Tuesday, July 30, 2013

Becca Keenan's Internship, Summer 2013 - Part 5

Hi Folks,

Yet another busy week at the increasingly busy COAPS offices, which are getting ready to relocate down the road next week.

I have spent more time on materials, finalizing a deep-water corals fact sheet and drafting another fact sheet especially for policy makers, which highlights the effects of the spill and the importance of oil to the Gulf economy.

I have also started putting together a comprehensive contact list of relevant policy makers and Deep-C spokespeople to allow for better communication about the many important aspects of Deep-C’s work.

Then, on Thursday, some of the other interns and I went down to the FSU Coastal & Marine Laboratory. This was great fun and very interesting. It is always nice to see what other institutions are doing. On the way back, we over-indulged and ate our body weight in Hamaknockers BBQ.

The survey is also coming along really well, with now over 130 completed surveys. This is very exciting and wouldn’t have been possible if so many groups, research institutes, and businesses hadn’t been so helpful. Two particularly helpful groups have been the Woods Hole Oceanographic Institution and a great surf shop in St. Augustine called Surf Station.

The week couldn't have ended better: we went down to Cape San Blas on Friday evening, where we enjoyed the most beautiful sunset surf and camped out just off the beach. We then spent the next day chilling on the beach and catching a few waves. It was a great weekend with great friends - you couldn't ask for much more.  

Posted By:
Becca Keenan, Florida State University

Monday, July 29, 2013

Taylor Shropshire's Internship, Summer 2013 - Part 2

For the past two weeks I have been continuing what I focused on during my first week, which is the relationship between salinity and chlorophyll a in the Mississippi river plume, and working with MATLAB. I have been progressing towards the goal of developing a linear model to create a salinity field from observed satellite chlorophyll a concentrations. The relationship could possibly be used to validate salinity fields near and around the Mississippi river mouth produced by hydrodynamic models such as HYCOM or NCOM. This chlorophyll a surface salinity relationship, which I am deriving from the output of ELCOM-CAEDYM, can also be compared with field data, providing possible validation for the aquatic ecosystem model (CAEDYM).

On Thursday of last week I toured the FSU Marine Lab. Earlier that week I got to visit some of the biological oceanography labs on FSU campus, and the week before that I toured the Mag Lab, all of which were very interesting.

On a side note, it's the season for scallops in Florida, and I got the chance to do some scalloping this weekend, giving me the opportunity to put on a mask,snorkel, and get in the water, which is something I never pass up! Made for a nice dinner with colleagues from COAPS.

Posted By:
Taylor Shropshire, Florida State University

Tuesday, July 23, 2013

Dana Fields's Internship, Summer 2013 - Part 4

I’ve decided to “dedicate” this blog entry to a brief discussion of my experience performing data analysis using MATLAB vs Excel.

There is absolutely no doubt that MATLAB is a better platform for those who know how to use it!

With Excel I was able to plot graphs showing temperature and depth fluctuations recorded by one of the CTD-Divers for a day, a month, two months, and 4 months. I could see the tidal fluctuations and even match the “blip” in late August to Hurricane Isaac and the shorter “blip” in June to Tropical Storm Debbie. The main point in favor of Excel is that I know how to use it! Another point that I favor is that I could provide the data set to my more advanced high school students and expect them to be able to use Excel to plot similar graphs and, hopefully, make similar correlations between blips on the graphs and storm activity in the Gulf of Mexico.

On the other hand, MATLAB can be used to do so much more… if you know what you are doing. We were able to plot the temperature and depth data for all of the DCT-Divers on each mooring on the same page. This made it easy to see which variations were reflected from near surface all the way to the ocean floor.

As I mentioned in my previous entry, knowledgeable MATLAB practitioners can go much further with the data, applying filters and performing spectral analysis with an eye toward learning as much as possible from a relatively simple (although humungous) data set. I’m still working on a better understanding of how it all works. I have a feeling that I’m not going to become an expert in the next few days… but I’ve gained a keen appreciation for how statistics and mathematical methods can be applied to understand the physical aspects of our Earth’s oceans.  

Posted By:
Dana Fields (Florida State University)

Monday, July 22, 2013

Becca Keenan's Internship, Summer 2013 - Part 4

Hiya Folks

Sorry that I haven’t posted a Blog for a few weeks as it has been very busy. A few weeks ago we went to The Dauphin Island Sea Lab, which was also very busy, but I still had time to chat with the interns there, and on a more gory scale watch a manatee dissection, which was fascinating but also sad. Amelia has made an awesome video of our antics whilst we were there.

Once back in Tallahassee I started to collect surveys, which was actually easier than I thought it would be. To be honest though I have never had trouble talking...

As usual we had a few adventures outside of work: last weekend we went paddling down the Wassica again and yesterday we conquered the St Marks Trail.

For Now Take Care and…
Keep Calm and Love the Gulf

Ps If you would like to take my survey here is the link.  I would also be very grateful if you could pass this on to anyone you feel would be interested. https://www.surveymonkey.com/s/GulfofMexico-PublicOpinionSurvey

Posted By:
Becca Keenan, Florida State University

Friday, July 19, 2013

Taylor Shropshire's Internship, Summer 2013 - Part 1

My first week at the Center for Ocean-Atmospheric Prediction Studies was an interesting one. The first few days I was busy meeting people and presenting my past project on the numerical model ELCOM-CAEDYM. COAPS is interested in learning more about aquatic ecosystem models such as CAEDYM to simulate the biogeochemistry in the Gulf of Mexico. In my past project I was interested in primarily hypoxia in the Gulf of Mexico and hope to analyze, validate and add to my current simulation with the help of individuals here at COAPS.

I was introduced to MATLAB early in the week and have been able to load data from my ELCOM-CAEDYM simulation. MATLAB is a valuable skill and I am excited to start gaining experience. I created a salinity vs chlorophyll scatter plot and have started to familiarize myself with MATLAB basics.

I look forward to the next weeks and hope that I can make my short internship here at COAPS a productive one!

Posted By:
Taylor Shropshire, Florida State University

Chelsea McCurry's Internship, Summer 2013 - Part 10

The research team here at the Center for Environmental Diagnostics and Bioremediation (CEDB) is working on developing a process for analyzing sequence quality and output for bacteria, archaea, ciliates, and foraminfera.

We are hoping to develop a standard operating procedure for handling all of the clone libraries and single-cell polymerase chain reaction (PCR) products we have coming in. We are working to solve how to have high quality sequences and meaningful output data in each of the studies we are working on. 

Posted by:
Chelsea McCurry, University of West Florida

Curtis Okolovitch's Internship, Summer 2013 - Part 8

Now that I am entering the last few weeks of my internship, I’m spending the rest of my time tying up some loose ends and hoping to perfect the extraction method Kala and I worked on this summer. This past week I have extracted the hydrocarbons from the last of my cultures and started to analyze the total petroleum hydrocarbons (TPH) in these samples using Gas Chromatography. If all goes well, we could have some conclusive data on biodegradation of hydrocarbons using this new technique.

Since I do not have much exciting news this week, I thought I would introduce you all to some other members of the Kostka Lab working on the oil spill. In the photo on the right are is Will Overholt (right) and Nicandro Mandujano (left). Will is a graduate student at Georgia Tech studying for a Doctorate degree in Bioinformatics and Nicandro is an undergraduate from Elon University in the Research Experience for Undergraduate (REU) program. Together, they are combining genomic with geochemical data in order to analyze the response of the microbial community to the Deepwater Horizon Oil Spill. They have been using molecular techniques such as qPCR to examine the 16s SSU rRNA genes found in their samples to identify the key taxonomic clades in these marine microbial communities.  

Until Next Time,
Curtis Okolovitch, Georgia Tech

Thursday, July 18, 2013

Charnelle Bland's Internship, Summer 2013 - Part 3

Hello again! I had an awesome time on the R/V Weatherbird II for 11 days doing research and enjoying serene views of the sea! On our trip I worked with great scientists and crew members. I assisted Dr. Stan Locker with his sonar equipment and Dr. Ian McDonald with his millet operation. In addition, I filtered some more water samples and observed the different phytoplankton species back at the lab in Valdosta.

While on the cruise we mapped part of the ocean seafloor using the towfish. The towfish was monitored continuously when it was placed in the water. Everyone had two shifts: I worked the 4-8pm and 4-8am shifts along with Chelsea and Dana. As the towfish monitored the seafloor and mapped out the bathometry, sediment, temperature, velocity, and different characteristics of the ocean floor and the water in general, we had to monitor how far out it was being dragged in the water. There was a time (the early morning shift) where the towfish HIT the bottom of the seafloor and we ran out frantically to pull it up! However, it survived and so did we.

Chelsea, Stan, and I letting out the wire for the towfish to settle in the water.
The towfish also has many other capabilities, such as identifying where “lost” beaches were years ago, climate changes, sea level changes, habitats, sediment movement, contaminated water movements, and how the current moves on the shelves, along with many other interesting aspects! In addition to monitoring the seafloor, we also used the millet to view the different ocean communities and study physical sediment traits.

Towfish preparation for the “big drop.”
Additional commentary:

Here I am helping with the CTD for filtering!
Mauricio caught a huge Mahi, and we had it for dinner!
Thanks for reading!

Charnelle Bland, Valdosta State University

Wednesday, July 17, 2013

Dana Fields's Internship, Summer 2013 - Part 3

Well I’m back at a desk wrestling with MATLAB. Aided and abetted by my mentor, Dr. Nico Wienders, I’m starting to make progress.

In my first blog entry, I mentioned that I am working with data collected by the CTD (conductivity, depth, and temperature) divers that were deployed at the head of the DeSoto Canyon. Deep-C researchers have several mooring stations in the DeSoto Canyon area, but these particular instruments were located at mooring sites 1 and 3 (see Figure 1 for the mooring locations). These instruments were attached to mooring cables that were anchored to the ocean floor with three locomotive (train) wheels. The instruments were placed 5 to 10 meters apart along the cable. The mooring cable was held upright with flotation spheres, and the top of the cable was 15 meters below the surface to, hopefully, avoid fouling by boats. A marker float was attached to the top of the mooring with a 20-meter string. (Figure 2 is a diagram of the mooring cable deployed at Mooring 1.) As it turns out, the cable at mooring 3 was broken, probably by a trawling net, and all but the two instruments were lost.
Figure 1: Mooring sites 1 and 3 in the DeSoto Canyon area.

Figure 2: A diagram of the mooring cable deployed at Mooring 1.
The CTD Divers are nifty little instruments made by Schlumberger. They are traditionally used to monitor groundwater and haven’t been previously deployed in the ocean. These instruments were deployed May 2012 and recovered May 2013. Though the original intent was to collect data every 3 seconds for that year, in the final deployment they were configured to record depth, temperature and salinity every 15 minutes. (Trust me, that still ends up being a lot of data points!) Figure 3 shows a new CTD Diver and one of the recovered instruments. Notice that the deployed CTD Diver was covered with a shield to, again hopefully, prevent fouling by sea organisms (primarily barnacles). Unfortunately, the shield was only partially successful. Most of the instruments ended up with barnacles inside them, which interfered with the conductivity measurements, though depth and temperature seem to be unaffected.

Figure 3: A new CTD Diver (left) and one of the recovered instruments (right).
So anyway, 12 CTD Divers were deployed and 7 survived. One of the sensors (the top one) on Mooring 1failed so that no data could be retrieved. All but two of the sensors associated with Mooring 3 were lost completely. I’ve been using MATLAB and Excel to plot the collected data (Figure 4). I’ve already been able to identify how the tides affected the temperature and depth data. There are some interesting “blips” that we may be able to associate with storm activity… but I haven’t made it that far yet. I still have to learn how to apply filters to the data so we can screen out the responses we know about and identify other phenomena (currents, etc). By next week, I should know even more!
Figure 4: Using MATLAB and Excel to plot the collected data.
Posted By:
Dana Fields (Florida State University)