Thursday, August 23, 2012

Unforgettable Summer

Thought the sun set on my time at Shannon Point I will never forget it.
     What an amazing life affirming experience I had this summer with COSEE at Shannon Point Marine Center.  My only disappointment was that it went by way too fast and I was packing to return home before I knew it.  Luckily I'm not truly finished yet and still have some writing to do and most likely a conference with my adviser, Dr. Dinnel, in the near future. Plus, as I live close, I will return to volunteer on the continuing Olympia oyster restoration project monitoring whenever I can.  I plan to continue helping Denise Crow with any outreach projects that I can as well, which is always so much fun.
     This program reinforced my decision to make a huge life and career change moving from law to science.  Everyone I had the good fortune to interact with this summer was so amazing, friendly, helpful and excited about science.  Not only did COSEE help me become confident and comfortable in my decisions I was lucky enough that Shannon Point Marine Center is part of Western Washington University where I was accepted and will start in the fall.  I feel like I really have a foot in the door and more understanding of my program of study and the opportunities available to me at an undergraduate student.   I also am already planning to apply to be an REU student next summer, something I may not have done without this summers experience.
     When our final numbers were crunched it is evident that the oyster restoration project is  considered successful, a very happy moment for me.  Between this project and the City of Anacortes working to clean up their entire waterfront from historic mill operations the area is, and will continue to, recover ecologically.   Additional sites have shown to be promising as well and oyster seed will be planted this fall or next spring. 
     Thank you COSEE for an unforgettable summer and life affirming experience I will carry this forward with me using all I have learned to be a better scientist.

Crista working her magic with a camera older than herself.
Crista's installation, everyone's pictures and cyanotypes.
The wonderful students I was lucky enough to spend the summer with.
My individual shot. I love it!
The end of one adventure simply signals the beginning of another.


Tuesday, August 21, 2012

Such an amazing summer! Thank you, COSEE PRIME!

I'm not sure where to start...

This COSEE PRIME internship has offered me way more then I could have asked for. My experiences have ranged from helping grad students with literary searches, clamming on the coast line for the city of Newport, experimental design, all the way to captaining a research outing out on the ocean! My mentor, Vince Politano has offered me so many valuable perspectives and helped me to lay a solid foundation for future learning/research in the sciences. He has been an invaluable part of my learning this summer. I never felt like my experiences or training at Hatfield Marine Science Center (HMSC) were over my head, yet I was also challenged quite often this summer. I was also very glad to have some honest feed back on my strengths and weaknesses. Knowing ones own strengths and weaknesses is quite valuable when trying to move froward within their career, and this internship has surely helped me to gain prospective and direction to continue to build upon my strengths and develop my weaknesses.

HMSC has a great community feeling to it and I felt quite at home. A special thank you to Itchung for being very understanding and helpful while helping to balance my schedule, he truly contributed the the success of this summer. Coral, the OIMB COSEE mentor, has also gone above and beyond to make my journey here an amazing one.

I'll walk away from this summer with a wide range of skills! I'll also walk away with some great friends! All the other interns here have been great, and it has been a pleasure living with so many like minded people. I can only hope that my future endeavors will be half as successful and pleasurable as this one has.

Many thanks to everyone that played a part in making this summer one of the best of my life!



P.S. Perhaps some photos from this summer?

Thank You COSEE

Well that’s it, my summer with the COSEE program has come to an end and I am heading home. I am going to miss the community at Hatfield Marine Science Center and all of the members of the COSEE group. As I leave, however, I take with me the skills that I have learned and memories that will last a life time. I am so grateful for the COSEE program. What an amazing opportunity for a community college student to gain experience in scientific research and presentation. Every time I tell someone about this program they say, “I wish they had had a program like that when I was in school.” For me the opportunity was priceless and I would strongly encourage anyone with an interest in science to apply. Thank you COSEE.

Wow, Week Eight!

Wow. I can’t believe this journey is almost over. It’s week eight and we are still going strong. This week we went out to the Siletz River and collected snails. Many trematodes use a snail as an intermediate host and are released as cercaria. We collected two types of snails and placed them in petri dishes with a bit of lettuce and observed them as they released the cercaria. There isn’t really a way to predict what type of cercaria will be released, so every petri dish holds a surprise. Below is one of the cercaria that we found; it is nicknamed medusa for obvious reasons. It is composed of many single cercaria that attach themselves to each other at the tail. When they are ready to continue their life cycle they release and exist as single organisms.

Here is another trematode cercaria. One snail released thousands of these guys. They look like little pieces of ribbon in the bottom of the dish until they decide to move, and then they become more cylindrically shaped and move in a rapid figure eight motion. Watching a large group of them swim is hypnotizing. 

Here is a picture of the parasite that I’ve been studying, Nanophyetus salmincola. This is a picture of it in its cercarial stage. You can see in the picture that its tail is still attached, but when it enters the salmon it detaches and the body encysts.    

Snailing was fun but I have a presentation to give on Friday and I still have data to enter. Looking back at the pages of data that I have produced during this internship reminds me just how important it is. This is the first time this data set has been looked at, and once it is fully analyzed it should be very valuable in understanding the bigger picture of juvenile salmon habits.

Monday, August 20, 2012

Keira- Summer Reflection

This summer was a great learning experience for me. In addition to getting to play with lasers all summer, I learned to use really complex, valuable pieces of equipment such as the confocal microscope. The process of designing and carrying out experiments is different in a research lab from the classroom lab. There are more opportunities to make mistakes when performing an experiment that did not come out of a lab manual, but its also much more fun to be actively discovering new information. The most important skill I learned this summer was how to interpret data and look for patterns. My mentor was particularly adept at teaching me how to interpret experimental results. He gave me the opportunity for me to analyze the results on my own but also offered the support of his vast knowledge. I felt as though I was actually "doing" science this summer; it was inspiring and really fun. I would recommend applying for this internship to any community college student with a passion for science. It is great experience to prepare for graduate school and help you decide if you want to go to graduate school. I particularly like learning actively rather than out of a textbook and this internship was a great opportunity for that. 

Friday, August 17, 2012

Last few weeks in the field

The last few weeks provided us with some great conditions for field work, followed by this final week of dense fog allowing us to spend time in doors organizing and studying the data.  A few of our days out in the field we were lucky to get close to some of the resident gray whales that feed along the rocky shoreline outside of Sunset Bay.  I was surprised to see the whales so close to the rocks, with a few we saw appearing to be right up against some very shallow outcroppings, as if they were scratching their sides on the rocks!  I was told later that they were feeding on mysid shrimp found in the kelp beds, a behavior that the resident whales have adapted to the local habitat.
       We were able to get three days of field work in the week of the 25th along with a set of plankton samples on a day the front was clearly present at Sunset Bay.  It will be exciting to see how are samples differ from each other.  Samples were taken shoreward of the foam line at three different depths including the surface, offshore of the foamline at the same depths, and within the foamline  at the surface.   Up until now I wasn’t  sure of what the cause of the foam along the front was but was surprised when told that it is due to the release of lipids from certain plankton when they breakdown.  The break down of these organisms can actually be caused by the forces created at the front between the two water masses and also along the rocks where wave disturbance causes a lot of breakdown, producing large amounts of foam.   
On the week of the 6th winds had shifted to the south for a few days, giving us the chance to do some field work during downwelling favorable winds.  We were surprised to see that a foamline was still present and it was the first time that our drogues at 5.5 meters depth both traveled offshore, with the inshore drogues crossing the foam line.

Thursday, August 16, 2012

Short Reflection

This internship was a great opportunity for students at community colleges to experience a research facility before they decide if thats where they plan to continue their education pathway. This internship opportunity may open doors for students that plan on being scientists because they meet incredible people and learn how to conduct research. I encourage students to think about this internship opportunity because it could really change your mind or help you understand research in marine sciences. I am glad that I applied to this internship because it helped me gain more knowledge in ocean acidification and how important this research is for the future of marine environments.

Project Summary

The last week or so we have made some more changes to our systems. We even got the other two systems going like the one system we had running with CO2. We havent added CO2 to any other systems yet because we are still trying to get them to keep the gas in the water. To keep gas dissolved in the water is such a hard thing because we have flow thru water at Hatfield. The pH is different every day and the incoming water is always different than what we try to keep the pH at. The pH of seawater should be 8.1 and yesterday it was at the lowest 7.59 so we had a lot of experimenting to get the pH up to what we want. We changed the design in the sump to a much easier and effective design.

Before on left. After on right.

As you can see the newer design is much easier to look at and follow. We still have the white cylinder which was used as a countercurrent system, which has an air diffuser stone at the bottom and inflow of water at the top. This process helps incorporate the gas into the water. We ended up taking it apart and removing the gas going into the cylinder and adding a venturi to the inflow of water to the cylinder. The venturi adds the gas into the water before going into the cylinder. We also added one to the tubing that goes to a canister filter which leads to the systems with the algae in them. Adding the venturis to the system improved the amount of gas going into the water and changing the pH of the water more effectively. This is the end of the internship and its crazy to think its over tomorrow. It went by fast and I enjoyed this experience.

Chris - PRIME 2012 Reflection

The PRIME 2012 internship has been a tremendous experience for me. I have gained a wealth of insight into marine science and its careers, research opportunities, benefits, and drawbacks. I've also learned a great deal about the different methods of scientific research, how scientists operate, and the workings of a marine science station like OIMB. Most importantly, I have gained actual, hands-on experience performing science in the laboratory. This should aid me immensely in my future academic and occupational pursuits For these reasons, I would highly encourage other community college students to participate in the PRIME program. It is an excellent opportunity to gain invaluable research experience and to explore one's career, especially considering the limited availability of such programs for community college students.

Tuesday, August 14, 2012

Chris - Week 7: Final Scans and Project Summary

During Week 7, I concluded my project by examining two additional age groups with the scanning electron microscope. This time, I looked at 25 hour old and 36 hour old cohorts. My goals were to create cleaner specimens to scan (particularly with the 25 hr) and to observe any intermediate characteristics in the 36 hr group.

I was only partially successful. I avoided the globular objects that plagued my previous scans, only to find larger geometric objects. While interesting, they are just as vexing as the debris from last week. For whatever reason, these crystals were only present on the 36 hour specimens. On a more positive note, the 25 hour old group was very revealing, and the 36 hr group was more similar to the 48 hr than I would have guessed.

Figure 1: Posterior view of a 25 hour old
M. alaskensis larva
Figure 2: Angled anterior view of a 25 hour
old M. alaskensis larva

In Figure 1, note the indentation in the center of the specimen. This will continue to invaginate as the larva transitions to a pilidium, forming the esophagus and gut through the process known as gastrulation. Figure 2 shows that the apical organ is already forming at 25 hours. It is not clear from this image if the apical tuft is also present.

The specimen shown below in Figure 3 is covered with relatively large, geometric objects that have not been identified. Figure 4 shows the apical organ, which is rarely seen in this detail (cilia normally obscure it). Also note the relatively well developed apical tuft. Both specimens appear more similar to the 48 hour age group than they do to the 25 hour.

Figure 4: Angled anterior view of a 36 hour
old M. alaskensis larva
Figure 3: Posterior view of a 36 hour old
M. alaskensis larva

So that pretty much concludes the data collection phase of my project. I have examined M. alaskensis larvae from between 10 hour and 3 weeks of age over the course of this summer, utilizing both confocal and scanning electron microscopy. Now in the final week, I have to organize this large collection of micrographs and observations into a coherent and at least mildly interesting presentation. Wish me luck! 

Monday, August 13, 2012

Keira- Final antibody tests (Week 7)

Last week I showed you photographs of larvae stained with the phosphohistone antibody. This week, I'll discuss my findings about two more fluorescent antibodies I tested. A few weeks ago, I discussed the process of fluorescent antibody staining; I'll give you a quick recap now. First, the (already fixed) larvae are soaked in a primary antibody. This antibody has been developed to bind specifically to certain proteins of interest. After rinsing the primary out, the larvae are soaked in a secondary antibody. This fluorescently labeled antibody binds specifically to the primary. When excited with laser light, the secondary antibody will fluoresce, thereby showing us the location of the primary antibody.

The first antibody that I will be showing in this week's post is a MAPK (mitogen-activated-protein-kinase) antibody. MAPK refers to a key signaling pathway through which the cell responds to external stimuli. The antibody I tested is called p44. This will tag a certain "flavor" of MAP's; this "flavor" is the "44" part of the name. The "p" denotes that this antibody will tag the phosphorylated proteins. That is, only the activated proteins that are actively involved in signaling will be shown.

The first picture shows a D.excentricus larvae that has been stained with the p44MAPK antibody. This gives us a baseline for what the antibody looks like and what kind of signaling it is involved with in a normal, untreated larva.

The next photograph shows us a larva that has been deciliated. This is achieved by soaking the larvae in seawater at two times its normal concentration, which sends the larvae into hypertonic shock and causes them to lose their cilia.

 The p44MAPK signaling pathway is clearly activated by the stress of deciliation. We see much brighter labeling along the ciliary band as well as some illuminated skeletogenic cells.

Another antibody I tested was a SAPK or stress-activated-protein-kinase. It is in the family of MAPK and is activated by a variety of environmental stress and growth factors, among other things.

This is a photograph of the untreated larvae labeled with the SAPK antibody. The edges of the epithelial cells are illuminated, giving the larva a lace- or spiderweb-like appearance.

This larva has been treated with the same deciliation process. The deciliation appears to activate the SAPK signaling pathway as well. The ciliated band is bright and well defined. As the majority of cilia-possessing cells are located in the ciliated band, it makes sense that labeling in the ciliated band would be brightest because the effects of deciliation would be more pronounced where most cilia are located.

Research on the Centennial

For me, field research has to be the ultimate lab that one can have.  Spending time on the Centennial and working the CTD is a great opportunity.  It is the hands-on research that I think that I learned the most from.  But it is also being in environments that I'm studying seeing the beauty of the San Juan Islands and the waters that surround brings value to the research that I am doing. 
With the CTD we are able to take and activity temperature and depth readings.  The program gathers information on the salinity, temperature, fluorescence, turbidity, photosynthetically available radiation (PAR), depth in the water column and dissolved oxygen.  We also gathered water samples using the Niskin bottles at various depths.   From the samples gathered we are able to test for nutrient levels in the water but also to check for dissolved oxygen.

Many of the samples were taken right after the CTD came out of the water.  By filtering them from the Niskin and storing the filters for further lab testing.  Other samples are taken to the galley and ran through a larger filtering system.  It made it fun to try and run the filtering system when we hit rougher waters going out to the further parts of the Strait of Juan de Fuca.  To be honest, the rough waters were kind of hard on me and I had to go a top for air.  But these are the sacrifices one has to make.

 I’ve attached a video showing the CTD in action.  Sorry for the volume, you may have to turn up your speakers.

Thursday, August 9, 2012

New Parasites!

This week has been a lesson in parasite morphology. It has long been speculated that parasites in hatchery fish may be different than the parasites in their wild counterparts. In theory fish that develop in wild waterways consume the many invertebrates that carry trophic parasites. As the fish take advantage of this food source they take on passengers in their digestive tracts. Hatchery fish eat primarily pellets that they are fed and rarely have the option of consuming invertebrates. The first step in supporting this theory is gathering evidence.

The process of gathering this information is similar to the other parasite collections that we have done in the past. Coho salmon are retained from a hatchery (in this case one on Bingham Creek WA.) and wild ones from a nearby fish trap (also on Bingham Creek). The fish are examined under a dissecting microscope for signs of scarring, possibly caused by parasites entering through the skin. The weight and length are recorded, and the fish is dissected.

 In the past the organ that I have been involved in analyzing is the kidney. The dissection of these fish in this case also includes the stomach and intestines.
Great care needs to be taken when opening up the stomach and intestine because any parasites that are found need to have their location in the digestive tract recorded. It is also important to correctly identify what species the parasites are. At first they just look like many tiny grains of rice, with little to tell them apart, but with a keen eye (and some guidance) one can began to decipher the morphological code. Below are a few examples of what a person can expect to find in a coho salmon from Bingham creek.

Crepidostomum sp. Is identified by the half crown of two to six papillae, this gives the appearance of cartoon like ears. It is long and oval in shape and like the other parasites we look at they have two suckers.

Deropegus aspina. The body of Deropegus is slightly elongated when compared to the other parasites present. The most defining feature is the presence of vitellaria in two compact masses near the posterior of the trematode.

Plagioporus shawi. This parasite has a slightly flattened body, it is elliptical in shape. One of the defining features is a pair of testes visible in the center of the body. 
 In the end we hope to find a correlation between the parasites and where fish reared to better understand the importance of rearing strategies on trohpically transmitted parasites. For now I will work on honing my skills in identifying these little guys.

Wednesday, August 8, 2012

Chris - Week 6: SEM and Early Pilidia

During Week 6, I examined three new age cohorts; 21 hours old, 27 hours old, and 48 hours old. I used both confocal and scanning electron microscopy, in part to compare the results produced by the different techniques. I found that the 21 and 27 hour age groups were remarkably similar to the 15 hour cohort, both in shape and cilia distribution. The 48 hour age group was much different however, taking on the form of a pilidium rather than a disc.
 Unfortunately, this week was also fraught with difficulties. The confocal staining did not go as expected, producing results that are not worth sharing. I had better luck with the SEM specimens, although I did run into some problems with them as well. Some of the specimens, and all of the 27 hour, were covered in many small globular structures that we can't identify. Needless to say, such filthy specimens do not make for good images (at least not when the objects cover the structures being examined, i.e. cilia). 

Figure 1: A posterior view of a 21 hour
old M. alaskensis larva

Figure 2: An angled side view of a 21 hour
old M. alaskensis larva
 In Figures 1 and 2, note the somewhat "domed" shape of the specimens, as well as the patchy distribution of cilia. Figure 3 below shows the now characteristic bald patch, where Figure 4 shows that even the anterior portion is not completely ciliated after 27 hours. Svetlana believes that many of the bald patches seen so far in the 12.5 - 48 hour stages are centers for cell division, and thus larval growth. Only cells that are either mono-ciliated or are not ciliated at all can divide and reproduce; multi-ciliated cell are incapable of dividing. Also note the many globular objects covering the specimens. Their origin is unknown.
Figure 4: An anterior view of a 27 hour
old M. alaskensis larva

Figure 3: A posterior view of a 27 hour
old M. alaskensis larva

Figure 6: A posterior view of a 48 hour old
M. alaskensis pilidium

Figure 5: A side view of a 48 hour old
M. alaskensis pilidium

Figure 7: An anterior view of a 48 hour
old M. alaskensis pilidium 

The specimen of Figure 5 displays the characteristic shape (albeit developmentally early) of a pilidium. Note the beginnings of a ciliary bands along the posterior, of which Figure 6 shows in more detail. Figure 7 shows the apical tuft of the pilidium, which is the bundle of long cilia at the anterior-most portion of the specimen.