Oh FRAP!

One of my favorite experiments to do in my lab involves shooting cells with lasers. Yeah, that’s right…shooting cells with lasers! It’s part of a really cool procedure called fluorescence recovery after photobleaching or FRAP for short.

The fluorescent proteins that I wrote about before are useful way beyond just making glowing fish. They can also be fused to other proteins. This is done at the DNA level by taking the gene for one protein and fusing it to the gene for a fluorescent protein. The molecular machinery inside the cell transcribes this DNA onto a single RNA which is then translated into a single protein called a fusion protein. Fusion proteins can often do the same thing that the original protein did. (It’s very important to test that this is the case. Sometimes tacking on an extra piece can disrupt the protein’s function!) Here’s a picture of a fusion protein that I made. The protein is in the nucleus of a living cell, as seen under a fluorescence microscope. I have done various tests to make sure that it still does what the normal protein does. So far, it has passed all of my tests in cultured cells (in a Petri dish, basically), and I am now working to do similar tests in living flies.

So, what is FRAP? FRAP is a technique that can be used to study how fast fluorescently tagged proteins move around inside cells. The idea is actually pretty simple: You take a laser and zap the fluorescently-labeled protein in a little spot. (You do all of this with a high-tech microscope.) The laser is so intense that the fluorescent label goes dark or photobleaches. This is sort of like what happens when you leave colored construction paper out in the light for a long time. The dye molecules in the paper undergo photochemical reactions (chemical reactions caused by light) that cause them to lose their color. Similarly, a fluorescent molecule photobleaches when it undergoes a photochemical reaction that turns it permanently into something non-fluorescent.

The rest of the fluorescently-labeled protein, however, is still okay. It still glows as before. If the protein is free to move around, then the bleached protein inside the spot will diffuse out and the fluorescent protein surrounding the spot will diffuse in. You can determine how mobile a fluorescent fusion protein is by measuring how long it takes for this exchange to occur. The result is a recovery curve, like the one below. Proteins that are free-floating in the cell recovery quickly after photobleaching. Proteins that are stuck to larger things recover more slowly. You can figure out a lot about what a protein is doing in a cell by comparing FRAP curves of different mutants under different conditions.

In addition to FRAP, there are even more advanced fluorescence techniques that you can use to study how proteins behave in living cells…more on those later.

X-rays...from peeling tape?!

This is really wild...

In experiments reported in the prestigious journal Nature, scientists at UCLA have shown that peeling tape off a roll can produce X-rays powerful enough to take medical photographs like the composite picture of a human finger on the left.
This seems to be an extreme case of triboluminescence, the process in which light is produced by friction. Though it's still not very well understood how triboluminescence happens, it probably has something to do with electric charges being torn apart and then coming back together...it's the same sort of thing that happens when you create static electricity by rubbing your hair with a comb (see triboelectricity). What's incredible is that such intense radiation could come from doing something so simple with such an ordinary everyday material! Better understanding this phenomenon may allow engineers to produce simpler, cheaper, and more energy-efficient X-ray devices.
Here's an article about this from the AP: http://ap.google.com/article/ALeqM5jAOxqWhwZlFtsWTQQHllAoDukeRgD93VSQOG0
And here's a video from the Nature website: http://www.nature.com/nature/videoarchive/x-rays/ (I hope you can access it...)

Nobel Prizes

We're excited at the University of Chicago because one of our professors just won a Nobel Prize! Yoichiro Nambu received the Nobel Prize for his theoretical work in particle physics. To be perfectly honest, his contributions to the field are too far above my head for me to even understand, let alone explain. But suffice it to say, he one one of the key contributors to the Standard Model of particle physics and quantum chromodynamics, the theory that deals with interactions between quarks, the exceptionally tiny subatomic particles that make up protons and neutrons. He was also one of the early contributors to string theory.

The Nobel Prize in Chemistry was awarded to the people who discovered green fluorescent protein and developed it into a powerful tool for molecular biology (see my posts below). I for one am definitely grateful to them!

Cell Movie

Here's a really cool animation of a cell that some students at Harvard made. They took some artistic liberties, but it's overall pretty accurate. I especially like the little motor protein that is shown dragging a (relatively) huge vesicle along a microtubule. It's thought that's exactly how it works. I know some people at UChicago who study single motor proteins, and they're capable of exerting amazingly high forces to move large cargoes through the cell.

http://www.studiodaily.com/main/searchlist/6850.html

Lisa Randall on Colbert

Here's a shorter and more ridiculous (but still science-filled!) interview with Lisa Randall on the Colbert Report:

http://bravenewfilms.org/blog/29097-colbert-report-lisa-randall

Synthetic biology--drugs and biofuels

At the q-bio Conference (see my post from yesterday), we heard a really interesting talk from Tim Gardner of Amyris Biotechnologies, a new company devoted to synthetic biology--engineering new organisms that do cool and useful stuff. They have two projects going on right now that involve engineering E. coli bacteria to produce compounds called terpenoids.

One compound that they've successfully produced in bacteria is an anti-malarial drug called artemisinin. Artemisinin is found in nature in wormwood plants. But extracting and purifying artemisinin from this natural source is very expensive--much too expensive for people in the developing world to afford. So scientists led by Jay Keasling at Berkeley have engineered E. coli to produce artemisinin by sticking several genes from the wormwood plant into the bacteria. Amyris scientists are now working to commercialize this technology to produce low-cost anti-malaria drugs for people in developing countries.

Amyris is also engineering bacteria to produce other terpenoids that can be made into a type of fuel called biodiesel. Many people are interested in using biodiesel as a renewable alternative to fossil fuels, especially with concerns about global warming and energy security. Amyris researchers are doing metabolic engineering to try to maximize the amount of biodiesel that their bacteria produce. They plan on beginning large-scale production soon.

What was especially exciting for me about Tim Gardner's presentation was the idea that we may be able to use mathematical modeling to help us design better biofuel-producing bacteria. His team of scientists at Amyris are developing mathematical models of gene networks and biochemical reactions inside the bacteria. They hope to use these models to predict what genetic modifications to the bacteria will make them produce more biofuel. If successful, mathematical modeling may allow Amyris researchers to test their ideas in silico (on computers) before trying to implement them in the real world. This would be less expensive, and it might also lead to new ideas.

Large Hadron Collider

I'm really excited, because the world's largest particle accelerator, the Large Hadron Collider (LHC), is about to start spitting out data. Particle physicists are hoping to learn new things about the fundamental pieces that make up the universe.


Here's an article about the LHC:
http://blog.wired.com/wiredscience/2008/09/first-beam-circ.html



And here's an interview with Lisa Randall, a theoretical physicist at Harvard who has predicts that the LHC may allow us to discover extra dimensions! (She also came to my school to give a seminar a couple of years ago...she's a really amazing scientist.)
http://video.google.com/videoplay?docid=-45154219728824809

This summer, I went to the q-Bio Conference on Cellular Information Processing. You can see the website here: http://cnls.lanl.gov/q-bio/ It was a really interesting international meeting of so-called “quantitative biologists”—people who study biology in a way that uses numbers and equations.

This is something that I’m really interested in, because it seems like a very natural way to study biology. There are numbers everywhere in biology, after all, from concentrations of a protein inside a cell to forces tugging on a cell membrane. And ultimately, everything in biology works according physical laws, which we can express mathematically.

There’s a pretty good Wikipedia article about “Systems Biology,” which is similar to “quantitative biology.” There are also closely-related things called “computational biology,” “computational systems biology,” “mathematical biology,” or “biomathematics.” Sometimes I wish they would stop coming up with new words and just call it biology!!!!

Fluorescent proteins

Some of the most interesting things I get to work with in my lab are fluorescent proteins

Fluorescence occurs when a molecule absorbs light of one color (wavelength) and emits light of another color. For instance, you can shine ultraviolet light on certain rock
s like the ones below, and they’ll emit visible light of a lower wavelength.

It turns out that some organisms like jellyfish make proteins that are fluorescent. The most famous of these is green fluorescent protein (GFP). “How can a protein be fluorescent?” you might ask. The way that this works is that there are amino acids inside the protein that undergo a chemical reaction (shown below) to generate a fluorescent molecule or fluorophore. The amino acids within the protein have to be positioned next to each other in exactly the right way within the protein in order for this reaction to occur—it’s really an amazing chemical feat!

Here are some fluorescent jellyfish of the species Aequorea victoria

The GFP fluorophore absorbs blue light and then gives off green light. What makes all of this really useful for biologists like me is that scientists have been able to isolate and make copies of (“clone”) the gene that encodes green fluorescent protein. You can introduce the gene into other organisms and make them produce GFP and glow as well. Here are some GFP animals:

(Check out GFP Bunny and glowfish)

One way that this is useful for research is that you can place the GFP gene under the control of the promoter of another gene that you’re interested in. You can think of a promoter as a sort of biochemical switch that turns a gene on and off. The promoter of a gene regulates where (in which tissues and cell types) the gene is turned on or expressed. So if you put the GFP gene under the control of the promoter of another gene, you can see where that promoter is active in the organism. This promoter-GFP combo is an example of a “reporter gene.” It’s called that because it “reports” on where the promoter is active.

Here’s a really pretty example. This is an image of transgenic (“transgenic” means genetically engineered—with an added gene) fruit fly embryos and larvae in different stages of development. In these animals, the GFP gene is under the control of a promoter that is active only in motor neurons (the nerve cells that control muscles). And so the motor neurons glow and you can see them very clearly under a fluorescence microscope.

As you can probably imagine, there are many ways that this could be useful for biologists. It can not only show you where genes are active, but can also allow you to track different cell types by fluorescently labeling them. In fruit flies especially, there are some really awesome techniques that you can use to create patches of mutant tissue (known as somatic mosaic analysis). A GFP label allows you to distinguish mutant cells from normal (“wild type”) cells. I can talk more about that if anyone is interested…

Right now in my lab, I’m trying to create different fluorescent protein reporter genes to study the activity of different promoters. My ultimate goal is to develop a mathematical model of how those genes are regulated. My current model can be summarized with these equations:

(Don’t worry: You don’t have to understand all of that!)

My big challenge at the moment will be putting together an experiment to measure gene activity as a function of inputs and then use this data to fit and test the model. But more on all of this later!

Welcome to my blog!

Hi! Welcome to my blog! My name is Thomas Graham, and I was a student at Mary Gage Peterson Elementary School between 1992 and 2001 and Northside College Preparatory High School between 2001 and 2005. While I was at Peterson, I developed a very strong interest in science that has remained with me to this day. I'm writing this blog for the benefit of other students at Peterson who are similarly interested in science. I'd like to give you some idea about what doing science is like, and I'm really eager to answer whatever questions you might have.

Right now, I'm a college student at the University of Chicago, and I'm double-majoring in chemistry and biology. I spend my spare time working on a research project in collaboration with Professor Ilaria Rebay in the biology department and Professor Aaron Dinner in the chemistry department. Specifically, we're trying to develop mathematical models of gene regulation in fruit flies. Expect more on that later!