Tuesday, July 17, 2007
July 16th blog
This is our last week in the research lab and Dr. Fromme wants us to try different lab activities that we can use in the classroom. She made several suggestions as to the type of materials that will be accessible for us and still be able to bring in the concept of crystallization in the classroom. Chemicals such as sucrose, sodium chloride, copper sulfate, and potassium chloride would be easy for us to find in our chemistry lab. We can use glass vials, we used wool, cotton, strand of hair, silicone and made several experimental set-ups. I am really excited about what we have tried because we can bring in knowledge from the research lab and connect it to the concept that we normally teach in the classroom such as photosynthesis.
July 13th blog
We spent most of our morning listening to a powerpoint prenetation of one of the grad students. We have seen three presentations the past 3 weeks and we can tell that this presnetation was so much better than the others. The student was better prepared, very confident about his data and very confident about his presentation. The rest of the time was spent with Petra helping us with our powerpoint presentation. She gave us a lot of suggestions on how to organize thoughts in our powerpoint. Monday, we will start with lab activities that we can use for our own classroom. We really have been fortunate to be assigned with Dr. Fromme's lab. She has been very helpful not only in the research lab but also would like for us to take activities learned from the lab to use in our classroom.
Thursday, July 12, 2007
July 12th blog
We looked at our PSI crystals by microdialysis tubing. These crystals are entirely different shape from all the other crystals we have looked at with different techniques. These crystals are longer and thinner and when magnified under the polarized dissecting scopes, they look like neon colored glow sticks - beautiful. We each tried to seed our crystals onto another microdialysis tubing by fishing for crystals. This was a very neat experience to try to transfer a dot-size crystals from one end to another tube :).
Wednesday, July 11, 2007
July 6th-11th blogs
July 9, 2007
We started today with a different crystallization technique of PS I called microdialysis tubing. Dr. Fromme mentioned that this type of technique is something that she shows her students the last due to the difficulty of the process. This involves the preparation of materials (microdialysis tube) and probably a more careful and steady hand specially when we get to trying to “fish” for crystals to be seeded. The next part of this technique will be continued on Thursday.
July 10th blog
We worked today with Dr. Wachter and her technician named Nam. Dr. Wachter gave a powerpoint presentation on PCR (polymerase chain reaction) and she gave us a little background on DNA. They are also involved in crystallization of protein called GFP (green fluorescent protein) from a jellyfish. After the powerpoint presentation, we started working on the process of PCR . We combine all the chemicals needed for PCR and centrifuge the PCR ingredients. We were given a chance to again use the tools that they use such as micropippetors , showed us how to use the PCR machine and how to prepare the agarose gell needed to show the movement of chemical (DNA). The lab we did today is a different experience which gave me a very neat experience and understanding of how DNA is used in PCR. This is an experience that I can take in the classroom as we are in the age of biotechnology.
July 11th blog
We started our day with placing the agarose gel in the electrophoresis chamber, transferred the PCR cocktail of chemicals we prepared yesterday and left it for an hour. Meanwhile, Dr. Wachter gave a powerpoint presentation on their goals and background on their research which is the GFP protein. It was good to be able to follow what was going on in the lab since I had a little bit of background on DNA J.
We started today with a different crystallization technique of PS I called microdialysis tubing. Dr. Fromme mentioned that this type of technique is something that she shows her students the last due to the difficulty of the process. This involves the preparation of materials (microdialysis tube) and probably a more careful and steady hand specially when we get to trying to “fish” for crystals to be seeded. The next part of this technique will be continued on Thursday.
July 10th blog
We worked today with Dr. Wachter and her technician named Nam. Dr. Wachter gave a powerpoint presentation on PCR (polymerase chain reaction) and she gave us a little background on DNA. They are also involved in crystallization of protein called GFP (green fluorescent protein) from a jellyfish. After the powerpoint presentation, we started working on the process of PCR . We combine all the chemicals needed for PCR and centrifuge the PCR ingredients. We were given a chance to again use the tools that they use such as micropippetors , showed us how to use the PCR machine and how to prepare the agarose gell needed to show the movement of chemical (DNA). The lab we did today is a different experience which gave me a very neat experience and understanding of how DNA is used in PCR. This is an experience that I can take in the classroom as we are in the age of biotechnology.
July 11th blog
We started our day with placing the agarose gel in the electrophoresis chamber, transferred the PCR cocktail of chemicals we prepared yesterday and left it for an hour. Meanwhile, Dr. Wachter gave a powerpoint presentation on their goals and background on their research which is the GFP protein. It was good to be able to follow what was going on in the lab since I had a little bit of background on DNA J.
July 6th blog
We spent our morning in three places, the X-ray lab, computer lab and conference room. We first looked at one of our lysozyme crystals setup wil liquid nitrogen ready for diffraction. The liquid nitrogen is necessary to prevent the protein from drying out. We then went to the computer lab to obtain data set of the diffraction pattern. Raimund Fromme then showed us how to obtain pretty ribbonlike form picture of the protein from the data set using a specific program. This part was really exciting because I have seen these protein pictures from Biology books but never really know how it was made. We then spent the second half of our morning listening to one of the grad student's presentation.
Thursday, July 5, 2007
July 5th blog
We started our day in the lab looking at the phycocyanin protein crystals we prepared by vapor diffusion last tuesday. The crystals formed well after two days and in large numbers. The phycocyanin crystals were in deep blue color due to its (phycocyanin's) antennaes that allows it to capture green light. Its shape varies in shape and sizes. Although the shapes and sizes are different, the unit cell according to Raimund Fromme is still the same. Tomorrow, we will try to work on the diffraction of these crystals. On the second half of the day, we went to the x-ray lab and worked on the x-ray diffraction of the lysozyme protein that we prepared. Raimund Fromme showed us how to "fish" for crystals using the tiniest hook I have ever seen, in which case is only possible with the use of a powerful dissecting microscope. We attempted to work on two crystals, one of which has a beautiful diamond shape, which as it turned out, the beauty of crystal has nothing to do with the diffraction. We tried to work on another crystal and this time we were able to get a. diffraction. Tomorrow, we will work on more diffraction of crystals and this time we get to "fish" for our own crystals from our preparation.:)
Tuesday, July 3, 2007
July 3 blog
We worked today with Raimund Fromme (husband of Dr. Petra Fromme) on vapor diffusion of a different protein (phycocyanin). This was the protein that we centrifuged yesterday. In the next day, the crystals should form and we will be able to look at these crystals when we come back on Thursday. Following will be the x-ray diffraction maybe this week. The type of experiment we did today worked well without having to repeat the process, whihc means then that we are getting better withe use of materials such micropippetors :).
Monday, July 2, 2007
July 2
July 2, 2007
Jannette O. Nuestro’s blog
Dr. Fromme gave a powerpoint presentation on cyanobacteria, Photosystems I and Photosystems II. The question is why use Cyanobacteria (common term, blue green algae although not an algae), instead of plants? Cyanobacteria have been in use and is considered to be a free-living chloroplast, has large membrane antennae called phycobilisomes and PSII, which allows it to harvest light, better developed than plants and has complete visible light spectrum and collects green light unlike plants that only collects red and blue light and cyanobacteria is more stable than plants due to cytochrome present. Photysystems I (PSI) leads to reduction of energy NADPH which also allows an easier crystallization of protein than PSII . Photosystems II (PSII) role is to split water ( H2O) molecule to oxygen which is also Dr. Fromme’s goal and would like find out how plants perform this process. The second part of the day is the introduction to x-ray crystallography. Dr. Raimund Fromme will be handling our group this week for the x-ray crystallography of protein. He gave a power point presentation as a brief overview while we were waiting for the protein being centrifuged. Afterwards, the protein was stored in the fridge for lab tomorrow. The powerpoint presentation from both researchers was a great way for us to understand what was going on, although, I must admit my brain is a bit (a bit?) overwhelmed J.
Jannette O. Nuestro’s blog
Dr. Fromme gave a powerpoint presentation on cyanobacteria, Photosystems I and Photosystems II. The question is why use Cyanobacteria (common term, blue green algae although not an algae), instead of plants? Cyanobacteria have been in use and is considered to be a free-living chloroplast, has large membrane antennae called phycobilisomes and PSII, which allows it to harvest light, better developed than plants and has complete visible light spectrum and collects green light unlike plants that only collects red and blue light and cyanobacteria is more stable than plants due to cytochrome present. Photysystems I (PSI) leads to reduction of energy NADPH which also allows an easier crystallization of protein than PSII . Photosystems II (PSII) role is to split water ( H2O) molecule to oxygen which is also Dr. Fromme’s goal and would like find out how plants perform this process. The second part of the day is the introduction to x-ray crystallography. Dr. Raimund Fromme will be handling our group this week for the x-ray crystallography of protein. He gave a power point presentation as a brief overview while we were waiting for the protein being centrifuged. Afterwards, the protein was stored in the fridge for lab tomorrow. The powerpoint presentation from both researchers was a great way for us to understand what was going on, although, I must admit my brain is a bit (a bit?) overwhelmed J.
Blogs from June 26th-29th
Jannette O. Nuestro
Blogs from June 26th -29th
Photosynthesis Fromme
May I express my apologies for not having been able to post my blogs online. I wasn’t connected to the internet until today. However, I have been keeping and writing my reflections for each day regarding my experience in the research lab with Dr. Fromme.
June 26th Tuesday
We started today with our lab with the help of one of Dr. Fromme’s graduate students named Yana. She took us for a tour of the different lab areas where they perform the crystallization of protein. The plan for the day was to prepare the chemicals needed for the crystallization of protein called lysozyme in plants. Yana was very helpful, willing and patient in reviewing and reteaching us the chemical equations necessary to arrive at the desired units of measurements for the chemicals needed for the lab. It was an experience that took me back in time many, many years ago when I had chemistry in class. I feel like a student again having to jog my memory of solving chemical equations. When the chemicals were prepared, Dr. Fromme took us into her office for a powerpoint presentation on photosynthesis. The presentation gave us an introduction to the research that she has worked on and gave us an overview of the different experiments that will be performed in the next few days.
June 27th Wednesday
Today, we worked in the lab with Dr. Fromme in crystallizing lysozyme in plants. The method we used today is called batch crystallization, where the lysozymes or enzyme will be crystallized inside the thin glass capillaries. The chemicals used where lysozyme, sodium chloride, acetic acid and sodium acetate – these were the chemicals that were peepared yesterday. We used different materials in the lab, such as micropippetor , plastic vials, capillaries, permanent markers and tape. I had to mention permanent markers and tape to emphasize its importance along with the micropipettors because these items are as we found out are just as important as in keeping track of our experiment. Everyone of us in the group had a nice turn in working in the experiment using the pipettors in obtaining accuracy of the mixture in chemicals. And we all found out that just as our students in the classroom, we made our mistakes and had to repeat our mixture of chemicals at least two times. We were just glad that one of us noticed the mistakes and we were able to correct it.
June 28th Thursday
Today, we looked at the capillaries form the batch crystallization hat we have prepared from
yesterday.We made two groups of cru=ytallization with varyig amounts of lysozme. We labeled the first
group with 100 mg./ml. of lysozyme as batch A and the second group with 50 mg./ml. of lysozyme as
batch B. Both groups had the same amount and
mixture of chemicals of sodium acetate (NaAc), sodium chloride (NaCl)and water (H2O). Different
capillaries have varying amounts of proteins that have cruystallized depending on the amount of
repetitions and mistakes the group made yesterday. But, like any science experiments, there is always
room for errors J. In addition to seeing the results of our experiment from the previous day, we also
started with two more experiments. The goals of these experiments was to use different methods of
crystallizing protein. The first one which was much easier to prepare was called free interface-diffusion
The protein solution used for the experiments use 50 mg/ml lysozyme and the same amount of sodium
chloride with sodium acetate as the precipitant. The second experiment is called vapordiffusion. This
experiment stores the chemicals in a reservoir
with mixtures of the same chemicals, sodium acetate, sodium chloride and water. On a
separate glass slide is the protein solution. This will be stored overnight and be observed the
following day.
June 29th Friday
Today, we had the opportunity to sit with the graduate students under Dr. Fromme and to listen to one of the student’s powerpoint presentation on his experiment. His presentation was on the expression of protein in Spinach in E.coli bacteria. It was a very interesting experience to watch the grad students listen and offer suggestions on the presenters experiment. After this experience, we went back to the lab to look at the results and take pictures of our experiments from thursday. Once again, with pride and enjoyment, we were successful and have seen beautiful crystals formed under the dissecting scopes. Dr. Fromme explained the differences in the amount and sizes of the crystals formed and showed us how to take pictures of the crystals. Pictures that we can take in the classroom to show our students and post in our wiki J. The whole week was a wonderful and productive experience with Dr. Fromme . She had been very professional, dedicated, willing to teach and help and encourage us to experience for ourselves being in the research lab by actually doing the experiments and using the materials in the lab. She had been very accommodating, very well organized and prepared us well everyday for each experiment.
Blogs from June 26th -29th
Photosynthesis Fromme
May I express my apologies for not having been able to post my blogs online. I wasn’t connected to the internet until today. However, I have been keeping and writing my reflections for each day regarding my experience in the research lab with Dr. Fromme.
June 26th Tuesday
We started today with our lab with the help of one of Dr. Fromme’s graduate students named Yana. She took us for a tour of the different lab areas where they perform the crystallization of protein. The plan for the day was to prepare the chemicals needed for the crystallization of protein called lysozyme in plants. Yana was very helpful, willing and patient in reviewing and reteaching us the chemical equations necessary to arrive at the desired units of measurements for the chemicals needed for the lab. It was an experience that took me back in time many, many years ago when I had chemistry in class. I feel like a student again having to jog my memory of solving chemical equations. When the chemicals were prepared, Dr. Fromme took us into her office for a powerpoint presentation on photosynthesis. The presentation gave us an introduction to the research that she has worked on and gave us an overview of the different experiments that will be performed in the next few days.
June 27th Wednesday
Today, we worked in the lab with Dr. Fromme in crystallizing lysozyme in plants. The method we used today is called batch crystallization, where the lysozymes or enzyme will be crystallized inside the thin glass capillaries. The chemicals used where lysozyme, sodium chloride, acetic acid and sodium acetate – these were the chemicals that were peepared yesterday. We used different materials in the lab, such as micropippetor , plastic vials, capillaries, permanent markers and tape. I had to mention permanent markers and tape to emphasize its importance along with the micropipettors because these items are as we found out are just as important as in keeping track of our experiment. Everyone of us in the group had a nice turn in working in the experiment using the pipettors in obtaining accuracy of the mixture in chemicals. And we all found out that just as our students in the classroom, we made our mistakes and had to repeat our mixture of chemicals at least two times. We were just glad that one of us noticed the mistakes and we were able to correct it.
June 28th Thursday
Today, we looked at the capillaries form the batch crystallization hat we have prepared from
yesterday.We made two groups of cru=ytallization with varyig amounts of lysozme. We labeled the first
group with 100 mg./ml. of lysozyme as batch A and the second group with 50 mg./ml. of lysozyme as
batch B. Both groups had the same amount and
mixture of chemicals of sodium acetate (NaAc), sodium chloride (NaCl)and water (H2O). Different
capillaries have varying amounts of proteins that have cruystallized depending on the amount of
repetitions and mistakes the group made yesterday. But, like any science experiments, there is always
room for errors J. In addition to seeing the results of our experiment from the previous day, we also
started with two more experiments. The goals of these experiments was to use different methods of
crystallizing protein. The first one which was much easier to prepare was called free interface-diffusion
The protein solution used for the experiments use 50 mg/ml lysozyme and the same amount of sodium
chloride with sodium acetate as the precipitant. The second experiment is called vapordiffusion. This
experiment stores the chemicals in a reservoir
with mixtures of the same chemicals, sodium acetate, sodium chloride and water. On a
separate glass slide is the protein solution. This will be stored overnight and be observed the
following day.
June 29th Friday
Today, we had the opportunity to sit with the graduate students under Dr. Fromme and to listen to one of the student’s powerpoint presentation on his experiment. His presentation was on the expression of protein in Spinach in E.coli bacteria. It was a very interesting experience to watch the grad students listen and offer suggestions on the presenters experiment. After this experience, we went back to the lab to look at the results and take pictures of our experiments from thursday. Once again, with pride and enjoyment, we were successful and have seen beautiful crystals formed under the dissecting scopes. Dr. Fromme explained the differences in the amount and sizes of the crystals formed and showed us how to take pictures of the crystals. Pictures that we can take in the classroom to show our students and post in our wiki J. The whole week was a wonderful and productive experience with Dr. Fromme . She had been very professional, dedicated, willing to teach and help and encourage us to experience for ourselves being in the research lab by actually doing the experiments and using the materials in the lab. She had been very accommodating, very well organized and prepared us well everyday for each experiment.
Thursday, June 28, 2007
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