The ramblings of a working, knitting, writing wife and mother.

Tuesday, April 29, 2014

Welcome to Caltech

So my niece sent us a drawing of herself with the instruction to take her to our places of employment and show her around. My actual job is kind of dull, but the people I work with are all sorts of interesting. So interesting in fact that whenever anyone comes for a visit and we're thinking of things we want them to experience while they are here, a visit to Caltech is in the top three (there is also a turtle / koi pond on the grounds - it's not all microscopes and bacteria around here).

Here's what Danyelle saw when she came to visit.

Behold the impressive Broad center, where science is happening.

Science is fun and interesting, but the first thing you need to do before you enter a lab is learn about lab safety! Always wear proper shoes, clothes, and sometimes even goggles and lab coats. Also, know where the first aid kit is and know how to use the emergency shower station in case you spill something on yourself that you need to wash off in a hurry.

Our biology lab specializes in taking the best pictures in the world of some of the smallest living organisms. Some of our favorite things to take pictures of are Caulobacter crescentus bacteria (a cousin of e. coli), mycoplasma pneumoniae (the bug that causes pneumonia), and the HIV virus.

Before we can take pictures, first we have to grow our bacteria in tubes. You can grow bacteria in just about anything. We use liquid solutions called media. Some of our solutions even have gold added to them! It only takes a few hours for bacteria to grow, so you can start a solution in the morning and take pictures of it after lunch! Once you have a nice group of cells to image, you need to place them on a slide or a grid so they can go into the microscope. Our lab uses both - a wet slide for light microscopy (the kind you're probably used to)

or a copper grid to put into our special, big electron microscope.

Since a drop of media can contain thousands and thousands of bacteria to take pictures of, we only need a tiny bit for each slide or grid. To help us, we use a special tool to pipette small amounts. It works just the same as a straw.

When your grids all have bacteria on them, it's time to take them to the basement where the electron microscope has its own special room to help protect it from movement and sound. Because when you're taking pictures of very small things, it helps to be as still as possible.


Taking pictures of things with an electron microscope is tricky because when you beam electrons on your bacteria, it makes them fall apart after a short time. And trying to figure out the structure of a bacteria after it falls apart is like trying to figure out how a watch works by looking at one that's been smashed by a hammer! Right, not very helpful. Scientists try to get around this issue by mixing their samples with special chemicals, embedding them in plastic, or freezing them.

Our lab uses a method called plunge freezing to create our samples. We use a machine called a Vitrobot to freeze our bacteria. Freezing protects the bacteria from the electrons and keeps them looking almost exactly the same as when they were swimming around in the media, but you have to freeze your samples very, very quickly in order to create clear, see-through ice. Freezing things too slowly will create crystals, and crystals will make for bad images just like having static on your television set will disrupt the picture. We drop our bacteria grids in a mixture of liquid nitrogen and ethane so they freeze instantly.

After they are frozen, the grids have to stay frozen solid. If they warm up even a little bit, the ice can make crystals. So we put the frozen grids in a cryo-holder (it's like a thermos filled with liquid nitrogen) until they are ready to put in the microscope.

The next step is to put the grid into the vacuum of the microscope and take your images. Our microscope is hooked to a series of computers that save the pictures you take. We also do a special technique called a tilt-series where you take a whole bunch of pictures of one bacterium at different angles.

After you take all the pictures you want to, the last step is to analyze your data - or look closely at the pictures you took. For a tilt-series, this last step is called reconstruction. It's where you take all the pictures and stack them on top of each other to create what we call a tomogram. Remember that gold we put into the solution? Under the microscope, that gold shows up as large black beads that we can use as markers when we are stacking images. This gives us a complete 3-dimensional image of our bacterium - a real break-through for seeing new things and figuring out how things work!

Here's an example of how a tomogram is put together to form a 3D picture and how it helps us learn about bacteria cells.


Thanks for taking a trip to our microscopy lab at Caltech today. I hope you learned a lot!

No comments:

Post a Comment