Here we go again.

It seems that every week as I finish writing my blog update I think, maybe next week will be the week when I will be able to post positive results.

Not the case.

Don't get me wrong, I am not discouraged in the least. If anything, the lack of results is a motivator. Getting good genetic evidence of what I am trying to prove has now become sort of a personal challenge (or vendetta?). I am running out of time for this semester though.

Upon completion of the PCR amplification of the DNA extraction, I conducted another gel electrophoresis. As I have seen many times this semester, the material did not travel in the gel. Under UV light, the wells containing the PCR results from the Sigma extraction did glow, but there was no evident travel through the gel.

Electrophoresis separates the molecules based on size. Larger DNA strands will travel much slower than the smaller ones. After a period of time with 100 volts pulling the negatively charge DNA molecules toward the negative pole of the gel box, a separation of the fragments can be seen. Based on this principle behind the separation, I am now questioning if the issue has to do with the size of my sample's DNA fragments. Is it possible that the fragments are simply too big to travel through the gel? In my research I have not come upon anything regarding this.

The gel used is a 1% agarose gel. It is made by adding 1 gram of molecular grade agarose to 100mL of 50x TAE buffer, and heating/mixing it to a clear solution and then pouring it into a mold (the gel box tray) and allowing it to cool. My newly developing theory is that if the DNA fragment is too large to travel through the gel, why not alter the concentration of agarose to make it easier for the fragment to travel. I have no idea if it will work, but today I made a 0.5% agarose solution and poured a gel. I did not have enough time to run the gel, but I will be able to do so tomorrow. Maybe it will work, maybe not.

I am now up against the wall as far as being able to present results at MetroTech, and complete my research paper. Should I obtain the positive results I hope for tomorrow, I am not sure that I have enough time left to interpret them. I believe what I am going to have to do is focus on structuring poster for presentation and the my research paper around the observational work I have done - mapping and imaging of the site it itself showing the spatial interrelation of the subjects and their respective root systems (or better stated the portions of the root systems that can be seen). This will not be near as exciting as what I hoped to accomplish, but it is something. I do not know if I will be selected for renewal of the S-STEM scholarship for a third semester, but I certainly hope so. I want to prove the Palo Verde does reproduce through cloning in addition to sexual reproduction.

This is the best picture of potential cloning in Parkinsonia microphylla I have taken. It is quite obvious that the root system coming from the main portion of the biomass on the left is in fact sending up additional shoots. Notice the large developed shoot on the right and the smaller/newer shoots between the two. They all originate from the same root system.