BISC 219/F10:Calendars/Planner

BISC219 F10 Lab Calendar

Monday	Tuesday	Wednesday	Thursday	Friday
Sept. 6 Labor Day Holiday	Sept. 7 Lab 1	Sept. 8 Lab 1	Sept. 9 Lab 1	Sept. 10 Lab 1
Sept. 13 Lab 1	Sept. 14 Lab 2	Sept. 15 Lab 2	Sept. 16 Lab 2	Sept. 17 Lab 2
Sept. 20 Lab 2	Sept. 21 Lab 3	Sept. 22 Lab 3	Sept. 23 Lab 3	Sept. 24 Lab 3
Sept. 27 Lab 3	Sept. 28 Lab 4	Sept. 29 Lab 4	Sept. 30 Lab 4	Oct. 1 Lab 4
Oct. 4 Lab 4	Oct. 5 Lab 5	Oct. 6 Lab 5	Oct. 7 Lab 5	Oct. 8 Lab 5
Oct. 11 Fall Break No Lab	Oct. 12 MON. Sch. Lab 5	Oct. 13 Lab 6	Oct. 14 Lab 6	Oct. 15 Lab 6
Oct. 18 Lab 6	Oct. 19 Lab 6	Oct. 20 Lab 7	Oct. 21 Lab 7	Oct. 22 Lab 7
Oct. 25 Lab 7	Oct. 26 Lab 7	Oct. 27 Tanner Conf. No Lab	Oct. 28 Lab 8	Oct. 29 Lab 8
Nov. 1 Lab 8	Nov. 2 Lab 8	Nov. 3 Lab 8	Nov. 4 Lab 9	Nov. 5 Lab 9
Nov. 8 Lab 9	Nov. 9 Lab 9	Nov. 10 Lab 9	Nov. 11 Lab 10	Nov. 12 Lab 10
Nov. 15 Lab 10	Nov. 16 Lab 10	Nov. 17 Lab 10	Nov. 18 NO Lab	Nov. 19 No Lab
Nov. 22 No Lab	Nov. 23 No Lab	Nov. 24 No Lab	Nov. 25 Thanksgiving Holiday	Nov. 26 Thanksgiving Holiday
Nov. 29 Lab 11	Nov. 30 Lab 11	Dec. 1 Lab 11	Dec. 2 Lab 11	Dec. 3 Lab 11
Dec. 6 Lab 12	Dec. 7 Lab 12	Dec. 8 Lab 12	Dec. 9 Lab 12	Dec. 10 Lab 12

Schedule of Experiments

Series	Title	Lab #
1	Worm Boot Camp; Autosomal vs. Sex-linked Traits	1-2
2	Gene Mapping	2-6
3	RNAi	7-12

Graded Assignments

Lab Assigned	Lab Due	Assignment description	Point Value (Total 200)
Lab 1	Lab 2
Lab 2	Lab 3
Lab 3	Lab 4
Lab 4	Lab 5
Lab 5	Lab 6
Lab 6	Lab 7
Lab 7	Lab 8
Lab 8	Lab 9
Lab 9	Lab 10
Lab 10	Lab 11
Lab 11	Lab 12
Other		Discretionary Points: Preparation & Participation	5

BISC219 F10 Weekly Lab Planner

Lab	Date	In-Lab Work	Outside of Lab Work	Assignment
1	Tues. 9/7 to Mon. 9/13	LEARN WORM HUSBANDRY; View worm videos; Examine worms learn difference between stages and sexes; Practice picking worms; Set up autosomal and X-linked crosses	3 days after lab: pick (2) wild type worms from each A and X cross to new plates (3 plates total); Examine the phenotypes of the progeny – hermaphrodites and males	Familiarize yourself with the information in the BISC_219/F10:Resources section; Read all of Series 1: Gene Mapping; Be prepared to discuss the concepts used in the experimental design & to identify the experimental question(s); Design homework to explain autosome and X-chromosome & a way to check for scoring worms correctly. – email in after they score so we can be sure they are seeing the right phenotype?
2	Tue. Sept. 14 to Mon. Sept 20	Series 1: Count and examine phenotypes of autosomal vs. X-linked crosses; Series 2: Perform mutant hunt: Pick (3) putative Dpy mutants to separate plates	Series 2: Examine mutants from hunt: check phenotype – if Dpy then cross L4 mutant hermaphrodites by L4 N2 males (2 plates – duplicate)	Homework:Data Analysis (Results)of your autosomal vs. X-linked testing (15pt) due next lab. Grading rubric & Assignment info at: BISC_219/F10: 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: 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