Thursday, October 23, 2014

Deep-C Fish Ecology Cruise Possibly Finds A New Species

Unknown skate - ventral (underside)
Reprinted from October 22, 2014 article on the FSU Coastal and Marine Lab website -- Dr. Dean Grubbs, Dr. Chip Cotton, and crew recently returned from a 10-day (October 1-10, 2014) Deep-C fish ecology cruise in the Gulf of Mexico, where they caught their third specimen (since 2012) of a skate believed to be a new species. Multiple taxonomic experts have examined this skate (or pictures of it) and determined that it is likely new to science! If this is confirmed, the team will write a description of the new species and give it a Latin name. Alternatively the skate might simply be a species that was not previously known to inhabit the Gulf of Mexico. With nearly 300 described skate species globally, this will require some time to rule out that possibility.

Unknown skate - dorsal (upper side)
They did not stop there. Drs. Grubbs and Cotton and their crew also caught two six-gill sharks at deeper depths than they have ever caught them before (one caught at 1,100 meters (3,600 feet), and the other caught at 1,300 meters (4,300 feet) deep). They attached an archival satellite tag to one of the sharks (approximately 15.5 feet long). This tag will record depth, temperature, and light levels for 3 months and then will pop off of the shark and transmit data to a satellite that will forward the data along to Dr. Grubbs and Dr. Cotton. Although the crew has tagged several other sixgills in the Gulf of Mexico, they are particularly interested in the movement patterns of this shark because it was caught much deeper than the others they have previously tagged.

King snake eel (Ophichthus rex)
Participants on the cruise included the two ship’s captains, Robby Shakespeare and Bobby Francis, and seven science crew on each “leg” of the trip (before and after their port call in Panama City). The science crew was led by Drs. Grubbs and Cotton, and included seven students from Florida State University (Jo Imhoff and Bianca Prohaska), University of North Florida (Arianne Leary, John Whalen, and Hannah Hart), and University of West Florida (Beverly McAcy and Mariah Pfleger). These students were there to collect samples for their respective projects and to generally assist with the work on the cruise.

Red deep-sea crabs (Chaceon quinquedens) and giant isopods (Bathynomus giganteus)
During the cruise, the team fished 38 “stations,” which is a demersal (bottom) longline with two fish traps attached. The depths for these stations ranged from 173 to 1860 meters (560-6100 feet) deep. The overall catch from these stations yielded a total of 343 fishes from 35 different species: 15 species of elasmobranchs (sharks, skates), 17 species of bony fishes, and 3 species of hagfish. They also caught 181 invertebrate specimens from 8 different species, mostly deep-sea isopods and various species of crabs and shrimp. Approximately 3000 samples were collected for studies of oil and mercury contamination, life histories (age, growth, reproduction), phylogenetics (relationships among groups of organisms) taxonomy (classifications), diet, and food webs. Most of these samples support several ongoing graduate student research projects.

Stay tuned to find out whether their “new” skate is indeed a new species and we will report more about that DEEP sixgill shark after the tag pops off in three months!

Wednesday, August 27, 2014

Interns Gain Real-World Research Experience With Deep-C Scientists

This summer, nine students were paired with leading scientists and experts in their fields to work on Deep-C research projects at the University of West Florida, the Naval Research Laboratory at Stennis Space Center, Florida State University, and Valdosta State University. From isolating microorganisms and extracting DNA to building an ROV, developing marine data apps to measuring nitrogen concentrations, enhancing a GIS Map Viewer to assisting in aquaculture projects and cataloging marine collections into a database, these interns received on-the-job learning experiences that enabled them to explore potential career opportunities. Even after their internships were completed, some of them plan on continuing to work with their Deep-C mentors on projects. Some interns even said the internship helped them to decide what they want to do as a career.

“Experiences such as these -- internships and other opportunities within the field you want to work in -- are what help you narrow down what you want to do for the rest of your life. At the same time that you are developing skills and getting exposed to how things work in the scientific community, you are also developing interests in various areas that will help you figure out what path to choose later on.” – Meaghan Faletti, Spring 2014 Intern

Katherine Vaccaro – Molecular Microbial Oceanography
Interned with Dr. Richard Snyder at the University of West Florida. Katie collected and analyzed samples of microorganisms using microscopes and a FlowCam, and then extracted samples of DNA to better understand their distribution and ecology. She had the opportunity to join Dr. Snyder on a Deep-C research cruise to collect samples in the Gulf of Mexico. “Fun people, awesome crew, great food and lots of science!” Read Katie’s blog.

Rachel Holladay – Adaptive Ecosystem Climatology
Interned with Sergio deRada at the Naval Research Laboratory at the Stennis Space Center. Rachel built an ROV (remotely operated vehicle) equipped with a GoPro camera system, Arduino powered temperature and depth logging system, active and passive water collector systems, and a carefully designed buoyancy system designed to allow the ROV to sink and float as needed. High school students will use the ROV to collect marine data in the Gulf. “My mentor’s extreme enthusiasm and dedicated work ethic always inspire me.” Read Rachel’s blog.

Sam Holladay – Adaptive Ecosystem Climatology
Interned with Sergio deRada at the Naval Research Laboratory at the Stennis Space Center. Sam worked on developing an iPhone app for water-testing kit users to send in water collection data, for use in their adaptive climatology model. “Working on this iPhone app has given me my first experience with graphic design. I'm not exactly an artist, but seeing the app screen finally look presentable feels very good.” Read Sam’s blog.

Herbert Johnson – Using Nitrogen Isotopes to Characterize Nitrogen Cycling
Interned with Dr. Angela Knapp at Florida State University. Herbert investigated nutrient cycling in the Gulf of Mexico, by measuring nitrogen concentrations in water samples. He utilized Ocean Data View (ODV), a tool used to plot oceanographic data sets, to plot water column profiles of nutrient distributions to gain insight into the location of the sources and sinks of nitrogen to and from the Gulf. “It is an invaluable resource for chemical oceanographers or anyone studying ocean chemistry.” Read Herbert’s blog

Harshul Pandav – Deep-C Web GIS Map Viewer
Interned with Olmo Romero Zavala at FSU’s Center for Ocean-Atmospheric Prediction Studies (COAPS). Harshul was tasked with increasing the efficiency of Deep-C’s Gulf of Mexico Atlas (a GIS Map Viewer) and learning about various web based technologies for interactivity and design. The Atlas now has enhanced tooltip features and can be read in another language. He was also working on designing a mobile device interface for the Atlas. “This internship will definitely broaden the scope of my versatility, knowledge and creativity.” Read Harshul’s blog.

Emily Goetz – Developing an Atlantis Model for the Gulf of Mexico Reef Fisheries
Interned with Dr. Stephen Gosnell at FSU’s Coastal and Marine Laboratory. Emily researched existing models and gained an understanding of Atlantis. She also assisted with oyster aquaculture projects, and created a digital guide of sessile invertebrates of hardbottom reefs in this region. “Simply being at the marine lab fosters relationships with scientists in related fields and provides opportunities to assist with additional field and lab work.” Read Emily’s blog.
Erica Levine – Fish Diversity in the Deep Gulf of Mexico
Interned with Dr. Chip Cotton at the Florida State University’s Coastal and Marine Lab. Erica helped organize the marine collection and create a searchable database for all the specimens in the collection. After some investigating, she identified the correct paper type and best printer for making ethanol resistant labels. The marine lab now has a collection that is phylogenetically organized and cataloged. The jars were all entered into a digital database, along with all the 500+ previously identified items. “The work we have accomplished over the past month will make it much easier for others to continue expanding the collection and find items already stored at the FSU Coastal and Marine Lab.” Read Erica’s blog.

Deep-C sponsored two NOAA-NGI Interns

The Deep-C Consortium supported two students selected for participation with scientists Drs. Richard Snyder (University of West Florida) and James Nienow (Valdosta State University) acting as their mentors and facilitating the interns' research:

Cynthia Kane (to the left) interning at the University of West Florida used several microbiology techniques including polymerase chain reactions (PCR), gel electrophoresis, and clonal library creation to analyze water and sediment samples collected from the Gulf of Mexico to determine the different types of Archaea present. To learn more, read Cynthia's blog.

Chris Horruitiner (to the right) interned at Valdosta State University (GA) to investigate the impacts of the Deepwater Horizon event on the phytoplankton populations in the DeSoto Canyon region of the northern Gulf of Mexico. Chris used a combination of net plankton samples (across the entire water column), pigment samples (for HPLC), and discrete Niskin bottle water samples from several depths across the water column analyzed using SEM and imaging flow cytometry to address how phytoplankton populations change with depth and with season in this area. To learn more, read Chris' blog.

Visit the DISL website for information about future NOAA-NGI internship opportunities.

Advice for Future Deep-C Interns

“Be braver than you feel”. – Rachel Holladay

“If you give something enough time and dedication, you can become great at it.” – Sam Holladay

“Don't take roadblocks and problems you can't solve yet, personally. This is science, it's not going to be like studying for a test. Here no one knows the answers and we get to try to figure them out as we go.” – Benjamin LaBelle

“Absorb the knowledge your mentor has to offer.” – Christopher Horruitiner

“Explore every opportunity that arises. You never know what connections you will create, things you will learn and memories you'll make by trying something new.” – Meaghan Faletti

From Deep-C’s Education and Outreach Staff, 
Thank you mentors and students for all your hard work and dedication this summer. 

Deep-C's internship program matches students majoring in STEM fields to research opportunities proposed by Deep-C scientists at the various Deep-C member institutions. The program offers participants opportunities to conduct research in various fields of science as well as gain real-world experience working with scientists on projects that support the Deep-C mission. For more information, visit our website:

Posted By: 
Brittany Pace
Deep-C Internship Coordinator


Emily Goetz's Internship, Summer 2014 - Part 4

Last week was my final official week of working at the lab. I plan to continue some projects through computer work, but I am done with one of my main commitments for the summer--the oyster aquaculture experiments. The experiment will continue for the next six weeks or so before Erica will take down the experiment and weigh and measure the remaining oysters. In the next couple of weeks, I plan to finish up the sections of the invertebrate digital guide on which I have been working. I also hope to work more on the Atlantis ecosystem modeling project.

Posted By:
Emily Goetz, Florida State University

Tuesday, August 19, 2014

Emily Goetz's Internship, Summer 2014 - Part 3

Hello again!

These past few weeks, I have been busy helping with a medley of different projects around the lab. I have been assisting with one of Dr. Gosnell's oyster aquaculture projects, in which he is testing the non-consumptive effects of blue crabs and king conchs on oyster growth with different periods of exposure to the predators. The project has been running for almost a month now, and, last week, we removed the first half of oysters from each of the cages to measure their growth. With 20 oysters removed from each of the 52 cages in the experiment, we have been pretty busy measuring and weighing. In addition to assisting with the oyster projects, I have been working on a digital guide to the sessile invertebrates of the hardbottom reefs in this region. So far I have been assembling a collection of photos and information related to the corals and sponges of the reefs. Next, I plan to start on the tunicates, bryozoans, and mollusks. Although this is the last week I will physically be at the lab, I hope to continue working on some of these projects or to at least keep up with their progress.

Posted By:
Emily Goetz, Florida State University

Friday, August 15, 2014

Rachel Holladay's Internship, Summer 2014 - Part 6

...and the end. Well, basically. Today is the last day of my internship.

Since my previous blog post, some of the team drove down to Bay St Louis to test the ROV in the bay, take some samples and measurements and discuss the upcoming plans with the high school teacher we are working with. It was an extremely enlightening experience that really helped things move forward. The water samples we collected were subjected to a large round of aquarium kit testing which gave details on the conditions.

The ROV has the many tweaks that are customary of the end of prototyping and I am pleased to include these pictures of its (for now) final form. Its capabilities include: GoPro camera system, Arduino powered temperature and depth logging system, active and passive water collector systems and a carefully designed buoyancy system designed to allow the ROV to sink and float as needed.

As this is my final send­off, I want to thank the Deep-C Consortium for this opportunity and this summer, its been a pleasure. I particularly want to thank my mentor, Sergio deRada, for his several years of kind and enthusiastic teaching and guidance. I have spent my past three summers at the Naval Research Laboratory and it has been an absolute joy so I thank everyone who has made my experience possible.

And so...the end.

Posted By:
Rachel Holladay, Naval Research Laboratory

Wednesday, August 6, 2014

Emily Goetz's Internship, Summer 2014 - Part 2

Hi everyone! Things have been busy these past few weeks, and I can't believe my internship is already halfway over. I have been getting adjusted to living and working at the lab, and time has flown by. My work on the Atlantis project thus far has been largely based in research, with the goal of developing my preliminary understanding of the project. I have been reading about the existing models and am starting to build a deeper understanding of Atlantis and the goals for the northern Gulf of Mexico model. In addition, living at the lab has given me the opportunity to assist with other projects, and, in addition to working on Atlantis, I have been helping with the field data collection for some of Dr. Gosnell's other research endeavors, specifically his projects related to oyster aquaculture. In the next few weeks, I am looking forward to applying my research on Atlantis to the actual model and begin the implementation phase of the project.

Posted By:
Emily Goetz, Florida State University 

Tuesday, August 5, 2014

Sam Holladay's Internship, Summer 2014 - Part 4

Recently I have delved further into communication between the iPhone app and the server that receives its messages. The idea is that the iPhone app should communicate data to the server, which can then write data for later use. I have tried several ways of getting the iPhone app to successfully communicate with the server, but several problems remain. The app is still a work in progress, but has improved over past iterations; while it does not communicate successfully, I believe its method is right and it just needs some iterational improvement to make it better.

I have also learned a great deal about the rather opaque dynamics of iOS development. When developing apps one can either use a visual, storyboard-based approach or a textual, code-based approach. I have learned how one can connect the two so the storyboard is supported by the code, which greatly simplifies many of the Internet tutorials and guides I have been looking at (since some use the storyboard, while others use just code). I have therefore designed the first “level” of the app, its homepage, and will soon add additional pages that can be reached with a button.

Posted By:
Sam Holladay, Naval Research Laboratory

Monday, August 4, 2014

Cynthia Kane's Internship, Summer 2014 - Part 3

Last week was a whirlwind! Between finishing up experiments, working on my final presentation, and packing, I hardly had a free moment!

Picking up where I left off in the last blog post, the DNA sequences from samples 16 and 36 are still being analyzed, and the results will arrive sometime this upcoming week. I tried to make clone libraries with several more samples, but they were much less successful than the other two; a little less than a fourth of the plates developed colonies, and even those that did develop only had about 10 to 20 colonies -- nowhere near enough for a clone library. Having tested all other factors, including the agar plates, the electroporator, the vector/salt solution, we think that that the problem is the E. coli cells. Joe ordered new cells, and they should arrive sometime this week as well. Hopefully we will see better results with the new cells!

Other than the clone libraries, I worked on my final powerpoint presentation. As part of the internship, I was required to give a 15-minute presentation, explaining where I worked, what I did, and the results of my 10 weeks. The presentation took place Thursday, July 31st, at Stennis Space Center. I spoke in front of the other NGI-NOAA interns, their mentors, and various people from NGI, NOAA, and Deep-C. I will admit, I was pretty nervous; I don’t really enjoy public speaking. After the first few slides however, I realized that it wasn’t so bad; I knew what I was talking about, and everyone there was just interested in what I had done. This realization made the presentation much easier! After the presentations, Tina, the program organizer, and Natalie, the intern coordinator, took all the interns out for a BBQ dinner at a place called The Shed. All and all, I’d say it was a perfect way to end the program.

Friday morning, Natalie drove us all to the Mobile Regional Airport. We all had the same 1:19pm flight to Chicago, IL. When we arrived at the airport, we were told that the flight had been delayed by an hour and a half. Due to the delay, I had to reschedule my connecting flight. It wasn’t bad though; Bruce, the man at the ticket counter, made sure everything worked out. After changing my flight arrangements, it was just a hop, skip, and jump home to DC!

Now, as I sit in my room writing this final blog post, I can’t help but be amazed at the summer I’ve had and all of the incredible people that I’ve met, including Dr. Snyder, Dr. Jeffrey, Joe Moss, Katie, Josette, and Marie. While I’m sad that it’s over, I’m also so grateful to have been given this opportunity. And so I’d like to thank Deep-C and the NGI-NOAA Diversity Internship Program for giving me a summer to remember!

Posted By:
Cynthia Kane, University of West Florida

Friday, August 1, 2014

Rachel Holladay's Internship, Summer 2014 - Part 5

It's alive!

With some large parts deliveries over the course of the past week and a lot of construction time in the lab, we have the first prototype of the ROV driving around. As of right now, the SeaPerch base is assembled with motors, controls and the attached plankton net while construction of the water sampler is waiting on one final part. I'm in the process of assembling two sets of the sensor suite and have completed most of the circuit board soldering and mounting. Unfortunately, the light sensor is now only produced in a much smaller size and my jumper cable attempts have resulted in mostly singed fingers and electronics.

So far, I've been conducting field tests in a pool behind my building. However, next week a few of us are going to go down to Bay St. Louis, MS to test the ROV in the bay, probably off a pier. In addition to being able to test the aquarium kits and samplers the ability to test the ROV in much more realistic, although unpredictable conditions, should yield some useful experience. During the planning stages, we were worried about the ROV having enough flotation to be buoyant, but recent testing in the pool shows that we actually can't get the ROV to sink! However, the salinity levels in the bay will almost certainly mean different performance, so we'll have to see how it plays out.

Since we attached a GoPro (Hero3 Silver edition) to the ROV, I've been taking footage of the dives. After the field testing, I'll try to compile a larger video showing off a bunch of test, but for now here is a link to an example of a test drive: (I do a lot of iterative testing, shown here is test 4 of 11).

Posted By:
Rachel Holladay, Naval Research Laboratory

Monday, July 28, 2014

Katherine Vaccaro's Internship, Summer 2014 - Part 5

Hello everyone!

Last week was a busy one. After lots of troubleshooting, we finally got results for our single cell ciliate isolates! 
TA-DA! Ciliate DNA bands in gel 
6 out of 8 cells worked (not including our positive sample) which is fantastic news! I cut the bands out of the gel and saved them in individual tubes. Later, when we have a few more samples, we will be purifying the samples to extract the DNA out of the gel for cloning and transforming. And if all goes according to plan, we will be sending out our samples for sequencing and I will have concrete results telling me the species of each ciliate I picked out!

Identifying our ciliates is especially exciting, since Marie Head and I came across an interesting organism while searching our samples for ciliates:
Mr. Mohawk, Unidentified 
Meet our strange little unknown friend! I’ve been calling him “Mr. Mohawk”. Very scientific, I know. After staring at him through the microscope for several minutes, Marie and I decided he had some tintinnid-like qualities and we grabbed him for DNA amplification. Worth a shot, right? When all was said and done, we had 6 out of 8 ciliate samples work, like I said before. The cool thing is, this guy was one of them. The band he produced was bright and clear (Band on the top right of the image of our successful gel)!

When talking to Dr. Snyder about this little guy, he suggested that perhaps he is an invertebrate pluteus (larvae) that had ingested a ciliate, resulting in ciliate DNA being amplified during PCR, but he agreed that it is entirely possible to have found a previously undiscovered ciliate! Marie and I are in the process of asking around our department to see if anyone has any insight into what this little organism might be. We sure are hoping that he is a ciliate, and we are very curious to see what sequence comes back.

So have I assisted in discovering a new species of tintinnid ciliates, or have I just found a (super cute) invertebrate pluteus who had a ciliate snack before we grabbed him from our water samples? Either way, I was part of a fun little mystery, and I got to play detective while trying to determine our little mohawk friend’s identity! Fingers crossed for a new species :)

Unfortunately, my internship ends in two weeks, so I won’t be able to report back to Deep-C on the results of “The Mystery of Mr. Mohawk”, but I still attend school here at UWF so I can continue to assist Marie and Dr. Snyder even after my time with Deep-C ends.

My time here in the lab has flown by! It seems like only a few weeks ago I was getting ready for our research cruise. Now I am getting ready to say goodbye! I still have 1 more blog post to write before my time is up, so stay tuned for my last glimpse into the world of an intern in Dr. Snyder’s lab at UWF!

Posted By:
Katie Vaccaro, University of West Florida

Herbert Johnson's Internship, Summer 2014 - Part 4

Hello everyone!

I have been conducting a primary literature search gathering data on the magnitude of nitrogen fluxes to and from the Gulf of Mexico to characterize the nitrogen budget in the Gulf of Mexico. I will also use the data visualization program Ocean Data View (ODV) to plot water column profiles of nutrient distributions to gain insight into the location of the sources and sinks of nitrogen to and from the Gulf.

I hope that you all are learning a lot and having a great experience with your internships!!!!

Posted By:
Herbert Johnson, 
Florida State University

Thursday, July 24, 2014

Cynthia Kane's Internship, Summer 2014 - Part 2

I can’t believe the ten weeks are coming to an end! It seems like just yesterday I was on the boat collecting samples! The last blog post ended with PCR and gel electrophoresis, so I’ll just pick up from there. After the gel was run successfully, the bands of DNA were cut out of the gel using a scalpel and stored in the freezer. When they were ready to be used, the samples were cleaned with a DNA cleaning kit called Qiagen. Basically, the kit was used to dissolve the gel, so that only the amplified DNA was left.
DNA Cleaning Kit
After the DNA had been cleaned, it was cloned and transformed, in preparation for making clone libraries. The DNA was first mixed with a vector and a salt solution (to maintain the pH) and allowed to incubate at room temperature to allow the cells to replicate. The solution was then added to electrically competent E. coli cells and then shocked to induce the uptake of the vector by the cells. Afterwards, the solution was incubated at 37 degrees Celsius (human body temperature) for an hour, and then the solution was plated on agar plates for the bacterial colonies to grow overnight. In order to select for only the transformed colonies, ampicillin, kanamycin and x-gal were added to the gel plates. Only cells that had taken up the vector would be able to grow on the plates, as the vector contained ampicillin and kanamycin resistance, while normal E. coli cannot grow in ampicillin or kanamycin. The x-gal allowed further selection of colonies by causing colonies that did not transform properly to appear blue/purple, rather than white.

The cloning and transforming part of this process gave me a lot of trouble, as many of the samples that I plated did not form colonies during the overnight incubation. In fact, only samples 16 and 36 developed enough colonies to be transferred to well plates. The cause of this difficulty remained a mystery for several weeks. We thought originally that it was the transformation kit that I was using, so I switched to a new kit. We tried using different agar plates, in case something had gone wrong in the preparation of the plates. When this still did not solve the problem, I used chemically competent E. coli cells instead of electrically competent ones, to see if there was a problem with the machine used to shock the cells. I reused two samples that had not previously worked, samples 28 and 34. After the 18-hour incubation, it was found that all six plates (three for each sample) had grown colonies!

Top left: me plating the transformed cells
Top right: a successful cloning reaction (sample 16); the white dots indicate successfully cloned and transformed cells, the blue dots indicate cells that did not take up the vector. 
Only white colonies were used.

The final step in the DNA analysis was to prepare the DNA for sequencing. To do this, a well plate of 96 wells was used, and one colony was carefully removed from the plate with a toothpick and placed into each of the wells. LB media was added to the wells (a solution to encourage the colonies to grow more overnight). The well plate was incubated at 37 degrees Celsius for 12 hours and then divided into three shipping well trays. A 50% glycerol solution was added to these trays to act as a buffer for the DNA during transport, and they were then sealed, labeled, and sent away for sequencing.

The empty well plate, along with the agar plates containing the transformed colonies
Me pipetting the LB media into the well plates
 The well plate in the incubator. The toothpicks were removed after one hour and the well was sealed with a tape cover for overnight incubation.
Unfortunately, due to the problems we had with creating the clone libraries, the sequencing for the samples will not get to the lab until after I leave. While this is disappointing, as it would have been nice to see the sequences firsthand, I understand that this is also an important part of research; learning how to deal with challenges such as this, which are just another part of research. Also, Joe Moss, my lab instructor, said he would send me the sequences when they are finished, so that I can see the fruit of my labors!

Posted By:
Cynthia Kane, University of West Florida 

Wednesday, July 23, 2014

Erica Levine's Internship, Summer 2014 - Part 3

As this internship draws closer to its end, it’s interesting to look back at where we started and where we've come. We were able to start with a relatively unorganized collection with no form of digital record and make it into the phylogenetically organized and cataloged collection it now is. We have almost completed entering all of the jars into the digital database, and should have all 500+ previously identified items entered by the end of the week. With our remaining time, we are using genus and species keys to identify and label new specimens as they come into the collection. We will also start cataloging the specimens that are stored in larger containers and tanks too big for the shelves.

While there is still some work to be done to catch up with the identification and cataloging of all of the collected specimens, the work we have accomplished over the past month will make it much easier for others to continue expanding the collection and find items already stored at the FSU Coastal and Marine Lab. While there were a few snags along the way, working to overcome the problems and get as far along as we have has allowed me to learn new things about working in a marine collection as well as about general problem solving skills. I have enjoyed my time in this collection and look forward to any future opportunities to continue used the skills I developed while working on this internship.

Posted By:
Erica Levine, Florida State University

Monday, July 21, 2014

Christopher Horruitiner’s Internship, Summer 2014 – Part 2

From June 19th to the 28th, I was on a research vessel called the R/V Weatherbird II. The objective of our cruise was focused on identifying hardbottom habitat along the outer shelf of the De Soto Canyon’s eastern margin (Figure 1). The Chief Scientist on board was Dr. Stan Locker, and his team was primarily interested in using a Teledyne-Benthos C3D interferometric sidescan sonar device to map the sea floor and give us a better understanding of benthic habitats and paleoshorelines. My team from Valdosta State University and I were interested in capturing whole water samples across the water column using a CTD carousel, which also measured the Deep Chlorophyll Max, sound velocity, temperature, etc.
Survey Areas - DeSoto Canyon's Eastern Margin

Anastasia Nienow and I loading samples from the CTD.
On this cruise, we collected pigment samples to later analyze with High Performance Liquid Chromatography (HPLC) and discreet Niskin bottle samples from several depths across the water column to later be analyzed by FlowCAM imaging cytometry, and Scanning Electron Microscopy (SEM) to see how populations (primarily diatoms) change with depth and with season and hopefully we can compile that with a data set going back to January 2011 to identify/understand the temporal-spatial patterns of phytoplankton populations in the DeSoto Canyon region of the northern Gulf of Mexico.

While onboard, the science crew and I had to work two four-hour watches per day, where we helped monitor data acquisition, keep track of navigation, and took a log of activities. We also enjoyed three amazing and nutritious meals a day made by the onboard chef Thomas Lee, who took the care to make me separate vegetarian meals.

With only 8 or so hours of scientific obligations per day on the cruise, there was more than enough time to enjoy living out at sea in the Gulf of Mexico.

The whole crew came onto the deck to take a look at the formation of a water spout.  You can see the tendril of another to the left.
Dolphins were a regular phenomenon whilst on the R/V Weatherbird II.
And I also enjoyed my first real sunset (as well as my first real night sky and my first shooting star(s), which were impossible to photograph at night).
A pod of dolphins!  There was even a calf as well.  We thought they were made curious by the sonar device, but even after it was turned off they continued to show up.  
I am looking forward to analyzing our samples using the new lab equipment!

Posted By:
Christopher Horruitiner, Valdosta State University

Rachel Holladay's Internship, Summer 2014 - Part 4

Hello! Phases II and III of the ROV construction have been delayed while we are waiting for the rest of the parts to arrive. We have, however, tentatively scheduled some field testing in Bay St. Louis once more progress on the prototype can be made. This testing will also allow us to try out the manual that I am currently developing that will assist the intended audience, high school students, to easily collect data.

As a computer scientist, I have little to no experience with using CAD (computer aided design) programs. However, wanting to model the ROV as well as provide some detailed drawings and schematics, I decided to download SketchUp Make and fiddle around. While it isn’t as powerful as many, more professional CAD services, its relatively small learning curve made it incredibly appealing. Below are some of the sketches I’ve made, including a full mock­up of the intended end­result and a heavily stylized idea of the ROV swimming along in the ocean.


Posted By:
Rachel Holladay, Naval Research Laboratory

Friday, July 18, 2014

Sam Holladay's Internship, Summer 2014 - Part 3

Over the past few weeks I have continued work on the adaptive climatology iPhone app. I have continued to conduct a great deal of research into the app, and began work on the user interface. However, I have encountered some problems with designing the app totally from scratch: learning all the iPhone development on my own is difficult, and unfortunately Web resources aren’t the best. After some consulting with my advisor, I have decided to try a new tactic and focus instead on the most important part of the app: establishing communication between the user and our server, so the user can send in information for us to use in our model.

When facing adversity, I have found that determination, repeatedly attacking a problem, usually works after a while. If repeated attempts do not work, then trying the problem from a different angle helps. I hope that working on this different facet of the app will yield better results. Even though I have been greatly frustrated by setbacks, I have still learned a lot about Objective-C and iPhone development, and hope to continue with progress.

Posted By:
Sam Holladay, Naval Research Laboratory

Tuesday, July 15, 2014

Cynthia Kane's Internship, Summer 2014 - Part 1

Hello everyone! Things here at the University of West Florida have been pretty busy - but super fun as well! About a week after I arrived, I went on a research cruise to collect water and sediment samples for analysis. The trip was very education and also very wavy; it took some time to get used to the swaying of the boat. Here are a few pictures of the cruise (also see Katherine Vaccaro’s first post - she has some really good pictures!)

Left: my wonderful partner, Katherine Vaccaro setting up our lab station before we left  
Right: The cruise was great for collecting water samples - and fish! Here is Dr. Jeffrey holding a wahoo we caught while out at the one of the deeper stations

 Us taking water samples from the SeaBird CTD machine

After the cruise, things started picking up; we began doing lab analysis work, including PCR, gel electrophoresis, DNA purification, and clonal library creation. It took some time to get the hang of all the different tests and tools, but it was also really cool to be able to gain first hand lab experience. I’ve included some photos below, mostly of my PCR work. PCR stands for Polymerase Chain Reaction, and is used to amplify very small amounts of DNA so that it can be analyzed.

Me making the PCR samples. 
The “hood” I’m working in is UV sterilized between each sample to prevent contamination.

Left: The gel visualisation machine (on the left) shines a UV light through the gel, causing the DNA to glow so we can see whether the PCR worked or not. 
Right: A successful PCR! The bright bands indicate that the correct fragment of DNA was amplified.

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Cynthia Kane, University of West Florida