bio125 Thu, Feb 5, 2015, gel electrophoresis

Section 1:
37C incubation

by 8:15, reviewed agarose gel

8:30 I did a demo. R code on RE recognition site. Length of DNA words.

http://youtu.be/U1EdV5liCok

9am paper exercise on RE site, compatible RE enzymes. (This is a question in restriction enzyme assignement)

https://www.youtube.com/watch?v=W_rgsBz12Tk

x Paper exercise using grid paper on RE compatible sites

9:10 started pouring gel. Experiment of gel electrophoresis

Every bench has a gel box and power set. Students were asked to pour their own gels.
35mL of Gel-EB mix in falcon tube in 60C water bath. Kioko said 35mL gave 0.5cm depth of well that can hold upto 15uL sample.

Make sure DNA run to the positive side, put wells on the black (negative side).
Make sure power setting is on Volts. Set to 120Volts. (VWR power setting is default to Volt).

The dye is 6X, so 2 uL + 10 uL sample.

by 9:38am. Many students have pour gels. I asked them to work on Rstudio exercise on DNA words.

by 9:50am. Gel are set up, buffer are poured.  DNA ladders in 5uL were given to students.

by 10:05pm, most group finished gel loading.

Ask one member of each group to stay after class to take picture of the gels.

10:20 mcat. I finished two questions and ask students to work on them after class.

10:45am. Lab instructor used  a hand-hold UV lamp.

Section2;
1:05pm, gave mcat restriction enzyme questions to student. Socrative quiz.
  Q: blunt ends and sticky ends

Paper exercise

1:44 R DNA word video from morning

by 2:33, finish paper exercise and sticky ends.

2:40  Gel is ready, buffer are poured. Student spin down the samples and started to gel running.

2:55pm gel loading started.
(Tip: Size ladder was given to students after loading dye have been used, thus avoiding disastrous mixing up that happened in the past).

Students ask why we have to run agarose gels:
1) Check plasmid, are they what we want?
2) Check plasmid concentration.

Students have 4pm bioseminar. So, one of them has to come back to take pictures of the gels.

At 5pm, students came back to take pictures.

Not used:
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MCAT questions on RE

Ruler for gel measurement. standard curve exercise again.

ApE exercise. Most students

GoogleDoc final project report

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Identification of mutation

Protein alignments

PCR principle

Cognant site, identification of mutations

week 2/2-2/6, 2015, plan for week 4:

day 1:

pre-class

overview for MSH2 (single, DW), chapter 20(genetic technology): restriction digestion (DW), molecular cloning (DW), pre-lab, build the math into it (DW)

In class:

digestion, XbaI ApaI, labnotes (DW), presentation on MSH2.

ApE_restriction enzyme&gel simulation, Video (HQ),

Rstudio on receipe (Qin)

Rstudio on RE site recognition, longer RE site should have few occurrence in sequences. permutation of all possible sequences given the number of basepairs  (Qin)

day 2:

pre-class:

electrophoresis (DW), pre-lab (DW),

in-class:

MCAT (HQ)

running gel (maybe do standard curve) (DW)

R code and standard curve (Qin)

data analysis (DW) as a backup activity