Sunday, November 20, 2011

November Update on Influence of RET

     As school has gotten under way, I've tried to put an emphasis in my courses on how to perform labs, analyze the data, and how to look at varied ways to perform the experiment. As a class, we have spent a lot of time looking at the varied factors in performing an experiment which can limit the precision of the results. These factors include procedural limitations, equipment limitations and human limitations.
      We have then delved into various ways that each of these limitations can be reduced in sinificance by makig changes to the equipment and procedures used. We have also looked into various statistical techniques which can be utilized to minimize the effects of outlier results.
      At this point, we are getting ready for two major uses of this information. The first is that the students will be asked to redesign and redo an experiment to improve on the results that they got the first time that they did the experiment. They can redo the experiment using any equipment and techniques that we have.
      The second exercise will be for each student to develop and test a device to protect a raw egg from breaking after it has dropped ten meters to the ground. Students will have to redesign their project until it is successful. Then, they will have to write a design paper detailing what their design is and what the unrlining physics principals are which explain how their design works. This analysis will include reference to such areas as Newton's laws of motion, kinematics, Hooke's Law, Impulse-Momentum relationship, Momentum conservation, Work, and/or Energy Conservation.
     Through this process, students should learn how to work in a research environment. They will learn how to revise lab procedures based upon their analysis of past results. They will also become more familar with utilizing the scientific method in a real setting.

Sunday, August 7, 2011

Research Reflections

     We are coming to the last week of our work on the IRIS and MALSI-TOF project. It is important to note that this is not the last week that work is being done on the project. Undergraduate and graduate students of Dr. Goldberg and Dr. McComb will be continuing the studies on this topic.
     The most important aspect for people to realize about research is that it is a continuing investigation. We are trying to work in an area that has not been studied before. We develop theories explaining what we think should happen. The research is to see if the theory matches up against the reality.
     In our research, we have found that the MALDI system is a good way to identify the composition of the materials even if there are very small amounts of the material in the sample. However, we need to refine the testing techniques utilizing the IRIS system to identify how much of the different proteins are present in the interactive system.
     We have discerned that there are difficulties in maintaining a consistent polymer coating over the oxide level in our chip. As we work on this project, we will be looking at alternative chip designs. During the upcomng week, we will focus our efforts on a design that Julian Anding came up with that will raise the polymer spot above the HMDS level. Hopefully, this will make it easier to maintain the polymer consistency as the antibody and antigen levels are added to it.
     The second area that we will focus on is to derive an improved method to clean the sample after the addition of the antibody and antigen levels so that we will not wash off materials measured in one level as we move onto the next. Following the antigen placement, we will be reducing the amount of washing done with the distilled water. Hopefully, this will help us to maintain the antibody material on the sample as the antigen is added.
     During our five weeks of work, we have been able to derive data which shows where the measurement difficulties have appeared. We have had too little time to work through all of the possible solutions to the problem and to test our solutionsmultiple times. Without this evidence, we cannot say that we have found a viable solution. The other piece of the research process that has been important is to only change one aspect of the test procedure at a time so that we can make our improvements. There were times when we wanted to jump ahead by making multiple changes in our test procedure. We then had to slow ourselves down so that we could maintain our certainty about what factors needed to be changed.

Thursday, August 4, 2011

Results of PSA samples

     Over the course of the last week, we have been trying to use the IRIS and MODI-TOF to make measurements of the PSA antigen. PSA is used to signal the possibility of prostrate cancer. Unfortunately, it has only about a 50% chance of being correct in making the proper diagnosis. We hope to make a better prediction of the diagnosis with more accurat measurements.
     We have had difficulty in making accurate measurements for two reasons. First, the polymer base to which the antibody attaches is not consistent in maintaining its leel of material. Second, as we clean off the antibody and antigen levels, we found that the levels of antibody and antigenchange.
     We spent much time trying different chip configurations in order to maintain the polymer, antibody and antigen quantities. Unfortunately, we couldn't make accurate measurements with the IRIS that woul let us dtermine the amounts of antibody and antigen involved in each bonding event.
     However, we were able to use the MALDI-TOF to show accurately that there were PSA antigen components which were singly, doubly, and triply charged during the MALDI laser interaction with the PSA.
     We have developed a new chip design and cleaning process to use in the preparation of our new chip. We plan to test this new design and process within the next week.

Friday, July 29, 2011

Reflections on Research

      Having been involved in research efforts at a variety of location before ( Washington University, University of Rochester, Natick Labs...), the part of the process which has been reaffirmed this summer at the photonics lab is the need for a team approach in undergoing the research. Not only is there the guidance of the Principal Investigator but also the needed input of those who are working in the lab. People need to be able to share ideas on how to approach problems. Furthermore, within the constraints of funding and stipulated grant proposals, researchers need to have the freedom to investigate new avenues which evolve in the research process.
     It is also important that researchers be able to follow leads sufficiently so that they can ascertain how it will direct future research. It is important to recognize that even negative results provide the researcher with information concerning how the process under study operates. It also provides the researcher with new avenues to be delved into.
     As a teacher trying to become part of the process, instead of just an observer, it would be helpful to designate more of the 6 week time period to working in the lab. This would provide the teacher with the time to get the background information needed, the lab experience needed and the time to figure out how their work fits into the overall research of the lab. This would permit the teacher to feel able to contribute to the research beyond the technician's role. However, in order to do this, either the time period of the project must be expanded to more than 6 weeks or the hands-on time in the lab must be expanded to closer to 5 full days per week rather than 3.5. This would help the teacher to really experience the research experience better.
     One potential outcome of this experience for my classwork deals with providing students with the opportunities to do multiple stage research. As we delve into our laboratory experiences, rather than each lab only occurring on one double lab day, students need to do follow up labs. For instance, they will do a typical first lab on some topic. Then, as part of the lab report, they will do a limitations analysis of the lab. Following this, they will be asked to redesign the lab so that they can reduce the number of limitations in the lab. Then, they will perform their revised lab and analyze their results.
      Later, this process will be expanded upon as they do their own semester long projects.
      It will be important for them to work on both the labs and projects in small groups so that they gain experience in sharing ideas during the research process.

Monday, July 25, 2011

Research Procedure Modifications

We have been having difficulty adjusting the test procedure being used in creating our samples so that there are fewer variations in the test results. We are focusing our attention at this time on trying to improve the techniqes used to lay down the polymer and antibody layers on the sample.

Wednesday, July 20, 2011

IRIS Specimen Research Revisions

We have been trying to find a uniform method of applying the polymer to the SiO2 surface. We had a method which seemed to provide excellent results with only 5% variation. Today, we retested this procedure but our result was only good to 21.7% variation. We will be looking to improve on this.

Immediately, we are also going to see if we can work on another difficulty dealing with the placement of antibody material to the polymer. We are going to test each of the steps used during the placement of the antibody and the cleaning off of excess antibody material from the polymer slid. Hopefully, in this way, we will be able to better discern what follow up steps are necessary.
The following is a video describing the nature of our research work with the IRIS and MALDI-TOF systems.

video

Saturday, July 16, 2011

End of Week Two

     Our project is testing the applicability of the IRIS and MALDI-TOF systems in measuring the combining of antibody-antigen structures. This project has several variables which need to be tested. They include :

     1. The techniques used to set up the target plate of silicon, SiO2, polymer, antibody, and antigen.These techniques include the spotting technique is developing the polymer-antibody-antigen spots on the target, the washing techniques used in removing the photoresistive material, and structuring the different levels of the photophilic and photophobic layers.

     2. The techniques used during the MALDI-TOF process in exposing the target to laser beams. Here, we control the intensity of the laser beam and the time duration used to maximize the clarity of the mass spectrometry spectrum.


In order to measure the validity and reliability of our results, we will compare our results with those of known measured  reactions developed using other measurement techniques. We will then repeat our measurement system to determine  how accurately our results are reached each time.

Yesterday, we attended a full day session at the Museum of Science to learn about a program developed by the museum to teach about the engineering principles used in industry. This program is based upon the same principles as the Principles of Technology curriculum. The main differences between the Principles of Technology curriculum and this Engineering the Future curriculum is that this new course focuses only on the engineering principles and not the physics underpinings of the technology. Due to this difference, there are only three major units in this program dealing with physics. They focus only on an introduction to thermodynamics, fluid flow and electric circuits. They then use these topics to go into further depth in various areas important for developing engineering techniques.

Wednesday, July 13, 2011

MALDI and IRIS labs

     Yesterday, we spent the day in the Mass Spectroscopy lab in the BU Medical School. With the help of Dr. McComb and another mass spectrocopy expert, we began our work in learning how to run tests on the MALDI-TOF.We worked with some provided specimens to get a handle on the lab procedures needed to run the upcoming tests. Eventhough it wasn't until very late in our session, we were able to learn what the test procedure will be that we will be using as we proceed to test our own test subjects.
     Today, we started developing the target samples that we will be usiing. The silicon- SiO2 surface was covered with a polymer. We then took this and started making our measurements with the IRIS system. Jess and I ran the equipment under Julian's supervision. This is our first step to being able to run our tests on our own.

Tuesday, July 12, 2011

Large Group Cleanroom Activity 1

     Yesterday,  we did two large group activities. During the first, we had a presentation by Dr. Selim Unlu on the practice of reasearch. He shared with us his philosophy concerning what qualifies as legitimate research and what practices should be followed in today's age in order to perform successful research.
     Foremost is the concept that you should not be fearful of failure. It is most important to follow your curiousity and to create an educatied plan to delve into new areas of study. You may be utilizing developed systems but you should be taking them into new directions.
     Be organized and meticulous in your record keeping and data anaylsis. Follow a code of conduct as you persue your research. It is of importance that you disseminate your research to get others' imput. However, be careful to do so while maintaining protection for your ideas. This protection mechanism may include the search for patents. Be aware that to receive a patent, all of your work must be properly documented and dated. This is why the maintenance of a lab book is necessary.
     Following Dr. Unlu's presentation, a group of us went to the cleanroom to work with Dr.Helen Fawcett in preparing target slides. We used a masking system to burn a sample pattern onto a plastic substrate. We used a centrifuge type device to place layers of HMDS and photoresistance onto the disk. Then, using the mask and an ultraviolet light, we removed some of the photoresistance from the surface. This leaves a surface that we will later go in and place a test sample structure on.

Saturday, July 9, 2011

Research Team Meetings

On Thursday, we attended a Research Team meeting for Dr. Unlu's research team. They are working on several biophotonics areasw. We were in attendance because much of their work deals with the use of the IRIS analysis system. It was interesting to see how others are using and refining the use of the IRIS equipment to make measurements.

In addition to this work, Dr. Unlu is also having his group developing materials to use for presentations that will be done with and for k-12 students.  There will be a course run this summer for high school students. Then, during the year, grad students will visit schools in the Boston area and used these tested materials to share their researchwork with students.

On Friday, we took part in a presentation by Dr. Tarik Borogovac who is a research assciate in the Electrical and Computer Science Department. His presentation dealt with the work being done in the field of Smart Lighting. Here, they want to use lights as a means of communication. Ultimately, they want to use overhead lights in a room to communicate with the internet. In turn, they see using light as a means for automobiles to communicate with each other. They hope to have cars communicate so that as one car makes a change which might affect the neighboring cars, they will be able to respond in a defensive manner to reduce potential dangers on the road.

Later in the day, Dr. Goldberg's group held a team meeting to share results from experiments which have been gained recently. Data from experiments were shared with Dr. Goldberg, Julian, Jessica, a grad student on the team named Aaron, and me. As a result of the analysis of this data set, the group will be reviewing the results from past experiments to see if the same conditions discovered now were also present before. This may lead to further changes in the experimental techniques being used.

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.