Wednesday, June 26, 2013

Geomorphology Cruise aboard the RV Weatherbird II

This 10-day cruise has the objective of surveying the geomorphology and benthic habitats of the northern rim of DeSoto Canyon and collecting water samples to filter for pelagic foraminifra. Co-Chief Scientist Dr. Stan Locker will be using side-scan sonar instruments to map the acoustic texture of the sea bottom. Co-Chief Ian MacDonald will be using the MILET benthic imaging platform to extend and ground-truth the side scan tracks with photographic sampling of the seafloor and acoustic measurement of the subbottom profiles. 

The science team members come from University of South Florida, Florida State University, and Valdosta State University: 
  1. Stan Locker, USF, Chief Scientist 
  2. Ian MacDonald, FSU, Co-Chief Scientist 
  3. Peter Lazaravich, FSU 
  4. Eric Howarth, FSU 
  5. Mauricio Silva, FSU 
  6. Anne Harvey, FSU 
  7. Samir Daneshgar, FSU 
  8. Dana Fields, FSU 
  9. Courtney Bryller, VSU 
  10. Charnelle Bland, VSU (Intern from Emory University)
  11. Chelsea Kuhs, USFSP 
  12. Leo Meirose, USFSP
In addition to the mapping activity, collecting water samples with the CTD rosette happens at every station. The CTD measures the temperature, salinity and depth of the water and the rosette of sampling bottles collects water at designated depths. 

Charnelle Bland and Courtney Kuhs from Valdosta State University
collect water from the rosette after a profile at the Mooring Site.

Success of the cruise depends on getting all the equipment to work correctly.  As is often the case, the team has to spend many hours coaxing complicated electronic equipment to function underwater. 
George and Chris from the Weatherbird II crew
lower a pole-mounted sonar into position.
Stan Locker is using his side scan sonar in two modes: as a pole mounted sensor for shallow depths and as in a towfish to access the deeper stations.  
Chief Scientist Stan Locker preparing his
sonar system for towfish deployment

The MILET (Modular Instrument Lander and Equipment Toolsled) will collect data from the deepest stations.  Initially, MILET has trouble communicating through the fiber optic cable that transmits its images and measurements back to the surface.  The FSU team spends the better part of two days disassembling and troubleshooting before locating the problem — a faulty cable, which was brand new for the cruise!

Ian MacDonald working on the MILET benthic imaging platform.
With all  the equipment working, the long hours of survey can begin.  The teams trade watches recording the data files and keeping the RV Weatherbird II on track by radioing instructions to the bridge.

Samira Daneshgar and Leo Meirose, with Stan Locker in the background,
are standing watch during a sidescan sonar survey of the mooring site.

Post Author:

Ian MacDonald,
Florida State University

Becca Keenan's Internship, Summer 2013 - Part 2

Hi Folks!

This has been a very productive week, I think. After deciding that Cold-water Corals, Sixgill Sharks and Bristle Worms would be the best Flagship species to represent Deep-C, I started to design some campaign materials.

I thought I would incorporate some Briticisms and decided to bring the good old fashion Bulldog Spirit to the Gulf. Taking inspiration from the wartime motivational poster Keep Calm and Carry On, creating the Gulf‘s very own version.

I also started designing some flagship graphics, but they are still a work process…

In addition to playing around in Photoshop, I also constructed some factsheets to help capture and inform the public about the flagship species. Here I suffered a bit of déjà-vu as I found absolutely everything I read and heard fascinating, and I struggle to fit it all onto one factsheet!

This week has been pretty good, and I have managed to build on my catalog of interesting and strange facts that the ocean yields. The week was topped off by a super full moon paddle in the Wacissa River and Springs, (I am now currently one big bite, but it was very much worth it)!

So for now, Keep Calm and Love the Gulf!  

Posted By:
Becca Keenan, Florida State University

Chelsea McCurry's Internship, Summer 2013 - Part 8

I continue to process my data collected. There are many databases out there that are used to determine identities of sequences (such as the National Center for Biotechnology Information, SILVA, and the Protist Ribosomal Reference [PR2] Database). I’m finding that there are inconsistencies between the databases. This could potentially mean that there are errors within the databases. I continue to look for solutions and different programs to help with the analyzing portion of my work. 

Posted by:
Chelsea McCurry, University of West Florida

Tuesday, June 25, 2013

Lauren Reilly's Internship, Summer 2013 - Part 3

Last week and this week I am preparing samples to be run by the mass spectrometer. Each sample requires 6 to 10 cibs in order to run 3 to 5 replicates of the same depth increment. When I am choosing which cibs to use, I make sure they are in good condition to ensure sound results.

It’s interesting learning and developing the methods and procedures for my project to prepare the samples. After I choose which cibs I am going to use, I write down which species they are and if there is any sort of imperfection such as a partially cracked test chamber or hole. It’s important to take good notes on the cibs because after I choose them, I use two small plates of glass to crush them into smaller pieces. Then I put the crushed, homogenized cibs into a vial, clean with methanol, and put them in the oven to dry. Next comes the most delicate part of preparing my samples. I have to divvy up the crushed cibs into samples weighing about 100 microns. Sometimes when using the microbalance I catch myself holding my breath! Losing any part of the sample at this point can mean losing the sample entirely or having to prepare a new one - and no one likes to redo their work.

As my lab neighbor likes to remind me, “Work smarter, not harder.” With more practice preparing samples, my time has definitely been progressing toward being spent in smarter ways!

Post Author: Lauren "Ren" Reilly, University of South Florida

Monday, June 24, 2013

The cutting edge of oil research

This is my third consecutive summer working in the Reddy Lab at WHOI (I interned as a high school student for two years: And having just completed my first year studying materials science and engineering at the University of Toronto, Dr. Chris Reddy suggested I put my educational experience to practical use. He asked me to engineer a device or system for slicing oiled rock scrapings at millimeter increments along the axis perpendicular to the scraping so we could investigate if the oil composition on scrapings is different the closer they are to the rock surface. We hypothesized that sunlight and water “weathers” the oil more at the oil surface than closer to the rock. 

I began by writing an abridged project requirements document (PRD) – something I had learned about in school. A PRD outlines the conditions for a product being constructed (i.e., what the device should be, what it should and must do, and where the device will operate). It was pretty exciting to apply what I learned in class to an actual project in the field. 

My work station with my initial ideas made from Post-it
notes, tape, and paperclips. (Photo by: Bryan James)
I realized I had two problems to solve: the first was how to separate the oil and the second was how to attain the necessary millimeter accuracy. I started brainstorming and making little paperclip mockups. Then I made 3D renderings of my two main ideas using the software Autodesk Inventor Professional. After a couple of trips to the hardware store and some time at the lab, my first two designs were built and ready to test out. 

My first design was primarily a measurement device -- we could use any blade to slice the oil (I was using common stainless steel razorblades). My second design was essentially a rock-scraping guillotine. 

My first two prototypes: the measurement device (left) and the oil guillotine design (right).
(Photo credit: Bryan James)
A rock I found on the beach with artificial rock
scrapings I made. (Photo Credit: Bryan James)
To test out my two prototypes, I made some artificial rock scrapings by softening tarballs collected on a previous sampling trip and I applied the pliable oil to some rocks I picked up at the beach. Next, I had to figure out how I was going to slice the oil. I knew that oil can be treated like a globular polymer, which is the category of materials with properties similar to that of everyday plastics. Polymers exhibit a phase change at different temperatures, in much the same way water can go from solid ice, liquid water, or gaseous steam. The temperature at which polymers go from being pliable, gooey solids to hard solids (much better for slicing!) is called the glass transition temperature. So I figured by freezing the oil, I could lower the temperature of the oil below its glass transition temperature and attain the properties I wanted for slicing. 

I froze the oil by spraying it with upside down aerosol dusters to remove its stickiness and to keep its form. Aerosol dusters contain a refrigerant that is released when the can is sprayed upside down. The refrigerant has a temperature of -20º F when sprayed which is cold enough to freeze the oil.

Slicing the artificial rock scraping with a razor blade after freezing with an aerosol duster.
Evidence of shattering is apparent in the little chips of oil scattered about. (Photo credit: Bryan James)
Unfortunately, when I tried to slice the frozen oil with a razor blade, it shattered. The oil was too brittle and would fracture sporadically, preventing a clean measured cut. If the oil was cut unfrozen, it stuck to the blade and curled in on itself making clean measured cuts just as impossible. 

So, it was back to the drawing board in search of another solution. 

Lo and behold, a few days later, I found myself in conversation with a man who had worked in the ice cream business. You may be wondering what ice cream and oil have in common. Well… ice cream exhibits a phase change similar to that of oil’s glass transition temperature. You can observe this for yourself with any carton of ice cream -- when frozen solid the ice cream is hard and stiff, but when warmed it becomes soft and malleable. 

The man I had met explained to me that in the ice cream industry they use hot wire cutters to slice and shape ice cream which has been frozen well below 0º F with liquid nitrogen. This got me thinking… maybe this approach could work for my problem. 

The hot wire cutter system: the 6V battery supplied the necessary 2 amperes of current (left),
the hot wire cutter insulated in electrical tape (center), and the retrofitted measurement device
insulated in electrical tape (right). (Photo credit: Bryan James)
So I set about building a hot wire cutter for slicing oil. My plan was to use my measurement device (design #1) and then use the hot wire cutter instead of a razor blade to do the slicing. I ran into one problem, though, during the construction phase in that the wire necessary for the cutting part is a specialty item not sold in your run of the mill hardware store. 

Using the hot wire cutter to slice a frozen oiled rock scraping
collected from the Gulf. (Photo Credit: Ben Freiberg)
What I needed was nichrome wire — a nickel-chromium alloy. It is a great heating element because it does not burn out at temperatures upwards of 600º F, which got me thinking about toasters, which use heating elements to heat bread. And that is how I ended up at Wal-Mart buying an $8 toaster to take apart and use for my oil slicer! 

I tried again to cut my artificial rock scrapings with my new slicer, and it performed beautifully. It sliced through the rock scraping like a knife through butter. Now, I was ready to try out my design on some real samples from the field. 

It was at this point that our sampling trip to the Gulf began. I traveled with Dr. Christoph Aeppli, a postdoc, and Ben Freiberg, a guest student. Find out more about our experiences in two previous blog posts: "A once and a lifetime experience" and "Getting back to the Gulf."

A large oiled rock scraping chock full of shells
and other debris recently collected from the Gulf.
(Photo credit: Bryan James)
We returned to the lab with two rock scrapings thick enough to be sliced. I tried my hot wire cutter on both samples without success. It cut right through the oil, but the samples were filled with debris. Rocks, shells, sand, and twigs blocked the wire’s path and clean cuts could not be made. Again, it was back to the drawing board. 

I decided to follow the example of geologists and biologists in the way they prepare thin-sections of rocks or tissue for microscope slides. The process involves encasing the sample to be sectioned in epoxy resin. In my case, I encased the rock scrapings in plaster of Paris, because it would not interact with the oil or solvents used for extraction of the oil. 

To slice the oil-plaster system, I introduced a new piece of equipment into the lab -- a Chef’s Choice 609 Deli Slicer. A deli slicer can slice at millimeter precision and thicker allowing for adjustability and they are astronomically cheaper than the cutting apparatus used for traditional thin sectioning. Of course, we used the deli slicer for its intended purpose first by slicing a hunk of roast beef. The lab is slowly and steadily becoming a delicatessen. 

Testing the deli slicer with a rod of plaster.
(Photo credit: Ben Freiberg)
A tarball encased in plaster of Paris that has been sliced.
(Photo credit: Ben Freiberg)

All it took was a deli slicer.
(Photo Credit: Bryan James)
In the coming weeks, I will fine-tune a method for slicing oiled rock scrapings. but the preliminary tests I have done with only plaster have worked phenomenally.  In the meantime... slice on. 

Posted by: 

Bryan James, Student
Woods Hole Oceanographic Institution