Learn How to Sequence DNA in Less Than a Day

March 05, 2014

Prof. Oliver Medvedik. Photo courtesy Oliver Medvedik

Prof. Oliver Medvedik. Photo courtesy Oliver Medvedik

Though less well known than the four degree-granting engineering disciplines -- chemical, civil, electrical and mechanical -- bioengineering has a place at The Albert Nerken School of Engineering. The practice of applying engineering principles to the life sciences happens chiefly through the Maurice Kanbar Center for Biomedical Engineering and through the Sandholm Visiting Assistant Professor of Biology and Bioengineering, a two-year position currently held by Prof. Oliver Medvedik. A native of New York City, he co-founded Genspace, a non-profit biotechnology laboratory for classroom and public use. Now into his second semester, Prof. Medvedik has begun rounding up students to attend iGEM, an annual, national synthetic biology competition. We sat down with him for a chat about iGEM, Genspace, his ambitions during his time at Cooper and why the thought of bioengineered terrorism doesn't worry him...too much.

How did you get interested in bioengineering?

I was always interested in fundamental questions of biology. So my Ph.D. was in molecular biology and I was looking at pathways that regulated aging and longevity in organisms. Senescence seems to be a universal phenomenon, and is found to operate in every living being, including unicellular organisms, which also grow old and die. It may seem odd to consider senescence for single-cells since they divide into identical versions of themselves and the batch keeps growing until it runs out of food. So where’s the aging component? It turns out that if you can track individual cells, the clock is reset on one of the cells but the other tracked cell progressively slows down its metabolism, accumulates damage and dies. So there’s an inherent asymmetry in the split.

But otherwise the cells are completely identical?

Yes. So I was using yeast as a microorganism model for aging and looking at genetic tweaks that may circumvent that process and extend its lifespan. It's something I’d like to revisit experimentally because it touches on such a fundamental biological process. The approaches use engineering principles, but there’s still much basic science that needs to be done to pin down the biochemical and genetic similarities between a microbe like yeast and a human when it comes to a aging. That’s what got me hooked on biology.

What are some well known applications of bioengineering?

There are a lot of well known applications people use and are not even aware they are using products of bioengineering, like every time they do their laundry. Genetically engineered enzymes appear in a lot of detergents. They break down the proteins and fats and allow the detergent to operate more efficiently at lower temperatures. If the detergent works as well with room temperature or lukewarm temperature verses hot water, that’s a tremendous energy savings. These enzymes are biodegradable, so you’re not dealing with a genetically modified organism that’s going to get out in the wild. But that’s just one application of bioengineering. In biomedicine the applications just go through the roof.

What's an example?

Injectable insulin used to be available only by extraction from slaughtered animals or cadavers and then chemically modified to prevent an allergic reaction. Now it is produced by genetically modified bacteria. So E.coli, something that is evolutionarily separated from us by hundreds of millions of years, can be made to produce a protein that is identical to the natural human protein. As far as your body is concerned it’s the same thing.

Tell us about the Genspace lab.

Genspace is a non-profit organization that I co-founded in 2010. We run an open biotech lab in Fort Greene, Brooklyn that has been set up for the public to use and run their biotechnology projects. They could be artistic projects, or entrepreneurial ventures or just for hobby purposes. We also teach classes there, so it has a strong public outreach component to it. It's open year-round. People contact us to schedule a time to come in. We also have scheduled events that happen on a regular basis. Some evenings we have a "PCR and pizza" night, where anybody from the public can come in and learn how to sequence and amplify DNA using polymerase chain reaction (PCR) technology.

Anybody can learn to sequence DNA?

Anybody. Even though the invention for sequencing won a Nobel prize, it is straightforward to describe. PCR and dideoxy sequencing, those are two separate Nobel Prize winning discoveries we discuss all over a slice of pizza.

Do you have any particular ambitions during your time here?

I have several different interlocking goals. One long-term goal is to try to put together a pretty solid and comprehensive curriculum for biology that is also project-based. The other near-term goal would be to send a team to the next iGEM competition in 2014.

What is iGEM?

iGEM stands for International Genetically Engineered Machines. Faculty at Harvard and MIT started it back in 2003. It’s basically a synthetic biology competition for undergrads, held throughout the summer. Students use genetic engineering to come up with something novel. Part of their project must be to make the genetic components open source so that other groups can freely use them in their own projects. The competition also focuses heavily on social impact and safety components, so students have to weigh the merits of the project they are working on. Back in 2011 we had a joint Cooper Union, Genspace and Columbia University iGEM team. We had a project where we were trying to use bacteria for a green manufacturing approach to producing these small semiconductor light crystals called quantum dots used in building LCD and plasma screens. They are produced using industrial organic chemistry so we thought it would be neat if we could get microbes to grow them instead. You feed the microbes a particular salt and they express a protein that nucleates the salt. So as the bacteria grow the crystals grow inside of them.

What else will you be focusing on during your time at the School of Engineering?

One project I’m having students work on throughout the semester is to try to build something I call a biohacker kit. It would be aimed at high schools with limited bioengineering resources. It would let them rapidly change the phenotype of a microorganism, meaning change its measurable activity, through a faster genetic engineering approach. So instead of taking weeks and months, students could do it in a few days. The system works like a modular biosensor. The microbe would pick up some input stimulus and it would give you an output. Perhaps in response to sunlight or UV light it turns purple. And if you don’t like that then you can swap out a genetic module so that instead, it turns purple in response to caffeine. So that would be an open-source project that would be very cool. I currently have two highly motivated students, Devora Najjar and Shoshana Sigal who will be working on this project for Independent Study, so I'm pretty psyched about it happening.

Is there a dark side to genetic engineering?

There’s a dark side to everything. That’s like asking, "Is there a dark side to a knife or an axe or a two-by-four." Sure there is. Nature is full of the bad and the good, which is all relative depending on which organism parasitizes which other organism. There are lots of symposia on biosecurity issues and ways to keep an eye on what’s going on. But that being said, genetically modified organisms have not yet been used to harm the environment or injure a person, which is quite the contrary to naturally occurring organisms. To put things in perspective, evolution has had a tremendously long run fine-tuning natural pathogens like small pox, anthrax, tuberculosis and HIV to thwart human defenses. It’s much more efficient than any genetic engineering lab or any consortium of genetic engineers out there. So that’s something that makes me sleep better at night, knowing that you can’t currently have any lone individual create an microorganism from scratch and fine tune it to such an extent that it will run rampant.

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