12/19/2012

     On this day, I learned about the various other methods of DNA seperating other then capillary electrophoresis. Of these several methods that I learned about, I was particularly interested about the method of gel electrophoresis.

     Gel electrophoresis is a method that is used to separate and then analyze DNA, RNA, and proteins on the basis of their size and charge. Particularly in the interest of my internship, it is often used to separate a mixed group of DNA and RNA fragments by length and to separate proteins by their charges. This process occurs in an agarose matrix. Agarose is a gelatinous mixture and it has a neutral charge and a lower degree of complexity--thus making it less likely to interact with biomolecules. Gels made from purified agarose have a relatively big pore size, making them useful for separating large molecules like DNA fragments. DNA is overall negatively charged and so when they are placed in a gel, an electric field is created across the very gel and so the negative DNA approaches the positive electrode while moving further away from the negative cathode. Shorter molecules move faster and travel further than the longer ones because they are able to move more easily through the pores of the gel. After the process, one will find that the different sized molecules have created distinct bands on the gel.  

    This method of DNA separation, however, is not commonly used by mentor as it is limited. For instance, the gel may melt during electrophoresis from the heat caused from passing a current across. In addition, comparing the relative quantity of the various molecules rely on the band darkness of the different spots in the gel. It's method consequently has a substantial degree of error. (That is why experiments are usually run several time to get viable results.) 

     Hopefully by the week I come back from winter vacation, my real mentor, Yolanda, will be back as well so that I may be able to start testing the various samples of DNA for myself!

http://m.youtube.com/?reload=9&rdm=mfca6b1q0#/watch?v=9f2VSyVhsGI&feature=related

<Above is a YouTube link demonstrating a slab gel separation.>

December 12

I was not able to go to my internship as my mentor Yolanda went home for the holidays.
____

        Although I was not able to go to my internship on Wednesday, I decided to research more about the particular field of analytical science and about DNA separation, both in which my mentor (and thus I) is involved in.
        DNA isolation is an process that extracts DNA from other sources. There are different methods for doing this but what they all have in common is that they aim to separate DNA present in the nucleus of the cell from other cellular components. While researching online, I found that this process is crucial for genetic analysis, which is used for medical, scientific, or forensic purposes. In the field of medicine, this application is used for diagnostic purposes. To my fascination, I found that this process of DNA separation is important in the field of forensics as it allows investigators to recover DNA for identification of criminals, and the likes. While the area of my internship deals with the primary step of separating two DNA strands of similar length into separate pieces, I found it very fascinating to see how this type of research benefits the real world outside the long white coats and enclosed space called the laboratory.

reference: http://www.enotes.com/dna-isolation-methods-reference/dna-isolation-methods

December 5: Getting Started

Today, I learned all about DNA separation through the use of capillary electrophoresis.

The separation of DNA (not a double but a single strand) of the same length starts with synthesized DNA that is dyed so that the capillary machine detector can detect the separated DNA at the end of the process. Scientists are aware of how to separate DNA with different lengths, but what they do not know and what my internship is focused around is how to separate DNA of the same length. This can simply not be done by adding common separating polymers to the tube, but by adding one of the four bases (adenine, guanine, thymine, and cytosine) which helps to differentiate the speed at which the DNA sample hits the cathode end (due to the phosphate group attached to the DNA which gives it a negative charge). Why adding the bases helps separate the genes is unknown and there is currently a limit to how many parts the DNA can be separated into—as of now, it can be separated into 7 pegs.

After understanding all this, I was then explained to about the lab procedures that I would be performing. The graduate student that helped me, Yolanda, walked me through and we prepared the DNA test samples that will go in the machine for analysis. At the end of my time, I was amazed at how far I had come (and it was only the 2^nd time here) as just 2 weeks ago, I had no idea what capillary electrophoresis was and as to me, it sounded like something in another language. I am looking forward to my next meeting, as I will be able to apply what I have learned today and play an even greater role in preparing the test samples for the lab.

November 28

Was not able to go to internship due to schedule change.

November 14

No internship due to my misunderstanding upon scheduling rides with Ms. Biggins.

D-1

             On my first internship day (11/07/12), I finally was able to meet my mentor, Linda. Although this visit consisted primarily of introductions, I was able to get a peek of what I would be doing for all throughout my internship experience. Although my mentor is Linda, I soon found out that I would be, for the most part, working with a 4-year graduate student named Yolanda.

            While conversing with both Linda and Yolanda, I found out that their field of specialty was titled, “analytical chemistry”. They explained to me that for the past several years, they had been researching on how to separate DNA by sequences. In addition to this, I was also told where I would come into play within all this. I would be helping Yolanda with her current project on the very topic stated above (separating DNA [and RNA] by sequences). Whether it be measuring out ingredients, creating gels for the lab, or more, I was excited to do it all. Curious to know more about this particular field of science, I can not wait until my next visit—in which I will actually get the chance to take part in the research process!

The Quest for Science!

My first blog! ;)

Throughout my day at the UMass science event, I attended 4 very different classes, titled: "Unveiling the Hidden Universe", "From Capillary Origami to the Lotus Effect", "Funtastic Food Science", and "The Singular Science of Paper, and Everything Else."

Of these 4 classes, I particularly enjoyed the food science workshop because I was really able to get involved and experiment.  Here I was shown how to change melted ice cream into the more common and tasteful, creamy texture we know today. For this experiment, only two ingredients were needed: liquid nitrogen (LN2) and (most importantly) ice cream! <& for safety, gloves were a must> Mixing all these ingredients together in the blender, I learned that the secret to the creamy ice cream all has to do with the rapid freezing of the mixtures. The liquid nitrogen caused the fat and water particles to stay extremely small, giving the ice cream its fluffy consistency. The main goal was to avoid the ice crystals, which are similar to what one gets when making milk.

In short, I really enjoyed my day and through this event, I was able to—though very briefly—see the various pathways one can travel with solely the love of science.