Sunday, June 30, 2013

Payton Hermanson - Week One

My name is Payton Hermanson, and this summer I am acting as an intern in the lab of Dr. Alan Shanks at the Oregon Institute of Marine Biology (OIMB). My home community college, from which I received my Associate in Arts and Sciences degree earlier this year, is Everett Community College in Washington state.  The interest which led me to apply for an internship through the COSEE PRIME program is the same as that which has brought me this far in my college career already: an acute interest in research and the biological sciences. This fall I will be attending Oregon State University (OSU), entering with credits equivalent to those of a junior, where I will be majoring in biology. My hope is to one day continue on to graduate school to study marine biology.

In Dr.Shanks' lab, myself and one other intern are working on two projects involving larval recruitment rates. What this means is that the lab is investigating the rate that the larvae of Balanus sp. (barnacles, the larval stage of which is called a cyprid) and Cancer magister (Dungeness crabs, more on their life cycle later) settle in an area. While the methods of the two projects are dissimilar, the intention of both is to determine whether larval recruitment follows a set pattern, such as that of the tidal cycle or larger atmospheric conditions.
Myself (on left) and Kaylynne (my fellow intern) emptying the light trap. Photo taken by
Sol Guerrero Ortiz.

This first week, we were trained to complete surveys on both the organisms in question, counting the number of cyprids to settle on three permanent grid plates installed on rocks at Bastendorff beach, near Charleston, and surveying the numbers of organisms caught within a device known as a light trap, located in the marina adjacent to OIMB. The light trap is composed of a large clear plastic jug with a light suspended within and funnel-shaped entrances, much like a crab pot. A cod end (a sea water filter with mesh small enough to retain zooplankton [animal plankton] within the sample) screws on to the base of the trap. Both devices are checked daily. Next post, I'll talk about the life cycle of the Dungeness crab and how samples from the light trap are quantified.

Leeah Whittier: Week 1 in the Maslakova Lab

Week 1 in the Maslakova Lab
My name is Leeah Whittier and I am a recent graduate from Umpqua Community College in Roseburg, Oregon. I will transfer in the fall of this year to the University of Oregon where I will study to earn a Fine Art undergraduate degree and a degree in Biology with a Marine emphasis. When I applied for the COSEE-PRIME internship I was mostly interested in the experiences that it would provide. This is a very hands-on program that gives community college students the opportunity to do real field studies and research that they wouldn’t normally be able to do. As part of the PRIME internship this summer I will be working in the Maslakova lab on the Oregon Institute of Marine Biology campus.

This week I learned mostly about how the lab operates on a daily basis. I met my mentors over lunch on Monday, Dr. Svetlana Maslakova, Dr. George von Dassow and PhD students Terra and Laurel Heibert. The Maslakova lab focuses primarily on a phylum of invertebrates called Nemertea, their development and taxonomy. In the coming weeks I will be working on a project to identify nemertean larvae and match them with their corresponding adult forms. So far I have become familiar with collection techniques of larval stages of nemerteans via plankton tows. In addition I have learned how to collect the adult nemerteans by digging in various mudflats in the area. On day three of my time here, Laurel showed me how to make a culture of pilidium larvae. These are hat-shaped larvae that belong to the species Micura alaskensis, the "bread and butter of the nemertean world" as George puts it. I was given a small culture to look after and see through to the end of their development.

Below are some pictures that I have taken over the week of my developing culture. From left to right and top to bottom are days 2 through 5 of my culture's growth.

Pilidium Development Days 2 through 5

Next week on Monday I will be learning how to do DNA extractions on some specimens that I had caught and frozen. I am also learning a lot of the names of the plankton and the members in the lab have been very helpful in teaching them to me. Below are four of the five specimens I preserved over the last few days.

1. Bivalve Vileger 2. Gastropod Vileger  3. Oikopleura   4. Unknown ciliated specimen with lipid spots
Finally for this week I have been drawing some of the adult nemerteans that are currently undefined in this area. Terra requested that I draw both a Micura and a Cerebratulus adult. I scanned some of my drawings from this week to share.

Kaylynne Marquez: Week 1 at OIMB


My name is Kaylynne Marquez and I have attended both Lane Community College and the University of Oregon (both located in Eugene, OR) as a biology undergraduate student. Spring 2013 was my first term dual-enrolled (attending both LCC and UO at the same time) at the University of Oregon. I have been interested in the ocean for as long as I can remember and decided at seven years old I wanted to study marine biology. Curiosity as to how marine organisms function has driven my interest throughout my childhood, all the way into adulthood. I was born and raised in Los Angeles, California where living closely to the ocean allowed me the opportunity to spend a lot of time exploring the Southern California coast. In September 2010, I moved to Eugene. Despite being torn having to leave the sunny weather and warm beaches, moving to Oregon was the best decision I have ever made. Shortly after arriving, I began attending LCC where I met great students and extremely driven instructors.

My Biology 212 and 213 instructor, Stacey Kiser, is the reason I am here at OIMB (Oregon Institute of Marine Biology) this summer. One morning I walked into class and Stacey called me to the front of the room. She handed me the COSEE PRIME flyer and said, "I hope you're not doing anything this summer". Stacey has been the most supportive and encouraging instructor I have ever had, and she even wrote me the letter of recommendation for my COSEE PRIME application. I cannot thank her enough.

This summer I am working with Dr. Alan Shanks and his graduate students in the Shanks Lab at OIMB. His focus is on the dispersal and recruitment (the number of megalopae migrating from the open ocean and shelf environments to near-shore or estuarine benthic environments) of Cancer magister (Dungeness Crab). Once C.Magister molts from its final zoeal stage (free swimming larval stage adapted for pelagic life lasting 2-3 months; total of five zoeal stages) into the megalopal stage (terminal, recruiting stage specialized to find suitable benthic sites to settle; one megalopal stage), they are ready to return and develop into juveniles. There are many factors affecting the recruitment rate of C.magister. By using data from an 11-year time series, Dr. Shanks' aim is to explore the affect of atmospheric forcing, amount of upwelling, and the spring transition on the recruitment rate of C.magister. This research explores the possibility of predicting the commercial catch of Dungeness crabs from the number of returning megalopae.

Each day, I collect samples from the light trap at the end of dock F in the Charleston small boat harbor in Coos Bay, Oregon. The light trap captures returning megalopae, who are attracted to the string of LED lights located inside the trap, along with many other organisms. Then, I take the sample back to the Shanks Lab and begin counting targeted organisms under a dissecting microscope. I really enjoy this task because it allows me to familiarize multiple genera of larvae using Dr. Shanks' identifying key book.
I am extremely grateful for this opportunity to work with these amazing researchers who are thankfully very patient (I ask a lot of questions). I look forward to the rest of my time here and feel that it is already passing by too fast.
Image: Another Shanks Lab intern, Peyton (left), and I collecting the light trap sample on a beautiful day. I think we make a pretty great team!

Natalie Coleman: Start of Summer

My name is Natalie Coleman and last term I finished my Associate of Science Degree at Portland Community College. I will be transferring to Oregon State University in the fall to complete my B.S. in Zoology with a Marine Biology minor. I was drawn to the PRIME program because research is a very important aspect of my career goals and obtaining research experience is very difficult without university connections.  The COSEE PRIME program offers an opportunity I would otherwise not have had.  I grew up in the San Francisco Bay Area in California and have been interested in marine science since I first went tide-pooling at the age of four.  My ultimate career goal is to work toward the conservation of marine life, especially mammals and sharks.

This summer I am working with Dr. Brett Dumbauld, a scientist working with the US Department of Agriculture, who is researching the effect of two species of burrowing shrimp on the oyster aquaculture in the Pacific Northwest.  The way in which these shrimp, Upogebia pugettensis and Neotrypaea californiensis, burrow causes the substrate—the mudflats where the oysters and shrimp live—to collapse or make it impossible for the juvenile oysters to settle and grow.  I will also be working with Dr. Dumbauld’s PhD student Katelyn Bosley to help build an age structure of Upogebia puttegensis. The population model she is creating will help scientists better understand how to help the oyster aquaculture without significantly damaging the shrimp population.  Currently Katelyn is using lipofuscin—a brain pigment which accumulates with age—to determine the age of the shrimp collected.  This summer I will try a new technique which utilizes the calcified eye stalks to age these shrimp.  The eye stalks have been found to contain annual rings, much like tree rings, in crabs and lobsters but I will be the first to try this technique on Upogebia and Neotrypaea shrimp.

This week I have already gone into the field at the Yaquina Bay estuary with Dr. Dumbauld to sample the smaller shrimp who are just returning to the mudflats from their pelagic—open ocean—lifestyle. These “recruits” help determine the condition of the populations of different estuaries. The next task was to measure the carapace—the shell covering the top of the shrimp head—and total length of these shrimp and preserve them in alcohol for further study.  I was able to analyze all of the recruits from Yaquina Bay and found nine, whereas the samples from Willapa Bay in Washington and Tillamook Bay in Oregon contained no recruits. The next field assignment was to take larger samples from the mudflats to retrieve larger shrimp.  I also measured the carapace and total length for these shrimp, but in addition I recorded the sex of each shrimp and whether or not they contained a parasitic isopod—a blood sucking invertebrate that latches onto their gills.  Though these parasites do not kill their host shrimp they make it impossible for the females to produce eggs because they lack energy, which reduces the population of Upogebia. Dr. John Chapman is working with Dr. Dumbauld to investigate the effects of this parasite on the shrimp populations.  Their research revealed that this parasite is an introduced—non-native—species from Japan.

My first week was extremely messy, fun, and informative. I cannot wait to see what next week will entail.

Natalie Coleman

Zac Swider - My first week of embryology in the Maslakova Lab

Greetings from the Oregon Institute of Marine Biology!

This marks the end of my first week as a COSEE intern and I can't express enough how thankful I am for being given this opportunity. I will be spending the next seven weeks working in the Maslakova lab under Dr. Svetlana Maslakova and her husband Dr. George von Dassow, as well as Ph.D. students Laurel and Terra.  Everybody in the Maslakova lab has been unbelievably generous with their time in assisting both Leeah (a fellow COSEE intern) and myself with training and becoming familiar with the lab.

This lab is intently focused of the unraveling the mysteries of the Phylum Nemertea - commonly known as the "ribbon worms" - and they use a number of molecular biology and embryological techniques to accomplish this. The project that I am working on involves the studying the larval development of a very specific nemertean, Micrura alaskensis, that has been studied extensively by the Maslakova lab due to its ease of availability and the fact that it displays a "classic" developmental pattern for a nemertean. The larva of this species (and that of its closely related kin) are referred to as pilidium larvae and undergo an extreme type of metamorphosis (to the adult form) that is not seen anywhere else in the animal kingdom.  A time lapse video of this metamorphosis can be seen below.  This video was taken by Svetlana Maslakova and is included in her recent paper, published in Frontiers in Zoology, describing the development of Micrura alaskensis 

What you are seeing in this video is the juvenile worm literally eating its way out of the larval body and swallowing it as it does so.  When a pilidium larva begins to develop from an egg, the larval body appears first and, after a week or so, the juvenile worms begins to grow and develop around the larval stomach.  During this time, the larva continues to swim around water column, feeding on microscopic plankton and nourishing the larval body.  Once development of the juvenile body is complete the juvenile must break free, but it remains attached the larval body at the mouth.  A neat solution to this problem is for the juvenile to simply consume the larval body as it exits, kind of like a living sock turning itself inside out and crawling away.

Micrura alaskensis
 My first couple of mornings in the Maslakova lab were spent enjoying the especially low tides to go into the field and collect nemertean worms from various mudflats around the OIMB.  Nemertean collection is accomplished by walking around on the mudflats with a shovel and very carefully sifting through the mud to separate the tiny nemerteans away from all of the other minuscule worms that look extraordinarily like them... given the wind, rain, mud, and biting Nereis worms (also found in the mud) - this was by far the grungiest (but most enjoyable) field work that I have ever done!

The rest of my first week has been largely spent training - learning how to accurately pipette extremely small eggs, start cultures of larvae, take care of these cultures, and how to mount specimens for DIC (Differential Interference Contrast) imaging without damaging the larvae so badly that they cannot continue to grow.  On Monday I will begin learning how to inject eggs with various fluorescent markers and DNA analogues designed to inactivate certain genes - more information on this to come next week!

As a small side experiment I have started several cultures of dissected blastomeres - to accomplish this I fertilized a few hundred Micrura alaskensis eggs and as soon as the fertilized eggs divided, I separated the resulting two cells (very carefully, with a very thin glass needle) and set them aside to continue growing.  The significance of this is as follows:  Some animals develop in a regulative manner, meaning that these separated cells ought to be able to sense that they had been separated and compensate for the missing cells to make a complete (albeit smaller) embryo.  Other embryos are incapable of sensing this separation and will continue to divide as if nothing had ever happened, resulting in an embryo missing about half of its cells.  Micrura alaskensis is thought to be somewhere in between these two scenarios, meaning that it can regulate... but not very well - hopefully we will find out soon!

This week has not been all lab work, however.  We had the opportunity on Monday morning to get up at 530AM with the Marine Ecology class to see the Lighthouse tide-pools on the lowest tide of the summer.  It was by far the best tide-pooling that I have ever done and I took hundreds of pictures of intertidal invertebrates.  Unfortunately, until I can find a memory card adapter for my camera, all I have to share is this cell phone picture of a hermit crab :)  Other activities around the OIMB include hiking, swimming, mushroom hunting, birding, photography, insect collection and much more.  I hope to share about a number of these activities soon, stay tuned!

Friday, June 28, 2013

Katlyn Haven: Week 1 at the Hatfield Marine Science Center

Hello everyone,

My name is Katlyn Haven and I just finished my first year at Chemeketa Community College this spring. I am working on my Associate of Science degree and an Associate of Arts Oregon Transfer degree. I plan to transfer to Oregon State University and pursue a degree in Zoology once I am finished at Chemeketa. I am interested in conservation and field biology, which is why I wanted to take part in the COSEE internship program. I am so excited to gain some real-world field research experience and see what it is really like.

This summer I am working with Dr. Waldo Wakefield and Matt Yergey on their juvenile flatfish research project. They are trying to determine the effects of hypoxic (low oxygen level) events on the juvenile flatfish populations since these fish are too small to migrate away from the oxygen-deprived water. They are also examining the behavior of the fish and trying to determine if their reaction times are slowed because of the low oxygen levels.

I have been helping in the project by cataloging data from 1977 through 1979 on fish catches, which will allow for a long-term dataset to be accessible on an online database. This dataset will make it possible for fish populations to be compared and more long-term conclusions to be made. I have also helped by working in the lab on current specimens, which I helped identify, measure, weigh, and preserve. This was very exciting because I was able to appreciate what the data from the 1970's actually meant and what took place in order to get it.

I am so excited to see what else is going to take place this summer and what opportunities I am able to receive from this experience!

Anna Russell: Hi Everyone

Hi, my name is Anna and I am a COSEE student at Shannon Point Marine Center (SPMC) in Washington. I recently graduated from Everett Community College and the Ocean Research College Academy (ORCA) and will be attending the University of Washington in the fall. My career interest is in epidemiology, which is the spread of infectious diseases. However, through experiences and opportunities at ORCA, I have become interested in the relationship between ocean and human health. Specifically, I want to look at the zoonotic diseases, which are diseases that spread between different species. I applied to this internship because I wanted more experience looking at the relationships between different species. I thought it would be a really fun way to spend the summer and I knew I would gain more knowledge about marine science and laboratory techniques.

I will be working with Dr. Sylvia Yang from Western Washington University. We will be looking at phenolic acids and eelgrass wasting disease. Phenolic acids are like the immune system of a plant. When the plant senses that an organism is eating it, the plant will send out the phenolic acids to make it bitter tasting, an herbivore deterrent. Likewise, when the plant senses a disease attacking the cells, it will send out phenolic acids to fight off the disease. In this study, I will be looking at whether the phenolic acids the plant produces when it is attacked by animals will help fight diseases as well. Specifically, my question is whether the acids will help protect against eelgrass wasting disease. This disease is caused by a protist called Labyrinthula zosterae. In the 1930's, eelgrass wasting disease wiped out 90% of the eelgrass meadows on the East coast and Europe (Larkum, Awd et al. 2006. Seagrasses: Biology, Ecology, and Conservation). Labyrinthula zosterae is present in the Puget Sound ecosystem but it hasn't caused a widespread outbreak like the 1930's epizootic.

To measure the presence and extent of the disease in this study, I will be using both phenolic acids and image analysis. I will take samples from both before I introduce the disease and after to measure the phenolic acid levels. I will also take photos and use some computer programs to analyze, by pixels, how much of the leaf is diseased or decomposed.

That is weeks in the future though. This afternoon, we collected our first eelgrass shoots and isopods and snails, which will be our herbivores in this study. Tomorrow, I will start to set up the tanks and learn how to take care of eelgrass!
We collected eelgrass shoots out at Ship Harbor Park. Bridgette (right), another student working on eelgrass, helped us. 

Natasha Christman: The Start of a Summer

You might not notice it when cruising the gorgeous Fidalgo Island in Western Washington, but there is actually a laboratory tucked into the corner of the deep coastal forests. It might be easy to miss on the roads, but this scientific hotspot at Shannon Point Marine Center is the reason why I've made the several hour journey from nearby Seattle to the small town of Anacortes. I'll be here as a COSEE intern throughout the summer- right in between the completion of my studies at Olympic College and my future at the University of Washington. It's only been a few days up here at Shannon Point, but I can tell already it is going to be a fantastic summer.

I have been blazing down a career direction of biology nearly my entire life; from even an early age, observing the wonders of nature has been one of my great passions. My interest in marine science first sparked from my experience living in Puget Sound for so many years. When I started volunteering at the Seattle Aquarium, I learned how truly magnificent the ocean is and how much it really means to me. From there, I started scuba diving and investing more of my time into water-related pursuits. The marine world hooked me in, and the PRIME internship provided a fantastic opportunity to pursue these interests, particularly in research-driven science and learning that I believe will be invaluable to my growth as a student and prepare me as I pursue a career as a researcher and scientist!

So this summer, I will be working with Dr. Jude Apple of Western Washington University. We are studying and monitoring low-levels of dissolved oxygen (hypoxia) in and around Bellingham Bay of Washington. This evaluation of water quality ties in with the plankton communities and health of the ocean as it is affected by human activities and climate change. Low oxygen levels can be disastrous to the delicate ocean balance, and the destruction can be seen in "dead zones" that can form in areas over a period of time. Added with other contributors to lowered water quality such as increased nutrient and sediment levels and contamination with fecal coliform, hypoxia is a prominent issue of ocean health and will be a major aspect of the summer research.

Thursday, the research vessel left the dock for the summer's first research cruise. We collected data and samples from several sites. After a few hours on the boat, the water became a bit choppy, but that did not stop the science! And Friday, we will analyze the data. So stay tuned for more from our research!

Natasha Renae Christman

Wednesday, June 26, 2013

Aaron Nelson: Greetings from Friday Harbor Laboritories

Aaron Nelson~ Greetings from Friday Harbor Laboratories!

It’s been a week and half on San Juan Island for me and everything is going great so far (I had an earlier start date than the rest the group). I traveled up here at the end of finals week at Lane Community College in Eugene, OR. Soon I’ll be transferring to the University of Oregon to get a bachelors degree in environmental science.

This is my first experience with formal research and it has been exciting to see how much creativity and problem solving is involved. It definitely works the brain a little differently than the memorization and concept building that we’re all used to in classes. I decided to pursue a COSEE internship in order to get general biology research experience. In fact, the marine biology aspect didn't play too much into the decision.  That said, I’m certainly a leisure admirer of the sea and I’m glad to be so close to it for the summer. Maybe I’ll be converted from my forest-centered focus of the past....

I’m working with Dr. Kelly Sutherland (from Univ. of Oregon) on determining the effects of small-scale turbulence on the movement and predation of jellyfish (hydromedusae in particular). Sutherland and others have performed previous research focused on jellyfish movement and its function in feeding, escaping predators, etc. However, this is the first study to be done that observes jellyfish in turbulent conditions; all the rest took place in still water tanks. It feels good to be doing research on a totally new aspect of things... nobody can tell us we’re wrong!

My lab partner, Clare, and I are just starting to get into the routine of conducting the tank experiments. Dr. Sutherland has allotted us the task of conducting a series of experiments in one of the 10-gallon turbulence tanks. Most of our time is spent looking at drops of water through microscopes and harvesting food for the jellies (various copepods and Artemia salina [also known as “sea monkeys”]). This is surprisingly fun! Since these tiny prey are still alive in the Petri dishes, they are moving targets, and it’s a bit like a game of “Asteroids” to chase them and draw them up into our tiny pipettes. We count up exactly 100 of each and then toss them in the tank to spend two hours of turbulence (or stillness for control data) and then see how many remain afterwards.  I’m afraid that if I say much more there won’t be anything to reveal next week!


Tuesday, June 25, 2013

PRIME 2013 is underway!

Welcome, everyone!  Orientation is over and PRIME 2013 is off to a great start.  In Oregon and Washington we have 13 community college student interns participating in PRIME that will also be contributing to the blog this summer.  Our three joint COSEE/URM (Undergraduate Research and Mentoring in the Biological Sciences) interns have been hard at work in Hawai'i since May.  With 16 interns, this is our biggest year yet!  

I am looking forward to hearing from everyone and reading about your research experiences this summer.  Best of luck with your projects!