End of Week 2

Today wraps up the second week in the program. Our week began with a seminar led by Professor Unlu on what "good research" is. He introduced us to the basics of figuring out a topic to research and then the process that leads to a published paper. We then spent that afternoon in the clean room where we created our own chip. These chips are used in machines like IRIS in which lasers and light are used as sensors to identify changes. For example, our specific project begins with a silicon wafer with a layer of oxide on top. We then use the spinner to spin photoresist on the oxide. Photoresist is a substance that does not react to the light; it acts as a barrier between the light and any substance beneath it. It is important that the layer of photoresist be even all across the chip which is why we use the spinner as it uses high rotation speeds to spread the substance. After the photoresist layer we use a mask to expose and develop certain areas of the photoresist layer, exposing the oxide. We then remove these exposed areas of oxide with a substance called hydroflouric acid. This is a highly dangerous substance as it can disintegrate your bones if it seeps into your skin!! No worries though, I was wearing the full clean room suit as well as a thick rubber apron, rubber gloves, and a face mask. At this point we have a silicon wafer with a layer of oxide that is patterned, meaning that there is only oxide present in specific areas. For our research, we then add a layer of HMDS. This is a substance that has a hydrophobic nature meaning that it "hates" water and therefore repels it. However, HMDS loves to bind with many other substances including proteins. Due to this, we must then spin another layer of photoresist which is also exposed and developed under a mask to reveal spots of HMDS. The chip is then washed with certain chemicals to remove those spots of HMDS. The next step (almost there!) is to coat the chip in a layer of polymer. The polymer will help bind our sample later on in the experiment. Finally, we remove the layer of photoresist under the polymer that we just placed down. This time however, the polymer is removed wherever there is photoresist beneath it. This is what you get in the end!

Patterned Polymer, Patterned HMDS, Patterned Oxide, Silicon

Aside from our work we did above at the Photonics Center we also spent time at the BU Medical Campus where MALDI is located. We were able to get a lesson on how to use MALDI as well as spotting a sample onto a chip to run in MALDI so we could see how the machine worked. Remember what MALDI stands for? It's Matrix Assisted Laser Desorption/Ionization. The laser was already in the machine so that left the matrix which we had to make. Making the matrix consisted of a few different chemicals that had to be combined in a specific recipe to produce the correct concentration of matrix. Once the matrix was created, we used a micro-pipette to stop 5 microliters of our sample protein on the chip. We then spotted 5 microliters of matrix onto the protein spots we had just created. After allowing these spots to dry we were able to place the chip in MALDI. When the machine was warmed up and ready to go, the camera allowed us to see the individual spots we had created at a highly magnified view. We then used the crosshairs of the laser to target the laser to specific points in the spot. Normally, if the protein and matrix worked effectively, we would be able to see crystals in the camera. We would then target the laser at these crystals and "blast" them with laser bursts to blow up the crystal. The particles that come flying out would be ionized such that they are in their smallest possible form. These particles would then fly through the vacuum tube towards the detector. Based on how long it took for the particles to reach the detector, MALDI can determine the mass per charge ratio and identify what protein it is! Unfortunately that did not occur for us this time around. But we have many more opportunities ahead!

Using the technology described above, our overall intent is to create a system that will allow for the detection of extremely small amounts of disease-specific biomarkers in substances such as blood or urine. Before we can do that however, we must see how sensitive the technology is. To do this, Ken and I will be working with Julian to run protein samples with varying concentrations to find the lowest possible concentration of biomarker that can still be detected. With each decreasing concentration of biomarker sample, we will compare our results from MALDI to the standard, a biomarker sample of high enough concentration where the protein can be easily detected and identified using MALDI. There are many concentrations we can test, as well as many combinations of concentrations as we can create dilutions of the matrix and protein sample. Over the course of a few weeks we intend to find the most accurate combination at the lowest concentration.