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