Friday, July 8, 2011

Beginning Work at the Boston University BioPhotonics Lab

     This has been the first week of a summer program for teachers working at the BioPhotonics Lab at Boston University. Five teams of two teachers each have been formed to work on ongoing research projects. I have been teamed with Jessica Long who is a biology education major at Boston College. We are working with a group of graduate and undergraduate students lead by Professor Bennett Goldberg and Dr. Mark McComb.
     We have spent this first week working with Julian Anding. Our project is dealing with developing a new system to monitor how biological systems bond with each other. The system is used to make measurements of what materials bind with each other and how the undergo this binding. The meauring process  can be used to see the bonding of proteins to proteins, DNA and proteins, DNA to DNA, antigens to antibodies in large systems.of interactions.

     We have already started being introduced to the techniques used in isolating the samples to be tested. To do this, we have worked in a clean-room in which the presence of floating particles  might  infect the sample with unrelated materials is greatly reduced. Through our work here and in a related preparation lab, we have created mutiple samples in which a silicon ladened slide has had a coating of silicon dioxide, HMDS (which is a hydrophobic material that repels water based materials), photoresistive material and a hydrophilic (a material which attracts water based materials) polymer merged together. The format of this slide is such that the there are a series of dots of the polymer sitting on top of the Silicon and silicon dioxide layers surrounded by the HMDS material. An antibody material will be placed on this slide. The antibody will bind to the polymer and will be repeled by the HMDS. This will provide us with targeting areas to which antigen materials will attach.
     We will be looking to select the antibody and antigen so that they will demonstrate how PSA antigen material attaches to the appropriate antibodies. The PSA test is used as a potential indicater for prostate cancer. The hope here is to develop an improved test for prostate cancer which may permit the diagnosis of prostate cancr to be made more quickly and more accurately than is presently possible.
     During the production of this slide, we are already making measurements of it to determine the depths of the Silicon dioxide, polymer, antibody, and antigen present on the slide. Knowing the depths of these materials will permit us to measure the masses of the materials as they combine together. This will help us to discern the ways in which the antibody and antigen react with each other.
      In order to create the sample plates, we started with the Si - SiO2 plates and used a rotating plate to place uniform layers of HMDS and a photoresistive material over the plate. Then, after placing a mask on top of the plate, we used a laser system to burn off some of the photoresistive material and exposing the Silicon dioxide. The hydrophilic polymer was then bonded to the silicon dioxide. An acetone was then applied to the plate to remove the photoresistive material. This, then, explses the HMDS material which surrounds the polymer.
     At thsi point, we brought the plate into a different lab to make depth measurements of the polymer layer. To do this, we utilized a spectral reflecting biosensing device called the IRIS (Interfrometric Reflectance Imaging Sensor). Light from selected light emitting diodes are shone onto the plate. Some of the light reflects from the top surface of the polymer while some passes through it to the SiO2 layer and reflects from the silicon layer. These two beams are then reflected into a CCD camera which is connected to a computer system. The camera and computer will then analyze the wave interference pattern established by the light beams.
      Since the beams which originally hit the polymer are in-phase with one another, the interference pattern which develops is based upon the pathlength difference of the two rays. The further the beam traveling through the polymer moves in comparison to the initially reflected beam, the thicker the polymer-silicon dioxide underlayer must be. In observing how much of a wavelength different the two rays arepermits us to make accurate measurements in the nanometer range of the coating thickness.
     Later, we will repeat this measurement process utilizing the IRIS system to determine the thickness of the antibody and the antigen layers.
     Onc we have made these measurements of the sample, we will bring it over to the BU School of Medicine's Center for Biomedical Mass Spectrometry.. We have already met with Professor Mark. McComb who, along with his graduate students, will guide our use of the MALDI-TOF (matrix assisted laser desorption ionization time of flight) mass spectrometer. Utilizing this device, we will be able to break our ample apart and make measurements of the actual chemicals in our sample.
     In using the MALDI-TOF, we will coat the sample with a matrix chemical that will absorb laser light shone on it and blow the sample along a tube. The time of the flight of the materials along with a measurement of the mass to charge ratio of each chemical to make the trip permits us to produce a chemical analysis of the sample.
     Over the course the remaing weeks of this project, we hope to perform this series of tests several times and then focus our efforts on the PSA sample.

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