Becky Ward, Aneil Mallavarapu, human cell lines, microtubules, and prions

After talking with Galit, I went with Becky on a quick tour of the offices and labs. A postdoc named Paul Chang showed me some live human cells under a microscope. These cells where from a line that was over 50 years old, originally from a woman with a particular kind of cancer. The researchers just keep growing new cells from this line to use in experiments. Paul was feeding the cells. I didn't even quite realize that human cells could live outside the body. How are these individual cells any more or less alive then the aggregate I call me?

I needed a break to check in on the outside world. While surfing, Becky came in and we got to talking about one of the cells that I had seen under the microscope and which had a dark line running down the middle. It had duplicated its chromosomes and was about to split them. The duplicated chromosomes align themselves along the center of the cell. To split them, tiny thread like structures called microtubules grow from opposite poles of the cell. They shoot off in random directions, hoping to catch a chromosome. Microtubules that hit chromosomes stick, while those that don't shrink back and shoot off in another direction. Once each chromosome is attached to two microtubules, one from each pole, the cell produces a protein that slices the chromosomes so that they can be pulled apart.

This shrinking and growing process would be interesting to reproduce on a much larger scale. Imagine robotic arms that navigated this way. Tim Mitchison, deputy chair of the DSB, has done a lot of work in this area, and hopefully I'll get a chance to chat with him.

Aneil Mallavarapu joined Becky and me. Aneil is one of the folks whom Becky introduced me to and that I became friends with before the residency. He's an interesting guy. Somewhat of a modern-day nomad, moving and working around the world, changing from experimental biology to computational biology, and able to talk about diverse topics, from biology to Buddhism. Once there, we got to talking about prions, the nightmare behind mad-cow and other fatal diseases.

Prions are simply proteins; not all of them are bad, although we don't know what they're good for. The problem is when you introduce one bad one into an organism it converts other prions into bad ones, and they link together into long thin fibers that muck up the system.

Galit Lahav and a negative-feedback loop

[This post is heavy on scientific details. I needed to prove to myself, and perhaps the researchers, that I could follow the science, at least to a degree. After this post I decided to focus the blog on things that resonated with me and my observations. Read or skip ahead as you are inclined.]

After a tour I spent some time talking to Galit Lahav about her research into the p53-mdm2 negative-feedback loop. She told me that p53 is one of the most studied proteins in the human body because of its role in cancer prevention. When it recognizes damage to the cell's DNA (found by other proteins), p53 starts a process that either fixes the DNA or kills the cell through something called apoptosis. We don't know how or why it makes a decision to fix or to kill, but people are trying to find out.

p53 is paired in a negative feedback loop with a protein called mdm2. When the amount of p53 goes up, the amount of mdm2 also goes up, but when the amount of mdm2 goes up, the amount of p53 goes down. Usually these types of oscillations either go on forever or get smaller and smaller until they disappear. This second type of behavior is called damped oscillation.

Biologists used to believe that the p53-mdm2 feedback loop was a damped oscillation. The experiments all seemed to show this, but they only looked at cell colonies. In other words, they measured the amount of each of these proteins over time in an entire colony of cells. These measurements showed a damped oscillation. In her post-graduate work, Galit measured the protein levels in individual cells and found that the loop oscillated a finite number of times with no reduction in amplitude. In other words, the levels of p53 and msm2 went up and down once, twice, three times or more and then stopped. No damping.

In her lab at SB they are trying to understand why the oscillation works this way. They develop theoretical models and then test them in the lab. Systems Biology seems to be about combining these two parts of biology: theoretical and experimental, or as those in the know say, dry work and wet work.

Galit showed me some movies of the cell proteins changing. To make the proteins visible under a microscope, scientists attach colored fluorescing proteins (CFP, cyan fluorescent protein, and YFP, yellow flourescent protein) to the p53 and mdm2. You could easily see the discreet oscillations. She also showed me beautiful movies of cells destroying themselves through apoptosis. They don't just fade away; they bubble and explode and form these bubbles called blebs (similar to my domain, blep!).

First day

My first day of the residency and I am very excited. I arrived at Harvard Medical School (HMS) at 12 noon, just in time to give an intro talk to a room of about 20-25 people, which felt like a good turnout. I talked about my background and showed some work. They seemed interested and asked good questions about the work and directions I might take. I was nervous at first, but loosened up when a few familiar faces, Becky Ward and Debbie Marks (see Intro I), joined.