Wednesday, August 28, 2013

Zac - Summer Reflection

This summer has been quite a learning curve for me and an absolutely priceless experience. I traveled to the Oregon Institute of Marine Biology during the summer of 2013 to work in the Maslakova Lab with Dr. George von Dassow on performing gene knock-downs in the nemertean Micrura alaskensis. I came to the Maslakova Lab with no experience in the field of embryology, other than a handful of research papers to read, but was immediately greeted with a lab full of highly intelligent people that were willing to take time out of their own research agendas to show me the ropes. I didn't even approach my own research topic for at least a week after arriving at the OIMB, simply because there were so many preliminary skills to learn before I could do so. Some of these skills included the identification and collection of wild-caught Micrura alaskensis, some fertilization and culturing techniques, the basics of loading and employing the microinjection apparatus, how to take the perfect picture using DIC and epifluorescence microscopy, and of course the basics of laser scanning confocal miscroscopy.

Once I actually did start into my summer research project, I was immediately immersed within the scientific method in a way that I had never experienced before. My summer research project involved analyzing gene function in early M. alaskensis larvae by using morpholino-mediated gene knockdown. There are a number of factors involved in this research, both technological and biological, and it immediately became clear that I would be spending a large amount of time carefully checking and cataloguing my work. The process of tracking an experiment from beginning to end, and carefully cataloging the result, is something that every young scientist should experience, and the sooner the better.

This internship has also given me the opportunity to experience the life of a research scientist from multiple perspectives. For example, working closely with my adviser and his long-time collaborator, Dr. Bill Bement, allowed me some brief but insightful glimpses into the way that research is performed over the long term. Working with Dr. von Dassow and Dr. Bement have also given me some insight into the way that scientific literature is published and how collaboration occurs between scientists, even over great distances. I have also had the opportunity to work with Ph.D. students Laurel Hiebert and Terra Hiebert, both of whom have been working in the Maslakova Lab for over a year, and gain insight on the life of a hard working Ph.D. candidate.

Internship programs for community college students are few and far between, and I feel extraordinarily lucky to have been chosen to be a part of the COSEE PP-PRIME internship program. The caliber of research being done at the OIMB is unlike any that I have ever had the opportunity to experience before and being a part of it has already opened many professional doors for me. For example, this internship represents the first time that I have ever had the opportunity to present work that I have done to a live audience composed of senior researchers and Ph. D. students. It has also opened up the reality of traveling to Austin, Texas, in the Spring 2014 to co-present a poster at the Society for Integrative and Comparative Biology (SICB) annual conference. This truly is a once in a lifetime opportunity that I certainly never expected to be able to achieve when I began this internship eight weeks ago. Not only has this internship supplied me with a plethora of professional skills, both mental and physical, but it has also supplied me a number of professional relationships that are likely to last well into my career as a scientist.

I would recommend the COSEE program for absolutely any community college student, whether you are specifically interested in marine biology or not. Programs like these are instrumental stepping stones for young, budding scientists and are absolutely crucial in helping the unsure find their way through the large complicated world that is the sciences. Are you interested in doing research? There is only one way to find out: get involved. 

Zac - One last adventure blog

Giant Green Anemone - Anthopleura xanthogrammica
With a summer of research behind me now, I have had a little bit of free time to wander around the Oregon coastline and experience some of the scenery.  My fellow intern, Cris Rangel, and I immediately took advantage of this free time by renting an outfit of SCUBA gear and immersing ourselves in the murky Oregon waters. Visibility was limited to just a couple feet but fortunately, being biologists, we were perfectly happy to keep our noses pressed to the holdfasts analyzing the incredible invertebrate biodiversity on these rocky shores. We did our first dive at Simpsons Reef (which involved a good ten minute walk in full SCUBA gear) and our second dive at OIMB beach. 
Sea Lemon - Anisodoris nobilis

Both of these locations offered a number of targets for our borrowed underwater cameras (thank you Richard Emlet!) but the images above and to the left were surprisingly the only ones worth sharing from Simpsons Reef. As it turns out, it is quite difficult to work a small camera while wearing 7mm gloves and the surging current certainly didn't help. OIMB beach, seen below, was far more conducive to underwater photography. As you can see, this is a picture perfect entry point and I think that we enjoyed this dive the most purely due to ease of access. 

A great day for diving at OIMB beach, the kelp forest dead ahead is our target location.
Dungeness Crab - Metacarcinus magister
The dive off of OIMB beach features a sandy bottom peppered with numerous dungeness crabs. The image to the right is a picture of me holding an especially large dungeness. The male crab (see the telson in the image at right) was holding onto a presumed female crab in a characteristic pre-mating display. These crabs can only successfully be inseminated immediately after molting so a male will hold onto a female - sometimes for several days - until she molts, at which point he will inseminate her. Other notable marine invertebrates included a number of "Crawling Beauties" (Janolus fuscus) - a relatively common aeolid nudibranch (below left) - and what appeared to be the siphons of many  rock boring clams (Penitella penita).
Rock Boring Clam - Penitella penita
Crawling Beauty - Janolus fuscus
These clams feed by extending their paired siphons into the water current to feed.  Water is drawn into the shell where both oxygen and nutrient rich particles are extracted. The incurrent siphons of these clams are decorated with branched projections that distinguish them from the simple circular opening of the excurrent siphon.

One last view of the Oregon coastline
After our diving it was time for Cris and me to head back down the coast to Santa Barbara, but not without making some stops to admire some of the coastal wildlife. We did not have to drive long before a gang of elk along the side of the road attracted our attention.

Roosevelt Elk - Cervus canadensis roosevelti
The Roosevelk Elk is the largest remaining subspecies of elk. The adult bull seen left is absolutely enormous; the antlers alone were at least the size of my torso. This particular gang (herd) of elk had at least 20-30 cows and a handful of young males. Our next target location was The Avenue of the Giants - in Humboldt Redwoods State Park. A quick walk down from the side of the road led us to a little hidden paradise featuring a broad, meandering stream filled with underwater biting things - as Cris can attest to - and lined with old growth redwoods. Of course my attention was immediately drawn to the plethora of insects.

Cardinal Meadowhawk - Sympetrum illotum
The image above features a dragonfly while the image below features a damselfly. These are both basal insects winged insects (evolutionarily speaking) and are relatively closely related to one another.  Both adult forms share fairly similar ecological niches but can easily be distinguished from one another.  As a general rule of thumb (but certainly not always) dragonflies are larger and spend more time flying while damselflies tend to flit from perch to perch, spending much less time flying. The most distinctive difference, however, is the way that they hold their wings.  Neither insect are capable of folding their wings over the abdomen the way the neopterans ("modern" insects) do, but damselflies hold them up above the thorax while perched and dragonflies hold them down horizontally.
American Rubyspot - Hetaerina americana

The images above and below feature the exact same species of damselfly (and if I remember correctly, the exact same organism) and both pictures were taken with more or less the same camera settings.  The significant difference in coloration of the insect between these images is purely due to the angle of light. This structural coloration is due to wave interference and depends strongly on the angle of viewing in relation to the angle of light
American Rubyspot - Hetaerina americana
The "pseudopupil" seen in the dragonfly below is not a true pupil, but rather a collection of photoreceptors (ommatidia) that are all collecting the light that would otherwise bounce off of the dragonfly's compound eye and be absorbed by your own photoreceptors. Essentially the pseudopupil represents the cluster of ommatidia that are all aligned directly with your own optical axis, so, this pseudopupil will be present no matter what angle you look at the eye and it will always seem to be looking directly back at you... creepy.
Cardinal Meadowhawk - Sympetrum illotum
We also found a cool praying mantis at a gas station in the middle of nowhere... here is a picture (check out those pseudopupils!)

European Praying Mantis - Mantis religiosa
Okay, enough nerding out for now, on to the next blog!

Zac - summer research recap

A quick recap of the summer’s research: I have been working in the Maslakova lab under my immediate adviser, Dr. George von Dassow, and Ph.D. student Laurel Hiebert. The Maslakova lab is very interested in studying the evolution and development of the pilidium larva, a distinctive larval form of ribbon worms (Phylum Nemertea) in the clade Pilidiophora. This larval form originally develops as a highly ciliated, hat-shaped larva, which eventually develops into a juvenile worm within its blastocoel. This juvenile worm forms as a result of the growth and intercalation of a number of distinct stem cell bundles (imaginal disks) that eventually fuse around the larval stomach. The result of this developmental pathway is a swimming larval form containing a digestive system that terminates inside of the juvenile worm. Since the larva and juvenile are essentially connected at the mouth, the transition from free-living larva to free-living juvenile culminates in a "catastrophic metamorphosis" in which the juvenile inverts the larval body and swallows it in the process. This mode of development is unique in the animal kingdom, and the fact that it appears to have evolved from a direct developing ancestor make it all the more interesting.

Pilidium developmental sequence, age increases to the right - images by Svetlana Maslakova
In order to study the evolution and development of the pilidium larva more thoroughly, the Maslakova Lab has identified Micrura alaskensis as a model organism. M. alaskensis makes a good model organism because it is readily available and easy to keep alive in the lab. The oocytes are easily obtained and fertilized externally and the resulting larvae can be reared through metamorphosis in a reasonable amount of time (six to eight weeks). Dr. Svetalana Maslakova has already done a very thorough job describing the development of M. alaskensis, and Ph.D. student Laurel Hiebert has recently constructed a high quality developmental transcriptome, which are essentially a list of genes that are expressed in the early development of this species. My summer project involved inhibiting the translation of four of these genes by using morpholino injections. Morpholinos are a fairly common tool in modern molecular biology to study genes by using a "loss of function" approach. This approach is somewhat analogous to studying an automobile assembly line by kidnapping a worker at the beginning of each work day and seeing what happens to the cars at the end of the day as a result. If the cars came out of the factory at the end of the day missing the rear windows then one could reasonably argue that the worker in question was responsible for installing these windows; and furthermore, that the installation of the rear windows is distinct from that of the front windows (logic by Bill Sullivan).

Morpholino treatments have never before been performed in this species of nemertean, and so one of the first big questions was simply: "Will morpholino treatments work?" We proceeded to tackle this question by performing a positive control: an experiment with a known outcome used to determine if things are working as we had hypothesized. In order to do so, we repeated an experiment published by Henry & Martindale (2008) that involved knocking down the production of beta-Catenin in a related nemertean - Cerebratulus lacteus. Henry and Martindale reported a lack of gastrulation and excessive apical tuft formation in C. lacteus. We were easily able to distinguish these same features in M. alaskensis, validating the assumption that the morpholinos we are using are targeting the genes that we think they are targeting.

b-Catenin morphant phenotype in C. lacteus (left) vs b-Catenin morphant phenotype in M. alaskensis (right)
Our next target was the Intra-Flagellar Transport 88 (IFT88) gene. The IFT88 gene product is supposedly crucial for the formation of cilia, and since M. alaskensis larvae are covered in cilia, we thought that it would be awfully nice to be able to knock out cilia production for the purposes of live (video) imaging if nothing else. Unfortunately, this morpholino did not work in the way that we expected it to work. Not only did we observe more or less perfect cilia formation but the larvae ultimately developed a nonspecific and overall unhealthy looking phenotype. The most likely explanation for this is that the morpholino knockdown was not 100% effective—we know for a fact that it never is—and that these larvae are still capable of developing cilia with whatever remaining IFT88 protein that manages to be produced. It is important to note that this result does not actually contradict our positive control. This experiment has never been performed previously and it is impossible to say that the nonspecific—and generally unhealthy—phenotype resulting from this morpholino treatment was due to nonspecific morpholino toxicity and not IFT88 knockdown. Since this morpholino did not do what we thought it would do, we decided to abandon it for the time being and move onto bigger and better things.

The next gene of interest is called the Mitotic Kinesin-Like Protein 1 (MKLP1) gene. The MKLP1 protein is crucial for cell division in all animals previously studied. That being said, clearly there must be some amount of it provided in the oocyte prior to fertilization in order for first cleavage to occur. Since we can only knock down the production of future MKLP1, we were curious to see how many cleavages our morpholino treated embryos could undergo before they depleted the endogenous MKLP1 and failed to complete cytokinesis. The movie below shows a 16-32 cell M. alaskensis embryo attempting to undergo cell division and failing. If you watch the bottom cells closely, you can see the cells almost complete cytokinesis before they fail to achieve abscission and relapse to become one cell instead of two. This is characteristic of MKLP1 depletion as seen in human cells, and other animal cells, and indicates that the endogenous MKLP1 present in these oocytes is only sufficient for three or four cleavages before it is depleted.

The brightly lit cells near the top of the frame serve as a positive control. These cells never received morpholino treatment and subsequently have no problem undergoing cell division.


I have also spent a great deal of time learning to use the confocal microscope to image both fixed and live larvae stained with various fluorescent markers. By using fluorescent stains that not only bind to different tissues or sub-cellular components, but also fluoresce at different wavelengths of light, we can use the confocal microscope to put together high quality images with different tissues or sub-cellular components marked with different colors.

M. alaskensis Pilidium Larva - Oral View (Image by Zac Swider)
For example, the image above shows a confocal z-projection of a M. alaskensis pilidium larva (oral view) composed of about 130 individual images stacked together. This compilation of images shows actin filaments (stained with phalloidin) highlighted in grey, DNA (stained with Hoechst 33342) highlighted in light blue, and cells actively undergoing division (stained with an anti-phospho-histone antibody) highlighted in bright green. I have been using these staining techniques, in concert with the confocal microscope, extensively over the past couple weeks in order to more thoroughly characterize the effects of one particular morpholino treatment. Unfortunately, due to the sensitivities of unpublished data, I will not be going into any more detail than that. Come to the annual SICB conference in Austin, TX, Jan 3-7 2014 to hear the whole story!

Sunday, August 25, 2013

Kaylynne - Reflection

I cannot believe how quickly this summer has flown by. Many thanks to the National Science Foundation, COSEE Pacific Partnerships, and the Oregon Institute of Marine Biology for this incredible program. I hope it continues for many years to come.

The day I was offered this internship was one of the most exciting days of my life which sounds silly I know, but these types of opportunities are rare and I was thrilled to have been accepted. Its not everyday that programs like COSEE are offered, let alone to community college students, so when you find an opportunity like this you just have to go for it. I have met many students and interns here at the Oregon Institute of Marine Biology that are not sure if marine biology or ocean science is the direction they want to go in life, but they are out here because they want to get their feet wet (literally) and see how it is to be in the field actually collecting data and conducting research.

It has been so much fun and I am lucky enough to be able to stay an additional month as a student employee through the University of Oregon for the Shanks Lab, covering Marley's work while she is away. I would have never thought that this internship would have opened doors so quickly for me, but it did and my gratitude is beyond comprehension.

My best advice to the current community college students out there is to keep your undergraduate degree broad and explore all of the possibilities that an overall science degree has to offer. Try something out of your comfort zone and apply for programs like COSEE. Why not find out what you like and what you don't like? It has been an experience I will never forget and it is hard to communicate how awe-inspiring my time here has been. I have made many new friends from all over North America, gained lab and field experience, met renowned researchers and had a blast while doing it. It is perfectly okay to be nervous coming into something like this, but you only live once and you have to take advantage of every opportunity available to you.

Left to Right: Jessie, Corey, Sol, Robbie, Sam, Payton, Hannah and myself!
Oregon Institute of Marine Biology
Summer 2013

Kaylynne - Catching Up!


I have been horrible with writing my weekly blog posts and I sincerely apologize. To make up for it, I will post bits and pieces of what I have been doing this summer. I have been working for Dr. Alan Shanks and the Shanks Lab graduate students, researching nearshore biological oceanography and larval recruitment. To be more specific, I have been working mostly for/with Marley Jarvis, who is a PhD candidate in the Shanks Lab. Marley's research is looking into the effects of nearshore fronts on the settlement of algae propagules and barnacle larvae, known as cyprids. She has taught me how to collect physical data for her research while she is on leave for over a month. It is pretty exciting that I was given this opportunity, trusted with her research and I feel pretty lucky to have gained experience that will benefit me greatly later on in my education.

This is Marley and she studies nearshore fronts and planktonic dispersal along the coast. However, her data currently being collected has yet to be analyzed and is part of an ongoing research project. 

This image shows a nearshore front which can be seen as a foam-line. A foam-line is only present during upwelling conditions.

How do these nearshore fronts form?

This is Sunset Bay, one of the sites under observation, and the yellow-green oval highlights a foam-line. The nearshore front is caused by the alongshore current interacting with the land’s topography, creating this foam-line. This nearshore front along the mouth of the bay is only present during phases of upwelling winds, which blow Southward from the North.

This is a red alga propagule. Propagules are good models for this research because once they are trapped in the bay by the front, they may have higher settlement rates.
Photo by: Zac Swider
Magnification: 40X dry lense, 1X trunk lense, 0.5X coupler
Marley has taught me how to collect physical data using the following oceanographic instruments:

CTD: Conductivity (salinity), Temperature and Depth. This device is lowered vertically into the ocean on both sides (inshore/offshore) of a foamline to gather data. This data can be used to form graphs which show distinct differences in salinity, temperature, chlorophyll content and backscatter. We call this a 'CTD Transect', because as the device is lowered it takes measurements of the water column that is under observation by cutting sections of the water transversely.
This is a large plankton net that is used during vertical plankton tows, which is where we drop the weighted net into the water and then bring it back to the surface once the weighted end touches the ocean floor. This collects plankton from the entire vertical column being sampled. 
This is a flow meter and it is attached at the mouth of the large plankton net that we use for vertical plankton tows. The flow meter can determine the water volume associated with each plankton tow, giving us an idea of the amount of plankton within that volume.
When someone is offshore on a boat, casting the CTD and the plankton net, someone must be onshore using a hand-held pump to collect the plankton that has gathered closest to the shore for comparison against the plankton gathered offshore.
By using modified Hester Dendy stacks, we can measure algae propagule settlement in the intertidal.

This is a modified Hester Dendy stack.
These modified Hester Dendy stacks are bolted directly into rocks in the intertidal and simulate the rugosity of the sandstone rocks, upon which propagules settle. Each set of stacks is left out for a period of 48 hours. 

I switch out the stacks with new ones and take the 48 hour old stacks back to the lab. The stacks are disassembled and I count each individual plate underneath a dissecting scope. I count each coralline spore and red algae propagule that I find and document these numbers in Marley's lab notebook.
To measure barnacle cyprid settlement, we use barnacle plates of two different textures:

Tile Plate
Imprint Plate
I go out into the field every other day to count a total of 18 plates at 2 locations. 
The cyprids settle into the tiny pores of the plates, so I use a hand lens to count them. These cyprids range between 450μm and 600μm in size.
These numbers are entered into a log book as well, to be compiled later in the year for analysis and comparison between different bays.

My time here this summer has taught me many things, but one of the most important things I have learned is to be creative and resourceful with the limited supplies available when conducting research. Funding is not always available and if you want to do the research, you have to find cost-efficient ways to do so. Reduce, reuse and recycle!

Saturday, August 24, 2013

Week 7-8 & Reflection

Week seven & eight involved breaking new ground using the computer program known as Microsoft Access. With some help from my mentors Justin and Mitch, along with a little luck, I was quickly on my feet doing some very basic computer programing. I used Microsoft Access not only to neatly organize my demographic shellfisher information but to also give me support in summarizing my findings. For instance, I was curious what percentage of my sample population was using the following sources to learn about shellfishing opportunities. So with the help of a frequency equation I was able to designate whether the interviewee said “yes” or “no” to either; Youtube, the internet, printed guides, or family and friends. Having the ability to bin answers when they are pertaining to multiple chose questions is an invaluable tool. It will be one that I am likely to use in the future.

Analyzing one’s research is just as critical as the collection process; however, after spending the last six weeks in the field, seeing abundant wildlife, and interacting with the public made sitting in a room for 9 hours straight for 10 days pretty rough. In hindsight, this data entry experience was a good one because I will remember how much my body and mind ached from being indoors. I will certainly now look for jobs down the road accordingly.

When I wasn’t summarizing my data or working on my PowerPoint presentation I was trying to finish restoring the old Cort Gion surfboard I found when I first arrived. My mentor Steve lent me a few power tools which I need to return to him rather soon, so I’m in a rush to get the job done!

I can recall reading a COSEE blog from a student last year and hearing how they had an amazing summer. Now after finishing my summer internship experience I can attest to their statement because I easily had the greatest summer of my life, hands down. I had the opportunity to meet so many great people, from peers to possible employers. It was just such a great environment for networking and getting your name out. I made some incredible friends this summer who I plan on keeping close in my life far into the future. I would highly recommend any Natural Resources or Biology students to pursue this internship if you are serious about succeeding and reaching your goal of making a career in the arena of science.

Friday, August 23, 2013

Ella- Week 8 and reflection

Throughout this summer, I have had plenty of opportunity to experience and reflect on the culture of science. As this was my first foray into scientific research "in the real world", I was often surprised by the obstacles that the professional scientists around me ran into. Questions such as "how do we communicate and work together in the best way possible?" and "what is the best way to design this experiment?" were very real obstacles in Hatfield research, just as they are in the classroom. I was, however general impressed by the level of cooperation that is in place here. From the weekly community donuts and seminars to collaborative projects between labs, to lunchtime soccer matches with the researchers from these various labs, one can tell that networking is an important aspect of research. Furthermore, it was very exciting to be able to be a part of the research being done here, because without investigating the coastal and oceanic environment, we would know nothing of this big beautiful natural resource we call the Pacific ocean.

I am very grateful to have been able to go through the COSEE program and the research ethics program here at Hatfield with the guidance of all my mentors Itchung, Waldo and Matt and with the support of my office mate, Katlyn. I am happy with the presentation that we put together on our work this summer and it has inspired me to further pursue a career in the sciences. I am also grateful for the skills that I was able to develop such as working with the programming language R, excel and powerpoint, and being able to analyze and present data. After being in an office working on these things, I know that I would like to be outdoors more, and I am also grateful for that lesson as well. In summary, this was such a great opportunity and I count myself lucky to have been able to work on this project. Below is the view from our office window. I was also able to visit the aquarium (literally two minutes walk from our dorms) on my very last day!
Our clear name tags from our office door take center stage
Adieu and thank you for a great summer!  

Thursday, August 22, 2013

Natalie Week 7: Data analysis and Curiosity

During my second to last week at Hatfield I started wrapping up all of the slides and dissections I have been working on this summer. I was able to explain my project to all of the interns at the Oregon Institute of Marine Biology, who came down for an exchange day. It was really helpful being able to explain my process and the driving forces behind my project to a small group before getting up and giving my final presentation.  I spent most of my week photgraphing all of the slide that I had polished and analyzing the photographs.  I was also able to learn how to create a graph in R programming language with the help of Katelyn Bosley. This allowed me to plot the data I collected of carapace length vs. the number of rings observed in the gastric mill portions.  After analyzing the photographs I had taken my curiosity got the better of me and I hijacked a couple large ghost shrimp that were meant for crab food and dissected out the gastric mills. I made the very exciting discovery that the ring structures I observed in mud shrimp occurred in ghost shrimp as well!

During this last week I was also able to help Brett with several projects aimed to assess the eelgrass habitats in the estuary. One project included deploying breeder traps to catch fish coming in at high tide.  When we collected these traps we found quite a few staghorn sculpins, gunnels, and even a couple perch. Another project consisted of taking juvenile Dungeness crabs with hooks superglued to their backs and tethering them into the ground in the eelgrass beds.  The idea was to catch fish who tried eating the crab with the hooks to get a look at predation on dungeness crabs.  Instead we ended up with a lot of live angry crabs with hooks still on their backs.....The last project involved deploying GoPro cameras underwater at specific sites and filming the organisms inhabiting the eel grass beds. After four hours we went out again and collected the cameras so the footage could be analyzed.  All of these projects share the same goal of learning more about the two eel grass species, Zostera marina (native) and Zostera japonica (invasive) and how this habitat is being utilized by different species.

Overall, this week was busy, exciting, long, and ended far too soon.

During week 8 I focused on my presentation and working with R to analyze the data I collected for mud shrimp. I was able to find a significant positive relationship between carapace length and the number of rings observed in mud shrimp by running a linear regression. The more time I spend researching these shrimp the more questions I seem to have!

Wednesday, August 21, 2013

Ella- week 7

 Some of our "R" code with a graph dislplaying the "eveness" of our data        .

As the summer drew to a close, we realized just how little time we had to put together a presentation that would include some preliminary analyses. Thankfully, we had the good fortune to be working with Matt Yergey, who is very capable working with statistics and R, which is the programming language we eventually used to process the data.

By the beginning of the second week, we had to acknowledge that we were not going to be able to finish entering the data in the binder Katlyn had originally started working on if we wanted to do any sort of write up of the data we already had entered. So we left the comforting zone of entering fish length and embarked on a more treacherous path of quality control, understanding statistical tests and communicating science. 

This was a very important part of our internship, as so much of our time had been centered on our data. As we had so much data, with so many different variables such as fish count, fish length, location of collection, time and temp of beam trawls, it was a little overwhelming trying to decide which variables we wanted to analyze, and in which way. We read various scientific papers that had similar data sets to see which kind of analyses were usually done on fish populations to determine and compare community structure and we thought about how we could perform similar tests on part of our data set. 

At first, we checked for outliers in the dataset, such as fish that were way larger than others, which may have been entered by mistake. We also looked for stations that had latitudes/longitudes that were not on the Oregon coast, or were further out from the coastline than other stations, and then went back and verified that the data was entered correctly. There is a map feature associated with the online database which will plot the latitudes and longitudes entered, which proved very useful. We did discover multiple stations in China (a result of the longitudes being entered without a negative symbol!). 

We then exported all of the data in FOIS, our database, saving it to file on our computer. The location where it was saved we named as our "working directory". When we used R to manipulate our data by performing the various statistical tests on them, we were able to "call" this working directory and access all of the information that had been exported from the database. 

Using R, we split the historic data from the current data and then sorted our data even further, keeping only those fish entries that had associated geographic coordinates and depth information. We then created "bins" of stations with similar depths and latitudes and found the diversity of these bins using a pre-written command in the package "vegan" that we were using with R. 

We sorted the data various ways and wrote instructions to display the information in tables, one of which you can see above. The eveness  was found using our diversity index and reflected how close two bins of information were to each other in terms of diversity. 

Our ultimate statsical test that we ran was an MRPP, which basically found and quantified differences in community structure within and between bins. By the end of the internship, literally a few days before our presentations, we were left with the responsibility of deciding which results to display and the  best way to do that. 


Tuesday, August 20, 2013

Doing Research is Fun - Reflection - Aaron Nelson

The things I've learned this summer can be divided into two main categories: "things I've learned about jellyfish and turbulence" and "things I've learned about conducting biological research." My biggest motivation for applying to COSEE was to add to the latter category, but that being said, the experience of learning about jellyfish has been an enjoyable and captivating process, and I am lucky to have been granted such an elegant research subject! Jellyfish were perhaps the perfect vehicle to deliver insight into the research process, and my experience this summer was very diverse: I've helped with experimental design and construction; I've conducted research trials with live jellyfish and plankton; I've written about our materials and methods and have summarized the background literature concerning our question; I've "quantified" the movement of jellyfish using video files; and I've even earned my first stripes with the dissecting scope, spending a hefty handful of hours counting and collecting plankton.

A majority of my time was spent working alone, while my mentor Dr. Kelly Sutherland was working in Eugene, and this situation granted me an autonomy over how and when I would work. The result of this often meant working late into the night and some long days; but also having the ability to make time for other plans outside of the lab. In short, I feel that I got a glimpse of what it's like to be a self-motivated professional researcher; working at a list of long-term tasks in the order I felt was appropriate rather than completing short-term tasks at the whim of a professor in a class setting. What it really comes down to is this: the classroom can never replace authentic research experience and I am grateful for this opportunity! While I have seen some of the infamously tedious side of research work, I have also witnessed its stimulating aspects that come with the frequent critical thinking and problem solving. These latter aspects have outweighed the tedium for me enough that I'm destined to continue down the path of research, and I'm happy to have gotten my start here.

Reading Through the Literature - Aaron Nelson

Lately, my COSEE experience has brought me a lot more "screen time" sitting in front of a computer. I was appointed the task of writing an annotated bibliography. The process has been both challenging and insightful and has really helped bring the research of the summer into a broad focus.

For those of you who are unfamiliar, an annotated bibliography consists of brief summaries of sources that contribute to knowledge of a specific topic. In my case, I was searching for scientific literature that addresses two things: jelly clearance rates (amount of water volume / time that passes through their tentacles) and plankton interactions in turbulence. The information is ultimately being used to build a backdrop for my summer's research concerning the effects of turbulence on hydromedusae feeding.

After I accumulated a pile of electronic and hard-copy articles, I began the long process of sifting through the pages hoping to glean out a few pertinent gems of knowledge from each source. This didn't always happen. Sometimes I would dive into a dense article and after an hour or two of translating the technical-speak surrounding turbulence calculus, I would realize that the article had nothing to contribute to my particular question. Oh well. Toss it in the pile and move on!

It was never easy to read, and it especially wasn't fast. But after a while, I started to get accustomed to the language that is used in published research literature. I also started to notice a pattern in the methods that researchers used; some would be the same and some would be different, and some would draw attention to just how different the results can be in the case of the latter!

I began to get familiar with the names of some of the authors and could even make out a narrative of their progress though time. Researchers of a certain topic would often be found together as co-authors at the top of the page, and if not, they were almost certainly listed as references at the end. Together they are helping to build a body of knowledge that hitherto didn't exist, piece by peer-reviewed-piece. The new is layered over the old, adding a strata that modifies and incorporates it. It's a slow process, and it really accentuates the cooperative nature of science: no one makes important discoveries based entirely on their own brilliance and wit; they are always standing on the shoulders of their colleagues. Discovery is a slow process and it was fun to get a glimpse of it while writing my first annotated bibliography.

Monday, August 19, 2013

Anna Russell- Reflections

My time at SPMC has helped to direct my future career and given me passion for doing science. Although I am not going into marine science, I have learned a lot of skills that will help me in any science career. I would highly recommend this program for anyone who is interested in going into science. It has exposed me to many different scientific techniques and equipment that I would not have otherwise been able to use. I also learned a lot about the process of science: designing a question and project, coming up with a hypothesis, data analysis, and interpreting that data. It was a fantastic way to spend the summer and I feel more prepared for a career in science.
Here are some pictures from throughout my summer:

Eelgrass growing in the tanks.

Isopods happily eating eelgrass.

Deception Pass Bridge


Laby cultures

My 'sterile' workspace

All the petri dishes drying after the experiment

Katlyn - Reflection

I cannot believe that this internship is already over! These eight weeks have flown by! This has been a great learning experience. I have met so many wonderful people this summer and I have been able to get involved in so many different aspects of field biology. I am so glad that I was able to have this opportunity this summer. It has definitely allowed me to see what it is really like to be a field biologist. It has also reinforced my love for science and the coast. The fact that I was able to be a part of this great program after only one year in community college was amazing and I feel so privileged to have been chosen. I will never forget this summer and I know that this experience will help me in my future career. Thank you COSEE, everyone at Hatfield, and everyone else who has been a part of making this a great summer!

Katlyn - Week 7 and 8 wrap up

A screen print of my R work
These last two weeks Ella and I have been able to do some statistical data analysis using the programming language R. This was intimidating at first because I have not had any other programming experience. However, after a few hours of explanation from Matt, we were able to get the basic idea.

After we started understanding the basics of R, we were able to export the data from the online data base into R. This allowed us to do some analysis on it. Since there was such a large amount of data (23,101 fish from 1977 and 1978 alone), we had to decide what main ideas we wanted to answer. We decided on examining the differences in fish communities based on differences in latitude and depth. Since not all stations had both GPS coordinates and depth, we separated the data into two groups, also called data frames, one containing stations with a GPS location and the other containing stations with recorded depths.

To examine the differences we did a Multi Response Permutations Procedure (MRPP), which basically tells you if there are any statistically significant differences between and within groups. After running this test we found that there were small differences between the depth groups that were statistically significant because there p-value was much less than 0.001. We also found that any differences between the latitude groupings we had were not significant because the p-value was too high.

After we analyzed the data we made a PowerPoint presentation and prepared a speech. At the end of the internship we gave this speech to a large group of researchers, staff, and other interns at Hatfield. I feel like this was a great experience because we got to see what it is like to present scientific findings to others in the science field.

During the last week I took a break from preparing our speech to go on a walk to the beautiful South Beach. I thoroughly enjoyed the gorgeous scenic surrounds. Being around nature and admiring a beautiful sunset allowed me to appreciate my last week at Hatfield Marine Science Center.

Friday, August 16, 2013

Anna Russell - Wrapping up..

In the 1930s, eelgrass (Zostera marina) beds were destroyed on the Atlantic coast of the US by eelgrass wasting disease. Eelgrass wasting disease is caused by a marine opportunist called Labyrinthula zosterae. While in recent history the outbreaks have remained localized, it is still not known what environmental factors create a suitable environment for an outbreak. Laby is thought to be an opportunist, acting as a decomposer, but given an opportunity, such as suitable environment or compromised host, it may become infectious. 
This summer, I focused on the effects of herbivory on eelgrass susceptibility to Labyrinthula zosterae. Herbivory could affect eelgrass susceptibility to L. zosterae because herbivory induced phenolic acids, secondary compounds which are thought to help the plant resist herbivory and pathogens. Therefore, I hypothesized that eelgrass that had been affected by herbivory would be more resistant to Laby because the herbivores had induced phenolic acids. Eelgrass that had sustained long-term damage by invertebrate grazers for five weeks, eelgrass that was only exposed to short-term damage by mechanical damage one day before infection and a unmanipulated treatment of eelgrass were all exposed to two strains of Labyrinthula zosterae in laboratory culture. Although almost none of the plants showed signs of infection after 9 days, the plants began to decompose at different rates. 
Using image analysis, I found that the decay rates of the short-term damaged eelgrass were significantly higher (p=0.0063) than the control or long-term damaged eelgrass, regardless of L. zostera inoculation. One possible explanation for this is that the environment had not been suitable for infection. Laby is only infectious if the conditions are right, otherwise it works as a decomposer. 
Looking at the data, I wanted to examine decomposition rates more closely so  I designed a new experiment. Three treatments of long-term damaged eelgrass (herbivory), short-term damaged eelgrass (mechanical scratching), long-term damaged and short-term damaged eelgrass, and a control (unmanipulated) are currently being monitored for decay rates. These samples will also be analyzed for phenolic acids compounds to look at plant resistance over time.  These results will help to determine the effect of herbivory on resistance of eelgrass to opportunistic decomposing microbes. 
I learned a lot this summer. Not just about eelgrasss, but science in general. I feel like I am better equipped for college and my future career. This experience taught me what to do in the face of failure and how to be persistent. Although things did not always go as planned, you always learn more from mistakes than when you do it right. I gained a lot from my time here this summer. Thank you COSEE, SPMC, and Dr. Sylvia Yang, my  awesome mentor, for giving me this experience! 

Sunday, August 11, 2013

Anna Russell- Week Seven

As I mentioned in my previous post, my experiment did not exactly turn out the way I thought. Almost none of the plants got infected with Labyrinthula. This was a surprising result, at least to me, because I thought that many of the plants would get infected due to the sheer number of Labyrinthula cells that were put on each leaf. However, this result has caused me to do a lot of background research into plant defenses in order to understand what I was seeing with my experiment.
When a plant (marine or terrestrial) senses a threat, it reacts through a process called basal resistance. Basically, it fortifies the cell wall to make it more resistant. This is a response to both pathogens and non-pathogenic threats. If the pathogen can still make it through, then the plant undergoes 'hypersensitive response' otherwise known as cell suicide. The cell infected with the pathogen and the cells around the infected cells will die. The plant purposely kills a bit of itself in order to keep the whole plant alive. If the pathogen still manages to sneak past that defense, the plant has one of two options. The first option works only on viruses and is called RNA silencing. The plant literally eats the RNA of the virus so there is nothing left to infect the plant. However, since not all pathogens are viruses, the plant can also undergo 'systematic acquired resistance' (SAR). SAR causes the plant to become more immune to all diseases for a long period of time. Scientists have figured out how to generate SAR in agricultural plants so that they will be resistant to diseases.
A plant goes through a very different process when it senses herbivory. Bugs and other herbivores release saliva when they eat plants. This saliva triggers a response in the plants to release 'volatile organic compounds' (VOC). The VOCs can do one of two things. They can either repel the herbivores through making the plant bitter tasting or cause it to have a bad odor. The other way VOCs protect against herbivory is by attracting predators of herbivores. The predators will then eat the herbivores and the plant will not be eaten anymore (hopefully).
Although in my experiment I will not be able to measure VOC levels or whether the eelgrass is exhibiting SAR, it is helpful to know some of the reasons why the eelgrass did not get infected. This information can also help direct future research questions about the mechanisms of infection for eelgrass.


Natalie Week 6 Fish Cutting and More

I cannot believe there are only two weeks left of my internship at Hatfield. This week I was given the wonderful opportunity to help with the NOAA's "fish-cutting party".  This is a three-day event where volunteers learn how to dissect juvenile salmon and collect data for many different projects.  All of the salmon from this session were caught in either the Columbia River or in curface ocean trawls in the Pacific near the mouth of the Columbia. There were four different types of salmon species including Coho, Chinook, Sockeye, and Chum.  From each fish the volunteers would collect some or all of the following parts: stomach, intestines with pyloric cecae, tail fin clip, otoliths (fish ear bones), anterior and posterior kidneys, and copper tags that were implanted in the fish noses. We also checked the body cavity and air bladders for nematodes and other worm-like parasites. The hardest part for me was dissecting out the otoliths, which are tiny little bones located on either sides of the spine posterior to the eyes.  The otoliths sit in fluid-filled sacs and help the fish balance and orient itself.  These bones can be used for aging and studying the condition of the water at different stages in the fish's life. Some of the stomachs I dissected had very interesting prey items still inside of them, including other small fish and even squid heads.  The stomachs, intestines, and kidneys will be used by Dr. Kym Jacobson to check for parasites and the stomach contents will also be used to conduct a dietary study for the juvenile salmon. The pieces of fin were taken for genetics studies and each dissected part was labeled with the fish ID number so the results could be correlated with the weight, length, and type of fish it came from, along with where the fish was collected. I was very excited to be a part of this process and it was very impressive seeing how efficiently everyone worked together to accomplish this goal.

This week I also looked at some of the slides I prepared from the lateral teeth of the gastric mills of mud and ghost shrimp (Neotrypaea californiensis shown below).  I was not able to find any ring-like structures or evidence of annual growth patterns so I did some further research and discovered that age rings were found in the ossicles of the gastric mills of larger crustaceans.  Ossicles hard structures (less hard than the lateral teeth) that make up the walls of the gastric mill and hold the lateral and median teeth (pictured above in a petri dish and then embedded in resin) in place.  I dissected some of these ossicles out of my remaining mud shrimp and discovered that there were some ring-like structures in a section of the pyloric ossicle that I polished.  I spent the rest of the week mounting a camera on a compound scope and photographing these images.  I hope to take some measurements and mount more slides with this same part from other shrimp to see how the ring number relates to the size of the shrimp. Overall it was a very promising discovery and I hope to learn more in the next couple of weeks!

Wednesday, August 7, 2013

Natasha Christman: The Phytoplankton Census

With such a great, fundamental role in the biological structure of the ocean, plankton are always sought to be understood. While they account for less than 1% of the Earth's plant biomass, phytoplankton are responsible for over 50% of the world's plant primary production and 95% of the ocean's primary production. Consequently, when monitoring water quality and investigating hypoxia along the way, knowing the quantity of phytoplankton present is important to get a better understanding of the delicate biological and chemical relationships found underneath the surface. But phytoplankton are microscopic, and unfortunately they are not capable of performing a reliable population census themselves. There can be an enormous number of individuals in one drop of water. So how do we measure the concentrations of plankton present?

Various phytoplankton in a water sample from our research station
near Eliza Island. 
The answer begins with a simple component of all plant life- the photosynthetic pigment chlorophyll a. Chlorophyll a is the primary pigment of photosynthesis, and it absorbs blue wavelengths of light while emitting (fluorescing) red light. Using this property to our advantage, we can filter a sample of water at a fixed volume and isolate the cell particles on a filter pad in the field. The filter is then dropped into a tube of 10ml of 90% acetone, and this solvent extracts the chlorophyll pigment from the cells with minimum alteration of pigment. After a bit more preparation back at the lab, this samples can be put through a device called a fluorometer. The fluorometer measures the chlorophyll pigments by hitting the acetone and extracted pigments with a beam of blue light. By measuring the amount of red light fluoresced back, the concentration of phytoplankton can be measured by its proportional relationship to emitted light.

The fluorometer in the chemistry lab, complete with
cat stickers (and no, they were already there).

When calculated, this data is a valuable contribution to the overall picture of the bay we are constructing. Comparisons of concentrations across transects can be made and crossed with other data collected, like the water column profiles, to further illuminate the research.

A graph of the chlorophyll concentrations at each station
visited on an early summer cruise.

Analyzing chlorophyll pigments on the fluorometer is a valuable tool and major contributor to our research this summer. It makes efficient a task that would be overwhelming, if not impossible on an accurate scale. Additionally, these measurements over time can describe the cycles of the plankton over generations and how these patterns coincide with other aspects of water quality.