DNA on Speeder Bikes or so I Thought

This week I am working on making more 2% Agarose gels in order to run some with my newly amplified Ant DNA. I ran the PCR last Thursday, and I am hoping for the bands in the gels to be clear. I need the bands to be clear in order to make a concise measurement of whether certain bands are similar to one another.
I ran my gel with the amplified DNA and there were no bands! I then ran another gel with my regular DNA samples and saw polymorphic banding. I wanted to make sure I actually had DNA in my samples and wanted to know why there was no DNA showing in the gels from the PCR. I will be running another gel next week on the same amplified DNA samples. I need to figure this one out.

The Old Republic

This week I began making new gels with 2% Agarose in order to see if the polymorphic bandings from the ants would seem clearer than the bands in a gel of 1% Agarose. It did not seem to work and I am wondering if I should just run another PCR on my ant DNA. I ran three gels with 6 microliters of DNA and 2 microliters of the orange loading dye. It occurred to me, after I reviewed my previous gels over the summer, there was barely enough DNA shown in the first gel from my amplified DNA samples. Here are the first three gels I had ran a couple of weeks ago from the first PCR in a 1% Agarose Gel:

Colony A



 

 Colony B

 

 Colony C

 

In the Colony A gel it shows barely any DNA, and when I ran a gel yesterday with the same DNA, but in a 2% Agarose gel, nothing showed up. I felt as though it was a waste of three 2% Agarose gels.



My poor agarose gels.

Storm Troopers on the Rise

I am happy to be back this Fall 2015 Semester! Good wishes to you all on this new semester! I'd like to share with you all the most interesting thing I have been researching so far about ants. I've been researching their many different adaptations. One of my favorite adaptations of an ant species is how they are capable of stealing another specie’s colony in order to survive. They kill the colony’s queen and all of her children. The tend to leave some of the larva alive in order to keep them as their slaves. This ant species is known as Polyergus breviceps or Slavemaker ants. They are basically ruthless serial killers.

Here’s a video of the ants about to embark into new territory:

 

The Never-ending Droids

In the week of April 30th I was finished with my DNA extractions and began running a PCR. I used four different primers. I had five DNA extractions in total due to the five different pharaoh ant colonies. I ran all five samples separately for each primer. After the PCR, I began running a gel from each primer set. I found a trend in the polymorphic bands while looking at the gel under the UV lighting. It seemed as though colonies 1&3 had similar polymorphic bands while colonies 2,4,&5 had similar polymorphic banding with one another. Below you shall see the gels of each different primer and the DNA amplification of each colony over five lines.

Gel with DNA samples amplified with Primer 1.

Gel with DNA samples amplified with Primer 2.

Gel with DNA samples amplified with Primer 3.

Gel with DNA samples amplified with Primer 4.

Running Trade Federation Gels

In the week of April 16th I ran gels on the DNA samples I amplified with the PCR. It did not turn out very well;I was a bit disappointed in how the amplification turned out. I wanted to see bright,beautiful polymorphic bands, but only recieved unclear, smeared remnants of my DNA in the gel. I had used primers 1 & 2 to amplify two sets of samples. I used four samples of DNA with primer 1; one control DNA extraction and four other DNA extractions with a novel method. I did the same samples for primer 2 as well. When I ran a gel on each primer to see which primer would amplify the DNA better, I did not see good results. Below are the pictures of the gels and how they turned out. 

Gel of amplified DNA with primer 1.

Gel of amplified DNA with  primer 2.

Amplification of the Trade Federation

The week of April 9th was one filled with new techniques. Matt helped me learn how to run a PCR! I was excited to see if the DNA samples I had would be amplified . The process was not as hard as actually doing a DNA extraction. After I was done running the PCR, I was taught how to run a gel with my amplified DNA which is different from the usual electrophoresis with non-amplified DNA. Aftter I ran my gel and looked at it under the UV lighting it seemed as though the primers had done well. I used both primers instead of just one each for my DNA samples. Below is a picture of how well both primers worked with my DNA extractions.

This is a gel containing both primers 1&2 from my first PCR.

On the Planet Genesis

In the week of April 23rd I was working on collecting ants from five locations on PC campus. I was happy to find five pharaoh ant colonies. I am pretty sure I looked like a crazy person scooping up ants into little eppendorf tubes with tweezers. I needed enough ants to have 25 extractions. I was planning on having five control extractions with E.Z.N.A. Insect DNA kit protocol and 20 others with the novel method. I happened to finish all the extractions in two days and ran a gel to make sure I had DNA. Below is a picture of the gel I ran with a couple of DNA samples.

The control sample from the E.Z.N.A. Insect DNA protocol.

The DNA samples from the novel method.

Not much DNA from the pharaoh ants, but there was enough to run a PCR.