Tuesday, September 15, 2009

PAVA Paves the Way

(Post Updated Monday, Sept. 21 with new image and links)

“Can we assure the safety of myriads of molecules? Can we use technological innovations in information science to learn from a legacy of scientific minds?” former Duke graduate student Rocky Goldsmith asked at the Sept. 11 Visualization Friday Forum.

Goldsmith currently works with The Exposure Dose Research Branch of the EPA's National Exposure Research Laboratory, mapping how the body absorbs and purges chemicals.

“An environmental chemical is not just the standard pesticide, but really everything around us,” Goldsmith said. He quoted environmental activist David Suzuki as saying “We all live downstream.” Distant actions can affect us in unseen ways.

Without actually testing on humans, Goldsmith and his colleagues must estimate chemical exposure results for humans by examining multiple exposure parameters: dosage, route of exposure (oral, dermal, inhaled), life stage sensitivity (infants or the elderly), complex chemical mixtures, and the effects of similar chemicals.

“We want to be able to extrapolate from exposure to dose,” Goldsmith said.
“If the body gets rid of it quickly, we don’t worry about as much. It all depends on the dose -- if you have enough water, you can die.”

Was there were a better way to visualize the available dosimetry data? According to Goldsmith, several factors motivated this exploration: easier target organ / tissue identification, more compact and portable format, and the removal of linguistic barriers for data interpretation.

Thus, Physical and Anatomical Visual Analytics (PAVA), an online interface for evaluating the extent of human exposure to chemicals. PAVA allows species and gender selection, and realtime updated anatomical representation of a human.

(Goldsmith says PAVA is not yet available to the public, "But our intention is to have it available by early next year. In the meantime we can generate biologically mapped data by request. goldsmith.rocky@epa.gov.)

(See the entire lecture)

Monday, September 14, 2009

Starvation Induced Arrest in Worms- Interview with an IGSP Fellow

Duke sophomore Ilka Felsen did not want to do summer school, but instead really wanted to put what she learned in class to practical use. "I came into the experience wondering how long does it take to answer a question in science. Like, why do we need 10 weeks to answer a question that doesn't even look that complicated?"

Ilka was one among the 15 students selected as IGSP (Institute of Genome Sciences & Policy) summer fellows. An Evolutionary Anthropology major and a Dance minor, her project involved starving 1 mm worms and seeing what happened over a ten week period.

Her research project was "The role of TGF-beta and insulin pathways in C. elegans L1 arrest and recovery." Her mentor was Dr. Ryan Baugh, Assistant Professor, Department of Biology.

"In simple terms, our research involved looking at C.elegans (nematodes/worms).
We wanted to explore the worms' response to starvation, and control the nutritional factors within the worms to see which genes were involved in the process," explains Ilka. "We wanted to identify which pathways are involved in starvation induced arrest, and to what extent."

Nematodes go into two reversible stages like hibernation if they are starved. If you starve them at an L1 larvae stage, they stop growing and can survive just like that, with an increased resistance to stress.

But the amazing thing is that once you give them food again, they will start again from where they stopped, as if a machine was restarted. "Worms can survive by eating a hard cuticle for almost four months."

"We knew that 2 pathways are involved in starvation induced arrest- the Insulin pathway and the TGF-beta (Transforming Growth Factor-beta) pathway. The main purpose was to understand to what extent the TGF-beta pathway was involved."

"I had seven different strains of worms, where one was the wild type while six had mutations. I starved each worm and analyzed how long they could survive over time. Through a variety of experiments and Micro X-ray experiments we found the TGF-beta pathway is involved."

The interesting part is that this kind of arrest creates hope for age-stagnation in humans too.

"I now understand how research in science is conducted at a professional level. It is a lot about taking big risks, as you never know to what extent your research is going to contribute to science."

She notes that research is a lot of thinking, as one needs to correlate a lot of things and scientifically and experimentally prove every single result.

"This was a wonderful experience for me. It was great interacting with my mentor, professors and other scientists who were doing really cool research. However, from this research experience, I also learned that pottery lessons are not science! And flies are really annoying to work with!"

So what are her future plans? "I am pre-health, and I probably want to pursue physical therapy as a career. Apart from many great things I take back from this summer fellowship, I figured out a simple cardinal rule for scientific research-- there is absolutely no room for mistakes!"