End of Week 4

I don't know where the time went! We have been learning and doing so much that I can't believe the program is almost over. If only we had more time!

The past two weeks have been a crash course in 'real' research. When I say 'real' I mean the kind that doesn't always work as you planned. Or work at all for that matter. As we continue to build and test our chips we have been running into a few issues. The main problem we are having is that the polymer layer that is used to hold down our antibody probe is constantly being washed off when we clean the chip before adding the antigen target. The first thing we tried to do was to change how we wash the chip. Remember that the standard pattern is 3, 3 minute washes each of PBST, PBS, and DI water. What we tried instead was 1, 5 minute wash of each solution as well as 3, 6 minute washes of each solution. Unfortunately, neither one worked. We then tried changing the way we layer the chip: instead of placing photomask down and then the polymer, we just layered the chip with polymer. As you might have guessed, this did not work as well. This afternoon was therefore spent brainstorming new ways we could try on the chip to prevent the polymer from washing off.

As frustrating as it is to have your experiments repeatedly fail, it's also exhilarating to brainstorm ideas to try and identify the problem as well as solve it. You have to use all the information that you know (like the stuff in class you always ask, "Where am I ever going to use this?") from many different areas and put them together. When you finally produce an idea that you think may work, you have to has out the details. It becomes more and more exciting as you get closer to actually conducting the experiment. And this is what research is all about. You get idea, try it out, and see what happens. If you run into problems you troubleshoot. If you get great results you look for the next step. Yes, some days can be very stressful and disappointing but none of that matters when things finally go right. The other thing that's great about research is it's a very social profession. Contrary to popular belief, you do not grow white frizzy hair and sit in a secret laboratory all day by yourself, working feverishly on some crazy experiment. In reality, you're working with many people who specialize in many areas. You all interact to brainstorm an experiment as well as to set it in motion. In fact, you may work with people in another country! You look at scientific journals and attend conferences to get ideas and to get the advice from other researchers who have doe experiments similar to yours. Before you know it, you'll know people in multiple states AND countries!

As awesome it is to be part of team like this, I'm also humbled by how brilliant my coworkers are. They know so much in their respectful fields. They say some of the most intelligent comments I have ever heard the same way I would announce that it is raining. But after talking to one of the researchers, he told me something that is very true: All these people sound brilliant because they have been practicing their specialty for years, day in and day out. I, on the other hand, have been practicing biology. When he asked me a question about the immune system I was able to provide him with a complete and accurate answer. He replied that I had just proved his point: I knew my field as well as any of the other team members knew theirs. And that's something very important to take away. You don't have to be knowledgeable in many different areas or be born with skills that help in research. Anyone can be a competent researcher; you just need to love what you do and get excited about working in teams.

When I head back to the classroom I definitely want to bring the reality of research into the curriculum. Following the procedures in a lab workbook is not going to cut it. Students need to develop a curiosity and learn to ask the right questions, or to even ask questions at all. More of the curriculum needs to be based on inquiry as students need to learn how to synthesize what they have learned so far to find the answer to a problem.

Thrid Week!

  

Here is a video about the two pieces of equipment that we use, IRIS and MALDI!

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.

End of Week 1

Today marks the end of our first week in the Research Experience for Teachers program at Boston University. This program is designed to introduce teachers to current topics in technology so that we can bring them back to our students. This summer we are working in the Photonics Center at BU with particular focus on Biophotonics. Photonics is the study of everything we know about light: what it's composed of, how we can detect light, how we can use light as a sensor, and much more. Therefore, biophotonics is an area of research where light is used to sense, detect, and analyze biological materials such as tissues, cells, fluids, and other materials that relate to fields like medicine, agriculture, and environmental sciences.

The particular group of researchers that I worked with was headed by Professors Bennett Goldberg and Mark McComb. The main goal of their research is to develop a technology that can quickly and efficiently analyze a biological sample to detect the presence of a biomarker of a particular disease so that doctors can immediately begin treatment of the patient, potentially increasing their chances of recovery. Now I bet you're wondering what a biomarker is. The term biomarker encompasses a broad range of substances but the basic concept is that a biomarker is an indicator of a particular biological state. For example, a recent study showed that children infected with HIV had much higher levels of a protein called Interleukin-6 (IL-6) than non-infected children. We can then say that very high levels of IL-6 would be a biomarker of HIV infection. Now, if we use the technology that Professors Goldberg and McComb are developing, we would be able to quickly identify the amount of IL-6 in the blood sample from a child. If the level of IL-6 is very high, we can assume that the child is infected wit HIV and begin immediate treatment.

While I just gave you  general overview of what we are diving into, I spent the week learning and understanding the physics, photonics, and biology behind this research. This includes the type of equipment that we will be using. One of them is IRIS, or the Interferometric Reflectance Imaging Sensor. This machine uses different wavelengths of light to detect differences of height as small as nanometers!! In case you don't know, a nanometer is extremely small; it is only one-billionth of a meter! Think of it this way, a strand of hair is about 100,000 nanometers wide so it's pretty difficult to imagine 1 nanometer. What's amazing is that this piece of equipment can distinguish the difference from one nanometer to the next. When you use IRIS to analyze a sample, that machine produces a set of data that will indicate the differences in height throughout the sample. These height differences indicate whether or not a specific target substance is present or not in the sample. We can then use a formula to get the amount of target substance is present. Once we know this amount, we take the sample to another machine called MALDI-TOF, a type of mass spectrometer. This particular spectrometer is a Matrix Assisted Laser Desorption/Ionization - Time Of Flight spectrometer. The general concept of this piece of equipment is that we can place the sample in the machine and blast the sample with high energy in the form of a laser to produce even smaller pieces of our target substance. As these pieces are produced from the blast, they fly into contact with a detector that can determine the mass and charge of the pieces. Based on this value, we can identify what the target substance actually is. Identifying target substances like this used to require  process that took several months. With MALDI however, it only takes a few minutes!

Being able to work with amazing technology such as this is an incredible opportunity. Stay tuned for more mind-blowing information to come!