Saturday, December 24, 2011
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.
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.
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.
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.
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