BISC 219/2009:Schedule
BISC219 F09 Lab Calendar
| Monday | Tuesday | Wednesday | Thursday | Friday | |
|---|---|---|---|---|---|
| Sept. 7 Labor Day Holiday |
Sept. 8 Lab 1 |
Sept. 9 Lab 1 |
Sept. 10 Lab 1 |
Sept. 11 Lab 1 |
|
| Sept. 14 Lab 1 |
Sept. 15 Lab 2 |
Sept. 16 Lab 2 |
Sept. 17 Lab 2 |
Sept. 18 Lab 2 |
|
| Sept. 21 Lab 2 |
Sept. 22 Lab 3 |
Sept. 23 Lab 3 |
Sept. 24 Lab 3 |
Sept. 25 Lab 3 |
|
| Sept. 28 Lab 3 |
Sept. 29 Lab 4 |
Sept. 30 Lab 4 |
Oct. 1 Lab 4 |
Oct. 2 Lab 4 |
|
| Oct. 5 Lab 4 |
Oct. 6 Lab 5 |
Oct. 7 Lab 5 |
Oct. 8 Lab 5 |
Oct. 9 Lab 5 |
|
| Oct. 12 Fall Break No Lab |
Oct. 13 No Lab |
Oct. 14 Wed. follows Mon. Schedule Lab 5 |
Oct. 15 No Lab |
Oct. 16 No Lab |
|
| Oct. 19 Lab 6 |
Oct. 20 Lab 6 |
Oct. 21 Lab 6 |
Oct. 22 Lab 6 |
Oct. 23 Lab 6 |
|
| Oct. 26 Lab 7 |
Oct. 27 Lab 7 |
Oct. 28 Lab 7 |
Oct. 29 Lab 7 |
Oct. 30 Lab 7 |
|
| Nov. 2 No Monday Lab |
Nov. 3 Tanner Conference No Lab |
Nov. 4 Lab 8 |
Nov. 5 Lab 8 |
Nov. 6 Lab 8 |
|
| Nov. 9 Lab 8 |
Nov. 10 Lab 8 |
Nov. 11 Lab 9 |
Nov. 12 Lab 9 |
Nov. 13 Lab 9 |
|
| Nov. 16 Lab 9 |
Nov. 17 Lab 9 |
Nov. 18 Lab 10 |
Nov. 19 Lab 10 |
Nov. 20 Lab 10 |
|
| Nov. 23 Lab 10 |
Nov. 24 Lab 10 |
Nov. 25 No Lab |
Nov. 26 Thanksgiving Holiday |
Nov. 27 Thanksgiving Holiday No Lab |
|
| Nov. 30 Lab 11 |
Dec. 1 Lab 11 |
Dec. 2 Lab 11 |
Dec. 3 Lab 11 |
Dec. 4 Lab 11 |
|
| Dec. 7 Lab 12 |
Dec. 8 Lab 12 |
Dec. 9 Lab 12 |
Dec. 10 Lab 12 |
Dec. 11 Lab 12 |
Schedule of Experiments
| Series | Title | Lab # |
|---|---|---|
| 1 | Gene Mapping | 1-5 |
| 2 | RNA interference | 5-8 |
| 3 | Plant Genetic Engineering | 1,4,7-10 |
Graded Assignments
| Lab Assigned | Lab Due | Assignment description |
Point Value (Total 200) |
|---|---|---|---|
| Lab 2 | Lab 3 | Autosomal vs. X-linked analysis | 15 |
| Lab 5 | Friday, October 23rd by 5 pm | Gene Mapping Paper | 40 |
| Lab 5 | Wednesday, October 14th by 5 pm Monday Lab ONLY: Monday October 19th by 5 pm |
Materials and Methods Write-up: Two M&M sections for your paper |
15 |
| Lab 8 | Lab 9 | Sequence Analysis write up | 10 |
| Lab 8 | Tuesday, November 17th by 5 pm | RNAi paper - Full paper | 45 |
| Lab 9 | Wednesday, December 2nd by 5 pm | Revision of Paper #2 | 20 |
| Lab 10 | Friday, December 11th by 5 pm | Transgenic Plant Paper - Science Style | 50 |
| Other | Discretionary Points: Preparation & Participation |
5 |
BISC219 F09 Weekly Lab Planner
| Lab | Date | In-Lab Work | Outside of Lab Work | Assignment |
|---|---|---|---|---|
| 1 | Tues. 9/9 to Mon. 9/14 |
Start tobacco transformation Examine C. elegans and learn to identify the stages and sexes Practice picking worms Set up your first crosses to examine autosomal vs. X-linkage (3 plates total) Perform a mutant hunt: Pick (3) Dumpy mutants to separate plates (3 plates total) |
3-5 days after Lab 1 transfer tobacco leaf tissue to new media with antibiotics 3-4 days after setting up your crosses pick 2 wild type worms from each autosomal vs. X-linked cross to new plates (3 plates total) be sure to examine the F1 progeny taking note of male and hermaphrodite phenotypes Examine mutants from hunt - check phenotype. If Dumpy then cross L4 mutant hermaphrodites by L4 wild type (N2) males (2 plates - duplicates) |
Familiarize yourself with the information in the BISC_219/2009:Resources section. Read the Introduction, Tools and Techniques, and first two labs in the Gene Mapping series: BISC 219/2009:Gene Mapping Read the Background and Creating the Transgenic Plants in the Creating a Transgenic Organism series: BISC 219/2009:Creating a Transgenic Organism |
| 2 | Tue. Sept. 15 to Mon. Sept 21 |
Calibrate micropipettes Count and examine phenotypes of autosomal vs. X-linked crosses Linkage: cross males from last cross to the (4) test strains (4 plates total) |
3 days after lab: Linkage: transfer (2) L4 hermaphrodites from each cross to 2 new plates (8 plates total) |
Homework:Data Analysis (Results)of your autosomal vs. X-linked testing (15pt) due next lab. Grading rubric & Assignment info at: BISC_219: Assignment Help- Data Analysis 1 |
| 3 | Tues. Sept. 22 to Mon. Sept. 28 |
Linkage: examine phenotypes and count to determine linkage Mapping: pick (5) Dpy worms from linkage plate to separate plates (5 plates total) |
3 days after lab: Mapping: Pick (3) double mutants to separate plates (3 plates total) Complementation: Cross Dpy mutant worms to N2 males (2 plates total) |
Homework: Read journal article #1 for discussion in Lab 4: Bruinsma et al., Identification of Mutations in Caenorhabditis elegans That Cause Resistance to High Levels of Dietary Zinc and Analysis Using a Genomewide Map of Single Nucleotide Polymorphisms Scored by Pyrosequencing. Genetics. 2008 June; 179(2): 811–828.
doi: 10.1534/genetics.107.084384. Full text available from PubMed or from Wellesley College Library at [1] |
| 4 | Tues. Sept. 29 to Mon. Oct. 5 |
Plant: Transfer tobacco shoots to root inducing medium Mapping: cross N2 males with double mutants (2 plates total) Complementation: pick males from complementation cross #1 and mate with known Dpy strains (4 plates total) RNAi: pick a single colony – circle and save for next week Discuss Paper #1 |
3 days after lab: Mapping: pick 3-4 males from previous cross to 2 plates and cross with d u/d u hermaphrodites for a test cross (2 plates total) Complementation: examine cross plates for Dpy males Set up an overnight culture of your colony on the day before next lab |
Homework: Start working on Mapping Partial Paper (Introduction section). See BISC_219/2009:Resources and BISC_219: Assignment Help- Partial Paper Mapping for help. |
| 5 | Tues. Oct. 6 to Wed. Oct. 14 |
Mapping: SCORE RNAi: Plasmid DNA isolation (mini-prep) Transform the miniprep into the feeding bacterial strain |
Determine map distance between your mutant gene and the known reference mutation. Make sure all transformations are successful. If not, contact instructor to problem solve The day before lab: Set up an overnight culture of your transformation |
Homework: Work on Gene Mapping Partial paper – Title, Abstract, Intro, Results, References – due 10/23. See BISC_219/2009:Resources and BISC_219: Assignment Help- Partial Paper Mapping for help. Write up practice M &M sections (15 points) on plasmid isolation and transformation BISC_219: Assignment Help- Materials and Methods – due Wednesday October 14th by 5 pm Read journal articles: |
| 6 | Mon. Oct. 19 to Fri. Oct. 23 |
RNAi: induction of bacteria for RNAi feeding Seed plates with induced bacteria and allow to dry Paper discussion |
4 days after lab: Add 2 L4 worms to your plates – N2, rrf-3 |
Homework: Gene Mapping partial paper due Friday October 23rd by 5 pm for all students |
| 7 | Mon. Oct. 26 to Fri. Oct. 30 |
Plant:Transfer plantlets to soil and remove them from their sterile world RNAi: examine the three sets of worms and determine their phenotypes Set up single worm PCR RNAi treated and mutant worms |
Complete Practice sequencing exercise | Homework: Work on M&M revisions for RNAi paper and additional M&M protocols |
| 8 | Wed. Nov. 4 to Tues. Nov. 10 |
RNAi: Clean up PCR reactions Run sequencing reaction and cleanup (columns) Load samples into Sequencer |
Instructors will post your sequencing data to the conference – analyze your results Examine and score histochemial data according to instructors directions |
Homework: Write up practice sequencing data analysis (10 points). BISC_219: Assignment Help- Sequence Analysis Due in lab next week. Read for next lab: Apse, G.P., Aharon, G.S., Snedden, W.A., Blumwald, E. "Salt Tolerance Conferred by Overexpression of a Vacuolar Na+/H+ Antiport in Arabidopsis" Science (1999) 285: 1256-1258. Available at: http://www.sciencemag.org/cgi/content/full/285/5431/1256 or in pdf form at http://0-www.sciencemag.org.luna.wellesley.edu:80/cgi/reprint/285/5431/1256.pdf and the Science perspectives article by Frommer Taking Transgenic Plants with a Pinch of Salt, Science 20 August 1999: Vol. 285. no. 5431, pp. 1222 - 1223. DOI: 10.1126/science.285.5431.1222 at [5]
|
| 9 | Wed. Nov. 11 to Tues. Nov. 17 |
Plants: Restriction enzyme digest of PCR reactions Agarose gel electrophoresis of cut PCR product Paper Discussion #3 |
_ | Work on Paper #2 – Full Paper – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References – BISC_219: Assignment Help- RNAi full paper- DUE Nov. 17th at 5 pm |
| 10 | Wed. Nov. 18 to Tues. Nov. 24 |
Plants:Spectrophotometric GUS enzyme activity assay Phenotypic analysis of plants Paper #2 review returned in lecture 11/24 for revision Discuss The Science of Science Writing by Gopen and Swan from the American Scientist (Nov.-Dec. 1990, Vol78, 550-558 (Available in the E-Reserves folder on the BISC219 course First Class) conference |
_ | Homework: Analyze all data & create figures/tables from course gusA and GUS data for the Workshop. Assignment help at BISC 219/2009: Mod 3 Analyzing the data on the putative transgenic and control plants
|
| 11 | Mon. Nov. 30 to Fri. Dec 4 |
Data Analysis:Effective Figure Design Workshop | _ | Homework: Write final paper on Genetic Engineering in Science style. Due: December 11, 2009 by 5 pm. Instructions at BISC 219: Assignment Help- Transgenic plants research report |
| 12 | Mon. Dec.7 to Fri. Dec. 11 |
TBA | TBA | TBA |
