BISC 219/2009:Schedule

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Wellesley College BISC 219 Genetics

Home     Lecture Syllabus     Lab Calendars/Weekly Planner     OWW Basics     Resources       Glossary    
Gene Mapping        RNA interference        Creating a Transgenic Organism        Assignments       

Contents

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 Methodsdue Wednesday October 14th by 5 pm

Read journal articles:
1) Fire et al, Potent and specific genetic interference by ds RNA in C. elegans in Nature Feb.19,1998 Vol.391 pages 806-811 (doi:10.1038/nature07759. Available at: [2]
2)Steiner and Plasterk's preview of the Yigid article, Knocking out the Argunautes, found in Cell 127, Nov. 17, 2006, DOI: doi:10.1016/j.cell.2006.11.004 available at: [3]
3) Yigid et al, Analysis of the C. elegans Argonaute Family Reveals that Distinct Argonautes Act Sequentially during RNAi in Cell Volume 127, Issue 4, 17 November 2006, Pages 747-757, (doi:10.1016/j.cell.2006.09.033), available at [4] for discussion in Lab 6.

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

Run agarose gel of PCR results

Practice sequencing data analysis with Sequencher software

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

Plants: Plant chromosomal DNA extraction from leaf tissue

PCR amplification of transgene

Histochemical GUS enzyme activity assay

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]
and Uddin MI et al., "Overexpression of a New Rice Vacuolar Antiporter Regulating Protein OsARP Improves Salt Tolerance in Tobacco". Plant and Cell Physiology (2008), Volume 49, Number 6 Pp. 880-890. Available at: http://pcp.oxfordjournals.org/cgi/content/full/49/6/880
and a Feb. 5, 2002 Boston Globe article by ME Malone, SCIENTISTS FOCUS ON THE TOBACCO PLANT AS A POSSIBLE CANCER-FIGHTER GENETICALLY ALTERED CROPS MAY SOMEDAY PRODUCE DRUGS TO COMBAT MANY DISEASES. Available from Lexus/Nexus Academic http://0-www.lexisnexis.com.luna.wellesley.edu/us/lnacademic/search/flap.do?flapID=news&random=0.7807457835138732

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

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



Work on revision of Paper #2 for resubmission by 12/2 at 5 pm

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



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