Thursday, August 25, 2011

Coty's Reflection

This summer internship opportunity through the COSEE pacific partnerships/PRIME program was an amazing experience. I lived at the Hatfield Marine Science Center in Newport, Oregon. I felt that I was treated with respect and taken care of by the program coordinators Itchung Cheung and Coral Gehrke.

During my time at Hatfield, I worked with the U.S. Fish and Wild Life Service for eight weeks helping wild life and refuge biologists conduct seabird surveys. My mentor Shawn Stephensen was an excellent person to work under. He always made sure that I was well equipt to conduct our surveys and that I was safe. I could also tell that he really cared about me learning proper data collection techniques. During my internship with USFWS I was was fourtunate enough to participate in several different surveys where I learned how to use different fieldwork skill sets.

My stay at the Hatfield student housing was a very plesant one. I felt comfortable in the appartment provided to me. The roomates I had were awesome and fun to live with. As the eight weeks of my internship passed on, I made several close friends that lived there in the housing. I admired how they all were very passionate about marine biology and excited about their internships. I was very sad to leave them when my 8 weeks was up.

Thank you for COSEE Pacific Partnerships, PRIME and USFWS for the amazing experience!

Wednesday, August 24, 2011

Coty's Final Weeks

Hey Everybody! Sorry that its been such a long time since my last post. In the last few weeks of my internship, I was involved with two more Seabird surveys with the USFWS. First we conducted a Coastline Cormorant Survey and second we did an Island Strom Petrel Survey.

The coastline cormorant survey took two days to conduct. The objective of the survey was to count Comorant nests along a stretch of shorline from Deopoe Bay to Yaquina Bay. The first day was a on-foot patrol of the Yaquina head location.
The second day My metnor and I took a boat form Depoe Bay to Yaquina Bay while slowly surveying the shorline with binochulars for cormorant nests. In past years there have been close to 1000 Comorant nests in this stretch of shoreline, but this year we observed that manyof the spots where there once were hundreds of nests, are now completely vacant :(

The Island Storm Petrel Survey took place off the Southern
Oregon Coast. There were four islands that we were interested in surveying, but we could only get on to one of them due to bad weather and strong tides. There were two objectives of this survey, 1. To obtain data that would later help generate am estimate of the petrels population size and 2. To gather samples of any invertebrates/ vertebrates that exixt on the island. The Petrels on these islands build their nests in burrows, so in order to obtain data about the population we "grubbed". Grubbing is the action of carefully slipping your arm down into the burrows and feeling around with your finger tips for burrow content. To conduct the survey we used a 100 meter transect along the hillside of the island, and took a 1m X 1m quadrat sample at every 10 meter mark along the transect.We found there was an average of 8-12 burrows per quadrat sample and nearly all of the burrows had either eggs or chicks in it! We had to wear snowshoes while we were on the island because we didnt want to step into the burrows with our feet and possilby disturb the petrels nesting within.

Monday, August 22, 2011


This experience is one that I would strongly encourage other community college students to participate in. Throughout the summer I have been given the opportunity to work in a diverse environment that has allowed me to learn about a wide variety of topics within the umbrella of marine science. Even if you are unsure if research is something you would be interested in pursuing, this internship is an excellent way to test the waters and learn more about what other opportunities may be out there and may be more suited to your particular interests. This will become just one step of many that will lead to my ultimate education and career goals and it is an excellent starting point to have. I have gained many helpful skills, made contacts with both the advisors in the lab and the other interns from all across the country, and been introduced to the other opportunities that I can pursue after this. Throughout the course of this summer I have faced challenges and obstacles, experienced great successes, learned a lot, and have enjoyed myself while doing it, as well anyone else who also participates in this program.

Thank you everyone at COSEE for this wonderful opportunity!

Final Post- Wrapping It All Up

After having completed all four research cruises in Bellingham Bay, I have been able to create various maps to track the bottom dissolved oxygen concentrations in the bay as well as look at the side view of the transects we performed to identify where the hypoxic layer was located. These maps showed that the hypoxic water layer was much more mobile than we initially thought it to be. Going into this project, I had assumed that the hypoxic area we found would be located at the bottom of the bay and would remain there from week to week. Instead, it traveled up and down the water column and was never in a consistent site. This indicates that tides and currents may be another factor to consider when looking at the hypoxic zone of water in Bellingham Bay.

This graph of the bottom water dissolved oxygen concentrations in Bellingham Bay is from the first week of testing. This was the week when the hypoxia was the most severe and extensive. After creating this map, I used it to calculate the volume of the hypoxic zone so I could find a comparable value. I calculated that the hypoxic zone had a total volume of 3.6 billion cubic meters, which is roughly equivalent to the volume of 35 Metrodomes (the Minnesota Viking football stadium). This value will be useful to have in the future to compare the sizes of hypoxic zones to examine trends as to whether the hypoxia is becoming more extensive.

I also worked on comparing Hood Canal to Bellingham Bay from July 2007 to February 2011 to see if there were any correlations between the two hypoxic systems. There were not any
significant correlations between the two bodies of water; however, they did follow some of the same annual trends and patterns. One of the most interesting similarities that was noted between the two bodies of water was a salt water wedge that came over a sill, which is a feature that both of the systems have. As deep marine water that has a high salinity, low temperature, and high density is pushed over the sill, it forces the hypoxic water at the bottom to move upwards in the water column. As the water is pushed up, it can move into more shallow areas, where fish may become trapped in the hypoxia and cause a fish kill. This process is shown in the figure.

Overall, the research that I have worked on this summer has helped identify some of the patterns that hypoxia in Bellingham Bay follows. However, it also raised many more questions about causes and influences, duration, location, and behaviors of hypoxia in the bay that require additional research.

I would like to thank my advisor Dr. Apple for taking me in this summer for this research project. I have enjoyed my time here and appreciate all of the help and guidance you have provided throughout the summer. Hopefully I will get the opportunity to continue this research with you in the future!

Wednesday, August 17, 2011

Akiko- Final Post

My goodness, I can't believe that the weeks passed by so quickly.

Before I came here, I knew that I wanted to work in the ocean, but I wasn't sure whether research was my thing. The only exposure that I'd had to research was in my science classes. I didn't think that I would enjoy microscopy very much, since I had generally found microscopy in my science labs to be rather boring. My viewpoint definitely changed as soon as I started my project. Looking at a prepared slide of dead organisms is not nearly as cool as looking at living organisms. I was constantly impressed with the abundance and the variety of life to be found on my little petri dishes. I was more dedicated and invested in my project than I expected to be, because it was *my* project-- no one was telling me what to do or what to look at.

I have had such a wonderful time here at the Oregon Institute of Marine Biology. I'm sad that the summer is over, but honestly thankful and happy to have had such a great opportunity to do research in marine science. I would highly recommend the COSEE PRIME program to any budding marine scientist.

Akiko- Week 8: Almost done

Hey all, Akiko here.

In the eighth week, my adviser asked me to stay at OIMB for one extra week, in order to polish up the website. I happily agreed, so I'll be here for a total of nine weeks. The website definitely needs a good deal of work so I am happy to put in more hours on it. Though to be honest, photo processing is exhausting work!

Most of this week was spent preparing for final presentations, which took place on Friday. I spent most of Tuesday reviewing notes on good ways to structure presentations. I gave a few practice presentations to my friends and felt ready to present on Friday. The presentations took place in a classroom at the Oregon Institute of Marine Biology. Unfortunately the Hatfield Marine Science Center interns did not come down to Charleston for the day, but we did get the chance to see their presentations via Skype.

During my presentation, I spoke briefly about my future plans for the website (, which I made to house the identification key which is my summer project. With my extra time at OIMB, I hope to label the basic anatomy of the juvenile settlers, and post a few photos of what each settler looks like as an adult colony. The website needs a lot of editing, and I have received many helpful comments about how to improve it. I hope that I have enough time to apply them all!

This is me looking through the dissecting microscope, which I used for the bulk of my work. Every day, for four weeks or so, I looked through this microscope to take pictures of the settling organisms.

A friend of mine took this photo of me and some ascidians. The large orange blobs are Distaplia occidentalis colonies, growing on a piece of netting that has been submerged for several months.

Friday, August 12, 2011

Winkler Method vs YSI meter

Week 4 Blog
Lance Brockie

My agenda for this week was focused solely on my research pertaining to Smugglers Slough. One of my main concerns was that I was getting out of the ordinary results or findings when comparing the two testing methods (YSI vs. Winkler Method). When expressing my concerns to Dr. Apple he advised me to set up an experiment to compare the two methods using 100 percent saturated water to see if they come up with the same dissolved oxygen reading. After completing the experiment I found that there was no significant difference between the two testing methods.
Upon finding that there were no flaws in my testing methods, Dr. Apple suggested that I standardize the sodium thiosulfate I’ve been using to get as approximate N-value (Normality). After completing the standardization of the sodium thiosulfate I discovered that I had been working with the wrong N-value this whole time. This was a big relief to me as now I knew why my results have been so out of the ordinary.
This week I learned that there are a lot of factors you need to take into consideration when using the Winkler Method. One being that you should insure that the reagents that you’re using are not too old. I discovered that during my study old reagents are capable of affecting your results during the titration process. Another thing that I discovered was that when calculating the milliliters of titration (ml of titration) that was used to get the milligrams per liter (mg/L D.O.) dissolved oxygen, you need to insure that you’re using the proper N-value. I discovered that if you use the wrong N-value your results will be inaccurate. Now that I have obtained this information, I now feel a lot more comfortable and confident about utilizing the Winkler Method.

Wednesday, August 10, 2011

Week 3 Blog
Lance Brockie

This week was a little different from the activities that I’ve been involved with so far involving this internship. On Tuesday, we participated on a working cruise aboard the R/V Centennial, which is a research vessel based out of Friday Harbor Labs. The purpose of this cruise was to conduct depth profiles utilizing the Conductivity, Temperature, Depth Sensor (CTD), as well as to collect water samples at various depths which would be used to measure the chlorophyll and dissolved oxygen levels back at the Shannon Point Marine Center Lab.

Each intern who participated was assigned a specific task to perform aboard the vessel. Another student (Mike Murphy) and I were assigned with lowering the CTD into the water as well as bringing the CTD back aboard once it made its descent to the bottom and back to the surface (see picture). Once the CTD was back aboard, I was then tasked with collecting water samples from designated niskin bottles which are located on the CTD. Once the BOD bottles were filled I then added the Winkler reagents (Manganous chloride, and Alkaline iodide) to each sample and stored them to be analyzed later at the Shannon Point lab using the Winkler Method.

This was a great learning experience not only for me but I would have to say all the other interns as well. Once learning about the CTD and visually seeing what this instrument measures in the water column (see figure below), I now have a greater understanding of what is going on at various depths of the ocean. I consider myself very lucky that I got the opportunity to learn how this piece of equipment operates and was able to work with it firsthand. I would have to say that this week has been the highpoint of this internship thus far, and I’m certainly looking forward to the next time we get to participate on another cruise.

Monday, August 8, 2011

Blog 3- Bellingham Bay Research

The cruises in Bellingham Bay have been the main focus for my research on hypoxia. So far we have gone on three research trips in the bay in order to collect a large amount of data with the CTD. For these cruises, we perform a transect of ten stations from north to south and eight stations from east to west, as well as CTD casts at eight historic sites in the bay. Water samples are also collected at the surface of each site for chlorophyll a analysis and from deep water at selected sites for dissolved oxygen and nutrient analysis.

Our first cruise was rather long because we had to figure out where exactly to send down the CTD, then create a rhythm in our data collection to make everything go as smoothly as possible. At the fifth station we sent the CTD down at, we found hypoxic conditions in the deep water. From there, we found many other sites also showed evidence of hypoxia in the deep water. All of this was in support of what we believed we would see due to the trends that had been found in the past. First I drew graphs of the data by hand to allow myself to visualize the hypoxic area. Then I made contour plots using a computer program called Surfer, which I will be using to make graphs for the data I collected at later dates as well. Graphing the data in Surfer will allow me to look more accurately at the hypoxic areas in Bellingham Bay and potentially find the volume of the hypoxic water mass.

After finding hypoxic levels on the first cruise, I fully anticipated seeing either the same results or intensified hypoxia on the following two cruises. However, this was not the case at all. The two figures below are the graphs for the concentrations of oxygen for the second research cruise. There was a small hypoxic area higher in the water column, but the concentrations for this cruise fell higher in the 2-4 mg/L range than the hypoxic areas the week prior. Based on all of the wind and mixing that had taken place, we hypothesized that the hypoxic area we had found at the bottom dispersed as a result of the mixing. The most recent cruise we went on, I expected the hypoxic area to return as a result of layers becoming stratified once more. Instead, the water column had the same general trend as the week before and did not have a significant hypoxic area.

These results are quite surprising and it will be interesting to see what we find on our final research trip later this week. I will soon begin analyzing and visualizing my data to calculate the volume of the initial hypoxic area that was found in the first week.

Akiko- Week 6 & 7: Crunch time!

Hey Everyone, Akiko here.

The weeks have flown by! I have been hard at work. During the sixth week, I finally stopped taking daily photos of the settlers. It's fun to do work under the microscope, but hard when you're doing it every day! I compiled all of the photos I took (over 2,000!) and began sorting through them in order to find the highest quality ones for each species. Once I had chosen the nicest photographs, I began the long process of modifying them with Adobe Photoshop. Since I am new to both microscopy and photography, most of the pictures that I took were blurry, too dark, too bright or off-colored. Additionally, many of the organisms that I photographed are translucent, making them even harder to see on a picture. With Adobe Photoshop, I can adjust the photo to make the image clearer and more representative of the actual organism.

In addition to image quality modifications, I can also use Photoshop to create composites of multiple images. This is a very useful way to deal with the limitations of microscopy. With microscopes, the focal plane-- that is, how much of the object is in focus-- is very thin. This means that at any one time, only some parts of the 3D organism will be in focus. In any one picture, only a portion of the organism will be in focus and the rest of the organism will be blurry, as shown below. However, with Photoshop, I can slice out the parts from each picture that are in focus, and combine them together to make a composite image in which most of the organism appears to be in focus.

Here, the base of the organism is in focus.

Here, the top part of the organism is in focus.

This picture is a composite that I have made using Photoshop, by combining the two above images.

Photo processing takes a good deal of time to do, and I spent many hours going through the photos in order to get them cleaned up and presentable. In addition to that, I also began to learn how to make a website on using the "Weebly" website creation page. Thankfully, the interface on the Weebly page is very user-friendly. I am still ironing out the finer points of the web page but so far it is looking good! It is still under construction, but is viewable at: .

Wednesday, August 3, 2011

Outreach Work

It has been a while since I last updated all of you, and I have quite a bit to catch up on. I have been working hard on collecting my data, both during cruises in Bellingham Bay and the San Juan Channel, as well as spending time on the weekends doing outreach with SPMC. In order to cover as much as possible, I will focus each of my upcoming blogs on a separate aspect of my work these past few weeks. This outreach has been a way for everyone here to help raise awareness in the community about what it is we are working on at SPMC and about the environment that is right in their own backyard.

The last two Saturdays I have helped bring a touch tank from Shannon Point to the Kids Are Best Fest and Bivalve Bash. I worked with some of the other interns and graduate students to share some of the local intertidal organisms with the people of the area. This was a chance for me to work on allowing people to work on answering their own questions and inquiring further about the animals in the area when interacting with them at the tanks. It was hard at first not to immediately answer the question and end the interaction, but after a bit of practice I was able to have a dialogue with the people who were visiting the touch tanks.

Each festival had an entirely different target group who was visiting. At Kids Are Best Fest, we were mainly sharing the animals with, you guessed it, kids. Parents were often interested in the organisms as well, and helped their children work up the courage to touch some of the more unusual looking animals. One of the favorite animals of all the kids was the leather star we had (pictured below), mainly because of its size and color. It was great to see all the kids get the wide-eyed look of astonishment as I would pull the huge star out of the water and let them all feel it. One of the most common questions asked was whether or not the sea stars were alive or dead or if they were fake. Without the typical head with the eyes and mouth that most children expect to see on an animal, the sea stars and many of the other organisms we had in the tanks helped them learn more about the variation in the animals on this planet.

At Bivalve Bash, we had a much wider audience of people who came to check out the animals. Most commonly, it was adults who were visiting, but they often just wanted to look at and discuss the animals rather than touch them. The kids who came by, though, were more than eager to get a chance to feel some of the organisms. Working with more adults was a chance for me to really work at helping challenge them to puzzle their way through figuring out what the animal was by using what prior knowledge they had. Although it was often tempting to simply rattle of the common name and a few random facts about the animals, having them answer their own questions allowed them to learn more and helped create a conversation about the organisms in our coastal waters.

It was wonderful to be able to help the people who have lived here most of their lives learn more about the animals that live in the environment around them. Some of them had no idea about what sort of animals live in the tide pools around them and were pleasantly surprised to learn about the interesting creatures living right in their own backyard.

Tuesday, July 26, 2011

Akiko- Week 5: Visitors

Hey all, Akiko here again.

In the fifth week of the internship, all of the OIMB interns in Charleston and the Hatfield Marine Science Center interns from Newport got the chance to come together and show off our projects. The COSEE PRIME program makes a huge effort to support communication and collaboration among scientists, which is such a great initiative. Having spent many hours in the lab, I can see how a researcher could become so involved in their work that they don't get the chance to see what other scientists are doing in similar fields. However, collaboration is so important, because the results that you get under a microscope could heavily influence the work of another researcher doing a similar project.

On Wednesday, Coty and Drew came down to Charleston with their adviser Itchung. I showed them all my project and let them watch the little ascidians pump water into themselves. Every once in a while, the organisms will contract their branchial baskets and close their siphons as if they are coughing or exhaling. From what I've read, this is to keep large particles from entering their incurrent siphons. This reaction is touch-sensitive, so sometimes I will tickle the ascidian with a single hair (that's how small and sensitive they are) and watch them contract. Later on that afternoon, we all went out with Professor Jan Hodder to see some marine mammal action at Cape Arago. Seals and sea lions sunbathed on the rocks, and a few gray whales broke the surface every few minutes.

On Thursday, Karyn, Jess, and I with our adviser, Coral, went up to Newport to visit with the interns there and see their projects. This was the first day in over 3 weeks that I took a full day off and didn't look at my petri dishes! It was nice to have a little break and it gave me time to reflect on my project progression and to write in my research notebook. We got to stomp around in the mud with Drew, and visit Coty's bird-watching location. It was a nice trip, but good to come back home!

Playing around in the mud was fun. I got to use a huge siphon to suck shrimp out of the mud. We saw ghost shrimp and mud shrimp.

We had a blast at Cape Arago looking out at the marine mammals.

Drew - The Tide is in...

Monday of this past week allowed for just enough low tide to finish the GPS work needed to generate a population density map of both species of shrimp in Yaquina Bay. However, the data has to be differentially corrected using the NAD 83 UTM 10 North GPS information system and that requires waiting at least 24 hours. By Tuesday I was knee deep in ARCGis and related computer software trying to generate an inverse distance weighted interpolation of our data. That was my last chance to work on the map because on Wednesday, all the COSEE interns took off at 8am to visit Charelston, OR.

We went to visit the Oregon Institute of Marine Biology (OIMB) and to meet the other COSEE PRIME interns (who were all awesome). In the photo to the right is Akiko showing an experiment in progress in the boat harbor. We toured their facilities, asked lots of questions (about the interns research and graduate school), and enjoyed all-you-can-eat dining hall meals. Thank you OIMB for a great visit!

The following day the COSEE interns came to Hatfield. Here we all are listening to Brett
introduce our project. No one got stuck in the mud...but it was a close call :)
This next week my focus will be on writing up a draft paper, completing that population density map that I keep talking about, and towards the end of the week the tide will finally be low enough to warrant a day of field work, collecting some of our last samples for this project.

Monday, July 25, 2011

Introduction to Bellingham Bay and Smugglers Slough Study

Lance Brockie
Blog #2

This week of this internship I participated on a couple of projects, the first project being the Bellingham Bay Hypoxia Study with Dr. Apple where we measured dissolved oxygen levels in the bay as well as levels of chlorophyll and nutrient levels. Being that this is my second summer participating in this study I’m excited to see what’s going on in Bellingham Bay this summer compared to last summer. This year we are implementing depth profiles where we could measure the quality of the water from the bottom of the water all the way to the surface. As the summer progresses I’m excited to find out and see what’s going on with the water throughout the bay.
I also began collecting water samples at various locations along Smugglers Slough, which is a body of water that is located on the Lummi Indian Reservation. With these samples I will be measuring the levels of dissolved oxygen at various locations throughout the slough. My main focus throughout this study will be to try to determine if the oxygen levels in this particular slough are healthy or high enough to sustain juvenile salmon populations. This past year the Lummi Tribe reconnected the Smugglers Slough with the Nooksack River in hopes that by doing so juvenile salmon will utilize this particular body of water on the Lummi Reservation.
For the Smugglers Slough study I will be utilizing the YSI-556 meter to collect dissolved oxygen levels as well as temperature, conductivity, and pH levels. Also I will be measuring the dissolved oxygen levels utilizing the Winkler Testing Method to try to determine which is more accurate when testing for levels of dissolved oxygen. I must say that I am very excited and am looking forward to continuing with these studies in the weeks to come as I am learning more and more about water quality every day.

Akiko- Week 4: Photos of settlers

Hey All, Akiko here.

My goodness the weeks are passing by so quickly! During the fourth week, I watched my six new plates get colonized by a variety of settlers. The plates are fouling quickly, which is good because it means that a lot of organisms are settling down on it, but is also difficult because algae and particles have clouded the petri dish and make it hard to clearly see the organism in photos.
I decided to make a little side-experiment out of the redeployment. I actually deployed 12 plates with velcro on the sides instead of underneath. Of the 12 plates, six of them have abrasion on the top side (I scrubbed them with sandpaper to make the surface rough) while six of them are simply smooth plastic. I did this because supposedly settlers prefer to settle on roughened surfaces, and I figured that I could keep track of the rate of settlement on the clear plates versus the smooth plates. I'll count the number of settlers on each plates at some future time during the experiment and see whether the settlers really prefer rough over smooth.

For my main experiment, every day is the same procedure: get the petri dishes out of the water, look at each of them under the dissecting microscope, take photos of specific organisms, and keep track of new species that arrive on my plate. It sounds easy, but the entire process takes about 3-4 hours, and I do it every day (even the weekends). I am trying hard to be a good scientist, even if it means sacrificing my days off. On the bright side, once I start looking at the plates I'm often so absorbed in observing the changes that go on from day to day that the time goes by faster than it would otherwise.

Here are some of the new organisms that have collected on my plates. I haven't had time to adjust the images or put in scale bars, but suffice to say that they are really tiny!

This is probably Schizoporella japonica, a bryozoan. Bryozoans are little animals that settle onto surfaces and reproduce asexually to form larger colonies. This kind of bryozoan is an encrusting bryozoan, meaning that it will continue to spread over the surface in a hard thin layer, like dried paint. When this bryozoan gets bigger, it will begin to reproduce assexually to form a colony.

The spiral shell in this photo belongs to what I believe is a serpulid polychaete worm. You can see little feeding structures sticking out of the mouth of the shell. That is the worm. With these guys, I have to wait for them to peek out of their shells before photographing them.

Sunday, July 24, 2011

Coty Spies on Costal Birdies Weeks 3 & 4

Hey everybody! Sorry for the delay on the blogs! I will briefly talk about week 3, but I'd like to focus my discussion on what I have been doing for the past week or so.
During week 3, I continued monitoring the colony of birds in Deope Bay. It was important to do follow up data collection beyond the day after the fireworks because often times abandonment, and predation of the nests can take take place up to several days after a disturbance. From what my data shows it seems that the birds were long term disturbance and no abandonment of nests. to the right is a picture of a Brant's Comorant, the bird that this study mainly focused on. One of my favorite features of Brant's comorants is the bright blue colored patch that they have on their throats. Only the sexually mature adults have this blue patch while the juveniles have a tan patch or no patch at all.

For the past week and a half I have not been surveying the Depoe Bay colony... Instead, I have had the opportunity to participate in a few other really awesome experiences. For part of the time, I have helped other biologist who are surveying colonies of Common Murres out at the Yaquina Head in north Newport. The main study that I have been a part of out there is determining the frequency and type of feeding that the Murre chicks receive from their parents. We also have been keeping track of the predation events on the Murres that the local Bald Eagles have been instigating. In a 6 hour monitoring shift I witnessed three times when a Bald Eagle attacked the colony, and made off with either an adult or chick Murre.
The picture on the right shows me surveying the Murres on Flat Top Rock at the Yaqunia head location with a Swarovski spotting scope. Something that I was astonished by was how physically packed the Murres were on the rock....They are practically nesting/roosting shoulder to shoulder in these colonies. The picture below shows a both how tightly packed the Murres can get on the rock and a Bald Eagles predation attempt!

The other awesome experience that I really enjoyed was when I got to go down to OIMB with Itchung and Drew to go visit the other COSEE interns and Staff. I was fascinated by the research that the interns down there were conducting! I was very impressed with the respect and quality of work that their mentors gave them. I also enjoyed the presentation that a speaker gave on the parasites of Hermit crabs....sooo much detail....and sooo much interesting information that I never knew!!!

Arriving at OIMB

I arrived at OIMB this week, a big change from Monterey. Never having gone anywhere for an extended amount of time without knowing anyone as well as never having even been to California, going to Monterey was a whole new experience that made me excited and extremely nervous at the same time. Within two week's time this brand new life-style became my normal routine and the only nervous feelings I had left came from the anticipation of my final presentation (those feelings are still there). Coming to Charleston wasn't as nerve-racking because I just went through a similar experience and was prepared for the change. The first night of going to sleep not knowing what was in store for the next day was a little strange, especially without everyone that became my little biology-team family right down the hall. It didn't take long to get used to though, and by Friday Alan was back to work in the lab and I had my nose back in a microscope.

One of the questions I was asked was how did we collect the samples that we spend so many hours counting? Well, there are a few answers to that question. Collecting samples from the surf zone was done by using this pump set-up. We secured a hose to poles that were driven roughly four feet into the sand. With the intake stationed in the surfzone, we connected the other end of the hose to a pump that sucked water from the surf up through the hose and routed the water through a sand-trap (the box apparatus in the picture) to reduce the amount of sand in the sample. Water was filtered through a net for ten minutes per sample, and we took three zooplankton samples everyday at high tide. Phyto samples were taken by filling liter jugs with water from the sand-trap.

To collect samples from offshore we did plankton tows from a kayak. I discovered that I easily got sea-sick so Daniel and Marley mostly did this job and I stayed on shore working the pump. They most often collected samples doing vertical tows, where they would lower the net to the bottom of the bay with the net tied to a rope with marked increments and pull it straight up. But they also did horizontal and newston tows. Horizontal tows are samples taken by dragging the net parallel to the surface of the water for a measured amount of time. A flowmeter in the net records how much water is filtered through the net, but it doesn't always work. Newston tows are plankton tows taken at an angle where the net starts deep and as you move the kayak you pull it up at an angle. Keeping track of which samples are from what method is done with waterproof paper and numbered jars. When we have the samples, we process them (meaning will kill the zooplankton with formalin or fix the phytoplankton with iodine) and concentrate them down, put them under a microscope and start counting. Yay!

Monday, July 18, 2011

Stuck in the mud

I didn't really get stuck in the mud but this past week was a workout. I have not spent any time on a mud flat or experienced mud of such a sticky and viscous nature. I believe it was on Monday that Lee, Sam, and I drove out to sample a high intertidal location and it was here that I experienced a frustration with mud that I have never known before. I was lugging a bucket, a sieve, and the GPS unit. After I dug a hole in the bucket core and transfered mud to the sieve, I had to transport the sieve to water. It was this step of the process that my boots would slide right off my feet. Basically, as I took a step forward, I would fall over and my boots would come off leaving me struggling in the mud to put my boots back on. This was a low point in the week for me. But then I decided to find these straps for my boots and life has been much better since. I am going to donate them to the next intern (they keep your heel from sliding out of the boot).
The early half of the week I spent learning some of the basics of ARC-gis and helping Lee or Jessica collect a few more samples for their projects. I was supposed to clean Katelyn's shrimp tanks.... but I'll do that next week.
So the question I am helping answer is how many shrimp are in Yaquina Bay. An outline of the whole process is in order. First, we walked the edges of the shrimp populations with a GPS unit. We then uploaded these GPS locations to ARC-gis and doctored the information into a group of polygons that represented where the shrimp live on a map of Yaquina Bay. Using information from previous studies we know that the number of burrow holes roughly correlates to the number of shrimp. We are using this relationship to map the population densities on our map. After transfering the data to R, we generated 300 random points to sample. We navigate to all of these points with the GPS and use a quadrat to count the number of burrow holes per 1/4 sq meter.
Katelyn and I have completed most of the Ghost shrimp and next week we will finish the Muds. The next step is the 10 random cores for each population and sorting the samples.

One last picture of a shrimp coming out of the sieve and going straight into our sampling bag.

Sunday, July 17, 2011

Wrapping up in Monterey

Yesterday was our last day of field work in Carmel, our last day at the lab in Monterey and Marley and I are leaving this morning from Pacific Grove. We were really busy yesterday, which isn't very different from our everyday normal, but instead of collecting samples and counting them and trying to keep things straight and organized, we were removing all of our equipment off of the beach and packing up the lab equipment and playing tetris with trying to fit everything into Alan and Marley's cars. After we finished loading everything off of the beach Alan accidentally locked his keys in his car (which was actually pretty funny) so we had some time to kill while we were waiting for AAA and Daniel and I decided to go snorkling. It was pretty fun for a while until the water got too cold for our heads. I didn't know you could get a brain freeze without drinking anything cold. I wasn't able to get pictures of any of this because my camera was on the fritz and it was taking me too long to figure it out.

It's been so hard to keep track of time here. Without having any days off for reference and with doing almost the exact same routine everyday, days start to blend together and it's hard to keep track of the date, yet alone which day of the week it is. It seems crazy that we are leaving, it feels like we just got here. We are going to drive back up to OIMB where Alan has informed me that me and Daniel are going to be working on a side project besides counting samples and I'm pretty excited!

Barnacles are one of the main points of Alan's interest in this project and cyprids are barnacle larva. We have found a variety of species, from left to right we have been classifying them as semibalanus, crenatus, tetraclita, chthamalus and pollicepes. The one we are calling semibalanus is the species we found most often. At first we were calling it balanus until we found another species that contradicted that.

This picture shows, from top to bottom, semibalanus, crenatus, glandula and tetraclita. Semibalanus and glandula are very similar at first glance, but with more careful examination there are subtle differences that convinced us that what we originally thought of as glandula actually is not. We still don't have a consensus on what our most common cyprid is, but semibalanus seemed like the best choice for now. So this is what Daniel and I will be working on at OIMB. We will catch cyprids and grow them up into barnacles so we can determine what species our mystery cyprid is. The only one we will not be able to work with is tetraclita because it is not native to the Oregon coast. I'm excited for the next chapter of my internship. I hope everyone else is getting to have as much fun as I am! Have a good day!

Thursday, July 14, 2011

Akiko- Week 3 Trial and Error

Hey All, Akiko here.

In the third week of my internship, I spent a lot of time focused on my research project. I spent a lot of time diligently following, photographing, and observing the little ascidians that settled on my plate. I used velcro on the backs of my petri dishes to attach them to a large plate hanging in the bay. However, this velcro created a problem in that it obscured the light from the microscopes when trying to take pictures of the ascidians. Furthermore, I found that my original intention of setting out 20 petri dishes was too ambitious: I quickly found myself inundated with work trying to photograph 20+ organisms each day!

I decided that I needed to rethink and redo some parts of my project. With the guidance of my adviser, Professor Richard Emlet, I made new petri dishes that had velcro on the sides of the plates rather than underneath them. That way, the velcro wouldn't distort the light. I also decided to downsize the number of petri dishes deployed. Now I have six clear petri dishes to keep track of instead of twenty. I also decided not to take pictures of all of the organisms each day, but to rotate through them.

On the up side, I am learning something new every day. Each day I dedicate a lot of time (around 3 hours) to observing and photographing the tiny organisms under the microscope, and then I put in a few hours to tidying up the images with photoshop. I'm learning how to recognize settlers of different species too! Here are some that are easy to identify.

Do you recognize this one? This is Botrylloides violaceus, the pictures that I posted on my last blog entry. They are generally easy to recognize because of their huge sunburst-like ampullae and their red, orange or purple hue. They are also relatively large compared to the other early settlers that I see under the microscope.


These next two images are of a different species of colonial ascidian. This is called Distaplia occidentalis. In these photos, you can see three or four little ampullae that look like legs of a tripod in contact with the surface of the petri dish. You can also see a large cylindrical shaped structure that looks like a mesh tube. That is called the branchial basket, and it's connected to the organism's
incurrent or branchial siphon- the nozzle that sucks water into the organism.

Yet another organism that fouls my plates: the sponge. Unfortunately, I don't know the scientific name of this one. However, I do get a lot of sponges on my plates and I take pictures of them, even though they aren't as charismatic as the colonial ascidians.

Tuesday, July 12, 2011

Lance Brockie - Northwest Indian College Summer Project

First I’d like to start by introducing myself, my name is Lance Brockie I’m an enrolled member of the Gros Ventre tribe from north central Montana. I’m currently a senior attending Northwest Indian College where I’m hoping to be graduating this December with my bachelor’s degree in Native Environmental Science. After hearing of this particular internship I decided to apply for PRIME after seeing that one of the scientists who will be mentoring is Dr. Jude Apple. I had the privilege of working with Dr. Apple last summer on the Bellingham Bay Hypoxia Study here at Northwest Indian College. Throughout the summer I acquired huge amounts of knowledge while working under the tutelage of Dr. Apple. Dr. Apple makes learning fun and interesting as he really takes his time when teaching to ensure that the students really get a good understanding of what ever projects they might be working on. After working on the Bellingham Bay Hypoxia Study I took a strong interest in marine science, I came to the conclusion that the marine environment has so much to offer when it comes to learning about its varying and numerous ecosystems.

This summer I’ll be working with Dr. Apple once again in the Bellingham Bay Hypoxia Study as I’m looking forward to see what findings we will find over the summer sampling period. Also this summer I’m conducting my own study to determine if the Smugglers Slough ecosystem will be a suitable habitat for juvenile salmon in regards to the levels of dissolved oxygen levels at different location throughout the slough. When conducting my study I’ll be utilizing and comparing two testing methods. The first method will be utilizing the YSI-556 meter to check the levels of dissolved oxygen as well as other Meta data. The second testing method I’ll be utilizing will be the Winkler Method to determine the levels of dissolved oxygen using chemical reagents and titration. By comparing the two methods I’m hoping to determine what method is the most accurate when measuring levels of dissolved oxygen.

Monday, July 11, 2011

Jess - Bugs and Worms and Microscopes, "Oh my!"

Collecting our plankton samples takes only a small portion of our days. Most of our time is spent in the lab at the Naval Post-graduate School counting the samples. This means we spend hours looking through microscopes and counting zooplankton species (we have phytoplankton samples too but as of right now Alan is the only one counting them, Daniel and I will learn how once we return to OIMB), keeping track with tally marks and "clicker" counters. To keep our minds from going crazy we alternate between listening to music and Science Friday because it is difficult to hold conversation while trying to keep count. Most often we see the same animals over and over again, but every once in a while we find something exciting and everybody comes over to look in your scope to see why you're so excited.

We see worms regularly (polychaetes), but it's not very often that we find ones with tentacles. With the naked eye this guy looks like a small little speck, something you wouldn't expect to be a living is much more intimidating when looked at with a microscope. It's rather fascinating actually. The whole time I'm looking at all these microscopic organisms my brain can't help but think about all the things I've swallowed when I accidently take a big gulp of water when I'm swimming. My awareness of the water around me has definitely taken on a whole new perspective.

Drew - Gearing up for a big muddy week

Tuesday morning started with a boat ride upriver to some particularly muddy experiments in progress. Brett, Lee, Sam, Jessica and I were collecting data for Jessica's project on Dungeness crab recruitment. She had placed liter size mesh bags containing oyster shells on the mud flats at varying intertidal elevations hoping that Dungeness crabs would arrive and call it home. We recorded some information about the algae or eel grass present, collected and sieved one inch of mud within the quadrat and threw all the sample into labeled plastic bags to be sorted back at the lab. We saw a lot of small crab living in these bags and I believe she is assembling the data next week. I had a great time though it was really hard to move around in such thick black deep mud and I was definitely sore the next day.
Wednesday involved more hard work out on the flats doing some core samples for shrimp. The muddy experience of Tuesday made Idaho Flats seem like a walk in the park.
Here is Sara (left) and Katelyn digging some holes and sieving for shrimp. Don't worry I helped out too. The bucket that Sara's shovel is in, is a 60cm tall pot with the bottom cut out that we sunk into the mud. It allowed us to regulate the total area of each sample (these shrimp can burrow up 120 cm but most don't go past 60 cm). We collected ten of these and I will be doing that again sometime soon for the population assessment project.

Earlier we had done a juvenile assessment just like this one in an area where we knew the age of the shrimp but this sampling is the adult version of a variety of age classes. We will compare the two this next week and see how it effects our sampling plans.

On Thursday Katelyn and I finally tackled Lee and got him to help us with the GPS map that we had collected and here is what he created. This is showing Idaho Flat in yellow, land in grey, and water in white. The blue represents the Ghost shrimp population and the red is the Mud shrimp population. All of those dots are locations I have to visit at some point next week and collect data such as burrow holes per sq. meter, soil type, and algae type. This information will allow us to generate a new map of population densities just like the one created in 2008. You might notice that ours is incomplete. We will get to mapping the rest, don't worry.
Well the tides aren't supposed to be great for collecting data from those random points on our map till Thursday. Till then I will be learning a little bit about ARC-map, a mapping/graphing program, writing up some rough drafts for the materials and methods section of a report, practicing R, and whatever else I can get involved with.

Enjoy the week!

Sunday, July 10, 2011

Ben - Anthopleura and their algal symbionts

Hi, my name is Ben Holzman and I am an intern at SPMC (Shannon Point Marine Center) located in Anacortes, WA through the COSEE PRIME program. Since this is my first post on the site, as well as my first blogging experience period, I would like to give a brief introduction before I delve into the details of my project.

I have attended Cascadia Community College for the last two years with the intention of transferring to the University of Hawai’i at Mānoa to obtain a degree with a major in marine biology and a minor in Zoology. I learned about the COSEE PRIME opportunity through my biology teacher at Cascadia who saw the posting and forwarded the link to me. Because my future career goals involve working with Cnidarians and the symbionts which many species contain, the listing for an internship working with intertidal sea anemones and the algal symbionts they are host to seemed to be the perfect fit.

Now that my introduction is out of the way we can get to the fun part…the science! While at SPMC I will be working with Dr. Brian L. Bingham and focusing my work on two specific anemone species, Anthopleura xanthogrammica and Anthopleura elegantissima. To provide an in-depth introduction to these two species would involve writing an essay for my first post so I will only briefly compare the two.

A. xanthogrammica is the larger of the two species and while an individual can be found in close proximity to others it is a solitary anemone.

In comparison, A. elegantissima is relatively small when compared to A. xanthogrammica and is clonal which means that large groupings of A. elegantissima are can be found with individual animals in direct contact with their neighbor.

In terms of reproduction, A. xanthogrammica reproduces only sexually while A. elegantissima is able to reproduce both sexually and asexually. A fascinating point to make about A. elegantissima is that when an individual reproduces asexually it is through the process known as fission which means that if one was to look at a large colony of A. elegantissima all the individual anemones would be clones of the original anemone produced through sexual reproduction.

For my project I will be working with the anemones as well as the symbiotic algae that they host. Both species are capable of hosting two different algae which each can influence the color of the anemone itself. The two algae are zooxanthellae which appear brown and are able to tolerate greater temperature changes and the second is zoochlorellae which appear green. There also exists a state in which the anemones do not contain zooanthellae or zoochlorellae yet remain healthy.

A major focus of my project is on anemones which contain zoochlorellae. Because zoochlorellae is not able to withstand elevated temperatures as well as zooxanthellae appears to be able to we are interested in looking at the two anemone species any differences that may be present in how they interact with the algae.

In the weeks to come I will be able to go into my more detail about my project and methods as I begin to collect data. It looks to be an exciting summer and I’m looking forward to sharing it with everyone out there.

Until next time.

Friday, July 8, 2011

Sarah- Hypoxia Study

My name is Sarah DeLand and I am a COSEE PRIME Intern at Shannon Point Marine Center this summer. I graduated this month from the Ocean Research College Academy (ORCA) at Everett Community College with my Associates in Arts and Sciences as well as from Jackson High School with my high school diploma. This upcoming fall I am attending Western Washington University and I am planning on majoring in marine biology.

Last year, I knew the PRIME student Darrick Dickerson and heard about this program. It immediately caught my attention because I am interested in pursuing a career in marine research. At ORCA I was able to begin performing independent research on the concentration of the heavy metal mercury in the sediments of Possession Sound. With my current research experience at Shannon Point, I will be able to get even more experience in performing research both in the field and in the lab with people who have a background in this career.

This week I worked with my advisor Dr. Apple to begin preliminary research. I worked alongside the REU student Hannah Clark to collect data on the levels of chlorophyll a in the water column as well as the concentration of dissolved oxygen in the water around the San Juan Islands. The samples were collected using a CTD probe, which stands for conductivity, temperature, and depth. The probe gathers information on the salinity, temperature, fluorescence, turbidity, photosynthetically available radiation (PAR), dissolved oxygen, and depth in the water column. The probe is also equipped with Niskin bottles to collect water samples at depth. The samples gathered for measuring dissolved oxygen were used to analyze the oxygen consumption of the surface and deep layers of the water using Winkler titrations. The Winkler titrations were done by preparing triplicate samples immediately after being collected and preparing the final three samples after a 24 hour incubation period.

After completing the first research trip and analyzing our initial samples, I discussed the outline of the projects for this summer with Dr. Apple and Hannah. This summer, I will be working to map the extent and volume of the hypoxia in Bellingham Bay both this year and historically. The data and trends I find will be compared to the hypoxic conditions found in Hood Canal in an attempt to identify any correlations with the extent, duration, and volume of the hypoxic regions.

Wednesday, July 6, 2011

Coty Spies On Costal Birdies Week #2

Hello everybody!!! I hope all is going well and you had a happy July 4th!

Last time I blogged I discussed the basic methods of data collection I have been using to determine the effects of fireworks on a colony of birds in Depoe Bay, OR. In this post, I will explain how the general process is done and some of the observations I have made.

Starting on Jun 27 I began my "core monitoring period". During this time I have been going to Depoe Bay and surveying every day from the 7:00 am - 2:00 pm. Some days go by quickly while others seem to drag on forever! The three main species of bird that I am observing include Brant's Cormorants, Western Gulls and Black Oyster Catchers.  Starting at 7:00 am I count all the birds (one species at a time) that I can see on the rock. This count usually takes me about 10-15 minutes to finish. I repeat this count every two hours until 2 pm. In between counts I take down data such as Adult bird activity and nest contents. Some days the surveying goes really smoothly and I can collect a lot of data and others are painstakingly slow. Usually if the weather is nice the birds are more likely to move around which make its easier for me to see what they are doing and what their nests contain. However there have been a few days where the weather is very poor, and I find myself battling fog, wind and rain! On these days the birds hunker down in their nests and don't do much of any thing!.. which makes my surveying much harder to do. Fortunately in the past two weeks I have witnesses three events occur within the bird colony that have made those long days of staring through a telescope worth it...

Last week, I watched a Bald Eagle fly in from nowhere and take a gull chick out of a nest. I had no idea that there was an eagle close to the colony, until I heard the colony suddenly start making lots of distress calls. Immediately I looked all around to see what was causing it and in came the Bald Eagle! Although seeing a gull chick taken out of its nest is slightly sad, I thought it was an amazing event to watch.

This week I watched a raven pull a gull egg from an unattended nest, break it open and begin to eat the unborn gull chick. The parents then rushed in to save the egg, but it was too late. As the raven and the parents were playing tug-of-war with the contents of the egg, another adult gull came to the scene and stole the unborn chick from the parents and the raven, and then took it to its nest and fed it to its own chicks! yikes!!!

Lastly, one day as I was staring at a nest I saw a parent gull stand up and look down at it's egg. The egg began to move and all of a sudden a beak popped out and a chick stared coming out!

As mentioned before the primary focus of this survey is to determine if the 3rd/4th July fireworks displays in Depoe Bay disturb the colony. Everything that I have discussed so far has been leading up to the fireworks display. As of right now I have not been able to analyze the data that was collected that night, so I will not be able to discuss the results of the survey until next week. However I will mention that two nights ago the fireworks flew in Depoe Bay and data was collected using infrared cameras and audio recording equipment. From the simple observations made that night by biologists and then me the next morning, it seems that the fireworks had a minimal affect on the colony of birds, but this is speculation and not confirmed yet.

On a side note, I have not posted pictures of my experience yet because all the pictures that I take or use while working for the USFWS, belong to them. Since they are government property I have to get clearance/permission to display the photos publicly. I hope by next week I will be authorized to do so!

Tuesday, July 5, 2011

Akiko: Petri dishes in the ocean

Hey All, Akiko here. So I spent most of the first week researching and designing my project, and during the second week I got to finally start implementing it. After a lot of planning I figured out a way to catch some pictures of microscopic settlers as they mature.

First I sanded the surface of a few petri dishes in order to make an abrasive surface. Supposedly, invertebrate settlers find the roughened surface more appealing to attach to. Then I attached velcro strips to the back of each petri dish with glue. I put longer strips of velcro on a large rectangular plate. This large rectangular plate has four holes drilled into it and rope tied to it, such that it can hang from a dock and be suspended in the water column. After lots of preparation, I attached my petri dishes to the backing plate and lowered them into the water for a few days, checking them every day.

I kept track of individual organisms by making a small grid that can fit over each petri dish, so that I can track their location and confirm that it's the same organism. It's very hard to keep track of them when they are so small! Every day, I took a photograph of each invertebrate settler. I have found that it is difficult to get good images when you're taking a picture through a microscope, but with some lighting adjustments and Photoshop help, I hope to get images that could be used for identification.

These images are all of the same organism. I'm pretty sure that the scientific name is Botrylloides violaceus. I have had quite a number of these settle on my petri dishes. They are easy to identify because of their ampullae: the sunburst-like ring around them.

Monday, July 4, 2011

Jess - Sometimes We Have To Adjust

To collect samples of zooplankton and phytoplankton from the surf-zone we use a pump that sucks water up from the surf through a hose. The zooplankton (animal plankton) is concentrated in a plankton-catch net and put in samples jars that are to be counted later. The phytoplankton (photosynthetic plankton) samples are collected by filling bottles with the water that we are sucking up with the pump and are then fixed with iodine. So we don't have to hold the hose out in the surf everyday when we are collecting the samples (which could be pretty risky and dangerous) we put a line of poles from the middle of the surf-zone to midway up the beach to secure the hose to with u-bolts and brackets. We did this the week of June 12th, and as you can see from the picture it took a number of people to do it successfully. Because the ocean is very powerful and constantly changing the physical structure of the beach and moving the sand, this last week two of our poles became dislodged.

We needed to get the poles back in as soon as possible and because it is difficult to get the poles in while getting pounded by waves we needed to do it at the lowest tide possible, which just so happened to be at dawn. We arrived on the beach before daylight and got to work. It was early and chilly but we got to see this amazing sunrise. The picture doesn't do it justice. Watching it rise in the company of a bunch of awesome people made me happy to wake up in the dark and start work at dawn.