Deja Vu Birney's TRAIN Blog

    This week in lab, I learned how to make and load a gel. For this blog, I will be discussing the protocol on how to make a 30mL gel. Before starting the process of making my gel, I had to figure out what percent of agarose we should use. For my practice gel, I did 1% agarose (percentage determined by how small or large the DNA is that you're using). For my conversion, I did the following equation: 30mL  *  0.01  *  1000  =  300mg             (percent  (conversion              agarose)    to mg)      I measured 30mL of TAE buffer in a flask a little over twice the volume. I then measured 300mg of agarose on my scale, added it to my buffer, then swirled until cloudy. Before putting my gel solution into the microwave, I made a stopper out of paper towel. After inserting the stopper, I put the solution in the microwave at 30 second increments until i...

      This week during lab, we were working on cleaning up left and right fragments. We are cleaning the sample of everything except the DNA that we want. The protocol I learned for this cleanup is as follows: We diluted the left and right samples with the DNA Cleanup Binding Buffer according to a 5:1 ratio recommended for fragments. We then loaded sample into a column that was within a collection tube and spun for 1 min at 13,000 rpm. We then proceeded to discard the flow through. After we re-inserted the column in another collection tube, adding 200µL of DNA Wash Buffer and spun again for 1 minute. We repeated the last step once more before transferring the column into a 1.5µL microfuge tube. Finally we added 10µL of DNA Elution Buffer to our samples, ensuring that its going into the center of the matrix. Then, we waited for 1 minute before proceeding to spin it for another 1 minute at 13,000 rpm. After our first elution cycle, we put the samples on the nano drop, the r...

    This week during lab we completed a gram stain on Deinococcus radiodurans after it was grown in MHA (mueller-hinton) media. Deinococcus radiodurans is an extremophile bacteria that we are growing in our lab. We are trying to grow  Deinococcus radiodurans  for 24 hours, in a media that we've never had in before, to see if it's successful.       To complete my gram stain, I first started by drawing a wax circle on my slide for and an indicator in the top right corner, to ensure my slide wouldn't be upside down at any time. I then ignited my Bunsen burner then sterilized my loop with the flame. After allowing the loop to cool, I unscrewed my tube containing the  D. rad  in MHA media, ran the top of the tube over the flame, collected my culture, ran the mouth of my tube over the flame once again, before finally screwing my tube shut. After closing tube, I smeared my culture within the wax circle on my slide. I waited about 2 minut...