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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.

Research in Bioengineering

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.

Research in Bioengineering

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).

  

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I plan to continue working on this project during the upcoming academic year. Further work needs to be carried out to test the effects of Vitamin B6 on bone at different doses, specifically a higher amount than what was carried out in this study. Also, there needs to be other modes of mechanical testing besides RPI to get a better picture of what is happening to the mechanical properties of bone after glycation. In the near future, we plan on working with collaborators in the Mechanical Engineering Department to use various modes of mechanical 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 a summer 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, John Riordan, and the Mechanical and Civil & Environmental Engineering departments for all the help they provided in 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

Research in Art History and Curatorial Studies

Artistic Responses to Presidential Elections and other Political Challenges

By Mariah Tarentino

 

The United States has a rich history of politically motivated art, from the first political cartoons of the American Revolution to the socially conscious artists involved in civil rights movements of the 1950s and 60s and leading up to works of today disseminated on social media and as street art. In 1972 Andy Warhol created “Vote McGovern” for the George McGovern Presidential campaign. Rather than portraying McGovern, Warhol decided to represent his opponent in a negative light. During the 2008 elections, the Barack Obama “Hope” poster–designed by the renowned graffiti artist Shepard Fairey–was widely described as iconic and came to represent the 2008 presidential campaign. The image became one of the most important aspects of Obama’s campaign messages, and arguably affected the perception of Obama in a positive way. By contrast, graffiti art and posters of President-elect Donald Trump, produced by designers and graffiti artists, were largely negative. Why do artists react to presidential elections? How does art affect the decision of voters? What can we learn from these artistic interventions? By looking at the trajectory of these artistic responses, we can better understand the relationship between art and politics: the ways in which art making can have an impact on the general public and how art becomes a tool of resistance for political dissidents.

 

Left: Andy Warhol’s “Vote McGovern.” Courtesy of MOMA. Available at https://www.moma.org/collection/works/68705 © MOMA; right: Shepar Fairy’s “Hope.” Courtesy of Wikimedia. Available at https://upload.wikimedia.org/wikipedia/en/5/55/Barack_Obama_Hope_poster.jpg © Wikimedia.

 

In the 2016-17 polarized election cycle in the US, artists used their platforms to make a stand for their beliefs. The political art of the past year has come to the forefront of protests, awareness campaigns and the like. This art has focused on a wide range of themes, from women’s rights, racial justice, LGBTQ+ rights, and criticism of the economy, to foreign policy, and politicians themselves.

These depictions of political issues have clear and cutting messages. Through examining the works of artists, one can gain greater insight into the current unrest within our nation. And by analyzing what makes political art effective in its goals, artists can gain greater understanding of how to successfully use their skills to become an activist who is engaged in the society.

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My fascination with the topic of artistic responses to Presidential elections and other political challenges is owing to my interest in art and activism. I major in Art History with a minor in Women’s and Gender Studies. In the past three years, I have been a student employee at the Center for Women, Gender, and Sexuality (CWGS) at UMass Dartmouth. During my time at CWGS, I have been involved in multiple projects, including facilitating bystander intervention training and organizing awareness campaigns for issues like street harassment, domestic violence, and sexual assault. Additionally, I have had the opportunity to attend conferences on reproductive justice, which instilled in me a sense of civic duty and activism. In April 2015, I combined my passion of art and social issues through an exhibition featuring the art of sexual violence survivors. Through this exhibition process, I saw firsthand the power art has to convey powerful messages. I have seen this again in the current political climate. As the University of Massachusetts has a respected art college and a strong sense of civic and community engagement, it seems appropriate to conduct a research on the topic of art as activism and the role of the artist as an activist. In what follows, I provide a summary of my research, which was supported by a generous fund from the OUR, granted to me in Spring 2017.

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2016 was a year of rising socio-political tensions, which the election only seemed to bring to a boiling point. Between the Dakota Access Pipeline, Flint, Michigan still in need of clean water, arguments of religious freedom and gay rights, the disentrancement of the working class, and the ever-growing list of innocent Black Americans killed at the hands of police- everyone seemed in agreement that something had to give, but few agreed on what. The country held its breath as election results trickled in and a collectively exhaled, some in relief and some in shock, when Mr.Trump became President Trump. In all this unrest and apprehensiveness, art found itself in the center of the conversation.

Art worked to facilitate debate and convey messages, and it varied as much as the issues it attempted to address. It was seen on protest signs, in art museums, and on the internet. However, the common thread appeared to be that the art made use of appropriation and irony to convey its messages; it referenced images and messages of the oppressor, in part to illuminate the wrongs and in part to reclaim the very same images. Saint Hoax’s Make America Misogynistic Again is a prime example in this vein.

I was most interested in the protest images that came out of the election and inauguration. My OUR funded research consisted of two parts: 1) a research paper that examined this political art and attempted to place it in a broader historical context; 2) an exhibition of local artists’ works regarding the 2016 elections. The Frederick Douglass Unity House at UMass Dartmouth was gracious enough to host my exhibition (The Art of Resistance). The goals and values of the Unity House in creating discussion, providing support, and educating the community aligned perfectly with my goals for this exhibition.

Left: Poster of “The Art of Resistance,” a juried show designed and curated by Mariah Tarentino; right: Portrait of Mariah Tarentino near the Public Art Projects at the Rose Kennedy Greenway in Boston.

 

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My show facilitated a dialogue at the time when political issues effected our campus community and other surrounding communities we all belong to. It also gave students a platform to discuss politics in unique and creative ways. In my call to artists, I tried to keep submission guidelines as open as possible. I hoped that the exhibit would inspire and empower others to act, be it through art, protest, calling representatives, or other avenues. The exhibition took place in mid-April and featured the works of students Ashley Lima, Joel Rivera, Grace Augello, Shannon Morrell, and Chloe Bartlett, and alumni Johnus Derby. It included photographs, paintings, digital works, and protest signs. The diversity of the works on display was a small glimpse into the diversity of works from artists around the country.

Additionally, I wrote a paper analyzing works from all election cycles reaching from 2016 to Nixon. The paper revealed trends not only in art, but also in politics; through multiple case studies I discussed the ways in which artists and creative agents have approached political issues and described how they have chosen to agree or disagree. The research conducted for this paper allowed me to craft a theme for the 2017 UMass Dartmouth Art History Annual Undergraduate Symposium: Art and Activism. In my capacity as the President of the Art History Club, I was responsible for organizing this year’s symposium, which required coming up with a theme.

The research grant from the OUR also allowed me to advance my career goals by enabling my extra-curricular activities in the Department of Art History and I am grateful for that. The funding  facilitated a professional exhibition with ample publicity. It also provided support for my research at key libraries in the greater Boston area. I intend to attend graduate school in curatorial and museum studies. Eventually, I’d like to pursue a career in curation, featuring the works of artists who focus on challenging social and political issues.

 

Research in Music

Spheres of Influence

By John Dalton
 

My four years at the University of Massachusetts Dartmouth have been a personal artistic journey–a journey of self-examination, developing not only as a musician but as an innovator and a researcher. Throughout this journey I have constantly asked myself: Who am I as an artist? What should I do to find my own unique, creative voice? These are, of course, never ending questions. But for now I can say that being at UMD’s Music Department has given me a foundation to pursue a career in music that is more than just a performer. It is a career that is combined with research and innovation.

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 John Dalton’s Spheres of Influence. Click on the image to play the video.

 

Every senior music student is required to put on a recital to showcase what they have accomplished in their time at the university.  As an honors student, I knew I had to aim for something more ambitious. Therefore, I decided to put together a group of not only my peers, but of professional musicians and one of my Professors. The group includes current students (myself and Caitlin Walsh), two alumni (Miles Flisher and Sean Farias), and one of my professors (Jim Robitaille). This is a quintet that consists of saxophone (Caitlin), guitar (Jim), piano (Miles), bass (Sean), and drums (myself). Bringing together this group of people required not only research and coordination, but also financial support. Thanks to a grant from the OUR I successfully executed this complicated project.

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As a jazz musician one makes the decision to throw themselves into a continuum– the rich and vast legacy of many creative minds who advanced this form of music. I am interested in creating new jazz music and finding my own personal approach to both improvisation and composition. In doing so, I get inspired by many sources of influence. At my core, I am intrigued by the post-bop traditions of the 1960’s, which includes such artists as John Coltrane, Wayne Shorter, Joe Henderson, Herbie Hancock, McCoy Tyner, and Eric Dolphy. I have also begun to draw inspiration from successful contemporary jazz musicians,  including Brad Mehldau, Donny McCaslin, and Kneebody. Also, as a jazz drummer, I am inspired by masters of the instrument such as Elvin Jones, Roy Haynes, Jack Dejohnette, Tony Williams, Bob Moses, Paul Motian, Brian Blade, Jorge Rossy, Nate Wood, Mark Guiliana, as well as local drummers Luther Gray and Chris Poudrier. These influences continue to color my approach as I try to reach for something that is uniquely my own expression. To achieve this goal, I have created a group under the moniker of Spheres of Influence.

Spheres of Influence is my own modular ensemble, which aims to perform both my own music and the music that I resonate with. A Sphere of Influence is an international relations term which denotes the region in which one nation holds power or influence. I decided to co-opt this term for my own work as the name allows for the group to be modular. Each group under this moniker represents its own sphere and its own artistic place, thus changing the influences made by other groups. In improvised music the range of individual players in any particular configuration can change the nature of the music. What unifies the concept though is the overall character of the music played by the whole group. The music is always guided by certain aesthetic principles–principles that are universal between different iterations.

My vision for this group was to put on a free public concert in the College of Visual and Performing Arts’s main auditorium, showcasing a program of primarily original jazz compositions. The performance was also recorded and released as a high-quality video (view it above). While this concert was a collaborative effort between many musicians, a great deal of individual work went into it.

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Left: Rehearsal at the College of Visual and Performing Arts’s main auditorium; right: Portrait of John Dalton during performance. Photographs courtesy of Dan Waterman.

 

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Perhaps the best place to start describing my individual contribution, is the work I put in practicing my instrument. I also practiced particular material for this recital and this ranged from different grooves and time feels to soloing ideas. I had been thinking about the general idea of the recital in my practicing for some time, but there were still many concrete steps that I had to take.

Many of these steps taken have occurred in no particular order (in fact, they were often simultaneous). But I have compiled and listed them here in a fashion that makes sense in a chronological order. The first step I took was figuring out which musicians I wanted to work with. I knew right away that I wanted to have both Miles Fisher and Caitlin Walsh on the program, as they are two of my closest friends and collaborators. I also knew, pretty early on, that I wanted to have my professor and project advisor, Jim Robitaille. Professor Robitaille is a master musician who has worked with many talented musicians, in addition to being an excellent player and composer himself. I wanted to use this opportunity to collaborate and perform with him. Finally, I decided to hire Sean Farias to round out the group because he has an excellent reputation in the Boston area as a musician.

I also put a great deal of effort into writing and arranging some of the pieces. In this concert four of the nine tunes are my own compositions, including two new pieces I had written over the summer. I also had to compile the other pieces for the group, which included three more original compositions (each written by separate members of the group and two covers). During this process, I also thought about how the pieces should be arranged, according to both my tastes and the tastes of my fellow musicians.

After these preliminary stages, I began to figure out the details for booking the space. I decided to use the main auditorium as I felt it would be an appropriate venue for the musicians I had chosen. In this stage I also started to work on assembling promotional materials, which included designing a poster, as well as contacting various promotional outlets (for both inside and outside of the school). During the process, I came across the OUR grant opportunities, and decided to apply. I was lucky enough to be awarded a generous amount that helped support part of the recital and the research that went into the making of this music.

The next item on the agenda was organizing two rehearsals. Due to the busy schedules of the chosen musicians, I booked two rehearsals in October, well in advance. The first rehearsal was an interesting experience; it was my first time directing a group like that. It was especially strange having to give directions to Professor Robitaille and Sean, due to their reputations and stature as musicians. In the second rehearsal I was able to better ascertain my bearings and give more clear instructions. It was a great experience, as I learned to examine the group sound, and make sure that people were playing their parts. It was also interesting to experiment with different ensemble textures, which I felt needed to be worked in, making sure that pieces had a certain flow to them. If this were a more regularly working group, these sorts of textures and dynamics would not need to be said, as they could be formed spontaneously. However, due to time constraints it was the most logical choice.

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Spheres of Influence in action. Photograph courtesy of Dan Waterman.

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The day of the concert was very gratifying. Playing with musicians of this caliber is not only exciting, but also educational. There is also a level of comfort and trust; and this gives an amazing feeling. Indeed, this is part of the beauty of this kind of art form. Jazz is a communal experience, and the relationships one has with other musicians has an impact on one’s own musical style. When there is a deep connection between musicians, it can be felt in the way they play together.

Another interesting facet of this performance was the extent to which the results were different from my own personal expectations. Many of the solos took on different directions than what I had anticipated. I really enjoyed this aspect of the project, as it is those unexpected turns that bring about some of the most powerful moments in improvising. Of course, sometimes these risks don’t pay off, but they have to be done as part of the process. The thrill of improvising when everything comes together makes the process worth the risk of things not working out.

This performance was positively received by both my peers and mentors, which I greatly appreciate. My greatest achievement was that I inspired some of the younger musician peers at the University to work hard and diligently at their craft. Throughout the process of researching and developing this music, I learned that my art can be a positive force for change in the world– whatever that may be: from advocacy to suggestion of a better future, or even making someone’s day a little better.  I  hope that this concert can also contribute to my future research on the development of improvised music.  I look forward to searching for new sounds, while also pay homage to those that came before me. Above all, I hope that my music will continue to build upon the rich foundation that I, and many others here at UMass Dartmouth, draw inspiration from.

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As far as future plans, I would like to make this a regular, working group. Upon receiving the recordings, I was very pleased with the overall group chemistry, but I believe that this group could become a more cohesive unit. I felt that the performances ran into errors that would not be an issue if we were a group that played more regularly. Because of this, I would like to perform with this iteration of the group whenever the opportunity arises. Additionally, I would  like to start making inroads in the Boston jazz scene, performing with as many different musicians as possible– both as a leader and sideman. Overall, I am very happy with how this concert turned out. It was an honor playing with gifted colleagues and mentors, and I hope to do it again in the near future.

Research in Social Psychology

Researching the Psychosocial Well-Being of Siblings of Children with Disabilities

By Catrina Combis

 

Through UMass Dartmouth Honors Program and thanks to a research grant from the OUR, I launched a research study titled “The Relationship Between Having a Sibling with a Developmental Disability and Indicators of the Typically Developing Sibling’s Psychosocial Well-Being.” While brainstorming ideas in an introductory Psychology class at the beginning of my research process, I immediately thought of my own sibling. My sibling was diagnosed with anxiety and depression while we were both in high school, and the consequent unusual behaviors greatly impacted all of our lives. As a Psychology major I strove to learn more about my sibling’s diagnoses, and decided to dedicate my professional life to children with developmental disabilities.

 

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Left to right: Ramzy Rajeh, Kimberly Schoener, Dr. Christina Cipriano, and Catrina Combis. Rajeh and Schoener help code Combis’s interviews and Dr. Cipriano is Combis’s supervisor.

 

The purpose of my OUR-funded research is to determine how having a sibling with a developmental disability impacts a typically developing sibling (TDS). Once concluded, this research will hopefully fill the gap in the current knowledge about the TDS’s psychosocial well-being as well as other factors, including the relationship they have with their parents. It is essential to understand the relationship between both siblings in order to comprehend how that relationship affects the development and life of the TDS. The research will also highlight the indicators of the TDS’s psychosocial well-being.

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When a member of a family receives a medical diagnosis, it can have layers of impact on the larger family unit. Siblings of children with developmental disabilities are a classically understudied population. Only recently has there been a rise in studies on siblings of children with developmental disabilities (Stoneman, 2005). Sibling relationships are one of the most significant relationships that humans develop and are strongly related to psychosocial adjustment (Pollard, Barry, Freedman, & Kotchick, 2013). Although much is known about the impact and trajectory of the child with a developmental disability, less is known about their siblings.

Developmental disability is operationalized in this research as they are described in the Individuals with Disabilities Education Act (IDEA). The IDEA federally mandates that schools serve the educational needs of eligible students with disabilities and ensures students with disabilities have access to a free and appropriate public education (FAPE). It includes a diagnosis of Autism Spectrum Disorder (ASD), Intellectual Disability, Multiple Handicap, Emotional-Behavioral Disorder, and Learning Disability. Typical development is operationalized as the absence of an IDEA designation. Under the direction of Dr. Christina Cipriano, Assistant Professor in the Psychology Department, I submitted and received IRB approval to compile a list of psycho-educational batteries alongside my own developed questionnaire, to assess TDS mental health and well-being in the community. Using the Qualtrics platform, I recruited and surveyed participants, and then randomly selected a proportion of participants to take part in an information gathering interview. I am currently analyzing the Qualtrics and interview data using a mixed-methods approach. These include descriptive and inferential analyses, and open coding for themes. I will be presenting my findings at the Annual Meeting of the Council for Excepional Children (CEC) in Boston this Spring and will be writing up my findings for publication in a peer-reviewed psychology journal.

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I have always enjoyed spending my time with children since my teenage years and this interest has been furthered by the professional connections I have developed during my undergraduate education: While a student at UMass Dartmouth, I have worked for and interned for various organizations involving children. I worked for the America Reads Program through UMass Dartmouth’s Leduc Center for Civic Engagement where I tutored and mentored students in schools and after school programs in Fall River and New Bedford. I also interned with the South Coast Autism Center where I modeled social skills for young boys with Autism and learned a lot more about Autism through observing and interacting with many children. I am currently interning with Horizons for Homeless Children where I play and interact with homeless children in homeless shelters that have established therapeutic play spaces. As an undergraduate student, I have also worked for two professors, Dr. Christina Cipriano and Dr. Meredith Dove, on their respective research studies. Dr. Cipriano’s research is on the Recognizing Excellence in Learning and Teaching (RELATE) tool for special education classroom observation. Dr. Dove’s research is on nutrition and physical activity in childcare settings.  My experiences with children along with the research opportunities at UMass Dartmouth, have formed my professional trajectory. Right now I am in the process of preparing my applications for graduate school and I look forward to pursuing a career in supporting children and their families.

 

References

Pollard, C. A., Barry, C. M., Freedman, B. H., and Kotchick, B. A. (2013). Relationship quality as a moderator of anxiety in siblings of children diagnosed with autism spectrum disorders or down syndrome. Journal of Child and Family Studies 22 (5), 647-657. doi:10.1007/s10826-012-9618-9

Stoneman, Z. (2005). Siblings of children with disabilities: Research themes. Mental Retardation 43 (5), 339-350.

Research in Mathematics

Strong Stability Preserving Sixth Order Two-Derivative Runge–Kutta Methods

By Gustavo Franco Reynoso

 

This past summer I joined Professor Sigal Gottlieb and PhD student Zachary Grant in their Computational Mathematics research on “Strong Stability Preserving Sixth Order Two-Derivative Runge-Kutta Methods.”  It was a great experience that has helped me understand my abilities and my interests. Before I explain the project, I would like to go back in time to provide some background information about my research.

When I first started taking Computational Mathematics curriculum courses back in 2012, I never thought research is what I wanted to do. In 2012 I joined a class called CSUMS that was centered on independent undergraduate research.  Even though I enjoyed the class, research was not on my mind.  Eventually, I started taking higher level classes and realized that research was the base of everything I did, whether it be in my Civil Engineering classes or in my Math classes.  Subsequently, I decided to do research independent of classwork.

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Left: Portrait of Reynoso at work; right:The first page of a study conducted by Reynoso, Gottlieb, and Grant.

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This past summer I approached Dr. Gottlieb to see if she would let me join her research group. She warmly accepted and started to instruct me in the topics I needed to learn. This was just the start. Shortly thereafter an OUR summer grant enabled me to work with Dr. Gottlieb on a research titled “Strong Stability Preserving Sixth Order Two-Derivative Runge-Kutta Methods.” Hyperbolic partial differential equations (PDEs) describe a wide-range of physical phenomena in a variety of fields, such as aeronautics, oceanography, and astrophysics. These equations describe solutions that have wave-like behavior, such as fluid flows and gravitational waves. In many cases, the physical behavior of this phenomenon and the related solutions to the hyperbolic PDE develop sharp gradients or discontinuities. In such cases, the numerical methods used to approximate the solutions in space and evolve them forward in time need to be very carefully designed so they can handle the discontinuities and remain stable and accurate.

The design of high order Strong Stability Preserving (SSP) time-stepping methods that are advantageous for use with spatial discretizations and that have nonlinear stability properties needed for the solution of hyperbolic PDEs with shocks, has been an active area of research over the last two decades. In particular, the focus has been to design high order methods with large allowable time-step. SSP methods in the multistep and Runge-Kutta families have been developed. However, these methods have order barriers and time-step restrictions. The focus of this project was to develop new SSP time discretizations by further exploring the class of multi-derivative Runge-Kutta methods.

My main job at the beginning was to derive the order conditions needed to design higher order multi-derivative methods. I derived the two derivative Runge-Kutta order conditions up to 6th order using what is known as Butcher trees.  Just the one derivative derivation had 37 trees, after including the second derivative, it increased tremendously. Some trees had around 15 sub-derivations; this was a tedious job that taught me a lot on how to be efficient and optimal. After deriving all the order conditions, they had to be included into a code that finds numerically optimal multi-derivative Runge-Kutta methods and tests these methods for accuracy and for the sharpness of the SSP condition on test problems used previously in the SSP field. We were able to find methods that gave us sixth order accurate, and after doing so we found that there are 7th order methods that work as well.

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This experience led me to realize how I want to further my education. Thanks to a summer grant from the OUR as well as help from Dr. Gottlieb and Zack Grant, I have decided to pursue a PhD at UMD in Engineering and Applied Science. This will be an amazing experience and I very much look forward to it. To all students out there who have yet to find the beauty hidden in the intricate curiosity that some call research, I recommend that you get involved in research as soon as possible. If you find that you don’t like it, it is easy to get out; but, if you find it luring and attractive, you will feel like you have lost time not doing it earlier. Research is not boring, as many students might think. It is challenging and never definitive or monotonous. You’re always learning something new. Even if you try it once and don’t like it, you could still try it again, because there are so many topics unexplored that you are bound to find something you find interesting.

I’d like to leave you with this quote by the American biochemist and peace activist, Linus Carl Pauling:

“Satisfaction of one’s curiosity is one of the greatest sources of happiness in life.”

 

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