Thursday, July 14, 2011

The Reality of Research

As you get farther away from life experiences, certain specifics tend to fade. The big lessons remain, but some of the details drop from the forefront. It has been 3 years since I have worked in a research lab and the idea of how to do research is still fresh (hammered home by an excellent lecture by Dr. Selim Unlu this week), but the ease with which projects can be delayed slipped from my memory. I often tell my students that science requires patience and my partner and I have had to exercise our own this week.

In our quest to create a multi-layered chip that can be used to detect viruses and proteins, we have hit a series of minor roadblocks. Our first thiol monolayer experiment appeared to go smoothly. Theoretically, it should look something like this (the red represents the sulfur group):

(image from

But the question is, how can we determine if this actually happened? The molecules are so small that we have no method to actually see them aligned as they are above, so we need to measure them indirectly. The first way we do this is using an ellipsometer. This apparatus measures the change in polarization of light after it is reflected off of a surface. This change, when coupled with a refractive index, can give you the thickness of the deposited layer. Our results came out to be a reasonable 1 nm (to give some perspective on the size, 1 nm is to the thickness of a human hair as 1 football field is to the distance between New York and Los Angeles). So we were confident that we could add layers 2 and 3. I will delve into more depth about these layers in future entries, but they will end up being used to bond the antibody of interest to our surface. The application process went smoothly, but when we went to check the new thickness of the ellipsometer, we ran into speedbump #1. The ellipsometer was down and the one person who could help us was out of the office. I had forgotten how frequently this happens in research, but instead of getting frustrated, we used the time to do more background reading on the topic. The delay allowed me to become more knowledgeable about my topic. With our short timeline, we feel rushed to move forward, but we forget that it is better to gather all information at each step in the process.

Speedbump #2 is getting trained on the FTIR (Fourier Transform - Infrared Spectrometer). While the ellipsometer tells you the thickness of the layer, it doesn't identify what is on the surface. We use the FTIR to tell use exactly what is on the surface (though it doesn't tell us the thickness, so we need both measurements to be sure). The FTIR is a complex machine, but in short, it emits a beam of infrared light onto the sample. The sample absorbs specific wavelengths depending on the bonds that it contains. The FTIR reads this absorbance pattern and can help us determine what we have. As is common with many analytical devices, it is tricky to use, so we need expert training (which we will get next week). Once this training is completed, we can test our chips to confirm that we have deposited the material correctly.

These 2 delays aside, the experimental plan is coming together nicely. Our first testable question is "Does our procedure provides consistent samples?. If we are successful, as judged by our ellipsometer and FTIR results, we will move on to "Can our chip be used to capture a specific protein?" This will involve a new set of tests, with a new set of vocabulary, but it is exciting to think of the possibilities!

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