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 and Sex-linked Traits	1-2
2	Classical (Forward) Genetics: Mutant Hunt, Linkage, Mapping, Complementation, DNA Sequence analysis	2-6
3	Reverse Genetics: Gene selection, Cloning & Making a feeding vector, RNAi, RT-PCR	5-12

BISC219 F10 Weekly Lab Planner

Lab	Date	In-Lab Work	Outside of Lab Work	Assignment
1	Sept. 7 to Sept. 13	LEARN WORM HUSBANDRY; View worm videos; Make your worm pick; Examine worms: recognize different stages & sexes & differentiate mutations; Practice picking worms; Start Series 1: Set up autosomal and X-linked crosses	3 days after lab: pick (2) wild type worms from each cross to new plates (3 plates total); Examine the phenotypes of the progeny – hermaphrodites and males - record all information in your notebook	Homework:Complete Entry Survey; Familiarize yourself with the information in the BISC_219/F10:Resources section; Read all of the background information on C. elegans found in BISC_219/F10:_Worm_Info and read the Lab 1 and Lab 2 information about our first Series 1: Autosomal vs. Sex-Linked Inheritance at BISC_219/F10:_Gene_Linkage & BISC_219/F10:_Lab_2; Complete Graded Assignment 1 explained at BISC_219/F10: Assignment_1_Lab1. Download and use for your cross diagrams: Media:Template_for_Crosses.ppt
2	Sept. 14 to Sept 20	Complete Series 1: Count and examine phenotypes of autosomal vs. X-linked crosses; Start Series 2: Classical (Forward) Genetics- Part 1- Perform mutant hunt: Pick (3) putative Dpy mutants to separate plates	3 days after lab:Examine mutants from hunt: check phenotype – if Dpy then cross L4 mutant hermaphrodites by L4 N2 males (2 plates – duplicate)	Homework: Read ALL of Series 2:background information and all work performed in Labs 2-6 on our Classical (Forward) Genetics project. Write a summary of our experimental question & goals. Outline the experimental process, including all parts of the experimental design: Mutant Hunt, Linkage Analysis, Mapping the Mutation to a chromosome and to a particular location, Complementation Analysis, Determining whether or not the mutation has been previously characterized, & Defining the gene sequence and protein change through DNA sequence analysis. Use this outline to write a 1-2 page summary of how you will determine the exact location and extent of the gene and protein change and include the significance of the mutation in worms and, if possible, broader significance in other species. Assignment explained and rubric found at BISC_219/F10: Assignment Series2_Outline_Summary Start Data Analysis (Results) of your autosomal vs. X-linked testing DUE at the beginning of LAB 4. Grading rubric & Assignment info at: BISC_219/F10: Assignment Help- Data Analysis 1; Read the journal article, Indentification of Genes that Regulate a Left-Right Aymmetric Neuronal Migration in Caenorhabditis elegans published in Genetics 164: 1355-1367 (August 2003), for discussion in lab next time. Full text of article found at: [1]; See BISC_219/F10:Questions to Guide Your Reading1 for information on how to prepare for this discussion
3	Sept. 21 to Sept. 27	Series 2- Part 2: Linkage Analysis: cross heterozygous males (+/d) from last cross to the (5) test strains (5 plates total); Journal article discussion	3 days after lab: Linkage: transfer (2) L4 hermaphrodites from each cross to new plates (5 plates total)	Homework: Draw crosses and diagram strategy for Series 2 Linkage Analysis due at the beginning of Lab 4. Information and grading rubric found at BISC_219/F10: Assignment_Series2_Linkage Testing Crosses Con't Data Analysis (Results)of your autosomal vs. X-linked testing DUE at the beginning of LAB 4. Grading rubric & Assignment info at: BISC_219/F10: Assignment Help- Data Analysis 1
4	Sept. 28 to Oct. 4	Complete Linkage Analysis: examine phenotypes and count to determine linkage; Part 3: Start Mapping: pick (5) Uncs from linkage plate to separate plates (5 plates total)	3 days after lab: Mapping: Pick (3) double mutants to separate plates (3 plates total); Part 4: Start Complementation Analysis: Cross Dpy mutant worms to N2 males (2 plates total)	Homework: Draw crosses and diagram strategy for Mapping the Location of your dpy mutation. Due at the beginning of Lab 5. Assignment described at BISC_219/F10: Assignment_Series2_Mapping Crosses; Read the journal article by Davis at al.,Rapid single nucleotide polymorphism mapping in C. elegans, found at BMC Genomics 2005, 6:118 doi:10.1186/1471-2164-6-118 and compare their mapping strategy to yours.
5	Oct. 5 to Oct. 12	Series 2: Mapping: cross N2 males with double mutants (2 plates total); Series2: Complementation: pick males from complementation cross #1 and mate with known Dpy strains (3 plates total); Series3: Reverse Genetics: Pick gene of interest; set up PCR reaction to clone the gene	Series 3:Reverse Genetics: Examine the results of agarose gel electrophoresis ;3 days after lab: Series2: Mapping: pick (4) heterozygotes from previous cross to individual plates (4 plates total); Series2:Complementation: examine cross plates for Dpy males - WHY?;	Homework: Explain complementation analysis in general and specifically how it will be used to confirm and expand your characterization of your dpy mutation. Due at the beginning of Lab 6. Assignment described atBISC_219/F10: Assignment_Series2_Complementation
6	Oct. 13 to Oct. 19	Series2:Mapping: SCORE!; Series2:Mapping: Gene Sequence Analysis Series3: Reverse Genetics:Restriction enzyme digest PCR product/clean-up/ligation into pPD129.36 vector/transformation into BL21 E.coli	Determine map distance between your mutant gene and the known reference mutation. Check control & transformation plates (save) – notify instructor if no colonies	Homework: DNA sequencing Analysis due at the beginning of Lab 7. Assignment description at BISC_219/F10: Assignment_Series2_DNA Sequencing Scientific research report on Series2 Classical (Forward) Genetics Project due week of 11/1 at the beginning of lab. 5%/day late penalty! See assignment directions at: BISC 219/F10: Assignment_ Series2_Classical Genetics Paper
7	Oct. 20 to Oct. 26	Series3:Reverse Genetics Colony PCR to look for bacterial transformants	Day before lab: grow overnight culture of positive colony	Homework: Continue working on your Series 2: Forward genetics paper due week of Nov 1
8	Oct. 28 to Nov. 3	Series3: Reverse Genetics: Plasmid isolation from BL21 cells/quantification of DNA/ transformation of plasmid into HT115(DE3)cells	Day before lab: grow overnight culture of single colony from transformation	Homework: Write all Series3 Protocols as Materials & Methods. Assignment described at BISC_219/F10: Assignment_Series3_ Materials and Methods. Due at the beginning of Lab 9 ; Read the original 1998 paper by Fire and Mello published in Nature 391: 806-811 (Feb.19 1998) at doi:10.1038/35888 ; Do your own library search to find and read a recent review article about RNAi in C. elegans. Also read the 2002 Simmer et al. paper in Current Biology 12:1317-1319 explaining the rrf-3 strain that we will use for our RNAi work at doi:10.1016/S0960-9822(02)01041-2 . These articles provide background information on how the mechanism of RNAi was worked out experimentally and will be helpful to you when you write the introduction section of your Series3 paper. Also read a published journal article by Green et al. (2009) Impact of Cigarette Smoke Exposure on Innate Immunity: A Caenorhabditis elegans Model. PLoS ONE 4(8): e6860, found at doi:10.1371/journal.pone.0006860. This study, like yours, uses reverse genetics to investigate gene function. There are questions to guide your reading found at:BISC_219:Questions to Guide Your Reading 2 . Be prepared to discuss those questions in Lab 9.
9	Nov.4 to Nov. 10	Series3:RNAi : Induction of bacteria and seed plates for RNAi feeding; Journal article discussion	4 days later: Pick2 L4 hermaphrodite worms of N2 and rrf-3genotype to 2 RNAi plates for each genotype and make 1 control 'mock"plate for each genotype (6plates);	Homework:Write a draft introduction section (including properly formatted Literature Cited page) of your next paper on our Reverse Genetics Project. Due at the beginning of Lab 10. Refer to BISC_219/F10:Resources Guide to Scientific Writing.
10	Nov. 11 to Nov. 17	Series3:RNAi: SCORING (collection)of phenotype of fed worms compared to control N2 worms & womrs with gene mutation; Collect treated worms for RNA purification	_	Homework: Construct figures/tables with properly formatted legends to illustrate the main findings of the RNAi part of your Series3:Reverse Genetics project. These figures are a draft of those that will be part of the results section of the research report you will write for Series3. Due on Nov. 24 for all students.
NO LAB	Nov. 18 to Nov. 26	Thanksgiving Break	_
11	Nov. 29 to Dec. 3	Series 3:Reverse Genetics RT PCR;	Instructor will run gel; when results available review and interpret gel image	Homework: Full Scientific Research Report on Reverse Genetics Project – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References See BISC_219/F10:Resources section Guide to Scientific Wriing and BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi
12	Dec. 6 to Dec. 10	TBA	TBA	Scientific Research Report on Reverse Genetics project DUE Dec. 10 (last day of classes) by 4pm for ALL students Assignment information at BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi; Complete exit genetic assessment. See First Class conference for link and for how to obtain your incentive points (2.5).

Links to Labs

Background: Classical Forward Genetics and Gene Mapping
Lab 2: Mutant Hunt
Lab 3: Linkage Test Part 1
Lab 4: Linkage Test Part 2, Mapping and Complementation
Lab 5: Mapping Part 2
Lab 6: Score & DNA sequencing analysis