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Research in Bioengineering

An Investigation into the Effects of Inverted Growing on Development and Strength of Basil

By Megan Scribner

My OUR research project was entitled ‘An Investigation into the Effects of Inverted Growing on Development and Strength of Basil’. The objective of the research is to determine if growing basil upside down influences the plant’s development and the mechanical strength of the stems. The initial plan to grow basil plants from seeds was modified for the sake of time; instead, adult plants were purchased and used for experimentation.

Portrait of Megan Scribner

Fifteen mature basil plants were purchased, numbered, and transplanted into larger pots. Plants 1-7 were planted traditionally, upright (displayed in Figure 1a), and plants 8-15 were planted in pots fashioned so that the plant would hang upside down (displayed in Figure 1b). Stalks that had a second set of true leaves, and sufficient space between the pairs to make a cut, were pruned.

Figure 1a (left): The upright basil plants
Figure 1b (right): Some of the upside down basil plants on a garment rack

 

After four weeks of growth, it was observed that stems of upright plants that had been pruned on Day 1 had established pairs of offshoot stems with two or three sets of leaves. Stems of upside-down plants that had been pruned on Day 1 had established pairs of offshoot stems with only one or two sets of leaves. This suggests that the upright plants experienced increased growth compared to the upside-down plants. Figures 2 and 3 display this growth difference.

Figure 2: Pruned stem of plant 6 (upright) with 3 sets of new leaves. The black circle on the left highlights the location of the pruning cut. The red circle highlights where the new offshoot stems and leaves grew from the main stem. The sets of leaves are numbered on the right.

 

Figure 3: Two pruned stems from plant 11 (upside-down), each with 2 pairs of new leaves.

 

Several obstacles were encountered in trying to maintain healthy plants. Challenges included: growing basil during the late winter/early spring months (which is not basil’s typical growing season for this region), securing an indoor location that met the environmental needs of basil, and the presence of insects.

Due to the complications with maintaining consistently healthy plants, no formal measurements with the experimental plants have been taken at this time, but there have been several practice measurements including extracting chlorophyll and measuring the wavelengths with a spectrophotometer, staining stem cross sections with toluidine blue and observing the plant vasculature under a microscope, and experimenting with different grip set ups for tensile testing. Images of the practice stained samples have been included below in Figure 4.

Figure 4: Two basil stem cross sections stained with toluidine blue and examined under a microscope

 

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Chlorophyll wavelength measurements were taken using a spectrophotometer. I am currently reviewing published literature for additional information about the effect of a plant’s health on its chlorophyll production.

Apart from the plants being used for experimentation, an additional basil plant was purchased in order to conduct practice tensile tests and find the most effective grip set up for successful testing. Due to the available pieces of testing apparatus not having fixtures suitable for botanical samples, there were no successful practice tensile tests. In the majority of the practice tests, the stem sample slipped through the grips. Examples of this are shown in Figures 5 and 6. In Figure 5, the stem slips from the start of testing. In Figure 6, the stem starts to deform as desired, but the sample begins to slip in the middle of testing. A successful tensile testing graph would look more like Figure 7. This graph was the result of one of the practice tests; however, the sample broke right at the bottom grip (displayed in Figure 8) which is not desirable. The sample should break more towards the center of the gage length. Breaking at the grips occurs due to improper stress concentrations through the sample; the grips are exerting too much force on the sample and weakening it at the grip points. Various materials such as sand paper and rubber were used to try to create more friction between the sample and the grips without applying too much force but these attempts were not successful.

Figure 5: Load vs extension graph of a stem tensile testing sample that slips throughout testing

 

Figure 6: Load vs extension graph of a stem tensile testing sample that starts to deform and then begins to slip around 2mm

 

Figure 7: Load vs extension graph of a stem tensile testing sample. The sample deforms until breaks at about 1.9 mm

 

Figure 8: A stem tensile test sample that broke at the bottom grip

 

An alternative idea for tensile testing has been investigated but not yet tested. It involves wrapping the ends of the stem sample around hooks instead of compressing the ends in grips. This is a method commonly used for testing the tensile strength of string samples. This set up does not have all the necessary components, but the available components have been gathered as seen in Figure 9. There may be some need for manufacturing in order to complete the testing set up. This will be explored further during the fall 2018 semester.

Figure 9: Top hook for future tensile tests. A bottom hook needs to be properly fashioned for this testing set up

 

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The current plans for the continuation of this project consist of obtaining and maintaining a new set of plants over the summer months in order to establish a healthier set of samples. Measurements from this healthier set of plants will be collected in the fall 2018 semester.
The research grant provided to me by the Office of Undergraduate Research allowed me to obtain many necessary materials including the plants and the various materials needed to care for them. While no conclusive measurements have been collected, these funds and materials provided me the opportunity to conduct valuable troubleshooting for this project. I would not have been able to pursue researching this unique application of mechanical engineering without the support of the grant. I would like to acknowledge my advisor Dr. Tracie Ferreira for her support and guidance with this project.

Research in Phychology

The Effect of Race-Related Words on Categorical Perception of Race

By Anna Sullivan

 

Categorical perception (CP) refers to the psychological phenomenon that occurs when we perceive a stimulus existing along a continuum as a set of discrete categories (for a review, see Fugate, 2013). One way to conceptualize CP is to think of a rainbow and the colors it produces. While we see a range of different colors, the physical composition of the rainbow is in fact a continuous range of visible wavelengths of light (Goldstone & Hendrickson, 2009). Due to the fact that we are unable perceive these wavelengths as they are, we counteract this by forming discrete categories in order to divide such objects, or in this case colors, occurring on a spectrum. From there, we can then differentiate the colors we see based on how we perceive their differences (e.g. Bornsten, Kessen, & Weiskopf, 1976). When this happens, the differences of colors in separate categories become more prominent while the differences of colors in the same category are less pronounced (Goldstone & Hendrickson, 2009).

 

Portrait of Anna Sullivan

Early psychological empirical research studied how speech sounds were perceived categorically (Liberman, Harris, Hoffman, & Griffith, 1957). Due to advancing technology and computer software, work on CP has also been extended to the human face. CP has been found to be present in the perception of facial expressions (Etcoff & Magee, 1992), familiar facial identities (Beale & Keil, 1995), gender information (Campanella, Chrysochoos, & Bruyer, 2001), and emotion (Fugate, Gouzoules, & Barrett, 2010). CP has also been studied in terms of race. For example, Levin and Angelone (2002) found that similar to gender, CP was stronger for different race facial morphs than for facial morphs of the same racial group.

In addition, categorical perception of social constructs, including emotion and race, are affected by a perceiver’s conceptual knowledge, including his/her language (see Barrett, 2006; Fugate, 2013). Specifically, when the meaning of a word is activated, people show more willingness to accept non-target emotional stimuli as a category member (Fugate, Gendron, Nakashima, & Barrett, 2017). Said another way, they are less “accurate” at matching images because their categories for that item have increased to include more instances. In this manner, people are becoming more “open-minded” and flexible with what constitutes a category member.  Directly related to the current project, Tskhay & Rule (2015) showed participants perceived racially ambiguous faces as belonging to different categories when they are preceded with either the words “Black” or “White”. Therefore, semantic information (i.e. top-down information) can interact with the stimulus characteristics (i.e. bottom-up information) to create differentiated judgments.

Poster of Anna Sullivan’s research project

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The research question for this project was: how do different race-related words affect the categorical perception of race? This study sought to further expand what is known of CP of race as it is affected by race-related words. To date, no research has directly studied the categorical perception of race and language (for a review, see Timeo, Farroni, & Maass, 2017). This type of research is important because it can provide more knowledge of how race-related words (and language more broadly) can affect our perceptions of important social categories, such as race.

The objectives of this project were to examine the ways in which certain race-related words affect an individual’s processing in categorizing racially ambiguous faces. This study examined how these cognitive processes are influenced by top-down information, such as language, and work to establish an individual’s perception of race within individuals. This work can lead to a better understanding of how people “see” race in the world and how the words used to describe race can shift perception and ultimately change biases. We are all affected by external sources of information, and therefore need to continue to explore the ways in which they affect our categorization of others into social and racial groups.

Categorical perception was tested through a typical two-stage paradigm (reviewed by Fugate, 2013). The first paradigm, classification (or identification), defined a participant’s categorical boundary (i.e. the point at which an individual distinguishes an image as either one race or another). The second paradigm, discrimination, was used to test for the hallmark of CP which is an increase in the ability to discriminate between pictures previously assigned to different categories compared with pictures previously assigned to the same category, even though the physical difference between the pictures is always held constant.

Detail from Anna Sullivan’s study

 

During the classification stage of this research, participants were presented with an array of racially ambiguous face stimuli that have been created using computer software (FantaMorph). These faces were created from combining two photos of different race individuals and creating systematic blends (known as morphs) which depict iterations between the two pictures Participants were then be asked to identify each stimulus as belonging to one of two categories, anchored by the picture endpoints or race-related words in different trials. We used several different race-related words to see whether a person’s threshold changes when evoking different race-related words and from when no words are evoked (match to picture condition).

During the discrimination stage of this research, participants were presented with two sequential morphs, which either span the threshold (established in part 1) or do not span the threshold (but constitute the same structural difference between the faces). The former trials were the “between-category” trials. Participants’ increased accuracy to discriminate better the “between-category” trials from the within-category is the hallmark of CP.   We predicted that when participants match to race-related words (compared to pictured endpoints), they will show increased thresholds (steeper category transitions). Moreover, the steeper transitions translated into enhanced CP, as demonstrated by participants having increased accuracy to the “between-category” pairs compared to the “within-category” pairs.

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Although similar types of studies and experiments have been performed, this project is unique in several key ways. First, no one has performed the full CP task (both identification and discrimination) on racial morphs. Second, the facial morphs are unique and were created specifically for this study from professional face sets. Third, no one has varied how (that is to what endpoint) participants match their choices. Words are almost always used as anchors. However, in a related CP study of emotion in the lab, Dr. Fugate and her students showed that matching to pictured endpoints (rather than words) increased the transition between categories but did not change CP. In addition, we will vary the type of race-related words (e.g. “African American” and “Black” and “not White” vs. “European American” and “White” vs. “Not Black”) to see if specific identifiers affect race perception differently.

Results from the identification portion of this research showed that language produces significant effects on race perception. Data analysis is still underway for the discrimination task, as well as the survey participants completed. This project was presented at both the UMass Amherst Undergraduate Research Conference and the PSI CHI Research Conference. It was also awarded second place at the 2018 OUR Undergraduate 3 Minute Thesis competition. I am grateful to my advisor Dr. Jennifer Fugate for her guidance and to the OUR for the financial support needed for this research.

 

Sources

Barrett, L. F. (2006a). Are emotions natural kinds? Perspectives on Psychological Science, 1, 28-58.

Barrett, L.F. (2006b). Solving the emotion paradox: Categorization and the experience of emotion. Personality and Social Psychology, 10, 20-46.

Beale, J.M., & Keil, C.F. (1995). Categorical effects in the perception of faces. Cognition, 57, 217-239.

Bornstein, M.H., Kessen, W., & Weiskopf, S. (1976). Color vision and hue categorization in young human infants. Journal of Experimental Psychology: Human Perception and Performance, 2, 115-129.

Campanella, S., Chrysochoos, A., & Bruyer, R. (2001). Categorical perception of facial gender information: Behavioural evidence and the face-space metaphor. Visual Cognition, 8, 237-262. doi: 10.1080/13506280042000072

Etcoff, N.L., & Magee, J.J. (1992). Categorical perception of facial expressions. Cognition, 44, 227-240.

FantaMorph. (2017). http://www.fantamorph.com/index.html

Fugate, J.M.B. (2013). Categorical perception for emotional faces. Emotion Review, 5, 84-89. doi: 10.117/1754073912451350

Fugate, J.M.B., Gendron, M., Nakashima, S.F., & Barrett, L.F. (2017). Emotion words: Adding face value. Emotion. doi: 10.1037/emo0000330

Fugate, J.M.B., Gouzoules, H., & Barrett, L.F. (2010). Reading chimpanzee faces: Evidence for the role of verbal labels in categorical perception of emotion. Emotion, 10, 544-554. doi: 10.1037/a0019017

Goldstone, R. L., & Hendrickson, A. T. (2010), Categorical perception. WIREs Cogni Sci, 1: 69–78. doi:10.1002/wcs.26

Levin, D. & Angelone, B. (2002). Categorical perception of race. Perception, 31, 567-578. doi: 10.1068/p3315

Liberman, A.M., Harris, K.S., Hoffman, H.S., & Griffin, B.C. (1957). The discrimination of speech sounds within and across phoneme boundaries. Journal of Experimental Psychology, 54, 358-368.

Timeo, S., Farroni, T., & Maass, A. (2017). Race and color: Two sides of the same story? Development of biases in categorical perception. Child Development, 88, 83-102. doi: 10.1111/cdev.12564

Tskhay, C. & Rule, N. (2015). Semantic information influences race categorization from faces. Personality and Social Psychology Bulletin, 41, 769-778. doi: 10.1177/0146167215579053

Research in Fine Arts

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.

Research in Rhetoric and Communication

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.

Research in English Literature

Temporary Meddlers: Friars in Measure for Measure and Romeo and Juliet
By Sarah Friedman
I am an English major and a member of the Honors Program at UMass Dartmouth. My paper “Temporary Meddlers: Friars in Measure for Measure and Romeo and Juliet” was originally developed as my final research paper for the Shakespeare course that I took in spring 2017 with Professor Jay Zysk of the English Department at UMass Dartmouth. During the course of the spring semester, my class visited the Boston Public Library’s “Shakespeare Unauthorized” exhibit to begin developing ideas for a paper topic.
Portrait of Sarah Friedman

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While I was at the Boston Public Library’s “Shakespeare Unauthorized” exhibit, I began to think about how Shakespeare portrays religion in his plays and I developed this concept into a research paper on Shakespeare’s friar characters. Last summer, Professor Catherine Gardner who is the director of the OUR informed me about the peer-reviewed Journal of the National Collegiate Honors Council (UReCA) and I decided to revise and submit my paper. The paper was recently approved for publication and in what follows I provide a summary of my argument. To read the entire paper, please feel free to click on the following image.
Front page of Sarah Freedman’s publication in UReCA

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During Shakespeare’s lifetime, religion was a controversial topic and the practice of Catholicism in England was illegal. I thought it was particularly interesting that Shakespeare uses Catholic friars as characters in his plays and I wanted to explore what those characters might suggest about Shakespeare’s religious beliefs. Shakespeare grew up in Stratford-upon-Avon and that community was at the center of Catholic resistance in England. His parents were connected with Catholicism and three of his grammar school teachers were Catholic, so that definitely had a strong presence in his early life. I focused my paper on Friar Laurence in the tragedy, Romeo and Juliet, and Duke Vincentio, who disguises himself as a friar in the comedy, Measure for Measure. In both of these plays, Shakespeare seems to be more sympathetic to friars than his contemporaries. He does not portray them as vice characters who break their vows, instead he portrays them as fallible human beings who try to help their communities. In both plays, friars keep secrets and manipulate politics. Friar Laurence performs Romeo and Juliet’s secret marriage, but he does so believing that it might end the feud between the Capulets and the Montagues. Duke Vincentio takes on the identity of a friar, but he uses it to try to stop the corruption that is happening in the city of Vienna. In conclusion, Shakespeare makes it clear that religion and politics are intertwined and earthly matters cannot be easily separated from spiritual matters.

Research in Biology

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.

 

 

Research in Chemistry

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.

Research in Biology

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.

 

 

Research in Marine Biology

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.

Research in Mechanical Engineering

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.

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