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.
Sunday, August 7, 2011
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.
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.
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.
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.
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.
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.
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