BISC 219/F10:Assignments: Difference between revisions

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! Lab 1
! Lab 1
| Lab 2  
| Lab 2  
| Complete entry assessment (2.5pts); Submit preliminary cross results Day 3 (1 pt);<br> Summarize experimental question, design; Diagram crosses; Explain data interpretation (9 pts) [[BISC_219/F10: Assignment_1_Lab1]]
| Complete entry assessment (2.5pts); Submit preliminary cross results Day 3 (1 pt);<br> Summarize experimental question, design; Diagram crosses[[Media:Series 1 Template for Crosses.ppt]]; Explain data interpretation (9 pts) [[BISC_219/F10: Assignment_1_Lab1]]
| 12.5
| 12.5
|-
|-
! Lab 2
! Lab 2
| Lab 3  
| Lab 3  
| Statement of Series 2 experimental question & goals. Outline of experimental process including : 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. 1-2 page summary of how you will determine the exact location of the gene and the sequence change likely to be associated with a phenotypic anomally [[BISC_219/F10: Assignment_Series2_Outline_Summary]]; <BR>Read the journal article,, and be prepared to discuss in LAB 3 the questions found at :[[BISC_219:Questions to Guide Your Reading 1]].
| Read Background information on your Series 2 Forward Genetics Project at [[BISC_219/F10:_Gene_Mapping_Info]]. Submit statement of Series 2 experimental question & goals. Outline our experimental process including : 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 and Wormbase work. Write 1-2 page summary of how you will determine the exact location of the gene and the sequence change likely to be associated with a phenotypic anomally [[BISC_219/F10: Assignment_Series2_Outline_Summary]]; <BR> 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: [http://www.genetics.org/cgi/content/full/164/4/1355]; See [[BISC_219/F10:Questions to Guide Your Reading1]] for information on how to prepare for this discussion
| 10
| 10
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|-
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! Lab 3
! Lab 3
| Lab 4  
| Lab 4  
|  Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work that you will do over the next several weeks. Highlight the progeny that will be used to continue each step of the process. Include a narrative description of the rational for the crosses and summarize the interpretation of the results that will allow determination of the linkage group to which your mutated gene of interest belongs.  Assignment information and rubric found at  [[BISC_219/F10: Assignment_Series2_Linkage Testing Crosses]]
|  Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work. Use only part of the template provided at [[Media:Series 2 Template for Crosses.ppt]] (Note that you will use and submit only through Linkage 2. (The Mapping part of the template will be used next week). Include a narrative description of this experimental design that you have drawn out on the template and summarize what you will be looking for in the results that will allow determination of the linkage group to which your mutated gene of interest belongs.  Assignment information and rubric found at  [[BISC_219/F10: Assignment_Series2_Linkage Testing Crosses]]
| 5
| 5
|-
|-
! Lab 4
! Lab 4
| Lab 5  
| Lab 5  
|  Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Mapping work that you will do over the next several weeks. Make sure you highlight the progeny that will be used to continue each step of the process. Assignment information and rubric found at: [[BISC_219/F10: Assignment_Series2_Mapping Crosses]]
|  Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Mapping work that you will do over the next several weeks by completing the templates provided. Make sure you highlight the progeny that will be used to continue each step of the process. Assignment information and rubric found 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 [http://dx.doi.org/10.1186/1471-2164-6-118 doi:10.1186/1471-2164-6-118] and compare their mapping strategy to yours.
|  5
|  5
|-
|-
! Lab 5
! Lab 5
| Lab 6
| Lab 6
| Explain complementation analysis in general and then explain specifically how you will use it to confirm and expand your linkage and mapping work. Assignment informaiton and rubric found at: [[BISC_219/F10: Assignment_Series2_Complementation]]
| Explain complementation analysis in general and then explain specifically how you use it to confirm and expand your linkage and mapping work. Draw out the crosses that you set up using the templates provided at [[Media:Complementation Template Crosses.ppt]]. Assignment information and rubric found at: [[BISC_219/F10: Assignment_Series2_Complementation]]
| 5
| 5
|-
|-
! Lab 6
! Lab 6
| Lab 7
| Lab 7
| Analyze your mutant gene's DNA sequence and write a 1-2 page summary describing briefly and generally how chain-termination sequencing is accomplished and then specifically describe the  mutation most likely to be responsible for your phenotype change by comparing the wild type sequence to the mutant's gene. Include the resulting protein or regulatory product change and its likely significance in the worm and, if possible, in other species. Assignment information and rubric found at:  [[BISC_219/F10: Assignment_Series2_DNA Sequencing]]
| Analyze your mutant gene's DNA sequence using the instructions that you can download from Lab 6. Construct a Results and Discussion section, WITH A FIGURE, for this analysis. Assignment information and rubric found at:  [[BISC_219/F10: Assignment_Series2_DNA Sequencing]]
| 10
| 10
|-
|-
! Lab 6
! Lab 7
| Week of Nov. 1
| Week of Nov. 1
| Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at [[BISC 219/F10: Assignment_ Series2_Classical Genetics Paper]]<br>
| Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at [[BISC 219/F10: Assignment_ Series2_Classical Genetics Paper]]<br>
| 50
| 50
|-
! Lab 7
| Week of Nov. 1
|  Work on Series2 Paper
|
|-
|-
! Lab 8
! Lab 8
| Lab 9
| Lab 9
| Convert all the lab protocols performed so far for Series 3: Reverse Genetics Using RNAi to M&M. Assignment information found at: [[BISC_219/F10: Assignment_Series3_ Materials and Methods]]; <BR>Read the original 1998 paper by Fire and Mello published in ''Nature''; read a later review by Yigit ''et.al'', DOI 10.1016/j.cell.2006.09.033, and the associated perspective,DOI 10.1016/j.cell.2006.11.004, both published in ''Cell''; also read a recent article by Trujillo ''et.al''in ''Genetics'',DOI10.1534/genetics.110.117341, that uses RNAi and other genetic tools that you have learned about in the lab and lecture sections of this course. There are questions to guide your reading found at:[[BISC_219:Questions to Guide Your Reading 2]] . Please be prepared to discuss those questions in Lab 9.  
| Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is 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 [http://dx.doi.org/10.1038/35888 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 [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 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 [http://dx.doi.org/10.1371/journal.pone.0006860 doi:10.1371/journal.pone.0006860]. This study, like yours, uses reverse genetics to investigate gene function.   Be prepared to discuss this paper in Lab 9.  
| 10
| 10
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! Other
! Other
|  
|  
| Exit Survey <br>participation  
| Exit Assessment participation. See First class conference for link and for instructions on how to receive your incentive points (2.5).
| 2.5  
| 2.5  
|-
|-
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Lab 5 Assignment:  [[BISC_219/F10: Assignment_Series2_Complementation]]<BR>
Lab 5 Assignment:  [[BISC_219/F10: Assignment_Series2_Complementation]]<BR>
Lab 6 Assignment: [[BISC_219/F10: Assignment_Series2_DNA Sequencing]]<BR>
Lab 6 Assignment: [[BISC_219/F10: Assignment_Series2_DNA Sequencing]]<BR>
Lab 6 Assignment: [[BISC 219/F10: Assignment_ Series2_Classical Genetics Paper]] Scientific Paper on Forward Genetics Project<br>
Lab 7 Assignment: [[BISC 219/F10: Assignment_ Series2_Classical Genetics Paper]] Scientific Paper on Forward Genetics Project<br>
Lab 8 Assignment: [[BISC_219/F10: Assignment_Series3_ Materials and Methods]] Convert all the lab protocols performed for Series 3 so far into Materials & Methods<br>
Lab 8 Assignment: [[BISC_219/F10: Assignment_Series3_ Materials and Methods]] Convert all the lab protocols performed for Series 3 so far into Materials & Methods<br>
Lab 11 Assignment: [[BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi]] Full Scientific Paper on Reverse Genetics Project using RNAi<br>
Lab 11 Assignment: [[BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi]] Full Scientific Paper on Reverse Genetics Project using RNAi<br>

Latest revision as of 06:59, 15 October 2010

Wellesley College BISC 219 Genetics

Graded Assignments

Lab Assigned Lab Due Assignment
description		 Point Value
(Total 200)
Lab 1 Lab 2 Complete entry assessment (2.5pts); Submit preliminary cross results Day 3 (1 pt);
Summarize experimental question, design; Diagram crossesMedia:Series 1 Template for Crosses.ppt; Explain data interpretation (9 pts) BISC_219/F10: Assignment_1_Lab1 		12.5
Lab 2 Lab 3 Read Background information on your Series 2 Forward Genetics Project at BISC_219/F10:_Gene_Mapping_Info. Submit statement of Series 2 experimental question & goals. Outline our experimental process including : 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 and Wormbase work. Write 1-2 page summary of how you will determine the exact location of the gene and the sequence change likely to be associated with a phenotypic anomally BISC_219/F10: Assignment_Series2_Outline_Summary;
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 		10
Lab 2 Lab 4
Results Section
BISC 219/F10: Assignment Help- Data Analysis 1
Autosomal vs. Sex linked inheritance
 25
Lab 3 Lab 4 Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work. Use only part of the template provided at Media:Series 2 Template for Crosses.ppt (Note that you will use and submit only through Linkage 2. (The Mapping part of the template will be used next week). Include a narrative description of this experimental design that you have drawn out on the template and summarize what you will be looking for in the results that will allow determination of the linkage group to which your mutated gene of interest belongs. Assignment information and rubric found at BISC_219/F10: Assignment_Series2_Linkage Testing Crosses 5
Lab 4 Lab 5 Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Mapping work that you will do over the next several weeks by completing the templates provided. Make sure you highlight the progeny that will be used to continue each step of the process. Assignment information and rubric found 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
Lab 5 Lab 6 Explain complementation analysis in general and then explain specifically how you use it to confirm and expand your linkage and mapping work. Draw out the crosses that you set up using the templates provided at Media:Complementation Template Crosses.ppt. Assignment information and rubric found at: BISC_219/F10: Assignment_Series2_Complementation 5
Lab 6 Lab 7 Analyze your mutant gene's DNA sequence using the instructions that you can download from Lab 6. Construct a Results and Discussion section, WITH A FIGURE, for this analysis. Assignment information and rubric found at: BISC_219/F10: Assignment_Series2_DNA Sequencing 10
Lab 7 Week of Nov. 1 Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at BISC 219/F10: Assignment_ Series2_Classical Genetics Paper
 50
Lab 8 Lab 9 Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is 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. Be prepared to discuss this paper in Lab 9. 10
Lab 9 Lab 10 Write a draft introduction section (including properly formatted Literature Cited page) of your next paper on our Reverse Genetics Project. Refer to BISC_219/F10:Resources Guide to Scientific Writing. 10
Lab 10 Nov. 24
for all students 		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. 5
Lab 11 Lab 12 Full scientific research report due Fri. Dec 10 at 4pm for all students. Assignment information found at BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi 50
Other Exit Assessment participation. See First class conference for link and for instructions on how to receive your incentive points (2.5). 2.5


Assignments

Lab 1 Assignment: BISC_219/F10: Assignment_1_Lab1
Lab 2 Assignment: BISC_219/F10: Assignment_Series2_Outline_Summary
Lab 2-3 Assignment: BISC 219/F10: Assignment Help- Data Analysis 1 Autosomal vs. Sex linked inheritance
Lab 3 Assignment: BISC_219/F10: Assignment_Series2_Linkage Testing Crosses
Lab 4 Assignment: BISC_219/F10: Assignment_Series2_Mapping Crosses
Lab 5 Assignment: BISC_219/F10: Assignment_Series2_Complementation
Lab 6 Assignment: BISC_219/F10: Assignment_Series2_DNA Sequencing
Lab 7 Assignment: BISC 219/F10: Assignment_ Series2_Classical Genetics Paper Scientific Paper on Forward Genetics Project
Lab 8 Assignment: BISC_219/F10: Assignment_Series3_ Materials and Methods Convert all the lab protocols performed for Series 3 so far into Materials & Methods
Lab 11 Assignment: BISC_219/F10: Assignment_Series3_Reverse Genetics Paper using RNAi Full Scientific Paper on Reverse Genetics Project using RNAi

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