraceus larvae. Knowledge on larval behavior in haloclines would enhance our understanding of how echinoderm larvae will respond to changes in surface salinity as a result of climate change.
The participating student would learn to prepare algal cultures; rear larvae to metamorphic competency, observe larvae in haloclines, prepare samples for protein determination and gel electrophoresis, and photograph larvae from the various treatments.
Past students have presented their research at regional (GAS) and international meetings (SICB), and are coauthors on 3 recent articles from research at FHL with one submitted to Marine Ecology Progress Series with minor revision. Past students have presented their research at regional (GAS) and international meetings (SICB), and are coauthors on 3 recent articles from research at FHL with two in preparation:
George, Sophie B. & Walker, Devoc. 2007 Short-term fluctuation in salinity promotes rapid development and metamorphosis of Dendraster excentricus larvae Journal of experimental marine Biology and Ecology. 348:113-130.
George, Sophie B., Fox, Colleen & Wakeham, Stuart 2008. Fatty acid composition of larvae of the sand dollar Dendraster excentricus (Echinodermata) might reflect FA composition of the diets Aquaculture 285: 167-173.
Tanya Pia; Johnson, Tiffany and George, Sophie 2012. Single and multiple fluctuations in salinity affect growth,
development and metamorphosis of the sea star Pisaster ochraceus. Journal of plankton research 34:590-601.
Sam Bashevkin, Daniel Lee, Paul Driver and Sophie George. Vertical distribution of brachiolariae larvae in haloclines is influenced by prior exposure to low salinity. In prep. (past Blinks-BEACON-REU scholars or grad students in bold).
Arthropods are the most abundant and diverse group in the animal kingdom – they occupy nearly every ecological niche in marine, freshwater and terrestrial habitats. Their extraordinary evolutionary success can be partly attributed to the remarkable diversity of mating systems found in arthropods. I am primarily interested in sexual selection, particularly within species that are sexually dimorphic – that is, where strong competition for mates has ultimately lead to divergence in the appearance of males and females. Exaggerated male traits can be the result of female choice, where females mate preferentially based on the male's expression of these traits, male competition, where males use armaments in intrasexual battles for access to females, or a combination of both. In such mating systems, males usually compete with each other for females in contests usually determined by differences in body size or weaponry which dictate fighting ability. Males may compete directly for access to females or may instead control resources essential for female survival and reproduction.
Earwigs are a model system for studying competition and reproductive behavior because they are distinguished by their possession of weapons (“forceps”), their high degree of maternal care (females aggressively guarding eggs and juveniles), and high densities that promote frequent interaction.
In most earwigs, both sexes use their forceps to capture prey, and female earwigs are usually larger than males, presumably due to a fecundity advantage seen in many arthropods. The maritime earwig Anisolabis maritima is unusual among the order Dermaptera, and this insect is particularly well-suited for studies of sexual selection because males differ markedly from females in both body size (males are more variable in size, and often substantially larger, than females) and weaponry (males possess asymmetrical, curved forceps whereas females have straight forceps; see photo). Furthermore, while females often kill conspecifics by using their forceps like scissors, males usually resolve their disputes non-lethally by squeezing each other’s abdomens, perhaps a means to assess strength and fighting ability (see diagram from Muñoz & Zink 2012). This summer we will continue lab and field investigations of the mating system of A. maritima by determining the roles of sex, size and weaponry on intrasexual competition and intersexual mating preferences, and by examining how same-sex and mixed-sex interactions (“social networks”) affect distribution patterns observed in the field.
Integrative Study of the Skin Material Properties in Sculpins
Fish skin is a complex structure characterized by long collagen fiber which wrap in a helical pattern around the body. Though all fish have this basic structure, details such as fiber arrangement and scale density varies extensively across species. For decades, scientists have been intrigued by these cross-helically arranged fibers. Several studies have looked at their structure both at a macro and microscopic level and some have even examined the material properties of the skin on a few specific fish (Danos et al., 2008; Lauder, 2015; Long et al., 2002). Other studies have revealed the importance of skin stiffness in the swimming behavior of certain fish, such as the Longnose Gar (Long et al., 1996). Despite this handful of studies, no one has extensively explored the role played by the skin in determining functional capabilities of important behaviors like swimming. In addition, no study has yet characterized the diversity of skin properties across an entire clade of fishes to answer question about how the diverse morphology may evolve.
The goal of this project is to characterize the stiffness and fiber angle of skin across a group of fishes that demonstrate a diverse morphology and ecology: Cottoidei (sculpins). To execute this study, the investigator will use techniques from both engineering and ecology. We will construct a bi-axial material testing system, and use an Arduino program to control it and collect stiffness data on skin from several species of sculpin. Next, we will use a dissection scope and camera to measure the fiber angle of the skin. Finally, we will integrate the results of hundreds of our material testing experiments with a database morphological and ecological data and the most current phylogenetic hypothesis for cottoids to identify the major covariates of skin stiffness and structural properties.
Morphological diversification across the marine to freshwater transition in temperate and tropical fishes
Evolutionary transitions from marine to freshwater habitats by different animals represent an interesting opportunity for examining adaptive evolution. Adaptive radiation is the process by which animals, when released from some constraint or presented with new resources, diversify ecologically to capitalize on these opportunities. This is perhaps best exemplified by classic case studies on Darwin’s finches and their evolution of different beak shapes to feed on different manners of prey in the Galapagos. Freshwater environments historically have offered new resources to invading marine fishes, resources potentially free from competition, an ecological opportunity.
The Amazon basin of today is far different than it was even 4-7 million years ago. Many of the modern fishes in South America evolved in a massive inland sea called the Pebas, a large, inland brackish lagoon. With the rise of the Andes, this inland estuary was isolated and then eventually started draining eastwards, trapping and redirecting the movements of the fishes within it. Partly due to this phenomenon the Amazon basin has the highest diversity of freshwater fishes in the world, including several conspicuously marine groups: pufferfishes, toadfishes, anchovies, herrings, needlefishes, and even stingrays. Little work has focused on determining how these fishes physically adapted to fit their changing ecological roles in the Amazon across the evolution of both the fishes AND of the basin itself.
In the Summer of 2017, we will examine how the overall form and function of these South American ‘marine-derived lineages’ of fishes (MDLs) have changed over the course of their 40-million-year history. We will also compare these patterns to similar fish systems in the Pacific Northwest, notably the many freshwater sculpins found along the Washington and Oregon coasts. Using computed microtomography scanning (micro-CT) of museum specimens we will (1) quantify shape change in the feeding apparatus and body shape of MDL fishes and their relatives to (2) determine whether rates of morphological evolution increased upon invasion of freshwater and (3) whether this diversification is correlated with changes in diet, habitat, or other factors pertaining to ecological opportunity. Students will learn: (A) how to use CT scanning and morphometric methods to quantify functional differences in skeletal and soft tissue anatomy; (B) how to build phylogenetic trees from downloaded DNA sequences from GenBank databases; (C) how to examine the evolution of traits using comparative phylogenetic methods; and (D) gain an introduction into museum curation and the field of biodiversity research. This research is in collaboration with international researchers from the University of Toronto, University of Western Michigan, Universidade de São Paulo, and elsewhere.
Past students of mine have presented their research at international meetings of the Society for Integrative and Comparative Biology (SICB) and several exceptional students are coauthors on publications in preparation for submission at the Journal of Zoology and Journal of Evolutionary Biology.
For a glance at similar sorts of research, this time on Australian freshwater fishes, see the following: http://link.springer.com/article/10.1007/s10682-013-9671-x
Rising atmospheric levels of CO2 are expected to lead to substantial lowering of ocean pH within the next century. Impacts of ocean acidification (OA) are being intensively studied at FHL and at other laboratories around the world, particularly with respect to organisms that make calcareous skeletons that become more difficult to grow and maintain in acidified conditions. Many studies have focused on veliger larvae of molluscs, because of the ecological and economic importance of these animals. Although many studies have documented OA effects on larval growth and survival, few have focused attention on the critical life history transition of metamorphosis, when pelagic larvae become benthic juveniles. This is a pressing area for research, in two respects. First, it is clear that larval experience may have profound latent effects on juveniles (1). Second, developmental effects of OA occur in the context of other influences such as nutrition, salinity, and temperature, so it is necessary to study such interactions (2).
In the summer of 2017 we will study interactions of OA and other environmental variables in larvae and juveniles of the gastropod, Crepidula fornicata. How do these factors affect the acquisition of competence for metamorphosis, larval behaviors that are related to settlement and metamorphosis, and post-metamorphic juvenile performance? C. fornicata is an ideal animal for this research. Much baseline information is already known about its development, metamorphosis, and life history. The veligers are large (up to 1.5 mm), easily cultured, and amenable to ecologically-relevant behavioral and neurophysiological experiments (3). Furthermore, C. fornicata is native to the eastern U.S. but has become established as a non-native species in many parts of the world (including Washington), and is of great interest as an invasive species in changing ecosystems (4). In this project students will learn elements of experimental design, as well as methods of larval culture, carbonate chemistry, metamorphosis assays, and techniques for analysis of larval behavior.
(1) Pechenik JA (2006) Integr Comp Biol 46: 323-333.
(2) Byrne M, Przeslawski R (2013) Integr Comp Biol 53: 582-596.
(3) Penniman JA et al. (2013) Invertebr Biol 132: 14-26.
(4) Bohn K, Richardson C (2012) Mar Biol 159: 2091-2103.
The BEACON Program will fund up to four students. Students will work under the supervision of Dr. Billie Swalla.
Evolution of Development in Molgulid Ascidians
Ascidians are a fascinating clade of animals, spending their time filter-feeding, stuck to the benthos. These amazing animals are actually one of our closest related invertebrate cousins. Ascidians are invertebrate chordates that share a number of developmental features in common with the vertebrates including a branchial basket, an endostyle, and a notochord inside a functional swimming larval tail. Molgulids are a monophyletic clade of ascidians in which a tailless phenotype has evolved multiple times independently. We investigate the differential gene expression of two species of molgulids, Molgula oculata and Molgula occulta.
Molgula oculata, has a typical tailed phenotype, but its sister species, Molgula occulta, has lost the tail and notochord, developing 20 notochord cells that do not converge and extend, but sit on the side of the larvae in a “notoball”. The two species can be hybridized: if the egg of the tailless species is used, then some of the resulting hybrids have 20 notochord cells that, in some cases, do converge and extend into a short, non-functional half tail. We have sequenced the genomes and embryonic developmental transcriptomes of these two sister species as well as hybrid embryos, and are searching for differential gene expression of known notochord related genes to attempt to identify the developmental changes responsible for the loss of the tailed phenotype.
This is a model system for looking at the evolution and modification of complex features. We are using modern molecular techniques to search for changes in gene expression between the two species and identify the underlying mechanisms behind this drastic life history change. Understanding how the notochord has been altered will help us understand how evolution can alter complex structures and how the underlying gene networks can be modified while not effecting the survivability of the altered organism.
In the Swalla lab you will utilize gene detection techniques such as database searching to find notochord related genes, confirming their identity in NCBI, and gene alignments to confirm homology and quantify change. You will also learn molecular techniques such as gene cloning, running gels, creating molecular probes, performing in situ hybridization to detect gene expression, and how to visualize results using microscopy.