Phenol-Chloroform Extraction

     This specific experiment is used to extract mixtures based on their solubilities. In this experiment we used it to extract RNA from DNA and protein. Protein is a non-polar molecule, it will be separated from the DNA which is a polar molecure. The RNA and DNA will end up in the chloroform, which is also polar. And the protein will end up the less polar solution, QIazol. The DNA will separate from RNA as it also moves into QIazol because the negative charge of DNA's backbone will be attracted to the H+ in QIazol. RNA is a single strand, so the exposed nitrogen bases will form hydrogen bonds with chloroform.

      After both solutions were transfered into the test tubes we added them to a centrifuge mixer for 15 min to create the separated layers. Because QIazol has a greater density than chloroform, the QIazol will reside at the bottom of the tube, and will give us easier access to the RNA at the top. Then we can take a pipette and carefully extract the RNA from the test tube.

     We also talked about the role of transcription factors. Transcription factors bind to DNA to make mRNA. DNA is wrapped around a protein histone, and some of it can be unwinded, and on the unwinded DNA there is a start and stop point. There are different stopping places for every different mRNA. And different mRNA's code for different functions and different proteins. There is also something known as "splicing", which means the DNA is cut from the middle, and this creates many message from the same gene.
     The transcription factors can turn on a gene by binding to the DNA, but can also turn off a gene when the gene is not unraveled from the histone leaving there no place for the transcription factor to bind to. Specifically in cancer cells, the transcription factors are always binded to the gene, which is also the reason for the cell's rapid growth. So if the transcription factors can be controled, then the cells would be able to maintain a more stable growth rate.

Capital Region Cancer Research Symposium 2014:

 New Strategies and technologies in Cancer Reasearch

        Today instead of the usual lab work and lab readings, we headed over to the cancer research symposium held at the Hilton inn at Albany Medical center. The purpose of the symposium is to promote cancer research interactions among differnt Albany facilities. There I sat and listened to the different cancer research project all across the capital district. Projects came from SUNY-Albany, RPI, Albany medical center, Albany college of Pharmacy and many more.
        One particular presentation that i found very interesting was "Collective Rotation of Epithelial Cells Exhibits Left-Right Asymmetry in a 3D system," given by Amanda Chin, a graduate student at RPI. Basically she concluded that left-right symmetry in a cell is vital for normal tissue growth. She concluded that inherent cellular chirality (left-right asymmetry) could be a force that moves cells during tissue morphogenesis, and the development of tumors.
        I left a little earlier, the symposium was held until 4:00pm and I left at 11:00am. However I was still able to observe the impressive researches that are happening in our community right now and I got to experience a science symposium, which I had never been to before this.

   

November 7, 2014

Lab meeting

Today during my internship, most of the time was spent in lab meeting; where we went through a paper that was meant to be read the day before. It was quite confusing for me to follow, but after my mentor and I sat down to speak about it, I began to understand the article a lot more. Primarily the article was about the changing of DNA sequence will change the overall function of that DNA, and this can cause "intellectual disabiliy disorder."

Article: NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

Cell Movies

After the lab meeting, my mentor and I talked about the cell movies, where we looked at the movment of previously cultured breast cancer cells. In the control, we can see that the movement of the cells is not as rapid and agressive as the other cells. Below are movie links to comapare two different cell movements due to different RNA concentrations. 

cell movie: control

cell movie

October 31, 2014

PCR and Gel Electrophoresis

Today in the lab, we worked on our agrose gel electrophoresis, which separates the dyed DNA products on the basis of size and charge. This way we can  visualize and analyze the PCR product, to determine the presence and size of the PCR product. Below are the two substances that we used to create our gel. First we added 1 gram of the agrose powder, and the added 100 ml of the solution. We also added Ethidium Bromide , which will help us "see" where the DNA is in our gel. Before we let our gel set, we added a tool to one side of the gel, which will create small groves in the gel where we will be able to insert our DNA. It is presumably a "starting place" for our DNA.

After we let our gel set, we added a blue dye to our genes to make it easier for us to see the movement of the DNA across the gel. I did 4 practice insertions with just a mixture of dye and water. Then I was able to insert the real DNA's more efficiently. To insert the DNA's we used a pipette, which is pictured below, to precisely measure and imbed the empty groove with the DNA. We had to be mindful not to puncture the gel, or else that would effect the way the DNA would move across the gel. So once all the genes were in place, we connected our gel box to the power supply, where a positively charged cord was connected to one end of the box, and a negatively charged cord was connected to the other. the charges coming from the power supply box is also separating the Hydrogen to one side, and the Oxygen to the other. And since there is double the amount of Hydrogen than Oxygen, we saw more bubbles on the right side of the gel box than on the left. DNA is also negatively charged, so the DNA was being attracted and pulled by the positively charged side, which is what is makig the DNA move across the gel.

To  interpret our results, we look at the movement of the genes through the gel. Smaller DNA strands will move quicker and further, while larger DNA will move a lot slower. This is because smaller genes have  higher velocity and because they are so small they are able to move through the open holes in the gel with ease, while the larger genes are not traveling through the open holes as quickly. This whole process is called, gel electrophoresis, and through this process we can actually physically cut out our purified genes from the gel.

The picture up top is a picture of pipette, which is a tool that is used to measure and transfer precise amounts of substances.

This picture shows the power supply connected to the gel box by the two charged wires. If you look closely you can see the blue dye at the top the gel box. As time passes we will see bars form in a ladder formation, which will show the movment of the dyed genes.

• Polymerase Chain Reaction (PCR) article: http://www.nature.com/jid/journal/v133/n3/full/jid20131a.htm

October 24, 2014

Today was the first day of my breast cancer research internship. In our research we will be trying to manipulate the expression of the RNA in a cell, and observe the affect that has on the movement of the invasive breast cancer cells. 

       First we went over the basic ideas involved in our study. We talked about the job of the RNA and the cells of normal breast tissue versus tissue on an invasive breast cell. After that I was able to work in the lab to create a solution that will magnify the RNA cells that we will be focusing on. 

I am interested in a STEM internship because I would love to learn new things outside of the classroom. Because of this STEM internship I will be able to feel satisfied with myself, knowing that I will be able to cotribute to a research and help in a specific field of study. I am also interested in science, and I am hoping to expand my oppurtunity as I graduate and go onto college. This internship will help me expand on my knowledge of science and will give me a boost start on what I hope to countinue in college. throughout the year, I hope to grow as a student and as a researcher. I would like to experience what it would be like working with others in a lab, and hopefully I can take the skills I learn this year and apply them in day-to-day life and later on in my life.