Seven New College of Florida students spent their summers in two major biomedical research institutes, examining lung cancer, pulmonary disease, degenerative brain disease and developing computer algorithms allowing scientists to share MRI scan data.
They worked at the Lovelace Respiratory Research Institute (LRRI) and the Mind Research Network (MRN), both in Albuquerque, New Mexico. New College has had an internship program with the organizations for seven years. LLRI, founded in 1947, studies a wide variety of lung diseases and environmental health issues. MRN studies brain disorders, including traumatic brain injury, and mental illness.
Four students, two from internships at each institution, discussed their research for this story.
Neal Lacey and Shane Caldwell worked at LRRI. Lacey worked with Dr. Yohannes Tesfaigzi, director of the institute’s Chronic Obstructive Pulmonary Disease program. COPD is a combination of lung damage and chronic bronchitis, in which an overproduction of mucous blocks the airways and makes it difficult to breathe.
The research team examined the reasons for that excess mucous production. They focused on a protein known as Bik, which is found in less concentration in the airways of mice and humans who have been exposed to cigarette smoke.
Bik plays a key role in killing cells, so its under-expression may lead to the excess mucous. Lacey studied the complex interaction of Bik and other proteins in the mechanism of how cells are killed. His group’s findings indicate that Bik works by mediating calcium release from a cell’s endoplasmic reticulum to its mitochondria, and found a relationship between other proteins that explains why some cells resist Bik-induced cell death.
Shane Caldwell also worked with Tesfaigzi to examine the role of the p53 gene, a vital tumor-suppressing gene in humans. A mutation in the gene is found in half of all lung cancers. His study’s goal was to look at other effects of the p53Arg mutation. They analyzed the gene expression data in primary human airway epithelial cells before and after exposure to cigarette smoke extract. They found a specific protein was reduced in the exposed cells, which would lead to increased mucous production.
Both presented their work at American Thoracic Society meeting in Denver.
Caitlyn Ralph and Bradley Baker worked at LRRI. Ralph’s work focused on a new neuroimaging technique called diffusion tensor imaging (DTI). This method can outline white matter tracts in the brain with much more detail than traditional MRI scans.
She used DTI to look for a biomarker for a neurodegenerative disease called Vascular Cognitive impairment, the second most common such disease after Alzheimer’s. She also did exploratory statistical analysis in conjunction with the lab work. This fall, she has been continuing her work remotely with MRN’s Dr. Arvind Caprihan and preparing to submit her work to scientific conferences.
Baker tackled the challenging problem of how researchers can share MRI data. Researchers at different institutions typically are interested in different questions, but their data might be of use to colleagues elsewhere. Patient privacy rules and lab regulations, however, may prevent that. Baker and MRN colleagues designed, implemented and evaluated an algorithm for a process called decentralized temporal independent component analysis, for use with functional MRI data stored on different servers and different labs.
They wrote a paper on the process, which was accepted for the Machine Learning for Signal Processing Conference 2015.
Students said the experience was transformative. Lacey appreciated the greater opportunities available at LRRI, such as being able to work with scientists from around the world – his mentors were from Ethiopia and Chile – and working with the most advanced lab equipment available.
Ralph got see the potential that certain fields of study have to offer. She has studied many subjects at New College, including psychology, math, writing, foreign languages and computer science. “I changed AOCs basically every week,” she said.
But she gradually focused on neuroscience and applied math, and was able to work in those areas in greater depth.
“MRN exposed me to more computer science, and I realized the endless possibilities that come with the field, one of them being computational neuroscience,” she said. “I’m convinced this wouldn’t have happened, and I would have stayed confused and overwhelmed for a while, if I didn’t see research played out in real life at MRN. I received irreplaceable exposure at this internship and gained skills only attainable after working directly in the field.”