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.




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).



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.



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, 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


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

Diamond blade saw used to cut bone beams

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

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

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

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


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


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


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


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


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


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

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

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



[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).

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

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