BISC219/F11:Assignments - Revision history

Tucker Crum: /* Graded Assignments */

2011-11-02T18:10:39Z

Graded Assignments

←Older revision		Revision as of 18:10, 2 November 2011
Line 49:		Line 49:
	! Lab 8		! Lab 8
	\| Lab 9		\| 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 ~~following~~ journal articles to use during a science writing workshop and concept discussion in Lab9~~: 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] ; 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 ]. The Fortunata and Frasier review~~ article ~~(Fortunato, A. and Fraser, A (2005) Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference. BioScience Reports, Vol. 25, Nos. 5/6, October/December pages 299-307 . DOI~~: 10.1007/s10540-005-2892-7)is a good one to read about the development and use of RNAi through 2005. Vastenhouw, NL et al. Long-term gene silencing by RNAi. Nature Aug. 24 2006. Vol. 442 (24) 882, will help you understand how gene knockdown in ''C. elegans'' can span generations.	+	\| 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 ~~to you~~ when you write ~~the introduction section of~~ 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.	+	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.
	\| 10		\| 10
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-10-31T20:04:40Z

Graded Assignments

←Older revision		Revision as of 20:04, 31 October 2011
Line 49:		Line 49:
	! Lab 8		! Lab 8
	\| Lab 9		\| 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 following journal articles to use during a science writing workshop and concept discussion in Lab9: 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 and bring 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 use this paper in~~ a ~~discussion~~ of ~~the structure of science writing 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 following journal articles to use during a science writing workshop and concept discussion in Lab9: 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] ; 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 ]. The Fortunata and Frasier review article (Fortunato, A. and Fraser, A (2005) Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference. BioScience Reports, Vol. 25, Nos. 5/6, October/December pages 299-307 . DOI: 10.1007/s10540-005-2892-7)is a good one to read about the development and use of RNAi through 2005. Vastenhouw, NL et al. Long-term gene silencing by RNAi. Nature Aug. 24 2006. Vol. 442 (24) 882, will help you understand how gene knockdown in ''C. elegans'' can span generations.
		+	These articles will provide helpful to you when you write the introduction section of 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.
	\| 10		\| 10
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-09-23T15:49:24Z

Graded Assignments

←Older revision		Revision as of 15:49, 23 September 2011
Line 29:		Line 29:
	! Lab 4		! Lab 4
	\| Lab 5		\| Lab 5
-	\| Explain complementation analysis in general and then explain specifically how you will use it ~~to confirm and expand your linkage and mapping work~~. Draw out the crosses that you set up using the templates provided. Assignment information and rubric found at: [[BISC219/F11: Assignment_Series2_Complementation]]	+	\| 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
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-09-22T13:23:15Z

Graded Assignments

←Older revision		Revision as of 13:23, 22 September 2011
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	! 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 (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 ~~1-2 page~~ narrative summary of the investigation [[BISC219/F11: Assignment_Series2_Outline_Summary]].	+	\| 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
	\|-		\|-

Melissa Beers: /* Graded Assignments */

2011-08-15T14:15:02Z

Graded Assignments

←Older revision		Revision as of 14:15, 15 August 2011
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	! Other		! Other
	\|		\|
-	\| 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
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-06-02T12:52:44Z

Graded Assignments

←Older revision		Revision as of 12:52, 2 June 2011
Line 29:		Line 29:
	! Lab 4		! Lab 4
	\| Lab 5		\| Lab 5
-	\| Explain complementation analysis in general and then explain specifically how you will 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]]	+	\| Explain complementation analysis in general and then explain specifically how you will use it to confirm and expand your linkage and mapping work. 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
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-06-02T12:52:12Z

Graded Assignments

←Older revision		Revision as of 12:52, 2 June 2011
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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. 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
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-06-02T12:50:33Z

Graded Assignments

←Older revision		Revision as of 12:50, 2 June 2011
Line 9:		Line 9:
	! 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 using template provided; 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
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-06-02T12:50:12Z

Graded Assignments

←Older revision		Revision as of 12:50, 2 June 2011
Line 9:		Line 9:
	! 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~~[[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) [[BISC219/F11: Assignment_1_Lab1]]
	\| 12.5		\| 12.5
	\|-		\|-

Tucker Crum: /* Graded Assignments */

2011-06-02T12:21:05Z

Graded Assignments

←Older revision		Revision as of 12:21, 2 June 2011
Line 63:		Line 63:
	\|-		\|-
	! Lab 11		! Lab 11
-	\| '''Wed. Dec 7~~<BR>~~for all students'''	+	\| '''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]]		\| 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