Tuesday, February 3, 2015

bio125, Tue, Feb 3, 2015

Section 1:
8-9:30am go over protocol. Mater mix was not understood.
I went with R code on digestion recipe

9:30-10:30am. Student started dilution DNA. 
Lab instructor took the original plasmid stock away as soon as student finished the dilution. 

_ most students have trouble with maxter mix recipe
_ some students shot 8ul in the air to the tube
_ students are confused by the serial number and plasmid names

Section 2:
1-2pm. went over protocol.

2pm. Student started to make DNA dilutions.

by 2:20pm. I went through master mix recipe.
by 3:10pm. Most student are done with reaction setup.

3:12pm, lab note 3 Moodle online assignment

=== thing postponed 
ApE exercise
Dilute plasmid DNA, label tubes group number, plasmid, concentration

GoogleDoc final project report
R code on RE recognition site
MCAT questions on RE

RE paper exercise,

Ruler for gel measurement

Identification of mutation

Protein alignments
Gel electrophoresis

PCR princple

Cognant site, identification of mutaitons

week 2/2-2/6, 2015, plan for week 4:
day 1:
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:
electrophoresis (DW), pre-lab (DW),
running gel (maybe do standard curve) (DW)
R code and standard curve (Qin)

data analysis (DW) as a backup activity

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