bio125 final exam

Paper exam and scantron as backups
Make sure there are enough ethernet cables in the room.
Ethernet cables
Random seatings
Backup calculators
Lockdown Browwer need to be installed on department computer every time.

Sec4, performance was poor. I was surprised that few students did the bonus point quiz that was designed to help student prepared for the final exam.

Sec4. I made one set of bonus quiz and one set of practice quiz. This time more students seem to take the quizzes. One student apparently studied hard but did poorly in the closed book exam.
The strongest and weakest students finished the exam quickly.


Reference:
http://hongqinlab.blogspot.com/2016/03/bio125-miderm-exam.html

yeast DNA repair genes

Gene Ontology Term: DNA repair

---

GO ID

GO:0006281

Aspect

Biological Process

http://www.yeastgenome.org/go/GO:0006281/overview

SIR2
protein  NP_010242.1
http://www.ncbi.nlm.nih.gov/protein/6320163?report=fasta

https://www.ncbi.nlm.nih.gov/nucleotide/296143322?report=genbank&log$=nucltop&blast_rank=1&RID=HJD968YR01R

RFA1

bio125 20160420 flow cytometer data analysis in R,

Section 3
video recording

9:10-10:10am, Flow cytometer data analysis in R using my own laptop. Helped some students with RStudio package installations.

Problems: In Windows 10, Rstudio has to be run as administrator to install packages.

10:15am, course evaluation
10:25am post-computing survey
10:35am lab 11.1_group

section 4

1-2pm. R Rstudio on flow data anlysis
Problems: R3.2.3. installation.  a/s/n warning.   Jumping lines. Setting working direcories.

2:11pm. Post survey

by 3pm.  review bioinfor_1

BIO125, 0420 Wed flowcytometer data analysis

https://github.com/hongqin/SBIO125/tree/master/20150415PI

bio125 cancer and ucsc genome broswer

Section 3:
2015 bio125 assignments are based on GRC37/hg19 assembled in 2009.
4 exercises in class
10:30am, class is over.

bio125 HU treatment of yeast cells

Get the HU experiment start as quickly as possible.
During the 1.5 hour incubaion time,
check FOA plate, take pictures
go over group exercises. 


Section 3:
Projector is set at a wrong station. A technician came and figure it out. 





During the incubation, flip tube occasionally to make sure cells are suspended. 

HU made cells arrested at G1 phase with round shapes. 
 
Section 4:

Problems: Because we did not sonicate the cells, so often cells in G1 phases are often chained together.  It is easy for students to count big circle with tiny dots as S phases, and everthing else as unbudded.
 
References
http://hongqinlab.blogspot.com/2015/04/bio125-hydroxyurea-induced-g1-arrest.html
http://hongqinlab.blogspot.com/2015/03/hydroxyurea-treatment-of-yeast-cells.html
https://youtu.be/yxA1-MvwZfQ  2014 HU video

MSH2, DNA mismatch repair, and sporadic colon cancer

BIO125 used MSH2
A Howard U and Johns Hopkins study on sporadic colon cancer and DNA mismatch repair
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713502/


Primer design to amplify your DNA signature, identify RE to distinguish the polymorphic sites.

bio125, 20160401Fri FOA

Materials: FOA plates, cells, serial water, Eppendorf tubes.

Section 3:
Ask the purpose of URA3 and FOA,

9:20, draw a diagram on the board. 

Go over previous student mistakes, not mix cells well, label the cover, adding cells to the cover. 

9:30, students started the lab. Students should have 9 tubes, and can be balanced triangularly in centrifuge. 

9:47. Students cannot see the pellet for OD=0.01. I remind them to orient their tubes the same way, so they can know where the pellet positions, even they cannot see the pellet.
One group only labeled OD on the tube but not strain names, and are confused after centrifuging
by 10:30, four groups are still working on the lab, because they have to redo the dilutions.
Forgot to ask students to label their section, and group on plates.

Section 4:

Emphasize that tubes during spin should be arranged 

One group was not sure that tips need to be changed each time for a different dilution.

Reference:
http://hongqinlab.blogspot.com/2015/04/bio125-foa.html
http://hongqinlab.blogspot.com/2014/03/bio125-foa-assay-of-msh2-mutants.html

bio125, 20160330Tue exercises, gene regulations

Section 3:
Review gene regulation 1,2,3,4. The spent 30 minutes on APE 11. Show a student video as demo.

Section 4.
Did most of the talk and the 4 exercises in 1.5 hours. Then let students work on APE11.

bio125 gene expression, go over exercises in class

section 3.
9-10am, finish 3 group exercises.
10am, T&T2
TT3: genetic complementation, biochemistry pathway
11am TT&4

Lockdown Quiz announced.
midterm grades to students.

section 4:
Students do not know "transcribe" is the action form of  "transcription".

2:10-2:40pm. TT3.

2:40-3pm, take pictures of transformation plates.

X Midterm grades

bio125 20160304Fri review midterm, research day abstract, go over syllabus

go over syllabus

review midterm, grades

show activity analysis and grades.

research day abstract submission

Major problems during sec 3 discussion:
'template strand' on ddCTP question
'promoter' on transcription, not translation.
plasmid features to be isolated from E coli.
plasmid RE and gel electrophoresis analysis

Genetic table reading is a problem. Some read it backwards. Some read the complementary code?!

students have trouble to understand how ampRistence marker work? how Ecoli will be selected.

bio125 miderm exam

Lockdown broswer need to be installed on department computer everyone time.

Wireless connections should be avoided during exam.

Make sure there are enough ethernet cables in the room.


Section 3:
One student has an error -105 on lockdown broswer. I quitted and submitted the error and quit the lockdown broswer. The student restart and continued her exam. I override her for extra time.
by 10am, some students started open book exam. One forget to exit lockdown broswer, and one did not know how to extract sequences from a ZIP file.  The earlier finishers are 20-30%.

by 11am. Several students finished open book exams.
One student was working on her last question before the exam closed on her. An extra attempt was given.

Section 4:
KA met Lockdown browser multiple times with 20 minutes passed. Paper exam and scantron is given.



Notes from previous exams:

- All phones must be OFF (even "sleep" mode is not enough, we had a couple of alarms going off). All bags and notes left at the front of the room for the closed exam. 

- Give students scrap paper. Ask them to take notes on their scrap paper (not their notebooks - open exam). Collect all paper at the end of exam.

- Ask students to plug in the computers to current and to the ethernet cable. Otherwise, wifi will crash (see below).

- Ask students to run their computers and start their Lockdown browser as soon as they come in. Make sure their lockdown browser is working.

- During my section (pm), during closed exam on Lockdown Browser, internet connection was lost for 75% of the students. We waited while plugging as many of their computers to ethernet cables as possible. In less than 5 min, connection came back, and exam could was taken. During that waiting period: Do NOT touch any button from the lockdown browser as it may block the student altogether. 

- Remind students: "Closed exam: after answering Q40, do NOT click NEXT if you are not ready to submit. Review that you have answered all the questions, then SUBMIT."

- if you need more computers: 

- main computer in the room: log in as bioadmin in the Mac version. ApE and LockdownBrowser should be on the Dock (right).

- Biolaptops (ONLY use Spelmanite wifi): 2 of them work (big pink sign on top "Lockdown Installed OK"), 

section 01 was able to complete under lockdown browser, and use ApE

section 02 was unable to use them for lockdown (message: "problem with the dashboard, ask instructor"), by then everyone else had started so I did not want to change any settings on the exam. I had 2 students take the (printed) exam with scantrons. 20 copies of the printed exam with scantrons are available with Steve, as well as 3 calculators that belong to Dongfang (in case students need them). Open exam and ApE worked well on biolaptops for section 02 as well.

- Both Dongfang and I used the following times for our closed and open midterms:

- closed: 1h 40min (good/fast students finished in 1h)

- open: 60 min (good/fast students finished in 45 min)

- If you have problems call MIT x5400, but it will be more efficient to try to fix the problems yourself with the students or send Steve to get MIT over...

- In many of my students' open exam they were unable to copy-paste the sequences of the primers from the exam... No idea why. It might have been a Mac issue?

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.

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

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

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

bio125 20150129 Friday, miniprep

===============
Section 3:
Mistakes:
Many students were confused by the difference from actual protocol and vendor's version
one group added twice amount of TE
tips were not changed for new samples in one group.
one group did not put zppy column inside of collection tubes.

Neutralization buffer were stored at 4C, and given to students when needed.
Reagent tubes were color coded. A good practice that seems to lead to few student mistakes.  

5ml cells were spun down and given to students.

9:45am, transfer neutralized supernatant to zppy columns.

10:30am. 3 groups started nanodrop measurement.
by 11am, students finished nanodrop readings, and submit labnotes_2.
Classed end 11:30am.

===============
Section 4:
Mistakes:
one student mistook 10ul as 100ul when pipetting.
One student poured away TE buffer. (This student did not read before lab).
Make sure three samples are done at the same time.
Kioko: from lysis to neutralization should be quick. 

2:30pm, most groups have finished elusion step.

bio125, 20160127, Wed, central dogma, dna repair, msh2 overview

-----------------

Section 3

Go over assignment and Student presentations 

problems: double-strand and single strand DNA

APE on GeneX

9:55am Replication 3
Problem: Some studens thought DNA was synthesized 3-5 on the lagging strand.
Seize this teachable moment, ask student to draw replication fork, leading and lagging strands on paper.

5 min break.

   mutation, HSV paper

http://www.ncbi.nlm.nih.gov/pubmed/20026654 ATM S1981 reference

by 11am, Rstudio usage on standard curves. I made a mistake on the dilution.

11am-> APE on MSH2 annotation.

video on miniprep for Thu

-----------------

Section 4: (due to snow, bradford assay and serial dilution lab data were not analyzed). 

Summaryize lab

1-2pm, Go over standard curve plot. 

2pm-3pm  APE pMSH2 annotation
KD was not practicing APE. 

Went through math5 standard curve as well.

No other inclass assignment were done. Did not went through preclass assignment.

===============

pre-class: central dogma, DNA repair , MSH2 overview (abstract reading),,

In-class: 
(1) Replication (in class, drawings-mutation), 
(2) mutation, HSV paper

(2) Math problem 5, standard curve

(3) MCAT

Running R code on linear regression, generating plot and save figures

ApE usage

replication assignment 3

mutation&repair  assignment 1

reference:
http://hongqinlab.blogspot.com/2015/01/bio125-jan-27-tue-central-dogma-dna.html
http://hongqinlab.blogspot.com/2014/03/bio125-central-dogma-review.html