BISC219/F11:Assignments

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(New page: {{Template:BISC219/F11}} <div style="padding: 10px; width: 720px; border: 5px solid #6600cc;"> ==Graded Assignments== {| border="1" |+ ! Lab Assigned !! Lab Due !! Assignment<br> descrip...)
Current revision (13:10, 2 November 2011) (view source)
(Graded Assignments)
 
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! Lab 1
! Lab 1
| Lab 2  
| Lab 2  
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| 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) [[BISC219/F11: Assignment_1_Lab1]]
+
| Complete entry assessment (2.5pts); Submit preliminary cross results Day 3 (1 pt);<br> Summarize experimental question, design; Diagram crosses using template provided; Explain data interpretation (9 pts). This assignment is described at: [[BISC219/F11: Assignment_1_Lab1]]
| 12.5
| 12.5
|-
|-
! Lab 2
! Lab 2
| Lab 3  
| Lab 3  
-
| Read Background information on your Series 2 Forward Genetics Project at [[BISC219/F11:_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 anomaly [[BISC219/F11: Assignment_Series2_Outline_Summary]]; <BR> Read the journal article, Indentification of Genes that Regulate a Left-Right Asymmetric 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
+
| Read Background information on your Series 2 Forward Genetics Project at [[BISC219/F11:_Gene_Mapping_Info]]. Submit statement of Series 2 experimental question & goals. Outline (or create flow diagram) our experimental process including : Mutant Phenotype description compared to WT; Linkage Analysis; Mapping the Mutation to a chromosome and to a particular chromosomal location; Complementation Analysis; Defining the gene sequence and protein change through DNA sequence analysis; & Bioinformatics to find homologues and to determine if the mutation is new or previously characterized. Write a narrative summary of the investigation [[BISC219/F11: Assignment_Series2_Outline_Summary]].
| 10
| 10
|-
|-
! Lab 2
! Lab 2
| Lab 4  
| Lab 4  
-
| <BR> Results Section <BR>[[BISC219/F11: Assignment Help- Data Analysis 1]] <BR>Autosomal vs. Sex linked inheritance<BR>  
+
| <BR> Results Section [[BISC219/F11: Assignment Help- Data Analysis 1]] <BR>Autosomal vs. Sex linked inheritance<BR>  
| 25
| 25
|-
|-
! Lab 3
! Lab 3
| Lab 4  
| Lab 4  
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|  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  [[BISC219/F11: 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 (through Linkage 2) of the template provided. (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  [[BISC219/F11: 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 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: [[BISC219/F11: 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.
+
| Explain complementation analysis in general and then explain specifically how you will use it in this investigation. Draw out the crosses that you set up using the templates provided. Assignment information and rubric found at: [[BISC219/F11: Assignment_Series2_Complementation]]  
|  5
|  5
|-
|-
! Lab 5
! Lab 5
| Lab 6
| 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: [[BISC219/F11: Assignment_Series2_Complementation]]
+
| 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: [[BISC219/F11: Assignment_Series2_Mapping Crosses]].
| 5
| 5
|-
|-
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| 10
| 10
|-
|-
-
! Lab 7
+
! Paper Series 2
-
| Week of Nov. 1
+
| Paper due Fri. Nov. 4<br>for all students
| Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at [[BISC219/F11: Assignment_ Series2_Classical Genetics Paper]]<br>
| Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at [[BISC219/F11: Assignment_ Series2_Classical Genetics Paper]]<br>
| 50
| 50
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! Lab 8
! Lab 8
| Lab 9
| Lab 9
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| Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is described at [[BISC219/F11: 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.  
+
| Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is described at [[BISC219/F11: Assignment_Series3_ Materials and Methods]]. Due at the beginning of Lab 9. Bring hard copies of the journal articles assigned to use during a science writing workshop and concept discussion in Lab9 and be prepared to lead the class discussion or summarize the major points of the article your group was assigned:  
 +
These articles will provide helpful information when you write your Series3 paper. A good published journal article (that you need not read for content) 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] uses reverse genetics to investigate gene function. It may be a helpful model when you write some of your M&M section for your final paper.
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| 10
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|-
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|-
|-
! Lab 10
! Lab 10
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| Nov. 24 <BR> for all students
+
| Lab 11
| 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.
| 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
| 5
|-
|-
! Lab 11
! Lab 11
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| Lab 12
+
| '''Wed. Dec 7 for all students'''
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| Full scientific research report due Fri. Dec 10 at 4pm for all students. Assignment information found at [[BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi]]
+
| Full scientific research report due Wed. Dec 7 at 4pm for all students. Assignment information found at [[BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi]]
| 50
| 50
|-
|-
! Other
! Other
|  
|  
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| Exit Assessment participation. See First class conference for link and for instructions on how to receive your incentive points (2.5).  
+
| Exit Assessment participation. See Sakai Announcement for link and for instructions on how to receive your incentive points (2.5).  
| 2.5  
| 2.5  
|-
|-
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Lab 2-3 Assignment: [[BISC219/F11: Assignment Help- Data Analysis 1]] Autosomal vs. Sex linked inheritance<BR>
Lab 2-3 Assignment: [[BISC219/F11: Assignment Help- Data Analysis 1]] Autosomal vs. Sex linked inheritance<BR>
Lab 3 Assignment:  [[BISC219/F11: Assignment_Series2_Linkage Testing Crosses]]<BR>
Lab 3 Assignment:  [[BISC219/F11: Assignment_Series2_Linkage Testing Crosses]]<BR>
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Lab 4 Assignment:  [[BISC219/F11: Assignment_Series2_Mapping Crosses]]<BR>
+
Lab 4 Assignment:  [[BISC219/F11: Assignment_Series2_Complementation]]<BR>
-
Lab 5 Assignment:  [[BISC219/F11: Assignment_Series2_Complementation]]<BR>
+
Lab 5 Assignment:  [[BISC219/F11: Assignment_Series2_Mapping Crosses]]<BR>
Lab 6 Assignment: [[BISC219/F11: Assignment_Series2_DNA Sequencing]]<BR>
Lab 6 Assignment: [[BISC219/F11: Assignment_Series2_DNA Sequencing]]<BR>
Lab 7 Assignment: [[BISC219/F11: Assignment_ Series2_Classical Genetics Paper]] Scientific Paper on Forward Genetics Project<br>
Lab 7 Assignment: [[BISC219/F11: Assignment_ Series2_Classical Genetics Paper]] Scientific Paper on Forward Genetics Project<br>
Lab 8 Assignment: [[BISC219/F11: Assignment_Series3_ Materials and Methods]] Convert all the lab protocols performed for Series 3 so far into Materials & Methods<br>
Lab 8 Assignment: [[BISC219/F11: Assignment_Series3_ Materials and Methods]] Convert all the lab protocols performed for Series 3 so far into Materials & Methods<br>
Lab 11 Assignment: [[BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi]] Full Scientific Paper on Reverse Genetics Project using RNAi<br>
Lab 11 Assignment: [[BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi]] Full Scientific Paper on Reverse Genetics Project using RNAi<br>

Current revision

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 crosses using template provided; Explain data interpretation (9 pts). This assignment is described at: BISC219/F11: Assignment_1_Lab1
12.5
Lab 2 Lab 3 Read Background information on your Series 2 Forward Genetics Project at BISC219/F11:_Gene_Mapping_Info. Submit statement of Series 2 experimental question & goals. Outline (or create flow diagram) our experimental process including : Mutant Phenotype description compared to WT; Linkage Analysis; Mapping the Mutation to a chromosome and to a particular chromosomal location; Complementation Analysis; Defining the gene sequence and protein change through DNA sequence analysis; & Bioinformatics to find homologues and to determine if the mutation is new or previously characterized. Write a narrative summary of the investigation BISC219/F11: Assignment_Series2_Outline_Summary. 10
Lab 2 Lab 4
Results Section BISC219/F11: 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 (through Linkage 2) of the template provided. (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 BISC219/F11: Assignment_Series2_Linkage Testing Crosses 5
Lab 4 Lab 5 Explain complementation analysis in general and then explain specifically how you will use it in this investigation. Draw out the crosses that you set up using the templates provided. Assignment information and rubric found at: BISC219/F11: Assignment_Series2_Complementation 5
Lab 5 Lab 6 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: BISC219/F11: Assignment_Series2_Mapping Crosses. 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: BISC219/F11: Assignment_Series2_DNA Sequencing 10
Paper Series 2 Paper due Fri. Nov. 4
for all students
Scientific Research Report on Series2 work Classical (Forward) Genetics. Assignment information found at BISC219/F11: 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 BISC219/F11: Assignment_Series3_ Materials and Methods. Due at the beginning of Lab 9. Bring hard copies of the journal articles assigned to use during a science writing workshop and concept discussion in Lab9 and be prepared to lead the class discussion or summarize the major points of the article your group was assigned:

These articles will provide helpful information when you write your Series3 paper. A good published journal article (that you need not read for content) 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 uses reverse genetics to investigate gene function. It may be a helpful model when you write some of your M&M section for your final paper.

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 BISC219/F11:Resources Guide to Scientific Writing. 10
Lab 10 Lab 11 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 Wed. Dec 7 for all students Full scientific research report due Wed. Dec 7 at 4pm for all students. Assignment information found at BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi 50
Other Exit Assessment participation. See Sakai Announcement for link and for instructions on how to receive your incentive points (2.5). 2.5


Assignments

Lab 1 Assignment: BISC219/F11: Assignment_1_Lab1
Lab 2 Assignment: BISC219/F11: Assignment_Series2_Outline_Summary
Lab 2-3 Assignment: BISC219/F11: Assignment Help- Data Analysis 1 Autosomal vs. Sex linked inheritance
Lab 3 Assignment: BISC219/F11: Assignment_Series2_Linkage Testing Crosses
Lab 4 Assignment: BISC219/F11: Assignment_Series2_Complementation
Lab 5 Assignment: BISC219/F11: Assignment_Series2_Mapping Crosses
Lab 6 Assignment: BISC219/F11: Assignment_Series2_DNA Sequencing
Lab 7 Assignment: BISC219/F11: Assignment_ Series2_Classical Genetics Paper Scientific Paper on Forward Genetics Project
Lab 8 Assignment: BISC219/F11: Assignment_Series3_ Materials and Methods Convert all the lab protocols performed for Series 3 so far into Materials & Methods

Lab 11 Assignment: BISC219/F11: Assignment_Series3_Reverse Genetics Paper using RNAi Full Scientific Paper on Reverse Genetics Project using RNAi
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