PCR Gels 1

This week in lab I took my final PCR product and ran it on a gel to see if the Polymerase Chain Reaction cut my DNA into the correct size of small fragments. The type of gel used for PCR products is exactly the same as the one used for genomic DNA, as well as the dye used to make DNA glow and the machine used to visualize the DNA. So in theory, if I had strong bands of genomic DNA after extraction, and I use the same gels and dye, as long as the PCR worked correctly, I should get pretty strong, clear bands of PCR product.

Unfortunately when I ran my PCR gels they did not come out as beautiful as my genomic DNA bands did. The PCR product was very difficult to visualize using the UV machine, and even where bands could be seen they were not of the right length for the primers I choose. I feel this might have been because I didn't mix my samples enough before putting them into the PCR machine. I am running another trial on my PCR to see if that was the case. If I still have weak bands I will have to trouble shoot the problem again.

Dilution Fail

This week in lab I ran a Polyermerase Chain Reaction for the first time. I wanted to be able to have the PCR done on Thursday so I could run a gel on Friday but, alas, I did not account for the time it would take to prepare my chemicals and was not able to complete the experiment. All day Thursday I diluted my stock solutions of primers and my DNA samples to have consistent concentrations of each in my tiny test tubes.

To be honest I'm a little annoyed that I didn't know to get that stuff diluted on Tuesday when I had so little to do in the lab. From now on I need to take more initiative and find out exactly what I need to do myself, not rely on the lab instructor when they say I didn't have any prep work.

Anyway today I ran my PCR. One basically mixed together very small quantities of clear liquids into baby sized PCR tubes and then puts them into a machine that does all the work. The PCR machine cycles between various temperatures causing the clear liquids to do different steps of a reaction depending on the temperature. Its all very technical. I'm not sure if mine will work because I didn't mix the tiny little drops when I added them to the tube.

Tiny Tiny Little PCR Tubes:


Tiny Tiny Little Clear Drops:

DNA Extraction Number 2

This week in lab I performed another DNA extraction on my most recent web samples as well as the positive control web I got from ASU West. Earlier today I ran two tests to see how good my extraction was.
The first test I did is called a Nanodrop. This machine basically vaporizes a biological sample, shines a light through it, and using wave length absorbency can tell you the concentrations of biochemicals like proteins or nucleic acids or what have you. The concentrations of nucleic acids in my samples varied widely, which could have been a result of the varying amount of silk collected at each site. I cant really understand the rest of the data the Nanodrop gave me. There were graphs and stuff but it was incomprehensible to me. I'll have to learn about that later.

#	Sample ID	User name	Date and Time	Nucleic Acid	Unit	A260 (Abs)	A280 (Abs)	260/280	260/230	Sample Type	Factor
1	J1	biology	3/10/2016 11:22 AM	31.8	ng/µl	0.635	0.399	1.59	0.28	DNA	50.00
2	J2	biology	3/10/2016 11:37 AM	40.7	ng/µl	0.814	0.463	1.76	0.22	DNA	50.00
3	HW1	biology	3/10/2016 11:38 AM	4.8	ng/µl	0.095	0.078	1.22	-1.24	DNA	50.00
4	RSW1	biology	3/10/2016 11:39 AM	13.5	ng/µl	0.269	0.229	1.18	2.28	DNA	50.00
5	FSE1	biology	3/10/2016 11:40 AM	7.7	ng/µl	0.155	0.095	1.62	1.84	DNA	50.00
6	+C1	biology	3/10/2016 11:42 AM	19.6	ng/µl	0.392	0.301	1.30	0.68	DNA	50.00
7	-C1	biology	3/10/2016 11:43 AM	1.5	ng/µl	0.029	0.017	1.76	-0.13	DNA	50.00

I also ran a gel today to see if there are any visible bands of DNA in my sample. The gel looked lovely. The first two lanes were an extraction process that Josh developed being done on known widow webs, the next three were my extraction process on unknown webs, the last visible band was extracted from a web built by a known widow with my extraction process, the next lane was a negative control and the last lane was empty. The four lanes I did my extraction process on had clear bands of genomic DNA. Even if the concentrations varied widely, at least I know the DNA is there.

Spring 2016 Web Collection

This week in lab I collected spider webs for an extraction next week. I went around campus and collected the webs of a few spiders that looked like they could possibly be black widows. I also went to ASU West and collected some webs from their lab spiders. I'm hoping the webs spun in captivity will have less contaminates than webs found in the environment so I can use them as a positive control. The DNA I extract from unknown webs on campus will be compared to the DNA extracted from the lab webs as well as a molecular weight ladder.