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Bridges to the Baccalaureate Program Directed Research 2015

 

golden gate bridge

NIH City College of San Francisco/Skyline College/Cañada College/San Francisco State University

Bridges to Baccalaureate Program
Directed Research Program

Summer 2015
Instructors:  Chantilly Apollon, Holy Names University, & Sally Pasion, SF State

 

 

 

 

 

 

Click here to see the ORIENTATION SCHEDULE - Monday 6/8/15

Click here to go to Part I (Weeks 1 - 4):  Directed Research Program - Sally Pasion

Click here to go to Part II (Weeks 5 - 8)-not yet available:  Directed Research Program - Chantilly Apollon

Monday, June 8, 2015:  Orientation Day

 9:00 am - 10:00 am
Introductions & Interactive Group Discussions, Getting to Know YOU!
10:00 am - 11:00 am
Discussions on Expectations
11:00 am  - 12 noon
Keeping a Lab Notebook
12 noon - 1:00  pm
lunch break
1:00 pm - 2:00 pm
Information Literacy
Searching for research articles  PubMed 
 
Task #1 web site: 
 
2:00 pm - 2:55 pm
Discussion on Guiding Principles 
2:55 pm - 4:00 pm
Lab Safety
 
 
 
 
Task #5 web site 2: Fume hoods
 
Task #7:  Scavenger Hunt 
  
Additional Safety web sites of interest
Lab Safety Song  
http://www.youtube.com/watch?v=WZ-1lfammjk
 
 
Laboratory Personal Protective Equipment:
Eye Protection: http://ehs.okstate.edu/modules/ppe/Eye.htm

Instructor: Sally Pasion, Ph.D.   Teaching Assistant:  Nainoa Richardson
NOTE: The agendas below are tentative and subject to change.
Computers must be returned to stockroom by 4:00pm
Week 1: Jun 8 - 12, 2015
Week 2: Jun 15 - 19, 2015
Week 3: Jun 22 - 26, 2015
Week 4: Jun 29 - Jul 2, 2015


click on this link to view course materials for Part II:  Weeks 5 - 8  (Jul 6 - Jul 31, 2015) (not yet available)
Week 1: Jun 8 - 12, 2015
Mon 6/08   Tue 6/09   Wed 6/10  Thu 6/11  Fri 6/12

For more information on fission yeast:  Pombe.net
For more information on a career in biology:  Women in Biology Internet Launch page 
Tuesday, 6/09/15
9:00 – 9:10 Introductions
9:10 – 10:10 Lab Safety
10:10 – 11:00 Mystery Box
11:00 – 11:30 Fission yeast morphology
11:30 – 12:00 Exercise 1: Fission Yeast microscope observation\
12:00 – 1:00 lunch break
1:00 – 2:00 Exercise 1: Fission Yeast microscope observation & Discussion
2:00 – 3:15 Introduction to bacteria and plasmids
3:15 – 3:50 Exercise 2-1: Plasmid DNA inoculation
3:50 – 4:00 Lab clean-up
 
Wednesday, 6/10/15
9:00 – 10:00    Introduction to fission yeast/media
10:00 – 12:00 Exercise 3-1: Genotype & phenotype
12:00 – 1:00     lunch break
1:00 – 3:50      Exercise 2-2: Plasmid DNA Isolation
3:50 – 4:00      Lab clean-up
 
Thursday, 6/11/15
9:00 – 10:30    Discussion
10:30 – 12:00  Exercise 5-1: Media preparation
12:00 – 1:00     lunch break
1:00 – 2:00      Exercise 5-1: Media preparation
DNA Replication Process (3D Animation):  https://www.youtube.com/watch?v=27TxKoFU2Nw
1:00 – 2:00      Restriction Enzyme Digestion
2:00 – 3:50      Exercise 4-1: Restriction Enzyme Digestion
3:50 – 4:00      Lab clean-up
 
Friday, 6/12/15
9:00 – 10:00    UV light and DNA damage
10:00 – 12:00 Exercise 6-1: Yeast UV sensitivity
12:00 – 1:00     lunch break
1:00 – 3:45      Exercise 6-1: Yeast UV sensitivity
1:00 – 3:50      FILM
3:50 – 4:00      Lab clean-up

Week 2: Jun 15 - 19, 2015
Mon 6/15  Tue 6/16   Wed 6/17     Thu 6/18    Fri 6/19
 
Monday, 6/15/15
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 6-2: Yeast UV sensitivity
Exercise 6-2 word file to download
12:00 – 1:00 lunch break
1:30 – 3:50 Exercise 6-2: Yeast UV sensitivity
1:30 – 3:50 Exercise 3-2: Genotype & phenotype
3:50 – 4:00 Lab clean-up
 
Tuesday, 6/16/15
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 3-3: Genotype & Phenotype 
12:00 – 1:00 lunch break
1:00 – 3:50 Exercise 3-3: Genotype & Phenotype 
1:00 – 3:50 Exercise 8-1: Independent UV Experiment
Some info on UV light
UV index forecast
http://www2.epa.gov/sunwise/uv-index

EPA info on UV index scale
http://www2.epa.gov/sunwise/uv-index-scale

National Weather Service
http://www.cpc.ncep.noaa.gov/products/stratosphere/uv_index/uv_current_map.shtml

UMN class on environmental hazards: UV radiation
http://www.enhs.umn.edu/current/5103/uv/character.html


UV index: Information (National Weather Service)
http://www.weather.gov/rah/uv

World Meterological Organization Solar Ultraviolet Radiation Site
http://www.wmo.int/pages/prog/arep/gaw/UV-radiation.html

Standardized UV Index for use worldwide--Global Solar UV Index: A Practical Guide 
http://www.unep.org/PDF/Solar_Index_Guide.pdf

3:50 – 4:00 Lab clean-up

 

9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 3-4: Genotype & phenotype

Exercise 3-4 (Word document)

Forsburg Lab web page Pombenet: http://www-bcf.usc.edu/~forsburg/index.html

Use Entrez/Pub-Med (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed ) to search for recent articles or reviews on the topic covered by the research article you selected.
PubMed tutorial (
http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/)

Consult the Online Mendelian Inheritance in Man (OMIM) for additional information about human genetic diseases:
(
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM)

The SFSU library has subscriptions to many biological sciences journals that will contain appropriate primary research articles. You can search online to see if the library has the journal you require (http://opac.sfsu.edu/search~S5). The subscription may be a paper subscription so you will need to go to the library to view it. The subscription may be an online subscription that you will be able to access from any SFSU computer. This web site allows you to check for SFSU online subscriptions:
http://sfx.calstate.edu:9003/sfsu/az/sfsu

Cell and Molecular and Microbiology Online journals available by SFSU subscription (along with some important journals that are not available online)
http://online.sfsu.edu/~pasion/SFSUOnlineCMMJournals.html


12:00 – 1:00 lunch break
1:00 – 3:50 Exercise 8-1: Independent UV Experiment
1:00 – 3:50 Exercise 9-1: Yeast Transformation
 

3:50 – 4:00 Lab clean-up 

 
Thursday, 6/18/15
9:00 – 9:10  Welcome/Agenda
9:10 – 12:00 Exercise 5-2: Media preparation
9:10 – 12:00 Exercise 8-2: Independent UV Experiment
Download Exercise 8-3 PREP form (word file)
12:00 – 1:00 lunch break
1:00 – 2:00   Exercise 5-2: Media preparation
2:00 - 3:50   Exercise 7-2: Mating type Check
Mating Type Tutorial:
 
3:50 – 4:00 Lab clean-up
 
Friday, 6/19/15
9:00 – 9:10 Welcome/Agenda
9:00 - 12:00 Exercise 8-3: Independent UV Experiment
12:00 - 1:00 lunch break
1:00 - 3:50 Exercise 8-3: Independent UV Experiment
3:50 – 4:00 Film or alternate activity
3:50 – 4:00 Lab clean-up
 
 
Week 3: Jun 22 - 26, 2015
Mon 6/22    Tue 6/23     Wed 6/24     Thu 6/25     Fri 6/26 

Monday, 6/22/15
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 8-4: Independent UV Experiment
12:00 – 1:00 lunch break
1:30 - 3:50 Exercise 7-2: Mating type Check
1:30 - 3:50 Exercise 4-1: Restriction Enzyme Digestion

DNA Restriction Animation:  http://www.dnalc.org/resources/animations/restriction.html
3:50 – 4:00 Lab clean-up

Tuesday, 6/23/15
9:00 – 9:10 Welcome/Agenda
9:10 – 11:55 Exercise 4-2: Restriction Enzyme Digestion
**11:55 – 1:35 lunch break
1:35 – 3:50 Exercise 4-2:  Restriction Enzyme Digestion
1:35 – 3:50 Exercise 9-2:  Yeast Transformation
3:50 – 4:00 Lab clean-up
 

Wednesday, 6/24/15
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 4-3: Restriction Enzyme Digestion
Exercise 4 REPORT (ppt)
12:00 – 1:00 lunch break
1:00 – 3:50 Exercise 4 – Restriction Enzyme Digestion & Report to class
1:00 – 3:50 Film or alternate activity
3:50 – 4:00 Lab clean-up

 
Thursday, 6/25/15
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 8-5: Independent UV Experiment
Exercise 8-6 PREP worksheet (word file)
12:00 – 1:00 lunch break
1:30 – 3:45  Exercise 8-5:  Independent UV Experiment
1:30 – 3:45  TBA
3:30 – 3:45  Exercise 10-1:  Make Diploid  
3:50 – 4:00 Lab clean-up

 
Friday, 6/26/15
9:00 – 9:10 Welcome/Agenda
9:00 – 9:15 Exercise 10-1:  Make Diploid  (17 hrs)
9:10 - 12:00 Exercise 8-6:  Independent UV Experiment
11:40 – 12:00 Exercise 10-1:  Make Diploid  (20 hrs)
12:00 – 1:00 lunch break
1:00 – 2:00 Exercise 8-6:  Independent UV Experiment
2:00 – 3:50 TBA
3:30 – 3:50 Exercise 10-1:  Make Diploid  (24 hrs)
3:50 – 4:00 Lab clean-up
   
Week 4: Jun 29 - Jul 2, 2015 
Mon 6/29     Tue 6/30     Wed 7/01    Thu 7/02

   Fri  7/3/15 July 4th Holiday Observed! 

Monday, 6/29/15 
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 8-7: Independent UV Experiment
12:00 – 1:00 lunch break
1:00 – 3:50 Exercise 8-7: Independent UV Experiment
1:00 – 3:50 Exercise 9-2: Yeast Transformation
3:50 – 4:00 Lab clean-up

Excel for Mac 2008: make a vertical bar graph (YouTube video)

Adding custom error bars in Mac Excel 2008 (YouTube video)

Tuesday, 6/30/15 
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 10-2: Make Diploid
 Streaking Bacteria for a Single Colony
9:10 – 12:00 Poster Prep
12:00 – 1:00 lunch break
1:00 – 3:50 Poster Prep
1:00 – 3:50 Film or alternate activity
3:50 – 4:00 Lab clean-up



Wednesday, 7/01/15 
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 11-1: Yeast Growth Curve
9:00 – 12:00 Poster Prep
12:00 – 1:00 lunch break
1:00 – 3:50 Exercise 11-1: Yeast Growth Curve
1:00 – 3:50 Poster Prep
3:50 – 4:00 Lab clean-up 

Thursday, 7/02/15  
9:00 – 9:10 Welcome/Agenda
9:10 – 12:00 Exercise 11: Yeast Growth Curve Report
9:10 – 12:00 Poster Prep
12:00 – 1:00 lunch break
1:00 – 3:50 Poster Prep
3:50 – 4:00 Lab clean-up

Friday 7/03/15 Happy Independence Day!