July 16th AM

The presentation on spider silk was very interesting. I was a molecular biology graduate student 20 years ago and I understood everything that she was doing. I like watching the silk fibers dropping down from the protein solution and the red eyes silkworm looked like aliens. It would be great if they can make silkworms produce colored silk like green silk, red silk, blue silk. Will be really cool. I could have done some similar molecular biology stuff if I am in the spider lab. I finished the lesson planing part one and will be working on the worksheets and curriculum mapping next week.

July 14th AM

Today, we waited on Nathan to come and scan precancerous cells on elasticity. He appeared at 10am. He got some cells from the incubator and changed the buffer so that the cells are all in the same buffer environment. Then he started the combi microscope and getiing the cantilever tip to focus in water at 37 degrees which is body temperature. The cells live as long as 6 hrs. at body temperature. they survive only 1 to 2 hrs. at 25 degrees or room temperature. It took him a long time to find the laser and he has to add more immersion oil.It is time for lunch.

cmap

July 13th AM

Today, we watch Rory repeat his experiments on precancerous cells to get more data on the elasticity or softness of the cells. Basically, you indent the cell at various points with the cantilever tip and pull back the tip and look at the force graph that is plotted. A gentle slope means that the cell is soft. A steep slope means that the cell is more rigid and less elastic. They pick the nucleus to test for elasticity so far. I think they should pick somewhere on the cell membrane if they really want to measure the elasticity of the cell. The nucleus is like the egg yolk of an egg. To test how hard the egg is, you would really test the hardness of the shell and not the egg yolk??? Just my opinion. I may be wrong.I worked on the lesson plan assignment while waiting for someone to appear at the lab.

July 12th PM

We worked on our posters and practise on Vpython. It is a cool software and we try different things on it like varying position, radius and color of the spheres, drawing arrows, and making a ball bounce on the floor. It would be fun for students to experiment with Vpython in their math classes to make the ball do different things.

July 12th AM

Today, Rory and Alex are looking at the data of the precancerous cells that they had collected last week. They probed 4 cell lines with cantilever tip to measure how elastic each cell was. They measure elasticity by indenting the cell with the tip at various regions, especially over the nucleus. The cells auto-fluoresce so thay can view the nucleus , nucleolous and cytoplasm easily. They hope to find a trend of elasticity across the cell lines. So far they have not gotten any good trend yet. There were different slopes on the force map for different cells, indicating different degrees of elasticity.

July 9th AM

We try to calibrate the combination AFM and confocal microscope with a new software. The goal is to align the image of the AFM with the image of confocal microscope. First, we looked at some ATTO molecules with the confocal microscope and measure the fluorescent lifetimes of the ATTO molecules. Olaf wants to test another way of drying the sample. It is an ACE duster moisture-free for cleaning computers. It contains tetrafluoroethane which is heavier than air. He intends to spray some of this gas onto samples in petri-dish. The goal of the new software is to make the AFM tells the confocal microscope the position of the cantilever and whether it touches the surface.

July 8th, AM

Today, Olaf put in a $30,000 camera that takes pictures instantly and that is maintained at minus 70 degrees Celsius. The camera can amplify the photons from fluorecent molecules and give a better image than the computer. We first looked at a picture taken of some fluorescent beads that is 10 microns in diameter. Next, we diluted some DNA and dyed it with YOYO which is a fluorescent dye. The DNA needs to be diluted so that we can see individual strands of DNA instead of a mess of DNA sphagetti stuck together. We have to fix the DNA onto mica. HEPES buffer was added which contains Ni ions. The Ni ions binds to the mica and holds the DNA onto the mica. We could see the fluorescent DNA under the eyepiece of the microscope. They need to buy the software that operates the expensive camera before we can take any pictures from the camera.

July 7th PM

We watch video 1 & 2 of RTOP training and scored the videos. We went through the scoring of video 1 and the expert's interpretation of the scoring. We learned a few things about how to score based on video 1. We viewed video 2 and scored them. Will look at scores tomorrow.

July 7th AM

Today, we look at the scans of different cells. The goal is to measure the elasticity of each cell and compare the softness of different cell lines. The sequence of precancerous cell lines from early to late stage goes from EPC to CPA to CPB to CPC to CPD. The cantilever tip is used to indent the cell at the nucleus and the elasticity or Young's modulus of the cell is measured. They expect the later stage cells to be very soft and elastic and to be able to squeeze between endothelial cells in capillaries and metastasize to other organs. A gentle slope on the graph indicates that the cell is soft or elastic. The cells auto-fluoresce so they do not have to dye the cells to visualize the nucleus. Next, they will look at the elasticity of the cells after incubating them in tamoxifen, an anti-cancer drug. They expect the cell lines that are killed by the drug should show less elasticity compared to cell lines that are not affected by the drug. Cells that are dyed with a fluorescence dte usually are stiffer than cells that are not dyed at all.

July 6th PM

Everyone discussed the research that they are doing. We got to understand RTOP principles. We grouped into 2 groups to discuss the topics that one observes in a walk-in the classroon. Adrian presented our ideas and Amber presented her group's ideas. I watched the RTOP video one and learn to assess the lesson that was presented.

July 6th AM

Today, we look at pre-cancerous cells from the human esophagus. They are from the CPD, CPA, EPC cell lines. The cells were dyed with fluorescent dyes that stain the nucleoli yellow and DNA blue. Cells were put on a petri-dish heater to heat them to body temperature of 37 degrees Celsius. The cells survive longer at 37 degrees than at 25 degrees or room temperature. Cells can survive up to 6 hrs. at 37 degrees compared to 2 hrs. at 25 degrees. The cells were scan with the cantilever tip in the oscillating mode. A picture of a cell with a big blue nucleus and a yellow nucleolus was seen. The cells were flattened on petri-dish and each squamous cell is about 20-25 micron.They zoom in on the nucleus of a cell to take another scan. Then, it is time for lunch.

coffee cup AFM

July 1st AM

Today, we built a primitive caveman AFM. We cut a flexible cantilever out of a coffee cup. Glue a plastic fork tip to the cantilever end and fasten a chip of Silicon wafer onto the back of the cantilever end that has the tip. We shine a green laser pointer vertically onto the Silicon reflector and saw the reflection of the green laser on a vertical white paper. It seems to work fairly well and we could use this caveman AFM in the classroom for measuring different heights of objects ,such as, coins, paperclips, erasers, etc. The cofee cup cantilever needs to be calibrated with objects of known heights first. A graph of deflected position versus known height can be plotted. The height of any object can be estimated from the graph when we know the delected position of the green laser. A cool cheap toy that is easy to make for the students. Students can also make their own macro version of the cantilever of an AFM.