OUR WORK

I.D.: Research and Exhibition on African-American Students at UMass Dartmouth

By Erick Maldonado

I am a senior Fine Arts major in the Department of Art and Design.  I also minor in Art History in the Department of Art Education, Art History and Media Studies. The goal my OUR-funded project was to highlight African-American student life on campus. I used the fund to do research, purchase painting materials, and organize a solo exhibition, featuring portraits of African-American students on campus. Every portrait is accompanied by a short narrative, describing the thoughts of the student models I chose to paint. My project was supported by Professors Pamela Karimi (Art History) and Bryan McFarlane (Painting) and I am extremely grateful to both of them for their guidance.

Erick Maldonado presents his thoughts on art and issues of displacement to a large crowd of audience at the New Bedford AHA! Festival. 

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As a Dominican-American on campus, I see women and men with different complexions living in complex environments. As students of color, we sometimes feel the barrier of living and communicating within our Institutions of education. At the same time, the African American culture has grown a sense of resiliency against the old racial assumptions. And this is largely thanks to the efforts of those protagonists who made America a better place for all of us. During the Harlem Renaissance, many African-American artists created works that resisted the racial oppression of their time. These artists wanted Black voices and Black stories to be heard, and by doing so they vocalized their own stories to stand up for their rights, by empowering a community and continuing to provide a dialogue, many musicians, artists, writers, and scholars gathered together to make a difference.

It is important to note that during this time there was also a demand for African-Americans to be proud of their racial heritage. In later decades many African-American artists continued to voice their perspective regarding racial oppression. For example, Betye Saar made The Liberation of Black Jemima. By creating an image of Aunt Jemima inside of a frame with a Caucasian child on her hip, Saar used iconographic imagery to state and comment on African-American women and their labor in American history. Romare Bearden, an African-American painter, developed a vocabulary with sudden burst of bright hues that at the time helped depict African-American men and women. His portraits represented black commonalities and helped address African-American living conditions. Lastly, our contemporary, Kara Walker, uses silhouettes and folklore to frame the complex social and living conditions of slaves and slave masters. These artists continue to inspire me to turn history into art and to use the beautiful language of art to address important issues in Black communities.

The ongoing political and racial issues that continue to develop mayhem in this country is what I planned to comment on through this research project that led to a solo exhibition, titled ID. In particular, I wanted to be able to give a strong voice to those UMD students who feel incapable of expressing themselves.

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Erick Maldonato’s solo show, I.D., at the 224 Gallery, UMass Dartnmouth.

Facing the everyday horror of trying to communicate stories, purposes, and lives, my exhibit is a reflection of my identity. My subjects include students from campus who have succeeded in bringing awareness to blackness, continue to inspire and change the frame of blackness on campus, and who elude and conspire a tradition of black representation that also emits the beauty of the community on campus. My overall vision of my project was to unite a group of people in the common goal of embracing culture. As evident due to our country’s divide, Black students are easily more targeted. This OUR-funded exhibit allowed me to create a dialogue where students were able to use their voice to express their identity and culture. Through my paintings and the interviewed that ensued students were able to communicate who they are. Black students are now more than ever are afraid to submerse themselves in a controversial dialogue. Therefore, I wanted to create paintings that would help project their narratives.

Details of Erick Maldonato’s paintings at the 224 Gallery, UMass Dartnmouth.

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It was truly an honor to be offered an OUR grant in Spring 2017. This successful experience gave me the courage and confidence to apply for external grants. And I am particularly grateful to my professors Pamela Karimi (Art History) and Suzanne Schireson (Painting), who encouraged me to apply and supported my application. The following summer, I applied and received a Mellon Summer Internship at RISD Museum.  My position at the museum was with the Contemporary Art department, where I worked closely with Richard Brown Baker, Curator of Contemporary Art, Dominic Molon and Nancy Prophet’s fellow Amber Lopez.

Some of my tasks included overseeing works and maintaining files of nearly hundreds of objects in the collection and preparing research of works for future exhibitions in the galleries. I learned so much from this program. RISD Museum’s Andrew W. Mellon summer internship program introduced me to museum work, the professional skills necessary to work in the arts, and the functionalities inside a museum. This experience shifted my perspective of how I view myself as an artist. The busy, continuous and challenging cycle of distributing art and curating work is one where it’s diligent, practice is valued, and production is a priority. One of the most exciting experiences in the museum was creating my own program for RISD’s Third Thursday. Third Thursday, is an open night where the museum audiences engage more with the collection. My program consisted of learning about color relationships and how they impact shape, form, line, symmetry, and space. It was rewarding working with such a community. I value my time in Providence and the exposure to such programs.

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In conclusion, the Office of Undergraduate Research provided the special skills and tools that I needed to enhance my knowledge of painting, curation and above all African-American life experience. Learning, exploring, and sharing stories of African-Americans in my community has been an advantage; it has helped me provide other students with an opportunity to find a space to express themselves. This project enabled me to become a better curator, painter and even artist. Above all, it helped me become a critical thinker; it allowed me to appreciate the importance of art historical and anthropological research and to want to encourage others to question the world we live in and instill a sense of pride in black communities.

Evolution of the Princess Culture: Discourse Analysis of Film and Merchandise Reviews

By Morgan Banville

I am a senior English Literature and Criticism, and Writing, Rhetoric and Communication major.  This research was partially supported by the OUR created for my Honors Thesis at UMass Dartmouth.  My project was advised by Katherine DeLuca and Caroline Gelmi.  Their hard work and dedication is greatly appreciated.

Portrait of Morgan Banville

The purpose of this study was to describe the ways in which film and merchandise reviews for Disney princess films such as Pocahontas, The Princess and the Frog, Brave, and Moana, depict Disney’s attempts at becoming progressive in their representations of female role models for young children.  The study was conducted in response to the ongoing discussion surrounding the Disney films and their inability to represent realistic and attainable role models for viewers.  The basic design of the study was conducted through coding and discourse analysis.  The study focused on how stereotypically racial and gendered rhetoric is used to describe the princesses, as well as the reliance on a male figure and various sexual innuendos.  Despite some progress, there are a few issues that remain with how Disney princesses are portrayed.  Both film and merchandise reviews continue to use coded rhetoric, which creates unrealistic expectations for young children as well as inadequate role models.

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When one hears the word “princess,” more often than not the image of a Disney Princess comes to mind.  The image of a Disney princess is usually standard throughout the line:  the women are heteronormative, accompanied most often by a prince, and oftentimes descendants of royal blood or married into royal blood.  The stereotype associated with the princess line are women who display incredible beauty, have skinny waists, sleek hair, and perfect clothing.  Although the flawless features of the princesses are a distinguishing feature, this also poses some issues for those seeking women who are not “perfect.”  In my research, I analyzed film and merchandise reviews because these mediums are primarily where the audiences are being influenced.  Both children and adults alike are highly influenced by visual rhetoric; an adult is more inclined to watch a film with their child and comment on it rather than a child going online and writing a review.  In this way, the data I gathered allows for an analysis of the perceptions parents have of the culture that is impacting their children.

Merida from Brave representations & Pocahontas Film versus Merchandise

In my research I found that Disney merchandising and films have racially charged rhetoric that impacts audiences’ perceptions of the princesses.  The film and merchandise reviews displayed terms relating to stereotypical racism in regard to expectations of that particular race, as well as terms demeaning the race.  Disney merchandising and films also perpetuate specific beauty standards.  The inclusion of demeaning physical descriptions of the princesses also serves to weaken their characters and perpetuate sexist ideals for women.  These perceptions, it seems, can lead to internal biases when examining the films and even could be a contributing factor to the disagreements regarding whether or not princesses are negative influences for young girls.

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I applied the methodology of Discourse analysis and coding method to the film and merchandise reviews.  Discourse analysis examines how language is used to construct “ways of being in the world.”  Coding categorizes language to make sense of dominant trends.  Using the coding method, I categorized the rhetoric of film and merchandise reviews into categories associated with racism/racial terms, gender ambiguity, sexual innuendos, and stereotypically feminine/masculine terms.  To categorize and code the films and merchandise, for example, I documented the typical masculine traits such as athleticism, bravery, or independence, as well as the feminine rhetoric such as any action or trait relating to showing emotion, physical features (pretty, beautiful, gorgeous), or being submissive.  After studying the merchandise and film reviews of the Disney princesses, the reviews, and thus the films, I found the merchandise and reviews reinforce traditional gender roles for the princesses and the negative portrayals of Disney princesses in reviews have the potential to impact the creation of positive role models for young girls by misrepresenting the characters that children often admire and emulate.  This research on the princesses could be extended to analyze the portrayal of other female characters in Disney movies, therefore contributing to the ongoing research on gender in media and the discourse between merchandise and films.

By Sarah Friedman

Behavioral Response of Mud Crab Megalopae to Chemical Cues from Fish Species and Adult Conspecifics

By Jerelle Jesse

During the summer of 2014 OUR funded my honors research with Dr. Nancy O’Connor. This research has recently been published in the Journal of Experimental Marine Biology and Ecology and in what follows, I provide a summary of this research for the OUR blog readers.

Snapshot from the official website of the Journal of Experimental Marine Biology and Ecology, where Jesse’s research results were published

Portrait of Jerelle Jesse

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In Massachusetts, Asian shore crabs have become more abundant than native mud crabs. Crab survival can be enhanced by antipredator behaviors in response to chemical cues released by predators.

Asian shore crab

The purpose of this study was to determine if and how mud crab megalopae (the last larval stage of the crab) respond to chemical cues from local fish predators and adult crabs of the same species and to understand the way local mud crab megalopae behaviorally respond to chemical cues. The study focused mainly on the importance of early life stages, the origin of the chemical cues, and their ability to respond to chemical stimuli. This could potentially shed light on how an invasive species can be more successful than a native species in this habitat.

Mud crab megalopa

Female egg-bearing mud crabs were collected from the rocky intertidal habitat during low tide periods. When the females became close to releasing larvae she was transferred to a small finger bowl, then placed in the incubator.

Egg-bearing female mud crab

Once the larvae were released they were cared for until they reached the megalopae stage when they were designated to an experiment.

Incubator with glass bowls of mud crab larvae before reaching the megalopal stage as well as females almost ready to release larvae in small glass finger bowls

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Chemical cues for the experiment were made by the fish species or adult mud crabs being held in artificial seawater tanks to let their cue release into the water. The chemical cue seawater flowed through the apparatus, a glass pipe-shaped piece of equipment with an inflow opening, outflow opening, and a middle opening on top. The middle opening was to drop the individual megalopa into the apparatus with the cue flowing through.

The chemical cue flowed from the reservoir to a flow stabilizer, then a glass apparatus, and finally the sink. The megalopae were dropped into the middle funnel shaped opening in the apparatus

Once the megalopae was dropped into the apparatus it displayed 1 to 3 different behaviors then flowed out into the sink. The behaviors were categorized based on the orientation to the flow, the limb position, and the action performed. These behaviors included: control swim, random swim, perimeter swim, cyclone swim, closed roll, open roll, swim out, sideways walk run, slide, and push.

Left: Control swim; right: this megalopa happens to be on its back

The data were analyzed using generalized linear modeling. The results show no difference in behavioral responses between the two mud crab species. However, more open rolling behavior was seen for the mummichog cue, and significantly more walking on the bottom was seen for the adult cue. This indicates that megalopae can detect and respond to chemical cues in their environment. Megalopae can also tell the difference between adult conspecific cues and predator cues, and they can perform a different behavioral response depending on the cue.

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My research experiences in Dr. Nancy O’Connor’s lab are some of my best memories from my time at UMass Dartmouth. I had so much fun conducting the research that summer, then rising to the challenge of analyzing the data, and ultimately getting the opportunity to present my work at multiple conferences. It was a rewarding experience that made my career at Umass Dartmouth truly special. Currently, I am working for the Division of Marine Fisheries and applying to graduate schools. I know that this research helped me become better prepared for fieldwork and graduate school. Being able to work with a master’s student, Ami Araujo, while I was an undergraduate gave me insight to the process and hard work involved with graduate school. Without OUR’s help I would not have been able to conduct this research, and help fulfill my dream of working as a marine biologist and going to graduate school.

Developing Inexpensive Catalysts for Buchwald Carbon-Nitrogen Couplings

By Diego Javier-Jimenez

Portrait of Diego Javier-Jiminez

Catalyzed cross-coupling reactions using aryl halide reagents have found a prominent role in synthetic chemistry. The most notable are carbon-carbon coupling reactions, for which Heck, Negishi and Suzuki received the Nobel Prize in 2010. Similar carbon-nitrogen couplings, known as Buchwald-Hartwig aryl-amination reactions, have also found great utility, with applications in natural product synthesis, medicinal chemistry, organic materials chemistry, and catalysis. The catalysts in almost all cross-coupling reactions are based upon the precious metal palladium (price: $58,000/kg). Our lab is currently exploring different routes for the formation of carbon-nitrogen bonds with less expensive metals. This summer, I studied one such reaction in detail, analyzing the mechanism that the reaction follows.

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My summer research involvement at UMass Dartmouth has been one of the most rewarding experiences of my undergraduate career. I had the pleasure of working with knowledgeable lab mates who were always willing to help, explain, and teach any skills necessary for me to be successful in my research. I would like greatly thank Dr. David Manke, working with him has inspired me to become the best chemist that I can and more. The experience has also significantly reaffirmed my goals of going to graduate school to obtain a Ph.D. in Chemistry. I would like to thank the Office of Undergraduate Research for funding this research, without their aid, this research experience would have not been possible. We are currently preparing two manuscripts that we hope to submit to peer-reviewed journals for publication this fall. I plan on continuing this work for the remaining two years at UMass Dartmouth, and hope that my research accomplishments will make me competitive for an NSF graduate research fellowship. The OUR has given me the opportunity to follow one of my life-long goals.

Identification of SIAT7 in Symbiotic Clownfish and a Closely Related Non-Symbiotic Fish

By Deborah Dele-Oni

Portrait of Dele-Oni

Clownfish live in a close symbiotic relationship with sea anemones. This relationship is often used as a teaching tool for students to learn about ecology, evolutionary mutualism, and species interactions. This mutualistic relationship may be due to a sugar the anemones detect in the mucus of the prey species. An enzyme class known as sialyltransferases has been studied because of its importance of sea anemone recognition of prey. This class of sialyltransferases adds chains of sugars to proteins found in mucus. Clownfish may lack a specific type of sialytransferases known as SIAT7, which could be a factor as to why the clownfish do not get stung. However, although SIAT7 was not initially seen does not mean it is not there; rather it could indicate inactivation. Alternatively, clownfish may have SIAT7 in their genomes but may not express it in the cells that make the external mucus. To test this, I am studying both symbiotic and closely related non-symbiotic species to determine if SIAT7 is present in these species. I hypothesize that SIAT7 will be present in both the symbiotic clownfish and non-symbiotic closely related species but is inactive in the skin of symbiotic species. My goals were to test primers on tissues of anemonefish and closely related non-symbiotic species to see where expression occurred.

To accomplish these goals, I will:

• Use degenerate PCR to obtain partial sequences of SIAT7 from symbiotic and non-symbiotic fish species.
• Use inverse PCR to determine the sequences of the regions surrounding the SIAT7 gene.
• Use quantitative PCR to determine which tissues express SIAT7 in symbiotic and non-symbiotic fish species.

To approach this, I knew that SIAT7 had been identified in close relatives of clownfish. If primers were designed based from those sequences and added to DNA of symbiotic clownfish, there would be a product formed if the primers found complementary parts of the DNA. In the spring, I completed degenerate PCR to try and acquire partial sequences of SIAT7 from non-symbiotic fish species. The degenerative primers were created from the bicolor damselfish (Stegastes partitus; Genbank accession XP_008298796.1), and PCR was done on cDNA samples from the ocellaris clownfish (Amphiprion ocellaris) and the non-symbiotic Springer’s damselfish (Chrysiptera springeri) which is a close relative. The PCR yielded some products which are bright bands in the gel below (Figure 1). The brighter the bands the more concentration of DNA, showing successful replication. These samples were then cleaned up and sent off for sequencing. The sequencing results were crosschecked with the NCBI database and matches that appeared were not of SIAT7.  Instead they matched to other genes like protein FAM20A isoform X3 inform the Southern pig-tailed macaque or monkey (Macaca nemestrina) (Figure 2) or to bacterial genes like protein A2680_02525 from the bacteria, Candidatus kaiserbacteria . These sequencing results are the DNA of one of the bands from the failed attempt using degenerate PCR. These results indicate that our DNA in the degenerate PCR was not successful at producing a partial part of the SIAT7 gene.

Figure 1. Gel showing the results of degenerate PCR searching for SIAT7 in springers damselfish (chrisyptera springeri, CSP) and clarks clownfish (amphiprion clarkia, ACL) genomic (gDNA) and skin cDNA samples.

Figure 2. Sequencing results and BLASTx alignment for a sample.  The BLAST results show a match with the protein FAM20A isoform X3 with the Southern pig-tailed macque (Macaca nemestrina) which is a medium-sized monkey.

Since the degenerate PCR primer was not successful at yielding a partial sequence for SIAT7, another approach to obtaining this sequence was taken. Marian Wahl, a graduate student in Dr. Robert Drew’s lab, had recently sequenced transcriptomes from several species of anemonefish and non-symbiotic fish.  Transcriptomes are all of the RNA that is made by genes of an organism. This is of interest because it shows exactly what is made and what will potentially be translated to proteins. This was not available in the spring but became available early this summer. I redesigned primers for four species of anemonefish (list species) and non-symbiotic fish (list species) to be used in the PCR. This provided me with a better chance of getting PCR product because the primers used in the PCR were designed from the exact species they would be testing in. Also, I would be able to see right away if SIAT7 was really present in the fish species because I would be checking their transcriptomes to see if it was present or not. If SIAT7 was present, I would get a gene sequence from the transcriptomes.

To do this a reference gene was identified from the bicolor damselfish (Stegastes partitus; XP_008298796.1). This reference gene was used to find matching sequences from the transcriptomes of the study species using Local BLAST. I found that SIAT7 appeared in all species transcriptomes that were checked. From this, I could say that SIAT7 is found in both symbiotic and non-symbiotic species of fish. However, the specific tissue or tissues it is expressed in and to what extent was not known from this information.

Figure 3. PCR Results using primers designed for Amphirion clarkii (ACL) species and Amblyglyphidodon curacao (AmCu) species.

After going back to look at the specific gene sequences that were used to make the primers, there was evidence that SIAT7 across these species may be paralogs. Paralogs are genes that have evolved by duplication events, resulting in two copies of the gene in different locations of the genome.  After duplication, these copies evolve independently, accumulating different mutations. After a long period, these paralogs may still encode for the same protein but can have very different DNA sequences. This is interesting to note because it could be evidence that clownfish symbiosis caused this duplication event to occur. We found paralogs in the Clarks clownfish but not in the other three species we tested which were the staghorn damselfish (Amblyglyphidodon Curacao), the three spot damselfish (Dascyllus Trimaculatus) and the three stripe damselfish (Dascyllus Aruanus). We found this out by aligning the different transcript that were gotten from the Local BLAST. When aligned I found that the Clarks clownfish transcripts with similar trinity numbers (numbers that appear after the letters “DN” in Figure 4) were more closely related than the ones with dissimilar numbers. If the sequence used to make the primers were made using one paralog, other paralogs will not be accounted for in the study and the PCR will not yield consistent results.

To account for paralogs, some bioinformatics was done to identify exactly where duplication events might have occurred and in what species. To do this, transcriptomes for the species of interest were identified and aligned to each other using computer programs such as MUSCLE, TranslatorX, and the NCBI Blast Website (Figure 4). When transcriptomes are aligned, the programs will put similar sequences together and dissimilar sequences further apart from each other.  This figure highlights that species with the same sequences (samples with the same Trinity numbers) may be from the same gene. For example, the sequences DN83440 and DN182523 from A. clarkii are probably paralogs but there are two copies of DN182523 which are probably splice variants or have alternative transcription start sites.

  Figure 4. Phylogenetic tree of SIAT7 cDNA samples from Clark’s Clownfish (ACL), Three stripe domino damselfish (DAR), Three spot domino damselfish (DTR) and staghorn damselfish (AmCu).

There is still much to do so I am continuing work on this project this fall.  This figure will be updated to include some well-studied fish and re-rooted to provide more accurate results. Some cichlid fish are more well understood in the evolution of fish, and using these as references for our SIAT7 sequences, can provide me with some information on paralogs. Once paralogs are completely identified, more specific primers can be designed that will hopefully yield consistent PCR results. Another approach that will be taken is to align protein sequences. Right now, the aligning that has been done has used cDNA sequences.

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From the work done this summer, I can say that SIAT7 is found in symbiotic and non-symbiotic fish that I studied, indicating that clownfish did not lose SIAT7 as part of the evolution of symbiosis with sea anemones.  However, I detected evidence of gene duplication which introduced paralogs. Going forward, I seek to understand when these duplication events occurred and if it is related to the clownfish-sea anemone symbiosis. I am looking to seeing if the evolution of paralogs in SIAT7 allowed anemonefish to live symbiotically with anemones or if it is completely unrelated to this.

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This summer research experience has provided me with an opportunity to continue with a long-term research experience. I stepped out of my comfort zone and experienced new things in the lab and learned immensely from bioinformatics alone. Being able to get results from looking at gene sequences and databases on local computers, and searching national gene databases, I could answer one of my research questions without even picking up a pipette. As a biology student, I underestimated the wealth of information bioinformatics shows and how important it is to do these steps in research.  Conducting experiments in the lab is rewarding but interpreting the data, and understanding it is the main goal. This summer research experience, I learned to think about long term goals and the bigger picture. Having participated in only short-term research experiences before, I was usually just thrown into a situation where I had to think quickly on my feet and do a series of experiments and interpret my immediate results. However, being at UMass during the summer, I could continue work I had started before. This allowed me to see what a long-term project entails. Data interpretation and relating results to a goal is something that I have strongly developed this summer. I feel much more prepared to pursue more long-term projects. I have developed myself as a critical thinker and a troubleshooter in my research and found a new appreciation for the study of bioinformatics.

Influence of UV Light on Marine Biofilms

By Alexandria E. Profetto

Currently I am a rising junior marine biology major at UMass Dartmouth. My career here at the university started late due to being a member of the Massachusetts Army National Guard. After delays from training and a deployment from 2014-2015, I could begin my long sought after pursuit of a degree in marine biology. Thanks to the funding from the OUR and additional assistance by the Dean’s Undergraduate Fellowship, I have been able to work on an antifouling project, originally started in 2016 by Boston Engineering Corporation (BEC) and Dr. Pia Moisander at the Biology Department. The project was focused around the reduction of growth on marine biofilms, specifically on capabilities of a prototype device, developed by BEC, based on LED-generated ultraviolet (UV) light for use as an antifouling method for ship hulls (UV-C band light).

Portrait of Alexandria E. Profetto (left) as a member of the National Guard

Biofilms can be found and formed on a variety of surfaces, varying from indwelling medical devices to natural aquatic systems. Formation of a biofilm (“fouling”) begins with an accumulation of microbial cells on a surface surrounded in a polysaccharide based matrix. Depending on the environment in which the biofilm has formed, non-cellular materials such as clay or silt particles can be found in the matrix (Donlan, 2002). In aquatic based biofilms, the solid-liquid boundary between water and the surface, such as a ship hull, offers an ideal environment for the attachment and growth of microorganisms. Bacteria and diatoms are the most dominate forms reported in biofilms and are coined as “microfoulers”. These microfoulers play a very important role by providing signals for the attachment of various macrofouling organisms ranging from algae and barnacles to oysters and polychaetes (Donlan, 2002). This can be a nuisance for aquaculturists as well as commercial and recreational fishermen. Traditionally, antifouling heavily relied on fouling-reducing marine paints that although reduced in toxicity, still contain some toxic chemicals which can potentially cause harmful environmental impacts. Limited options for environmentally friendly and effective eradication of biofilms have created a need for alternative antifouling methods (Kim et. al, 2016).

Left: 30C Plates post sampling one week into the experiment; right: 30C Experiment Bin

During my project over the summer of 2016, we had a few goals regarding methodology, toward development of a repeatable and controlled experimental system for growing marine biofilms in the lab. We also wanted to test the capabilities of the UV device on biofilms grown under a range of temperatures, using microalgal cultures isolated from Buzzards Bay by Dr. Moisander in 2016. The biofilms were grown for 1-2 weeks in 32L of inoculated microalgal cultures at two temperatures. Forty aluminum plates, painted to simulate a boat hull, with non-antifouling paint, were used to grow the biofilms on. At specified times, the plates were treated with the UV light with one of the three duration times (1, 10 or 20 minutes) and then placed back in the bin to continue growth. Triplicate plates were included for each treatment.  Samples were then collected from the treated and non-treated areas (one and two weeks after the UV treatment) to be analyzed at a later date. Samples were collected to investigate presence of chlorophyll a (representing microalgal abundance) and abundances of bacteria on the surfaces. A second experiment was conducted with bacterial mixed cultures in one temperature only and a 1-week post-treatment incubation.

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 Left: Front View of Setup with 22C Bin; right: Plate Arrangement of 22C Bin

By the end of the summer, all samples were collected for each analysis and experiments completed. I also finished the analysis of all chlorophyll samples using fluorometry, and started the bacterial counts using epifluorescence microscope. The data compilation for chlorophyll data is currently in progress, and I am continuing to complete the bacterial abundance counts over the next few months.

Left: 22C Plates after 1 week after the first UV treatment; right: 3D printed plate holder (by Boston Engineering) used for precisely sampling the plates

Overall, the UV device appeared to be successful in killing existing biofilm and slowing down regrowth in the already formed biofilms. The observations show that we were successful in creating artificial marine biofilms in the lab and demonstrate the effectiveness of the UV device on these biofilms, mirroring overall results from pilot experiments conducted by Moisander lab and the BEC collaborators with natural biofilms from Buzzards Bay in 2016.

UV device setup on top of plate prior to treatment

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My research experience this summer was very eye opening regarding where and how I want to work in my future research career. I thoroughly enjoyed coming up with an experimental design and tackling the research challenges with Dr. Pia Moisander, as well as seeing the project come to a successful completion. Without her mentoring filled with her wealth of knowledge and expertise, I can’t say my problem solving and critical thinking in terms of science would have progressed as well as I’ve noticed. Collaborating with other members of the lab team with in person lab meetings were truly priceless experiences that I am so grateful for being afforded. Getting other opinions, ranging from an REU undergraduate to a post doc, was a great way to expand my thinking on my project than to just “what does is this data?”. My hope for this upcoming academic year is to continue assisting with this biofilm project or any project, finishing up data analysis and learn as much as I can from Dr. Moisander and her three Ph.D. students. I’d also like to thank visiting post-doc Mar Benavides and REU undergraduate Clay Evans for allowing me to bounce ideas off them as well as learn from their research projects.

References

Donlan, Rodney M. “Biofilms: Microbial Life on Surfaces.” Emerging Infectious Diseases 8.9 (2002): 881-90. Web.

Kim, Minhui, Shin Young Park, and Sang-Do Ha. “Synergistic Effect of a Combination of Ultraviolet–C Irradiation and Sodium Hypochlorite to Reduce Listeria Monocytogenes Biofilms on Stainless Steel and Eggshell Surfaces.” Food Control. Elsevier, 03 May 2016. Web.

A Remote Sensing Study of the Relationship between Density Fronts and Phytoplankton Blooms in the North Atlantic

By Samuel Filliettaz-Domingues

My OUR Research for the summer of 2017 grant cycle was concerning the Sea Surface Density gradients to Phytoplankton blooms in the North Atlantic. Phytoplankton have an effect on the marine ecosystem and climate change. To show a link in the North Atlantic between surface density of the ocean, its gradi-ents, and phytoplankton blooms (rapid multiplication of phytoplankton) , I analyzed sea surface temperature and chlorophyll gradients taken from the Aqua/MODIS satellite for the years 2011, 2012, and 2013. I sorted each day using an algorithm. Small gaps in the data were filled using interpolation. Contour and gradient plots were used to graphically show the relationship between SST and CHL. A database was created of notable days where the SST and CHL plots showed a strong link between the two. Another algorithm was used to try and showed a trend between SST and CHL values throughout the year of 2013, but the results were inconclusive. Although there are many other factors involved within the ocean that can alter ocean properties in a way that triggers a bloom, such as wind stress, data suggests that there are cases in the North Atlantic in which the CHL growths are predominantly formed by the SST gradients. This topic needs to be further analyzed to determine how frequently this relationship occurs.

Poster of Filliettaz-Domingues’s research on a Remote Sensing Study of the Relationship between Density Fronts and Phytoplankton Blooms in the North Atlantic.

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In sum, the objective of the research was to find out how related are the Sea Surface Density gradients and Phytoplankton blooms and whether this relationship is the reason why blooms are seen sometimes earlier compared to other parts of the world than predicted between winter and spring time. Knowing this can help ocean oceanographers to better understand the North Atlantic. Computer simulations was conducted predicting that there is a relationship. And satellite data verified that it is indeed the case. The next step for this research would be to expand on what we found in terms of how frequent these density gradient induced blooms occur.

My research experience during the summer was very informative. It gave me a glimpse into what lab work for Mechanical Engineers who go into physical oceanography would consist of as well as a new perspective on the complexity of ocean mechanics.  I am grateful to the OUR for providing support for this project and to my advisor, Professor Amit Tandon for supervising my research.

An Ethical Analysis of the De-extinction of the Woolly Mammoth

By Carson M Longendorfer

During my time studying Bioengineering at UMass Dartmouth I have learned a lot about the vast potentials of biotechnology. I recall one topic that really struck a chord with me from my BIO 121 class, de-extinction. The professor described to us how a researcher in Australia, had brought the southern gastric brooding frog back from extinction in his lab by using the same technology that made Dolly the sheep a reality. He also briefly mentioned to us that another research group, wanted to use de-extinction to bring an ancient ice age species, the woolly mammoth, back into the wild. I was compelled to read up on this a little more and I learned that the project is lead Dr. George Church at Harvard University who is helping to develop the genetic editing technology known as CRISPR/Cas 9 (Shapiro, Beth). Using this technology he is attempting to swap out pieces of the genome of a somatic elephant cell until it resembles that of a woolly mammoth (Shapiro, Beth). This cell would then be implanted into an elephant embryo and carried to term by an elephant until the mammoth is born (Shapiro, Beth). I found this to be a really interesting use of biotechnology as well an intriguing ethical question, I was inspired. I became interested in further delving into the ethical implications of de-extinction, and so, I was very excited to learn about the summer grant opportunity from the OUR.

Portrait of Carson M Longendorfer

I decided to take a two-pronged approach in my research, first analyzing the scientific justifications and oppositions and secondly the philosophic implications that the de-extinction of the woolly Mammoth poses. One of the major justifications for Church’s project is its potential benefits to the environment. Sergey Zimov hypothesized that the changes to the environment during the transition from the pleistocene to the holocene era did not cause the mass extinctions that included the woolly mammoth but instead, It was the extinctions that caused the environmental changes (Zimov, S. A.). He was able to support this hypothesis by fencing off an area in Siberia and relocating a few species of large herbivores. The herbivores eat the grass and stimulate the growth of more completely transforming the swamp to grasslands within one year (Zimov, S. A.). Grasslands are preferable to wetlands because wetlands release greenhouse gases into the atmosphere causing global warming and when the wetlands are fed by the melting of the permafrost underneath, this could be very bad for the environment (Shapiro, Beth). Zimov wants to expand the experiment that he calls Pleistocene Park to cover a large area of Siberia and to include the woolly mammoth (Zimov, S. A.). The mammoth is especially good for this purpose because of its large size, it tramples the snow which acts as an insulator keeping the ground warmer (Shapiro, Beth). By disturbing the snow, it allows for more cold air to reach the permafrost keeping it more frozen (Shapiro, Beth).

Pleistocene Park, Russia. Photograph courtesy of The Telegraph.

In this way, a compelling Utilitarian argument can be made because the suffering of a few elephants as well as the objectification of the hybrid mammoth can be justified for the benefit of the entire planet and every species on it. Environmental ethicist, Robert Elliot claims that nature cannot be restored after having been damaged because original nature has an intrinsic value that can’t be regained because it can never be the same as it was (Elliot, Robert). Therefore, the only real way to preserve nature is to stop causing further damage and using de-extinction as a restoration method is unhelpful and even more damaging (Elliot, Robert).

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I plan to submit my research to the Penn Bioethics Journal, a peer-reviewed journal for undergraduates. I am grateful for the opportunity that the OUR has provided for me and I hope that this experience with bioethics research is only the beginning of a successful future career as a bioethicist.

References

Elliot, Robert. Faking Nature: The Ethics of Environmental Restoration. London: Routledge, 2007.

The Telegraph Editorial. “Is Jurassic World closer than we think?” The Telegraph, Telegraph Media Group, 3 Sept. 2015, www.telegraph.co.uk/film/jurassic-world/pleistocene-park-dna-dinosaurs/. Accessed 29 Aug. 2017.

Shapiro, Beth. How to Clone a Mammoth: The Science of De-extinction. Princeton: Princeton University Press, 2016.

Zimov, S. A. “Essays on Science and Society: Pleistocene Park: Return of the Mammoths Ecosystem.” Science 308, no. 5723 (2005): 796-98. doi:10.1126/science.1113442.

Investigation of In Vitro Vitamin B6 Treatment to Reverse Deterioration of Bone Mechanical Properties

By Jacob Aaronson

In the summer of 2017 I was granted a grant from the OUR to join Bioengineering Professor Dr. Lamya Karim’s lab and worked alongside undergraduate Bioengineering student John Riordan to conduct a research project concerning the testing of the properties of bone that were placed in a simulated diabetic environment. This was an interdisciplinary project that allowed us to work with techniques from bioengineering, mechanical engineering, biochemistry, and biology.  Ever since I took a class in Biomechanics in the third year of undergraduate studies, I have been interested in exploring the mechanical properties of human body tissues such as bone. Through this OUR-funded project, I exercised this interest through hands on research and design.

Portrait of Jacob Aaronson

From previous research it has been found that patients with type 2 diabetes mellitus have an increased risk of bone fracture compared to non-diabetics [1]. These patients have normal or high bone mass, which is typically beneficial for bone. This suggests factors other than bone mass, such as changes in bone quality, may play an important part in diabetic fractures. In this study, I looked at a possible method to inhibit harmful protein crosslinks that can accumulate in diabetic patients. I chose Vitamin B6 as the inhibitor because it showed promising results in rat bone [2]. However, it has never been tested in human bone. With this fact in mind, the goal of this project was to look at changes in protein crosslinks and mechanical properties of bone specimens after being placed in a simulated type 2 diabetic environment and to test how Vitamin B6 might prevent these changes.

Jacob Aaronson (Back) and John Riordan (Front) making solutions for incubation of cortical bone specimens

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In the first part of this project, my main task was to work with human donor bone (tibias or “shin bones”) that I cut and polished down to small testable sizes. I used a low-speed diamond blade saw and polishing machine to accomplish this task. Once all the specimens were ready, we then incubated them in control and type 2 diabetic environments (a chemical solution with ribose sugar) with and without Vitamin B6. The bone samples were incubated in these solutions for 10 days at 37ºC with pH maintained between 7.2-7.6 to represent the human body environment.

Diamond blade saw used to cut bone beams

The second part of this project involved gathering data on the incubated bone specimens. When first looking at the post incubation samples, we saw a significant difference in color between ribose and control groups. Samples in ribose solutions were brown, which indicates a buildup of the protein crosslinks. Meanwhile control groups had no significant color change. A biochemical assay was run to measure the crosslink content, and cyclic reference point indentation (RPI) tests were used to measure the mechanical properties of bone after incubation.

Cortical beams treated with ribose (top) and cortical beams treated with no ribose or vehicle group (bottom)

From the data, we did not detect our expected differences in crosslinks or mechanical properties between the Vitamin B6 treated group compared to the non-treated group. This may be due to our small sample size and/or the Vitamin B6 dose being too low. Although we did not detect any differences from the hypothesized inhibitory effects of Vitamin B6, we did have other key findings:

• In vitro incubation with ribose does increase AGEs (protein crosslinks) in human cortical bone
• Indentation tests showed there were deteriorated bone mechanical properties in a simulated diabetic state
• Bone specimens with higher crosslink contents had weaker mechanical properties

There was a trend for higher indentation distance (represnting weaker mechanical properties) and significantly more crosslinks in the ribose treated group (R) compared to vehicle controls (VEH).

By continuing my work with the mechanical engineering department, more mechanical testing data was derived from the incubated cortical beams. Specifically, we performed microindentation tests on the samples to measure bone stiffness.

Samples treated with ribose had a lower elastic modulus (measure of stiffness) compared to the control group. This trend was seen across all age groups (57-87 years).

We also carried out another incubation of cortical beams to test the efficacy of different concentrations of Vitamin B6 combined with the same concentration of ribose. The small dose of Vitamin B6 used in the previous incubation appeared to have no effect on AGE inhibition so we decided to increase this parameter. Vitamin B6 concentrations of 5.0 mM and 50 mM were used due to their positive effects seen in a previous study [3].

Results from the most recent incubation where two different concentrations of Vitamin B6 were used (0.5 mM and 5 mM). The 5 mM concentration seems to have a considerable effect on the number of AGEs when compared to the ribose treated group (R).

Since the 5 mM concentration shows promising results it is important to verify this in future studies. Therefore, the next step of this project is to confirm the correct amount of Vitamin B6 through additional incubations followed by mechanical testing, chemical testing, and structural analysis. Specifically, we would like to carry out bending tests because they will give a more complete understanding of how the mechanical properties of samples change after incubation. We also plan on measuring specific AGEs, such as pentosidine, in our assays so that we can analyze the exact AGE chemical structures that are forming.  Lastly, we hope to apply imaging techniques such as microCT analysis in order to measure microdamage in samples. A long-term goal for this project is to utilize our accumulated understanding of Vitamin B6 on the inhibition of AGEs in vitro to establish reason for animal model testing.

From this experience, I have learned that research projects require countless amounts of planning, organization, and collaboration. I am thankful that I have developed these types of qualities during my time as an undergraduate researcher. My plan is to apply this research experience to graduate school, industry, and everyday life. Working on projects that are aimed to help restore health to many people will be something I always find highly motivational and invaluable.

I would like to thank the Office of Undergraduate Research for presenting me with this highly sought-after opportunity. I would also like to thank Dr. Lamya Karim, Rachana Vaidya, Taraneh Rezaee, Kelly Merlo, John Riordan, and the Mechanical and Civil & Environmental Engineering departments for all the help carrying out this project.

References

[1] Janghorbani et al (2007), “Systematic Review of Type 1 and Type 2 Diabetes Mellitus and Risk of Fracture,” American Journal of Epidemiology 166 (5/1). doi.org/10.1093/aje/kwm106

[2] Saito, M., Fujii, K., Mori, Y., & Marumo, K. (2006), “Role of collagen enzymatic and glycation induced cross-links as a determinant of bone quality in spontaneously diabetic WBN/Kob rats,” Osteoporosis International 17(10). doi:10.1007/s00198-006-0155-5

[3] A. Ashley Booth, Raja G. Khalifah‡, Parvin Todd, and Billy G. Hudson. “In Vitro Kinetic Studies of Formation of Antigenic Advanced Glycation End Products (AGEs),” The Journal of Biological Chemistry 272 (9). Pp. 5430–5437, 1997.