Month: December 2022

Mary McGuinness completes MSc on alkalinity in Long Island Sound embayments

Posted on December 9, 2022December 9, 2022 by Manning, Cara

Congratulations to Mary McGuinness who presented her MSc thesis research on alkalinity in Long Island Sound embayments on November 17, 2022. Mary was advised by Dr. Penny Vlahos. Below is a description written by Mary about her research at UConn and her accomplishments during her degree. Check out the photos of her field work, too! Congratulations, Mary, and best wishes for the future!

I came to UConn in June 2020 after receiving the Crandall Fellowship for my commitment to diversity enhancement in higher education and science during my time as a undergraduate of the New Jersey Institute of Technology. While working on the Alkalinity of Long Island Sound Embayments (ALISE) project I was able to conduct field work across the Long Island Sound and help close the gap for alkalinity and inorganic carbon data in these rivers. Over a two year study I observed spatial trends for alkalinity across the Long Island Sound rivers, at their freshwater endmembers and detected help levels of acidification sensitivity. Lastly I produced an attributive model that indicated importance differences between the eastern and western Long Island Sound and presented novel controlling parameters which can be tested with the collection of further data to help fully resolve this system.

I was able to present my work virtually the Ocean Sciences Meeting (2022) and in person at the Long Island Sound Conference (2022) and Society of Environmental Toxicology and Chemistry Conference (SETAC) (2022). At the SETAC Conference I was presented with the best Oral Presentation Award.

Filtering for dissolved organic carbon at the Thames River

Collecting data in the Thames River with labmate Lauren Barrett

Finishing a day of data collection at the Housatonic River

Meet Dennis Arbige

Posted on December 2, 2022December 2, 2022 by Hannes Baumann

By Ewaldo Leitao.

For the longest time, Marine Science students and staff have known who to email first with any worries or equipment malfunctions: Dennis Arbige. Until recently, Dennis was the manager of our Marine Sciences Building, but Dennis has been so much more than a manager. A man of many hats, Dennis not only knows the building like the back of his hand, but is also a talented electrical engineer who deals with a multitude of equipment (and their problems) allowing research to go as smoothly as possible – always with a smile on his face. Dennis has now retired, after 29 years of service to the department. We conducted an interview to learn more about his path, his past, and the changes he saw while working here.

Dennis, thank you so much for agreeing to do this interview. What has been your career path and how did you get here?

Dennis: It’s my pleasure! So, I grew up with Jacques Cousteau books’. I think the first book I read cover to cover was a Jacques Cousteau book because I had to read it in high school and it was only 70 pages, so I picked that. I was like “Oh, this is pretty interesting” how they do scuba and things like that. I then became interested in oceanography, while growing up near the ocean in Rhode Island. In high school I went to the Coast Guard to get money for college. I wanted to be a marine science technician in the Coast Guard. I wanted to go out and measure things like salinity and temperature, and I thought that would be pretty cool. But when I got to the Coast Guard they were like “well, we don’t do this anymore”. So I became an electronic technician.

EL: How did you come back to oceanography?

Dennis: During my four years in the Coast Guard, I was stationed all over the country. I was in Boston for a while, and they used to fly me over on a helicopter as an aid to navigation, working in lighthouses and things like that. This was about the time they were changing to automated lighthouses, so they would drop me off on these crazy little lighthouses all over Massachusetts and New Hampshire. I worked with a team, and installed things like fog detectors, etc. This was back in the early 80s. Every single installation had its challenges, because these were all old structures. It was super fun, these lighthouses were historical and cool. So I did that for four years, and when I left the Coast Guard I joined Rutgers University for an electrical engineering degree. I worked in New Jersey for a while, and while I was there I got interested in physical oceanography. There were people working on satellite stations and satellite dishes, for NASA and NOAA. So I became interested in what they were doing, remote sensing, sea surface temperature, and things like that. I started taking graduate courses in sea-water interaction, because they didn’t have any physical oceanography courses.

EL: So did you finish grad school and applied for jobs in oceanography?

Dennis: When I was still in grad school someone sent me a job application for a place called Ocean Surveys, in Old Saybrook in CT, I interviewed and I got the job. They did a lot of bathymetry and ocean sensing, near shore coastal stuff. So actually while I was in Ocean Surveys, I worked in the attic, with these slanted roofs. One day I heard this voice complaining, one of the customers kept bumping his head on the ceiling, and I was like “who is that guy?” My colleague told me this tall guy was from the UConn Marine Sciences department, his name was Frank Bohlen. So I ended up sending letters here to UConn, because I thought that “this place sounds like fun”. Actually Frank said: “hey, come on in, we can talk”. There was another wave of retirements at that time, in the 80s, so eventually, I got a job. I came here as an electronic research technician, 29 years ago. And I just never left.

EL: You jumped from industry back to academia sort of in a way. Was there something that appealed to you in this academic environment?

Dennis: Yes, it seemed that it was more fun, it had more variability. When I was here I worked as a scientific diver, and I also had some boating experience. Back in the day there were fewer people here, so I got to run small boats and to dive. I used to tell my wife: I would do this job for free, and she would reply “you better stop saying this”. It was fantastic, it was so much fun being here.

EL: You’ve seen a lot of changes here clearly, including this building being built. Can you talk a bit about how it was to experience that?

Dennis: When we got this building, that was a game changer. We went from the old building to this new building in 1999- late 2000s. The faculty got to design this building from the floor to ceiling. They basically got a piece of paper and were asked “what do you guys want?”. The faculty decided to have environmental chambers, a wet lab, a hydrodynamics lab, etc. And so it happened, and that was thanks to Dave Cooper who had a lot of influence, and he was a very smart guy. The new building put us on the map basically. A couple of years later we also went from the old RV UCONN to the RV Connecticut. When we got the floating docks, all of the facilities were consolidated in one location, here.

EL: In this building, would you consider that you’re a jack of all trades and master of all? Haha

Dennis: Master of none! That’s what you mean! OK, at this point I know a lot about this building. It’s funny to even talk to the trades people that we hired to come in here, I tell them: “pay attention to that because that will affect x, y and z, which will affect something else” and so on. It’s good to pass this knowledge along because some of this stuff will be hard if you don’t know about it. This is a complex building with a lot of systems, and they’re all interconnected, but it might not be clear why or how, so that’s something that I had to learn over time, by default, because you keep coming back inside.

EL: What was one of the happiest moments that you experienced in your career?

Dennis: The ROVs (remotely operated vehicles) were really fun! I’ve seen shipwrecks, I've seen crazy fish that I've never seen before. One time we put the ROV in the bottom, and the bottom looked like it was moving. It is all dark and you can’t see much, so as the ROV was approaching the bottom we saw that it was covered with shrimp. These shrimp were like 4-6 inches long! We were trying to find a place to land not to crush all these shrimp, because they were everywhere. We were off of North Carolina. The captain and the crew were all fishermen at some stage in their lives, and they were all going crazy, like “we never seen shrimp this thick before!”. It was one of the coolest things I’ve seen in my life.

EL: You’ve seen so many cohorts of grad students. Do you have any advice for younger students?

Dennis: Don’t be intimidated by the faculty and staff, because they're good people. If you have a question you should just go and ask. We all want you to succeed. Everybody will pretty much go out of their way to help you, to make sure that the students succeed. Faculty are just regular people. For example, my own kids used to play soccer with the faculty here, and they realized that the faculty are just regular people, which greatly helped them get through college. So don’t be afraid to approach them and ask them questions.

EL: And since you mentioned soccer…

Dennis: I know, I can’t go through a conversation without mentioning soccer, haha

EL: When did this soccer thing start here? For how long has it been going on? Were you the one who started this?

Dennis: It has been going on for some time and it actually started with the Coast Guard. Again, the Coast Guard used to have about 200 people working here. They had a huge presence once I first got here. I started playing with the Coast Guard people and when they eventually moved out, they kinda bequeathed their nets to me. Some pop up nets that they owned. At that time it was just me and some other people, including Jim O’Donnell. Soccer has been going on since the beginning.

EL: Who are you bequeathing it to now?

Dennis: Oh, to Michael.

EL: Do you have a retirement plan?

D: My wife has a list of projects that I need to do in the house. So I told her I would do it but I’d have to quit my job. But now I am like, alright. I have actually learned a lot from working in this building and working with the contractors, so that helps me a great deal on how to do these home projects.

EL: But soccer is here to stay, right?

D: Oh yes, for sure. When you do these extracurricular activities your work is still getting done, but it’s getting done in a less formal manner. On the field and on the court. It’s an amazing community.

“Harmony of Nature”: environmental data becomes music

Posted on December 2, 2022December 5, 2022 by Hannes Baumann

By Ewaldo Leitao.

Science communication has many flavors, kinds, and sounds. One way by which that can happen is when nature or science produce “noise” that can be channeled into sounds. That can be done using architecture (Sea Organ), or reinterpreting a field of science (Quantum Computer Music). Sometimes, this combination of sound and science can be a deliberate choice, creating music.

DMS student Molly James and musician Hea Youn Chung (Sophy) combined their expertises and interests to explore this intersection between science and music. Molly plays trombone in her free time at a community orchestra. Sophy is a professional pianist and teacher at Yewon Arts School (Seoul, South Korea) who did her Master of Music degree in Piano Performance at The Juilliard School. What initially joined these two at the dead of the pandemic was a mutual language assistance: Molly wanted to learn Korean, and Sophy, back in South Korea, wanted to continue practicing English.

And that’s how “Harmony of Nature” was born. A beautiful collaboration that converts natural phenomena into sounds through coding technology and expresses them in classical music. The project was funded by the Art & Tech program by Arts Council Korea. The data was collected using temperature loggers deployed in several sites across South Korea, along with freely available data from several spots. “I statistically analyzed this data and created multiple graphs using the open-source coding language Python. I shared them with Sophy and discussed the scientific interpretations. Together, we collaborated on what scientific aspects became what musical aspects.” said Molly, about the process of data collection and curation, prior to its translation into music.

“Like expressing human emotions through musical instruments, I have always wanted to express natural phenomena that we cannot see but can feel through sound. While envisioning this project, I focused on conveying natural phenomena through sound.” said Sophy. “For various expressions, I try to incorporate nuances such as shape and texture into the performance. In this project, the weight of the waves, the ebb and flow of the waves, the temperature changes, and the appearance of rain can be realized by various musical elements such as rhythm, dynamics, etc.”

The composition “One Week in Incheon” directly came from hourly air temperature measurements collected at a weather station by the Korean Meteorological Administration Incheon branch 112. Other data, such as wave height, flow and ebb tides, were also analyzed in order to compose some pieces. “During this performance, I hope you can feel changes in temperatures, drops of rain, speed of the winds, and height of the waves”, says Molly. More songs can be found on Spotify or AppleMusic.

Science needs to reach out to the public, informing in different, inventive, artistic ways. Art is powerful. Collaborations between science and art will thrive as each part can use their unique skills to result in beautiful projects, such as this one.

From microbes to whales: alumna Susan Smith on her career journey

Posted on December 2, 2022December 2, 2022 by Hannes Baumann

By Ewaldo Leitao.

Dr. Susan Smith graduated in December 2020, during the pandemic, from UConn Avery Point with Dr. George McManus. Her work focused on the ecology and molecular biology of marine ciliates (a kind of eukaryotic microzooplankton). During her PhD, Dr. Smith (Sue) discovered a new genus and species, published the first tintinnid ciliate genome, and formed lasting collaborations with some remarkable scientists. Susan is currently a research scientist at the Mystic Aquarium, where she studies the microbiome of beluga whales.

Q: Tell us a bit about the research you have done during your PhD.

Sue: While at UConn, I had the opportunity to take part in every facet of research—we would take a boat into the Atlantic and sample, bring them back to the lab and do microscopical and experimental work, and then use those same cultures for downstream genomic and genetic analyses. We would often do what my mentor would call “old world” microscope work, but would then take that same single cell and sequence its whole genome, all in the same lab. That kind of work that runs the full gamut of biological research is so rare today, but was such a valuable experience, and really allows you to understand your subject. I think the UConn Marine Sciences Department presents that opportunity far more than your average academic research setting, which is especially important for graduate students.

I actually had the good fortune of doing my B.Sc., M.S., PhD., and my Postdoc at UConn Avery Point (I’m a bit of a stubborn forever-student). I finished my postdoc two months ago (~1.5 years in) and immediately started my new position as a research scientist at Mystic Aquarium (luckily our labs are on the Avery Point campus so I get to keep my parking space and continue my path towards being a permanent fixture on campus).

Q: You’ve had the opportunity to teach during your postdoc. How was your teaching and postdoc experience?

Sue: I had the great pleasure of filling in for my (lifelong) mentor and graduate advisor Dr. George McManus when he was on sabbatical, which allowed me to teach his graduate course, Biological Oceanography. Teaching Bio Oce was a unique opportunity to work with higher level students that were serious about their graduate/educational career, and I valued and enjoyed that immensely. Luckily, even with my full time research position at Mystic Aquarium, I get to keep an appointment at UConn, and am scheduled to teach Marine Biodiversity and Conservation this spring semester (still seats left!). I’m extremely grateful to remain a part of both scientific communities.
Continuing a postdoc position in the same lab I did my PhD in allowed me to complete projects I was excited but over-zealous about during my PhD, and also allowed me the autonomy to ask new questions that were a little off track from the direction of the lab. Of course, there’s a major benefit in going to a different lab for your postdoc, especially if you want to change course on your research goals, but these days most PhDs end up doing two postdocs before finding a faculty position, so it’s something to consider.

Q: How did your previous work align with your current job in the aquarium? What are you doing now and what have you planned to do in the aquarium?

Sue: The postdoc project I was most enthusiastic about involved these unique ciliate species that live in cetacean blowholes (as a part of their natural, healthy microbiome). Admittedly, this project all started as a blatant excuse to collaborate with Mystic Aquarium and interact with the beluga whales there. I worked with some REU students (Research Experience for Undergraduate students) during the summers to investigate this more. The major benefit of this work was that it formed a collaboration with Dr. Tracy Romano (VP and Chief Scientist of Research at Mystic Aquarium). Today, my work at Mystic Aquarium largely surrounds host-associated microbiota. To be in a position where you have so many samples and project options that you can’t decide which grant proposal you’re most excited to write, is a great feeling. I also now contribute to weekly sampling efforts, so I get to hang out with whales every week—that’s pretty awesome too.
Part of my work today focuses on how the microbiome of a new animal host changes as they are introduced to a different host population. I also have some other fun projects going on, including genetic sexing of penguins, microbiome analyses in sea turtles, and stress-response tests in stranded seals. In general, my research is focused on answering these questions using non-invasive methods that not only avoid stressing the animals, but also can be used in the conservation of wild populations that are impossible to have close contact with

Q: What is the best part about working in the aquarium?

Sue: The best part about working in the aquarium are my colleagues. It quickly became clear that every veterinary staff member, animal husbandry professional, and researcher, are concerned with animal welfare above all else. Further, all Mystic Aquarium research has an application in the conservation of wild (often endangered) populations, and even non-invasive interactions with our animals are extremely regulated, as they should be. Additionally, and although lesser known, MA also puts an enormous amount of effort and resources into our stranding clinic, from seals to sea turtles, where the rapid recovery and release of these animals is of highest priority. These stranders also allow for some opportunistic (non-invasive) research sampling that can go a long way in identifying threats and diseases afflicting wild populations.

Q: Do you have any hobbies and/or activities you do in your free time?

Sue: This question would have worried me as a graduate student, since any energy put towards extracurricular activities would have been an unthinkable waste of time. However, I’m grateful that my current position is structured in a way that prioritizes a separation between work and home, which is something I didn’t realize I needed. Today, I’m happy to spend nights reading some old science fiction novel with a glass of red wine and dogs by my side. However, I also truly get pleasure from my work and will gladly spend a Saturday at a coffee shop with a (likely late) manuscript.

DMS grad students do outreach in local elementary school

Posted on December 2, 2022December 2, 2022 by Hannes Baumann

By Ewaldo Leitao.

Academic institutions have a tendency to stay in the “Ivory Tower” and be distant from their surrounding communities. Scientific communication and outreach is a great way to minimize the gap between institutions and their communities, and to educate the new generation, especially about environmental awareness. We in the Marine Sciences Department try our best to be aware of this and reach out to communities in order to explain what we do. During the Ocean Week (June 7-9), Prof. Hannes Baumann and Dr. Zosia Baumann, reached out to the Catherine Kolnaski Steam Magnet School, in Groton/CT to give science talks about various marine science topics.

Zosia introduced the Long Island Sound and its importance to 2nd grade students. Then the kids split up to visit various stations. The stations were led by graduate students Ewaldo Leitão, Lingjie Zhou, Max Zavell, Jenna O’del (URI), Molly James, and Dr. Susan Smith. Each one showcased their area of expertise, but catered to 2nd graders.

There were four different stations. Ewaldo and Susan explained plankton and their importance, despite their tiny size, connecting with the kids using the famous Plankton from SpongeBob Squarepants as an example and how it was created based on copepods. To grab kids' attention, organisms were displayed in many different ways, with pictures, a dissecting scope that had a sample with shrimp, baby starfish, a concentrated sample of copepods, and finally a copepod under the microscope so that kids could see how similar copepods are to the Plankton.

Lingjie introduced the concept of DNA, and made the kids build their own DNA strand by using gummy candies and straws. She explained the bases of the DNA using gummies with different colors to represent each, and how they match in the strand. As a motivation, the kids could take their own DNA strand candy home.

Max and Jenna were explaining fish physiology and behavior. They used cleared and stained specimens to show bones and cartilage of the fish. These can determine important fish behavior such as schooling, which is easily observable in the wild.

Finally Molly explained the physics of the ocean. Using dyes to color water with different salinities, she demonstrated how salty water is denser and therefore stays in the bottom of the less dense, freshwater. These are not just important concepts for the ocean, it is why the kids can buoy easier in the ocean compared to lakes.

There’s an inherent joy and challenge in explaining scientific concepts to kids. We, scientists, are often told to have our elevator pitch in many levels of expertise, in order to explain what we do to our mom and to a potential employer. But explaining to kids is a completely different game. They can have a rather short attention span and yet get easily fascinated by new things. Therefore, explaining scientific concepts requires a combination of teaching them in an exciting way, that is also engaging but simplified so that they are able to retain the knowledge.

Having said that, it is a delight to end these interactions by asking the kids what they have learned, and listening to their excitement when they describe what they have just seen and experienced. Scientific outreach to our youngest generation is a great way to create environmental awareness and to build minds who will take better care of our planet.

Surveying ocean acidification on the Northwest Atlantic shelf

Posted on December 2, 2022December 2, 2022 by Hannes Baumann

By Ewaldo Leitao.

In August of 2022, Prof. Samantha Siedlecki and Prof. Craig Tobias, along with students Halle Berger and Alex Frenzel, went on the East Coast Ocean Acidification Cruise (ECOA-3). The cruise was led by scientists at the University of New Hampshire, joined through transdisciplinary partnerships with other universities, aboard the NOAA Ship Ronald H. Brown. The UConn Avery Point members joined the cruise to investigate the contribution of sediments to carbon chemistry and how that ultimately impacts ocean acidification.

Sam, Craig, Halle and Alex were the sediment coring team. The cores go all the way down to the bottom of the ocean and collect both the upper part of the sediment and the layer of water above it. This way, it is possible to understand chemical reactions in this zone between the sediments and the water above it. “The idea here is to understand how sediments control the chemistry of bottom water. There are sediment reactions that could help buffer acidity. But it's unclear how sediments talk to the water above it or how that communication might change in the future” says Craig. You can learn more on the Facebook page of research vessel Ronald H. Brown.

These measurements are valuable information because they are not only timestamps of what is happening at the moment of collection. Increasing the number of observations and fine-tuning the measurements of these chemical processes in bottom waters helps the research of modelers, like Sam. Models are important to test our understanding of ocean processes. We need more measurements like this to more accurately predict marine climate change. Part of Sam’s work is to use this information into regional ocean models to better constrain the role of sediments in the chemistry of the ocean.

Graduate student Halle uses modeling to understand how ocean acidification and warming impacts marine animals like Atlantic sea scallops. “I learned a lot about how all the different carbonate system parameters are measured, and it was great to meet other students and scientists working on ocean acidification. We got to see some whales and dolphins, amazing sunsets and starry nights, and ate a lot of delicious food. My favorite memory was at one station where all the multi-corer brought up was a single hermit crab (no sediment at all). We named him Fred.”, said Halle.

This was the third ECOA survey, which only happens every four years. The cruise starts in Newport, RI, travels to Portland, ME and then continues on to Nova Scotia. Traveling the Gulf of Maine, Georges Bank, Long Island Sound, Mid-Atlantic Bight, Chesapeake Bay, and the South Atlantic Bight. Each of these regions has their own physical processes that affect ocean acidification in each region, such as the Gulf of Maine receiving cold waters from the northern Labrador current and freshwater from rivers. In each of these regions, ocean acidification will likely have different effects. In the South Atlantic Bight, coral reefs, soft bottom corals, and therefore fish abundance may decline with ocean acidification. To better understand and accurately predict the impact of ocean acidification in different ecosystems, it is important to continuously do these measurements in order to understand how processes are changing over time in such dynamic environments.