RM's+Week+of+November+26

RM's Logbook


 * Monday, November 26, 2007**

Tomorrow, I will go to the lab, but today I read a paper (yes, another one). I'm trying to come up with ideas for my project by the time that I finish learning the basics of AFM. I still have some ways to go, such as actually setting up the microscope and exploring the software, but at least I've witnessed how the wafers and cleaned, how they're prepared, etc. The paper that I'm reading deals with DNA sizing using the AFM, and is associated with John Hopkins' School of Medicine. The reason AFM is very attractive for DNA sizing, I learned, is that it can be done at a lower cost, it has a high signla to noise ratio, and it can detect proteins bound to the DNA. This last part can also refer to DNA "decorating" with proteins, in order that specific information about the molecule may be obtained. The paper also contrasted using AFM to gel electrophoresis - I just found a tutorial website that explains the process in a little more detail.


 * Tuesday, November 27, 2007**

I was planning on working with the spectroscopy tutorial; however, the link did not function properly. As such, I began reading the DNA tutorial that I found on the web yesterday. I will be going to the ND lab today, but I cannot stay for too long. Perhaps I will just take a couple images. Anyway, gel electrophoresis, in easy terms, is this:

1. The DNA from crime-scene evidence or from a reference sample is cut with something called a restriction enzyme. The restriction enzyme recognizes a particular short sequence such as AATT that occurs many times in a given cell's DNA. One enzyme commonly used is called //Hae// III (pronounced: Hay Three) but the choice of enzyme varies. For RFLP to work, the analyst needs thousands of cells. If thousands of cells are present from a single individual, they will all be cut in same place along their DNA by the enzyme because each cells DNA is identical to every other cell of that person. 2. The cut DNA pieces are now sorted according to size by a device called a gel. The DNA is placed at one end of a slab of gelatin and it is drawn through the gel by an electric current. The gel acts like a sieve allowing small DNA fragments to move more rapidly than larger ones. 3. After the gel has separated the DNA pieces according to size, a blot or replica of the gel is made to trap the DNA in the positions that they end up in, with small DNA fragments near one end of the blot and large ones near the other end. The blot is now treated with a piece of DNA called a probe. The probe is simply a piece of DNA that binds to the DNA on the blot in the position were a similar sequence (the target sequence) is located. 4. The size or sizes of the target DNA fragments recognized by the probe are measured. Using the same probe and enzyme, the test lab will perform these same steps for many people. These sizes and how they distribute among large groups of people form a database. From the database a rough idea of how common a given DNA size measured by a given probe is found. The commonness of a given size of DNA fragment is called a population frequency.


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Steps and image found on: http://www.scientific.org/tutorials/articles/riley/riley.html

At the lab, I viewed my silicon sample just with the APTES. This time, I set up the microscope, so I understand how to do so much better now. At first, I was having trouble inserting a tip; however, it was finally done and I captured a few images. In order to capture the images, I had to learn how to use the software entiteld "Nanoscope": I learned what should be kept at the default settings and what I should change to obtain a desirable image. My image is saved as "rm4aptes".


 * Wednesday, November 28, 2007**

I'm not going into the lab today; however, Dr. Sarveswaran told me that she would send me some papers to read.

In the meantime, I'm reading yet another paper on AFM. This one is entitled "Integrated Confocal and Scanning Probe Micrscopy for Biomedical Research". It was written with associations with the London Center for Nanotechnology and published in The Scientific World Journal. It also discusses the potential use of AFM to detect diseases. In order to diagnose and detect diseases, however, an AFM needs to be set up in conjunction with another type of microscope. As I am brainstorming ideas for my research, I think that this would be a really interesting field to dive into. However, I will have to ascertain whether a dual-microscope setup will be feasible at ND.


 * Thursday, November 29, 2007**

Again, at ND, we went down to the AFM. This time, I viewed my silicon sample with APTES and plasmids deposited on its surface. I captured at least 4 good images. I also set up the AFM, and learned how to view different spots of the sample without damaging the surface. I named them "rm5dna.000, rm5dna.001, etc.". I also learned when to adjust the voltage point in order to obtain clear images using the AFM. Dr. Sarveswaran e-mailed me two papers during our session at the AFM.


 * Friday, November 30, 2007**

No school.

Week of November 19

Week of December 3