BISC219/F12:Calendars/Planner: Difference between revisions

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! 5
! 5
| Sept. 29 to<br> Oct. 5
| Sept. 29 to<br> Oct. 5
| '''Series2: Mapping:'''Self double mutants to keep viable true-breeding progeny;<BR>'''Series2: Complementation:''' examine cross plates for Dpy males - WHY?; '''Series3: Reverse Genetics:''' Pick gene of interest; set up PCR reaction to clone the gene
| '''Series2: Mapping:'''Self double mutants to keep viable true-breeding progeny;<BR>'''Series2: Complementation:''' examine cross plates for Dpy males - WHY?
| '''Series 3:Reverse Genetics:''' Examine the results of agarose gel electrophoresis
|
| '''Homework:''' Draw crosses and diagram strategy for Mapping the Location of your ''dpy'' mutation. (Complete template downloaded for Linkage analysis). Due at the beginning of Lab 6. Assignment described at [[BISC219/F12: Assignment_Series2_Mapping Crosses]]
| '''Homework:''' Draw crosses and diagram strategy for Mapping the Location of your ''dpy'' mutation. (Complete template downloaded for Linkage analysis). Due at the beginning of Lab 6. Assignment described at [[BISC219/F12: Assignment_Series2_Mapping Crosses]]
|-
|-
! 6
! 6
| Oct. 12 to <br> Oct. 18
| Oct. 12 to <br> Oct. 18
|  '''Series 2: Mapping''': cross N2 males (++/++) with L4 double mutant hermaphrodites (2 plates total);Self double mutants to new plate<BR> Series2: Characterizing the dpy mutation''' Gene Sequence Analysis <br> '''Series3: Reverse Genetics:'''Restriction enzyme digest PCR product/clean-up/ligation into pPD129.36 vector/transformation into BL21 ''E.coli''
|  '''Series 2: Mapping''': cross N2 males (++/++) with L4 double mutant hermaphrodites (2 plates total);Self double mutants to new plate<BR> Series2: Characterizing the dpy mutation''' Gene Sequence Analysis  
|  '''3 days after lab:Series2: Mapping:''' pick (4) male heterozygotes (++/d u) and Cross them with L4 hermaphrodite double mutants (d u/d u). <BR>'''Series 3:'''Check control & transformation plates (save) – <BR>notify instructor if no colonies
|  '''3 days after lab:Series2: Mapping:''' pick (4) male heterozygotes (++/d u) and Cross them with L4 hermaphrodite double mutants (d u/d u).  
| '''Homework''': DNA sequencing Analysis due at the beginning of Lab 7. Assignment description at [[BISC219/F12: Assignment_Series2_DNA Sequencing]]<BR>
| '''Homework''': DNA sequencing Analysis due at the beginning of Lab 7. Assignment description at [[BISC219/F12: Assignment_Series2_DNA Sequencing]]<BR>
|-
|-
! 7
! 7
| Oct. 19 to <br> Oct. 25  
| Oct. 19 to <br> Oct. 25  
| '''Series2:Finish Mapping:''' SCORE! Calculate Recombination frequency; <BR>'''Series3:Reverse Genetics''' Colony PCR to look for bacterial transformants
| '''Series2:Finish Mapping:''' SCORE! Calculate Recombination frequency;  
| Determine map distance between your mutant gene <BR>and the known reference mutation<BR>'''Day before lab:''' Series 3:grow overnight culture of positive colony
| Determine map distance between your mutant gene <BR>and the known reference mutation<BR>'''Day before lab:''' Series 3:grow overnight culture of positive colony
| '''Homework''': Scientific research report on Series 2 Classical (Forward) Genetics Project due Fri. Nov. 4 for ALL students. 5%/day late penalty! See assignment directions at: [[BISC219/F12: Assignment_ Series2_Classical Genetics Paper]]
| '''Homework''': Scientific research report on Series 2 Classical (Forward) Genetics Project due Fri. Nov. 4 for ALL students. 5%/day late penalty! See assignment directions at: [[BISC219/F12: Assignment_ Series2_Classical Genetics Paper]]
Line 125: Line 125:
! 8
! 8
| Nov. 2 to <br> Nov. 8
| Nov. 2 to <br> Nov. 8
| '''Series3: Reverse Genetics''': Plasmid isolation/quantification of DNA/ transformation of plasmid into ''E. coli'' strain HT115(DE3)
| '''Series3: Investigating Gene Regulation Using RNAi''':  
| '''Day before lab:''' grow overnight culture of single colony from transformation
| '''Day before lab:'''  
| '''Homework''': Write all Series 3 Protocols as Materials & Methods. Assignment described at [[BISC219/F12: Assignment_Series3_ Materials and Methods]]. Due at the beginning of Lab 9.
| '''Homework''': Full Research Report on Series 2 due at the beginning of Lab 9
 
|-
|-
! 9
! 9
| Nov. 9 to <br> Nov. 15
| Nov. 9 to <br> Nov. 15
| '''Series3:RNAi''' : Induction of bacteria and seed plates for RNAi feeding; <BR> Journal article discussion
| '''Series3: Gene Regulation & RNAi''' :  
|  '''4 days later:''' Pick 2 L4 hermaphrodite worms of N2 and ''rrf-3'' genotype to 2 RNAi plates for each genotype and make 1 control ''mock'' plate for each genotype (6 plates);
|  '''4 days later:'''  
| '''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 [[BISC219/F12:Resources]] Guide to Scientific Writing.  
| '''Homework:'''Write a draft introduction section (including properly formatted Literature Cited page) of your next paper on our Investigation of Gene Regulation Using RNAi. Write all Series 3 Protocols done so far as Materials & Methods. Assignment described at [[BISC219/F12: Assignment_Series3_ Materials and Methods]]. Due at the beginning of Lab 10. Refer to [[BISC219/F12:Resources]] Guide to Scientific Writing.  
|-
|-
! 10
! 10
| Nov. 16 to <br> Nov. 22
| Nov. 16 to <br> Nov. 22
| '''Series3:RNAi:''' SCORING (collection)of phenotype of fed worms compared to control N2 worms & worms with gene mutation
| '''Series3:RNAi:'''  
| --
| --
| '''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 to be used in a Science Writing workshop in Lab 11. Full paper on Series 3 Due last day of classes for all students. Read the [http://dx.doi.org/10.1038/35888 original 1998 paper by Fire and Mello] published in ''Nature'' '''391''': 806-811 (Feb.19 1998); 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 [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 explaining the ''rrf-3'' strain] that we will use for our RNAi work. 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) [http://dx.doi.org/10.1371/journal.pone.0006860 Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model] PLoS ONE 4(8): e6860. This study, like yours, uses reverse genetics to investigate gene function.  
| '''Homework''': Construct figures/tables with properly formatted legends to illustrate the main finding of your Series3 project. These figures are to be used in a Science Writing workshop in Lab 11. (Paper on Series 3 Due last day of classes for all students.) Read the [http://dx.doi.org/10.1038/35888 original 1998 paper by Fire and Mello] published in ''Nature'' '''391''': 806-811 (Feb.19 1998); 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 [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 explaining the ''rrf-3'' strain] that we will use for our RNAi work. 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) [http://dx.doi.org/10.1371/journal.pone.0006860 Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model] PLoS ONE 4(8): e6860. This study, like yours, uses reverse genetics to investigate gene function.  
|-
|-
! NO LAB
! NO LAB
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! 11
! 11
| Nov. 28 to<br> Dec. 2  
| Nov. 28 to<br> Dec. 2  
| '''Series 3:Reverse Genetics''' Science Writing Workshop & Effective Figure Design. Be sure to have read the [http://dx.doi.org/10.1038/35888 original 1998 paper by Fire and Mello] published in ''Nature'' '''391''': 806-811 (Feb.19 1998); 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 [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 explaining the ''rrf-3'' strain] that we will use for our RNAi work. 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) [http://dx.doi.org/10.1371/journal.pone.0006860 Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model] PLoS ONE 4(8): e6860. This study, like yours, uses reverse genetics to investigate gene function.  
| Science Writing Workshop & Effective Figure Design. Be sure to have read the [http://dx.doi.org/10.1038/35888 original 1998 paper by Fire and Mello] published in ''Nature'' '''391''': 806-811 (Feb.19 1998); 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 [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 explaining the ''rrf-3'' strain] that we will use for our RNAi work. 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) [http://dx.doi.org/10.1371/journal.pone.0006860 Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model] PLoS ONE 4(8): e6860. This study, like yours, uses reverse genetics to investigate gene function.  
| --
| --
| '''Homework''': Full Scientific Research Report on Reverse Genetics Project – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References See [[BISC219/F12:Resources]] section '''Guide to Scientific Wriing''' and [[BISC219/F12: Assignment_Series3_Reverse Genetics Paper using RNAi]].  
| '''Homework''': Full Scientific Research Report on your Investigation of Gene Regulation Using RNAi Project – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References See [[BISC219/F12:Resources]] section '''Guide to Scientific Wriing''' and [[BISC219/F12: Assignment_Series3_Reverse Genetics Paper using RNAi]].  
DUE Dec. 7 by 5 pm for ALL students. Complete exit genetic assessment. See Sakai site for link and for how to obtain your incentive points.  
DUE Dec. 11 by 4 pm for ALL students. Complete exit genetic assessment. See Sakai site for link and for how to obtain your incentive points.  
|-
|-
|}
|}
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Revision as of 11:46, 20 August 2012

Wellesley College BISC 219 Genetics

BISC219 F12 Lab Calendar


Monday Tuesday Wednesday Thursday Friday
Sept. 3
Labor Day
No Classes 		Sept. 4
Lab 1		 Sept. 5
Lab 1		 Sept. 6
Lab 1		 Sept. 7
Lab 1
Sept. 10
Lab 1 		Sept. 11
Lab 2		 Sept. 12
Lab 2		 Sept. 13
Lab 2		 Sept. 14
Lab 2
Sept. 17
Lab 2 		Sept. 18
Lab 3
Paper 1 due		 Sept. 19
Lab 3
Paper 1 due		 Sept. 20
Lab 3
Paper 1 due		 Sept. 21
Lab 3
Paper 1 due
Sept. 24
Lab 3
Paper 1 due 		Sept. 25
Lab 4		 Sept. 26
Lab 4		 Sept. 27
Lab 4		 Sept. 28
Lab 4
Oct. 1
Lab 4 Part I 		Oct. 2
Lab 5		 Oct. 3
Lab 5		 Oct. 4
Lab 5		 Oct. 5
Lab 5
Oct. 8
Fall Break
No Classes 		Oct. 9
Fall Break
No Classes		 Oct. 10
No Lab		 Oct. 11
No Lab		 Oct. 12
No Lab
Oct. 15
Lab 4 Part II/ Lab 5 		Oct. 16
Lab 6		 Oct. 17
Lab 6		 Oct. 18
Lab 6		 Oct. 19
Lab 6
Oct. 22
Lab 6 		Oct. 23
Lab 7		 Oct. 24
Lab 7		 Oct. 25
Lab 7		 Oct. 26
Lab 7
Oct. 29
Lab 7 		Oct. 30
Lab 8		 Oct. 31
Lab 8		 Nov. 1
Lab 8		 Nov. 2
Lab 8
Nov. 5
Lab 8 		Nov. 6
Tanner Conference
No Classes		 Nov. 7
Lab 9
Paper 2 Due		 Nov. 8
Lab 9
Paper 2 Due		 Nov. 9
Lab 9
Paper 2 Due
Nov. 12
Lab 9
Paper 2 Due 		Nov. 13
Lab 9
Paper 2 Due		 Nov. 14
Lab 10		 Nov. 15
Lab 10		 Nov. 16
Lab 10
Nov. 19
Lab 10 		Nov. 20
Lab 10		 Nov. 21
Thanksgiving Break
No Classes		 Nov. 22
Thanksgiving Break
No Classes		 Nov. 23
Thanksgiving Break
No Classes
Nov. 26
Lab 11 		Nov. 27
Lab 11		 Nov. 28
Lab 11		 Nov. 29
Lab 11		 Nov. 30
Lab 11
Dec. 3
Lab 12 		Dec. 4
Lab 12 '		 Dec. 5
Lab 12		 Dec. 6
Lab 12		 Dec. 7
Lab 12
Dec. 10
No Lab 		Dec. 11
Last Day of Classes
Paper 3 due for all students


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 2-7
3 Reverse Genetics: Investigating Gene Regulation Using RNAi 8-12

BISC219 F10 Weekly Lab Planner

Lab Date In-Lab Work Outside of Lab Work Assignment
1 Aug 30 to
Sept. 7 		LEARN WORM HUSBANDRY;
View worm videos;
Make your worm pick;
Examine worms: recognize different stages & sexes
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 BISC219/F12:Resources section;
Read all of the background information on C. elegans found in BISC219/F12:_Worm_Info and read the Lab 1 and Lab 2 information about our first Series 1: Autosomal vs. Sex-Linked Inheritance at BISC219/F12:_Gene_Linkage & BISC219/F12:_Lab_2; Complete Graded Assignment 1 explained at BISC219/F12: Assignment_1_Lab1
2 Sept. 8 to
Sept 14 		Complete Series 1: Count and examine phenotypes of autosomal vs. X-linked crosses;
Start Series 2: Classical (Forward) Genetics- Part 1- Examine mutant worms and compare to wild type:
Pick (3) putative Dpy mutants to separate plates 		3 days after lab:Examine mutants: 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 DUE at the beginning of LAB 3.
Grading rubric & Assignment info at:
BISC219/F12: Assignment Help- Data Analysis 1
3 Sept. 15 to
Sept. 21 		Series 2- Part 2: Linkage Analysis: cross heterozygous males (+/d) from last cross to the (5) test strains (5 plates total);
 		3 days after lab: Linkage: transfer (2) L4 hermaphrodites from each cross
to new plates (5 plates total) 		Homework: . Read ALL of Series 2:background information BISC219/F12:_Gene_Mapping_Info and about all work to be performed in Labs 2-6 on our Classical (Forward) Genetics project. Write a summary of our overall topic and experimental question(s) & goals. Outline the experimental process. 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. Draw crosses and diagram strategy for Series 2 Linkage Analysis. All due at the beginning of Lab 4. Assignment explained and rubrics found at Assignment Series2 Outline/Summary & Linkage Analysis
4 Sept. 22 to
Sept. 28 		Complete Linkage Analysis: examine phenotypes and count to determine linkage;
Part 3: Start Mapping: pick (6) Uncs of the linked unc strain to separate plates (6 plates total);
Part 4: Start Complementation Analysis: Cross Dpy mutant worms to N2 males (2 plates total) 		3 days after lab: Mapping:
Pick (3) double mutants to separate plates (3 plates total);
Series2: Complementation: pick males from complementation cross #1 and mate with known Dpy strains (3 plates total);
 Homework: Explain complementation analysis in general and specifically how it was used to id your dpy gene and to determine if the mutation of interest has been previously characterized. Diagram complementation crosses using template provided. Due at the beginning of Lab 5. Assignment described atBISC219/F12: Assignment_Series2_Complementation
5 Sept. 29 to
Oct. 5 		Series2: Mapping:Self double mutants to keep viable true-breeding progeny;
Series2: Complementation: examine cross plates for Dpy males - WHY? 		Homework: Draw crosses and diagram strategy for Mapping the Location of your dpy mutation. (Complete template downloaded for Linkage analysis). Due at the beginning of Lab 6. Assignment described at BISC219/F12: Assignment_Series2_Mapping Crosses
6 Oct. 12 to
Oct. 18 		Series 2: Mapping: cross N2 males (++/++) with L4 double mutant hermaphrodites (2 plates total);Self double mutants to new plate
Series2: Characterizing the dpy mutation Gene Sequence Analysis 		3 days after lab:Series2: Mapping: pick (4) male heterozygotes (++/d u) and Cross them with L4 hermaphrodite double mutants (d u/d u). Homework: DNA sequencing Analysis due at the beginning of Lab 7. Assignment description at BISC219/F12: Assignment_Series2_DNA Sequencing
7 Oct. 19 to
Oct. 25 		Series2:Finish Mapping: SCORE! Calculate Recombination frequency; Determine map distance between your mutant gene
and the known reference mutation
Day before lab: Series 3:grow overnight culture of positive colony 		Homework: Scientific research report on Series 2 Classical (Forward) Genetics Project due Fri. Nov. 4 for ALL students. 5%/day late penalty! See assignment directions at: BISC219/F12: Assignment_ Series2_Classical Genetics Paper
8 Nov. 2 to
Nov. 8 		Series3: Investigating Gene Regulation Using RNAi: Day before lab: Homework: Full Research Report on Series 2 due at the beginning of Lab 9
9 Nov. 9 to
Nov. 15 		Series3: Gene Regulation & RNAi : 4 days later: Homework:Write a draft introduction section (including properly formatted Literature Cited page) of your next paper on our Investigation of Gene Regulation Using RNAi. Write all Series 3 Protocols done so far as Materials & Methods. Assignment described at BISC219/F12: Assignment_Series3_ Materials and Methods. Due at the beginning of Lab 10. Refer to BISC219/F12:Resources Guide to Scientific Writing.
10 Nov. 16 to
Nov. 22 		Series3:RNAi: -- Homework: Construct figures/tables with properly formatted legends to illustrate the main finding of your Series3 project. These figures are to be used in a Science Writing workshop in Lab 11. (Paper on Series 3 Due last day of classes for all students.) Read the original 1998 paper by Fire and Mello published in Nature 391: 806-811 (Feb.19 1998); 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. 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. This study, like yours, uses reverse genetics to investigate gene function.
NO LAB Nov. 23 to
Nov. 25 		Thanksgiving Break _
11 Nov. 28 to
Dec. 2 		Science Writing Workshop & Effective Figure Design. Be sure to have read the original 1998 paper by Fire and Mello published in Nature 391: 806-811 (Feb.19 1998); 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. 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. This study, like yours, uses reverse genetics to investigate gene function. -- Homework: Full Scientific Research Report on your Investigation of Gene Regulation Using RNAi Project – Title, Abstract, Intro, Materials and Methods, Results, Discussion, References See BISC219/F12:Resources section Guide to Scientific Wriing and BISC219/F12: Assignment_Series3_Reverse Genetics Paper using RNAi.

DUE Dec. 11 by 4 pm for ALL students. Complete exit genetic assessment. See Sakai site for link and for how to obtain your incentive points.



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