“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.

Dr. Lingjie Zhou defends PhD on quantifying phytoplankton carbon biomass using DNA

Posted on November 30, 2022November 30, 2022 by Manning, Cara

Congratulations to Dr. Lingjie Zhou on her Ph.D. defense. Check out Dr. Zhou’s description of her Ph.D. journey and accomplishments below. We are wishing Dr. Zhou all the best for her future career!

I defended my Ph.D. dissertation entitled “Estimate phytoplankton carbon biomass using DNA” on Nov. 15^th, 2022. My Ph.D. research was aimed at establishing the correlations among the cellular contents of DNA, C, and rDNA in phytoplankton and I measured these parameters for 11 species spanning major algal lineages at different growth stages and under different growth conditions. The correlations would enable oceanographers to determine the species composition and species-specific carbon biomass in the phytoplankton community simultaneously. Throughout the Ph. D. study period, I gave presentations at conferences, including the Northeast Algal Symposium, Phycological Society of America, ASLO Aquatic Sciences Meeting, and Feng Graduate Research Colloquium. I have published several papers as co-author (listed below), and I’m still working on my own papers now. I have received the Student Research Award from the Ecology and Evolutionary Biology Department of the University of Connecticut (UConn) and the Connecticut State Museum of Natural History in 2019 as well as several summer research awards from the Department of Marine Sciences at UConn.

References:
Nanjing Ji, Jinwang Huang, Zhenzhen Zhang, Lingjie Zhou, Xin Shen, Senjie Lin, Identification and expression analysis of meiosis-related genes in the harmful alga Heterosigma akashiwo (Raphidophyceae). Harmful Algae, 2020, 92, 101736, ISSN 1568-9883, https://doi.org/10.1016/j.hal.2019.101736.

Nanjing Ji, Zhenzhen Zhang, Jinwang Huang, Lingjie Zhou, Shengxian Deng, Xin Shen, Senjie Lin. Utilization of various forms of nitrogen and expression regulation of transporters in the harmful alga Heterosigma akashiwo (Raphidophyceae). Harmful Algae, 2020, 92, 101770, ISSN 1568-9883, https://doi.org/10.1016/j.hal.2020.101770.

Chuner Cai, Feng Liu, Ting Jiang, Lingke Wang, Rui Jia, Lingjie Zhou, Kai Gu, Jianfeng Ren, Peimin He. Comparative study on mitogenomes of green tide algae. Genetica, 2018, 146(6): 529–540, https://doi.org/10.1007/s10709-018-0046-7

Zhou at the 56th Northeast Algal Symposium in April 2017

Zhou at the ASLO 2019 Aquatic Sciences Meeting in February 2019

Annette Carlson presents master’s thesis on oxygen and nutrient cycling in St. Helena Bay

Posted on November 19, 2022November 20, 2022 by Manning, Cara

Congratulations to Annette Carlson, who presented her master’s thesis on November 9, 2022. Annette‘s thesis was entitled “Quantifying interannual variability of shelf nutrients and associated hypoxia in St. Helena Bay with new metrics and tools” and she was advised by Professor Samantha Siedlecki. St. Helena Bay is located in the Southern Benguela Upwelling System off the coast of South Africa. During her master’s, Annette traveled to South Africa to work with collaborators at the University of Cape Town and gain experience collecting water samples, and analyzed an existing dataset to characterize and develop mechanistic understanding of the variability in nutrients and oxygen in this dynamic upwelling region.

Annette also presented a webinar on her thesis work to the Global Ocean Oxygen Network in October 2022, which is available on YouTube, and she participated in several conferences.

Congratulations, Annette, and best wishes in your future career!

Carlson’s thesis was funded by the US National Science Foundation through a grant to Dr. Samantha Siedlecki and Dr. Julie Granger.

Annette Carlson and colleagues (Raquel Flynn (left), Sina Wallschuss (right)) sampling for oxygen and nutrients in False Bay, Cape Town, South Africa. Photo credit: Pieter Truter.

DMS Kayla Mladinich shows that bivalves can reject microplastics

Posted on November 8, 2022November 8, 2022 by Hannes Baumann

8 November 2022. DMS is happy to share the latest publication by PhD student Kayla Mladinich, showing the surprising but good news that blue mussels and oysters appear not to ingest all microplastic particles floating in the water.

By Kayla Mladinich.

Oysters and mussels are filter feeders that draw particles in from the surrounding water to be eaten. These animals can select which particles are eaten or rejected depending on factors such as particle size and surface properties. This study was performed to determine what kinds of microplastics will be consumed or rejected by oysters and mussels. Both species rejected larger microplastics more than smaller microplastics and did not differentiate between different types of plastic polymers. The results suggest that oysters and mussels will not ingest all microplastics that they are exposed to in the natural environment!

Shell recycling will help restore oysters in Long Island Sound

Posted on November 7, 2022November 7, 2022 by Hannes Baumann

By Elaina Hancock.

7 November 2022. An unexpected find of a healthy, well-established oyster reef tucked away in a shoreline park inspired UConn Marine Science researcher Zofia Baumann to study ways to help these vital ecosystem engineers make a comeback.

Oyster habitats were largely destroyed by development, over-harvesting, and pollution, but in Long Island Sound, their numbers might be on the rise. Baumann and others hope to help restore Connecticut’s oyster populations.

Oysters build habitats where many species flourish, they improve water quality and make shorelines more resilient to erosion, but they need old shells to start building on. The site that became the focus of the project is one where oyster shells were deposited. Unfortunately, there is a shortage of shells in Connecticut and addressing this problem is the primary goal.

The project brings together members of the community, shellfish farmers, and regulators, as Baumann says, this effort relies on the community, otherwise, it will not work.

Dr. Yipeng He becomes the department’s newest PhD!

Posted on November 3, 2022November 3, 2022 by Manning, Cara

Congratulations to Dr. Yipeng He, who successfully defended his PhD thesis entitled “Air-sea exchange of mercury and its species in the coastal and open ocean” on October 28, 2022. Dr. He was a student in Professor Rob Mason’s group and his PhD research included research cruises in the Pacific Ocean (GEOTRACES cruise GP-15), Arctic Ocean, and Long Island Sound to collect measurements of mercury at the air-sea interface. Drs. He, Mason and colleagues have already published some of the thesis results in Environmental Science & Technology and Atmospheric Environment.

Check out some photos from Dr. He’s journey below!

Dr. He will be departing soon for another GEOTRACES research cruise to collect more mercury data!

Dr. Yipeng He and Dr. Rob Mason following a successful thesis defense!

Yipeng He and colleagues on an Arctic research cruise

Yipeng and colleagues coring ice in the Arctic

Yipeng and the Mason lab with their atmospheric mercury sampler

Outreach event for eelgrass restoration

Posted on October 29, 2022October 29, 2022 by Manning, Cara

On October 19, members of the Marine Sciences Department participated in an outreach event for a research project that is led by Professors Craig Tobias and Jamie Vaudrey, graduate student Shannon Jordan, and Chris Pickerell from the Cornell Cooperative Extension. The research is funded through the Long Island Sound Study. The researchers are aiming to improve the success of eelgrass restoration by adding a chemical amendment to the sediments when eelgrass shoots are transplanted to a new location.

The outreach event involved bringing community members and scientists together to prepare the eelgrass shoots for transplanting at the new sites in the Niantic River. Shannon and the team have also been conducting lots of field measurements and laboratory experiments in the lead up to the transplanting event. We look forward to learning how the eelgrass grows in its new habitat over the next year!