Genome annotation, metascape

http://metascape.org/gp/index.html#/main/step1

bio125, review 2014 closed book exam. Open book practice.

sec3, 4
go over exercises, practical exam, 2014 closed book
Major problem:
 primer on PCR template
 Restriction enzymes

oral presentation rubric, learning objectives

Did not have time to go over math problems in section 4.

Spelman research day, 2016 spring

The Research Day database is now open. Please use the link below to help students access the registration form and upload their abstract. The abstract deadline is Monday, March 14 at 11:59pm.  If you are having trouble opening the form, please copy and paste the link into a different browser.

Please note that research projects do not have to be complete in order to submit an abstract.

http://princess.spelman.edu/researchday.nsf

bio125 20160219Fri agarose gel of RE PCR fragments

For the lab:
Loading dye on student desks
100bp ladder will be put on instructor's desk, only given to students after they have used the loading dye.

During gel run, go over 2015 midterm open book part.

9am. section 3.
Lab instructor mistakenly gave ladder as loading dye to one group of students, luckily, the student discovered the error.

One group reversed cut-uncut on the gel. One group mistook loading dye as ladder. Both groups blame instructors for interfering their experiments.

Lockdown browser quiz test

Midterm open book test. 

The lab finished 30 minutes earlier.

1pm, section 4
Most students said that they did not how much volume of 6X loading dye to add to 20ul digestion.

gel run for 45 minutes

2:50pm. the lab ended.


Ref:
http://hongqinlab.blogspot.com/2015/02/bio125-thu-feb-26-2015-student.html
http://hongqinlab.blogspot.com/2015/02/bio125-tue-feb242015-agarose-gel-of-pcr.html
http://hongqinlab.blogspot.com/2015/02/bio125-feb-19-thu-digestion-of-pcr.html

R xlsx package on Windows7

library(xlsx) cannot be executed because rJava cannot be loaded. Re-installed JAVA, problem persisted.

Install Java SE development kits.

Problem fixed.

bio125 20160217Wed RE of PCR fragments

Before class:
Set 4 water bath/blocks: 60C,  37C, 55C heat block

Water is on their stations. Enzymes are in small -20 in the green ice block on top shelf. Buffers are in 2 boxes on the top shelf labeled buffers for RE enzyme and Restriction enzyme buffer. Each student can get a tube of the buffer that they need. After assembling MMix, the instructor should dispense the enzyme into their master mix for digestion. Water bath are set to 37 and 60. For 55 degree they should use heating block which is turned on and set.

Student samples are in the freezer by the tissue culture hood in the front with section labeled on the box

NEB reformulated their buffers. 
Buffer 2.1 = old buffer 2 + BSA

http://hongqinlab.blogspot.com/2015/02/bio125-feb-19-thu-digestion-of-pcr.html


Section 3:
9:10, go over the lab.  I did not put a tutorial video in the right place, and most group did not know which RE to use. I used a student video in class to let the student work on it.

by 10am, most students worked out the solutions.

Section 4
No groups submitted a preclass report that indicated RE needed.
Go over student video on RE identification
Showed student video from morning section.

by 1:41pm, three groups correctly found out RE needed.
by 2:12pm,  all groups knew their RE.

2:20pm, all groups start to set up reactions. One group was absent during last lab and did not do PCR. They were asked to finished APE 9 assignment.

bio125 20160212Friday PCR amplification of MSH2

Problem: for video on screen, red does not show on black background.

Section 3:
=>dilute plasmid to 5 ng/uL
9:25am, went over recipe

add large volume of water first. For 200uL pipette, round up the volume to the nearest integers.

Take away concentrated plasmids.

=>PCR master mix.
Go over PCR master mix recipe

9:38am  PCR beads are given to students

label  both sides of pcr tubes because they can be worn off during PCR. 

=> set up reaction.

9:50-

Problems: One group added master mix into diluted plasmids.

=> try respondus lockdown broswer

=> 30 minutes on PCR paper exercise.

Section 4:
 1:30pm, most group submitted wrong plasmid dilution recipe.

by 2pm, at least 3 groups have not started to dilute their pasmid DNA.
by 2:20pm, some groups finished their PCR reactions.

ask a group to finis paper pcr on boards.


========================
skipped:
homework common problems:
Wrong: HNPCC has no symptoms, a google trap.
Correct:

Reference
http://hongqinlab.blogspot.com/2015/02/bio125-thu-pcr-reaction-past-exams.html
http://hongqinlab.blogspot.com/2014/02/bio125-pcr-reaction.html

bio125 20160205Fri gel electrophoresis, RE compatible ends

Section 3:

9:30 most groups have gel running.

by 9:50am, do RE paper cutting exercise. Most students are chatting, but some students are working on it. Many student do not want to use razor.

During the gel running time, I went over RE enzyme recognition size and its expected number of sites.

Standard curve of gel and plots.

Section 4:

by 1:30, most groups started gel running.
Use paper and RE sites, cut with razor to explain compatible ends.

http://hongqinlab.blogspot.com/2015/02/bio125-thu-feb-5-2015.html

write to SEGATE NTFS disk from OSX,

On a OX 10.9.5 mactower system, purchased in 2012
Download Seagate's free NTFS driver
http://www.seagate.com/support/downloads/item/ntfs-driver-for-mac-os-master-dl/

bio125, XbaI + ApaI cut pMSH2, pRS413, pmsh2

Before class:
check 37C water-bath or heat block
Xba1 and Apa1 mix

=========
Section 1:
Problems:
Some students did not know that digestion and controls are do in parallel, not sequential.
How to make master mix
Many students have below 100ng/uL plasmid to start with
Some are not sure about diluted plasmid and reaction tubes.
Some students left their eppendorf tubes open all the time.
Do not add water to original plasmid stocks.

Lab instructor removed 10ul pipette because so many of them are broken by the students last year.

9am I started with master mix. This is a mistake. I should start with plasmid DNA dilution steps.

10am. most students are still struggling to the recipe.

10:15am, many finished master mix.

11am. Only one group is still doing the lab.

========
Section 2:
Problems:
What is master mix?
Students mixed up original DNA stocks and diluted DNA working stocks.

1pm, started overview of the lab.
1:10pm, explain plasmid dilution right away.

2:37pm, most groups are working on master mix.

3:15pm, incubation for most groups starts.


References: 
http://hongqinlab.blogspot.com/2015/02/bio125-tue-feb-3-2015.html
http://hongqinlab.blogspot.com/2014/02/bio125-xba1-apa1-prs413-pmsh2.html