Bard Features

From Baghdad to Bard

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Raed Al-Abbasee ’13 (left) and Swapan Jain
Photo by Richard Renaldi

Iraqi Refugee Finds Home in Science Research

by Swapan S. Jain
in the Bardian

Swapan Jain, assistant professor of chemistry, received his Ph.D. in biochemistry from the School of Chemistry and Biochemistry, Georgia Institute of Technology. He then worked as a postdoctoral fellow in the Chemistry Department at Boston University. His current research focuses on the development and testing of novel pharmaceutical agents that bind to DNA and RNA molecules. The Bardian asked Jain to describe his research with undergraduate Raed Al-Abbasee ’13, who came to Bard through unusual means.

The Journey to Bard
Biochemist Raed Al-Abbasee ’13 took an unlikely path to Bard that also led to publication in an important scientific journal. Born and raised in Baghdad, Al-Abbasee was a student at Al Mustansiriya College of Medicine, a prominent medical school in the Iraqi capital, from 2006 to 2008 (Iraqi students begin professional training after six years of high school). In 2008, Al-Abbasee and his family fled to Syria to escape the escalating violence of the Iraq war, including death threats toward members of the family. “People would be going to school and work across the street from a car bombing,” Al-Abbasee recalls. “I saw a lot of death. The main campus of my university was bombed. Why? Nobody knows. There was no military base in that neighborhood that would warrant making such a residential area a target for terrorist attack.”

Arriving in Damascus, where other relatives had fled, Al-Abbasee realized he could not continue his medical training: although Iraqis did not need visas at that time to cross the border, they could not, as refugees, attend public universities. “We left Iraq a few weeks before my second-year exams,” he says. “I was upset because I’d worked very hard to get into medical school and knew I wouldn’t be able to finish my education in Syria.”

He heard about the Iraqi Student Project, a nonprofit organization that helps displaced Iraqi students study in the United States, and applied. Felice and Yoram Gelman, and Hans Boehm, all of Rhinebeck, New York, are benefactors of the Iraqi Student Project who knew of Bard’s exceptional reputation in science and long history of assisting students from countries in conflict.

“We learned of the Iraqi Student Project through its founders, Gabe Huck and Theresa Kubasak, while they were on a speaking tour in the United States,” says Felice Gelman. “At the time, the program was just beginning, and they were searching for schools that would accept and provide scholarship aid for young Iraqi refugees of college age. Living in Rhinebeck, we were aware of some of the amazing things Bard does, and thought we would write a letter, asking for a scholarship for a student. The response, which was almost immediate, was, ‘Yes. Give us a strong student who is interested in science.’ We were thrilled. Bard pitched in, holding a meeting with faculty and students interested in the Middle East, to explain the program to them. Local people pitched in with contributions.”

She continues, “Our job, as a support group, was to raise the money for Raed’s room, board, and living expenses, and to help him deal with the dual shocks of a different culture and a different language. We helped him with summer work and, until his family arrived, with places to stay during academic breaks.” Al-Abbasee worked as a summer intern at Mount Sinai School of Medicine. He was elated and relieved when the Office of the United Nations High Commissioner for Refugees helped relocate his family, at the end of 2010, to Worcester, Massachusetts.

Al-Abbasee was awarded Bard’s prestigious Distinguished Scientist Scholarship, given to outstanding students in the sciences. He also received support from the Cornelia and Michael Bessie Foundation (of which Bard Life Trustee James H. Ottaway Jr. is treasurer), and Rally for Iraq, Inc., a nonprofit organization that provides higher-level education opportunities for Iraqis in the United States.

Boehm, treasurer of the Iraqi Student Project’s mid-Hudson chapter, is delighted that, by helping Al-Abbasee, “I have been able to pay back a little bit of the help I received some six decades ago when I obtained a Fulbright scholarship from Austria, which eventually led to my coming to this country for good.” He says of Al-Abbasee, “Raed is a remarkable person: very mature for his age, smart, polite, a hard worker. Considering the conditions both in Iraq and in Syria, I believe Raed will remain in this country and will be a valuable asset.”

Research into Enzymes and Cholera
Al-Abbasee and I met during his first year. Although a biology major, Al-Abbasee started work in my chemistry research lab in the fall 2010 semester; his project focused on the alcohol dehydrogenase (ADH) enzyme. Proteins, like machines in a factory, do the heavy-lifting work of a living cell. Myriad activities are carried out in the cellular environment, the cell being the basic-unit structure of all living entities. Some of these activities include making and breaking up molecules, transporting objects, transferring genetic information from a parent cell to the next generation, and harnessing nourishment from food particles to provide energy for cellular processes. This latter function formed part of the basis for Al-Abbasee’s research. Some proteins—enzymes—are catalytic in nature, which means they can increase the speed at which chemical reactions occur. ADH is a cellular enzyme that converts an alcohol into an aldehyde (a carbon atom doublebonded to an oxygen atom). For example, ADH can convert ethanol, which is present in beverages, into a compound called acetaldehyde. ADH can also carry out the reverse reaction, in which an aldehyde is converted back into an alcohol.

Al-Abbasee’s research project was conducted in collaboration with John Miecznikowski, assistant professor of chemistry at Fairfield University in Connecticut. The Miecznikowski lab is involved in making compounds that closely mimic the reaction center of the ADH enzyme. These “synthetic enzymes” can be used in place of natural enzymes to make alcohol and aldehyde molecules that can be developed for health care and industrial applications such as pharmaceuticals, paints, and plastics. Synthetic enzymes could prove more cost effective than natural enzymes and could also be used under extreme temperature and pressure conditions—invaluable assets when attempting to improve industrial product yields. For these reasons, it was important that a comparative analysis be undertaken that looked at the efficiency of a natural system compared to one that is created artificially.

As a biochemist who has worked with enzymes in both classroom and lab, I found this project fascinating. Al-Abbasee, who had taken several classes under my supervision, has an interest in molecular biochemistry that convinced me he would be a good fit for this project. His work focused on taking the natural ADH enzyme and looking at its catalytic rate using absorbance spectroscopy. This technique measures the concentration of a particular species by measuring its absorbance at a defined wavelength of light. We varied many experimental conditions—such as pH, temperature, and reaction time—in order to optimize the catalytic efficiency of the enzyme. In addition, we carried out mass spectrometry (MS) analysis—which can provide information about the weight of a molecule—on the compounds that were synthesized at Fairfield University. We found that the ADH enzyme performed more efficiently at room temperature and was also able to tolerate a greater number of substrates (the starting material used in an enzymatic reaction; in other words, the molecules on which enzymes act). On the other hand, while the synthetic enzyme was more effective at higher temperatures, it was limited to accepting only a small number of substrates.

In 2012, some of the results Al-Abbasee obtained were published in the journal Inorganica Chimica Acta, which focuses on inorganic and bioinorganic chemistry and adheres to a rigorous peer-review process. The paper was titled “Syntheses, characterization, density functional theory calculations, and activity of tridentate SNS zinc pincer complexes based on bis-imidazole or bis-triazole precursors.” Several Fairfield University undergraduates, and researchers from Boston College and Rochester Institute of Technology, were also featured as authors. Al-Abbasee was involved in describing his results and editing the manuscript during the review stages of the publication process. “My duties included preparation and presentation of the project poster, and presenting results to lab members and supervisors on a weekly basis in addition to participating in writing project’s abstract and manuscript for publication,” he explains. He also presented his results at two research symposiums held at Bard during 2011.

“In my summer internship at Mount Sinai Medical School, I worked extensively on performing sandwich ELISA—a technique used to detect the presence of an antigen of interest in a liquid sample,” he says. “On that project, I used sandwich ELISA to detect an antibody in mice serum. I also assisted staff in other duties, such as preparing reagents and buffers, performing analytical tests, and delivering specimens to the appropriate laboratory. I was introduced to the method of critical reading and effective writing of scientific papers, which was useful in the project I did on alcohol dehydrogenase with Professor Jain. Ultraviolet and visible (UV-Vis) absorption spectroscopy—the measurement of the attenuation of a beam of light after it passes through a sample or after reflection from a sample surface—and mass spectroscopy, SDS-PAGE, affinity chromatography, fluorescence, and dialysis were some of the techniques that I used.”

The Chemistry Program at Bard boasts state-of-the-art research labs, equipment, and instrumentation. Faculty members use these facilities to pursue their research activities with Bard students during the academic year and summer months. Students get hands-on experience with modern scientific instrumentation and gain from the expertise of their faculty supervisors. On average, five students conduct research projects in each faculty member’s lab at any given time.

During his research tenure, Al-Abbasee worked alongside Angela Potenza ’11 (chemistry), Wancong Zhang ’13 (chemistry), Rachit Neupane ’13 (biology), and Cara Black ’13 (biology). These students carried out independent projects that focused on small molecule interactions with DNA and RNA structures. Research students share valuable resources and ideas and develop a great sense of camaraderie and team spirit, which extends into their activities beyond the lab bench. James Sunderland ’13 (chemistry) is continuing Al-Abbasee’s project in my laboratory.

Sunderland has extended Al-Abbasee’s research for his own Senior Project. We are investigating the effect of substrate chemical structure on the reaction rate. Specifically, Sunderland is using the same alcohol dehydrogenase enzyme but he is using substrates that vary in their ability to donate or withdraw electron density from the reaction site. He has shown that variation in the electron density at the reaction site directly affects the catalytic rate of the enzyme. Analysis of the data reveals that the substrates can be logically categorized by examination of their chemical structure. He is also using another technique called cyclic voltammetry (CV), which helps in determining the electrochemical characteristics of substrates in solution. In our project, CV is being used to measure the mathematical constants that predict electron-withdrawing or -donating capabilities of these substrates.

Al-Abbasee’s Senior Project focuses on the cholera outbreak in Haiti in 2010, following the devastating earthquake in that country. His research examines the GlcNAc binding protein—the protein secreted by the Vibrio cholerae strain that caused the outbreak (scientifically known as the Haitian O1 El Tor variant)—that helps the disease’s molecules attach to the interior wall of the small intestine of humans. GlcNAc and chitin (a complex carbohydrate that forms part of the hard outer protective layer of insects, arachnids, and crustaceans, for example) are found on the surface of intestinal epithelial cells and in the exoskeleton of zooplankton. Research has been done to determine the role of GbpA in the colonization process in other V. cholerae strains; however, the protein’s role in the colonization process of the Haitian strain has not yet been explored.

In addition to GbpA, he is studying the HapR quorum sensing system, which activates the genes required to degrade GbpA at high cell density. The goal is to investigate whether or not the level of secreted GbpA protein is modulated by the proteins in this system, and how that secretion might affect the attachment and detachment abilities of this cholera strain. Understanding the function of GbpA protein in the Haitian O1 El Tor variant is crucial to understanding the mechanisms of aquatic and intestinal survival used by the isolate, or pure substance.

“My Senior Project research experience has been very enriching and it took me to a whole new level of thinking about the career of research,” says Al-Abbasee, whose Senior Project adviser is Assistant Professor of Biology Brooke Jude. “Unlike past projects, when I was given a research topic or area of study, this time I had to come up with my own. I also had to meet with Senior Project board members to explain my project, why it is important, and its timeline, so they could approve it. I am currently performing dot and western blot analyses and I am going to perform other techniques, such as inframe deletion and mutagenesis.” While his Senior Project research is not related to our published work on the ADH enzyme, some of the techniques from the earlier experiments have held him in good stead in his Senior Project efforts.

Al-Abbasee credits Bard with teaching him the rudiments of research. “Since my freshman year at Bard, when I began working as a lab assistant, I have been working with increased responsibility until I reached the point, now, where I can use my own judgment in making decisions and apply methods and procedures without close supervision or guidance,” he says. “Through the biology and chemistry courses I have taken at Bard, and the medical school curricula that I studied for two years at Al Mustansiriya College of Medicine, I was introduced to a wide variety of laboratory procedures and techniques, which gave me a solid foundation to start working on research projects.” However, unlike study at Bard and other institutions of higher education in the United States, medical students in Iraq attend lectures and conduct extensive observations, rather than performing their own research.

“In my internship at Mount Sinai School of Medicine, I followed instructions, but during my project at Bard, Professor Jain would often say, ‘Go find the relevant research articles and figure out a procedure,’” Al-Abbasee says. “I would conduct an independent literature review; then we would develop a suitable experimental plan. He inspired me to conduct more research.”

The Fruits of These Labors
Al-Abbasee plans to work as a research assistant before beginning graduate studies. “All these techniques, and many others that I performed in my lab science courses, helped me gain the confidence to explore my career options as a research technician,” he says. “I am looking forward to improving those techniques and learning new skills in order to be a better scientist in the future. I am hoping that a research opportunity will give me a better idea of what I really want to do in grad school.”

“Raed will be graduating with some very impressive accomplishments already under his belt,” says Felice Gelman. Adds Hans Boehm, “The years flew by so fast, I can’t believe that Raed’s graduation is just around the corner. It has been a very rewarding four years for me. I trust we will stay in touch with Raed.”

Al-Abbasee wants to put his newfound skills to use, in a place he knows and loves. “Although my family and I have begun to adapt to life in the United States, part of me is still back home in Baghdad. Unfortunately, the situation there is still not going as well as it could be. Violence is still a threat to millions of Iraqis every day. Politicians are busy fighting over power, ignoring their duty toward the country, which is being shredded to pieces by hate and violence,” he says.

“My friends in Iraq tell me about the state of the hospitals there,” he adds with urgency. “They need help. I hope a day will come when life in Iraq will go back as it was before the war, so that I and the other five million Iraqi refugees will be able to go back and help rebuild our beloved country.”

Read the spring 2013 issue of the Bardian:


More info: http://www.bard.edu/news/news.php?id=68

Post Date: 05-13-2013