BISC219/F12: Assignment Series3 Reverse Genetics Paper using RNAi - Revision history

Tucker Crum: /* Rubric for Each Question on the Reverse Genetics Project- 10 points each for total of 50 points */

2012-11-19T16:56:42Z

Rubric for Each Question on the Reverse Genetics Project- 10 points each for total of 50 points

←Older revision		Revision as of 16:56, 19 November 2012
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	! Data Analysis		! Data Analysis
-	\| '''3 pts.''' Identifies question addressed; includes a brief description of the experimental design related to the question; Uses appropriate experimental evidence and explains it effectively to a general audience. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge	+	\| '''3 pts.''' Identifies question addressed; includes a brief description of the experimental design related to the question; Uses appropriate experimental evidence and explains it effectively to a general audience. Includes all parts requested in assignment description. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge
-	\| '''0-2.5 pts.''' Missing question addressed, experimental design, appropriate experimental evidence or an inadequate explanation of the evidence. Inappropriate level of detail (either too much detail or too general). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.	+	\| '''0-2.5 pts.''' Missing question addressed, experimental design, appropriate experimental evidence or an inadequate explanation of the evidence. Does not include all aspects requested in assignment description. Inappropriate level of detail (either too much detail or too general). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.
	\| '''__/3'''		\| '''__/3'''
	\|-		\|-
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	! '''Discussion'''		! '''Discussion'''
-	\| '''2-2.5 pts.''' Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise	+	\| '''2-2.5 pts.''' All requested elements are included. Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise
-	\| '''0-1.5 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among findings missing or incorrectly applied. Conclusions incorrectly drawn, and/or not related to question. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	+	\| '''0-1.5 pts.''' Not all requested elements are included. Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among findings missing or incorrectly applied. Conclusions incorrectly drawn, and/or not related to question. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.
	\| '''__/2.5'''		\| '''__/2.5'''
	\|-		\|-

Tucker Crum: /* Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points */

2012-11-18T17:08:43Z

Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points

←Older revision		Revision as of 17:08, 18 November 2012
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	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.

-	==~~Answering~~ Each Question on the Reverse Genetics Project- 10 points each for total of 50 points==	+	==Rubric for Each Question on the Reverse Genetics Project- 10 points each for total of 50 points==
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Tucker Crum: /* Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points */

2012-11-18T17:08:02Z

Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points

←Older revision		Revision as of 17:08, 18 November 2012
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	! '''Figures/Tables'''		! '''Figures/Tables'''
-	\| '''~~3-4~~ pts.''' Figures/Tables are designed effectively to allow a general audience to visualize the most important findings and make the main message ease to grasp. Figure/Table titles include the main conclusion to be made from the data included. Figure/Table #, title and legend is formatted correctly.	+	\| '''2 pts.''' Figures/Tables are designed effectively to allow a general audience to visualize the most important findings and make the main message ease to grasp. Figure/Table titles include the main conclusion to be made from the data included. Figure/Table #, title and legend is formatted correctly.
-	\| '''0-3.5 pts.''' Figures/Tables are poorly designed or don't include appropriate findings processed to be visualized effectively: it is difficult for a general audience to grasp the main message. Figure/Table titles are missing, too general or fail to include the main conclusion to be made from the data or findings shown. Figure/Table #, title and legend formatted incorrectly.	+	\| '''0-1.5 pts.''' Figures/Tables are poorly designed or don't include appropriate findings processed to be visualized effectively: it is difficult for a general audience to grasp the main message. Figure/Table titles are missing, too general or fail to include the main conclusion to be made from the data or findings shown. Figure/Table #, title and legend formatted incorrectly.
-	\| '''_/4'''	+	\| '''_/2'''
	\|-		\|-
	! Data Analysis		! Data Analysis
-	\| '''~~7-8~~ pts.''' Identifies question addressed; includes a brief description of the experimental design related to the question; Uses appropriate experimental evidence and explains it effectively to a general audience. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge	+	\| '''3 pts.''' Identifies question addressed; includes a brief description of the experimental design related to the question; Uses appropriate experimental evidence and explains it effectively to a general audience. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge
-	\| '''0-6.5 pts.''' Missing question addressed, experimental design, appropriate experimental evidence or an inadequate explanation of the evidence. Inappropriate level of detail (either too much detail or too general). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.	+	\| '''0-2.5 pts.''' Missing question addressed, experimental design, appropriate experimental evidence or an inadequate explanation of the evidence. Inappropriate level of detail (either too much detail or too general). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.
-	\| '''__/8'''	+	\| '''__/3'''
	\|-		\|-
	! '''Conclusions'''		! '''Conclusions'''
-	\| '''3.5-5 pt.''' Appropriate conclusions come logically from investigation's findings.	+	\| '''0.5-1 pt.''' Appropriate conclusions come logically from investigation's findings.
-	\| '''0-3 pts.''' Unsupported conclusions or inappropriate conclusions	+	\| '''0 pts.''' Unsupported conclusions or inappropriate conclusions
-	\| '''__/5'''	+	\| '''__/1'''
	\|-		\|-
	! '''Discussion'''		! '''Discussion'''
-	\| '''12.5~~-15~~ pts.''' Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise	+	\| '''2-2.5 pts.''' Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise
-	\| '''0-12 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among findings missing or incorrectly applied. Conclusions incorrectly drawn, and/or not related to question. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	+	\| '''0-1.5 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among findings missing or incorrectly applied. Conclusions incorrectly drawn, and/or not related to question. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.
-	\| '''__/15'''	+	\| '''__/2.5'''
	\|-		\|-
	! '''Outside Sources'''		! '''Outside Sources'''
-	\| '''2 pt.''' Includes complete, properly formatted citation for each work cited in body of report. Cites all material used that is not commons knowledge. Uses an adequate number of reliable, appropriate sources including primary studies published in peer-reviewed journals.	+	\| '''0.5 pt.''' Includes complete, properly formatted citation for each work cited in body of report. Cites all material used that is not commons knowledge. Uses an adequate number of reliable, appropriate sources including primary studies published in peer-reviewed journals.
-	\| '''0-1 pts.''' Does not include complete, properly formatted citations for all references, lists works not cited in report, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources, or fails to use an adequate number of primary studies from peer reviewed journals.	+	\| '''0 pts.''' Does not include complete, properly formatted citations for all references, lists works not cited in report, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources, or fails to use an adequate number of primary studies from peer reviewed journals.
-	\| '''__/2'''	+	\| '''__/0.5'''
	\|-		\|-
	! '''Total'''		! '''Total'''
	\|		\|
	\|		\|
-	\| __/50	+	\| __/10
	\|-		\|-
	\|}		\|}

Tucker Crum: /* Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points */

2012-11-18T17:05:16Z

Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points

←Older revision		Revision as of 17:05, 18 November 2012
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	\| '''_/4'''		\| '''_/4'''
	\|-		\|-
-	! ~~Introduction~~	+	! Data Analysis
-	\| '''7-8 pts.''' Identifies ~~topic & central experimental questions~~; includes ~~appropriate background information; uses~~ a ~~level~~ of ~~detail~~ appropriate ~~for novice~~ audience. ~~Includes a brief outline of methods.~~ Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge	+	\| '''7-8 pts.''' Identifies question addressed; includes a brief description of the experimental design related to the question; Uses appropriate experimental evidence and explains it effectively to a general audience. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Source citations in proper format (''Genetics'' style) are included for all information not common knowledge
-	\| '''0-6.5 pts.''' ~~Does not correctly topic or identify~~ experimental ~~questions. Missing~~ appropriate ~~background information,~~ an ~~outline~~ of ~~methods, or reference citations for information not common knowledge~~. Inappropriate level of detail (either too much or ~~missing information needed for target audience~~). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.	+	\| '''0-6.5 pts.''' Missing question addressed, experimental design, appropriate experimental evidence or an inadequate explanation of the evidence. Inappropriate level of detail (either too much detail or too general). Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.
	\| '''__/8'''		\| '''__/8'''
	\|-		\|-
-	! '''~~Materials<br> & Methods~~'''	+	! '''Conclusions'''
-	\| '''3.5-5 pt.''' ~~Procedures are accurately, clearly & succinctly described~~.	+	\| '''3.5-5 pt.''' Appropriate conclusions come logically from investigation's findings.
-	\| '''0-3 pts.''' ~~Procedures incorrectly~~ or ~~unclearly described or omitted; uses too much detail.~~	+	\| '''0-3 pts.''' Unsupported conclusions or inappropriate conclusions
	\| '''__/5'''		\| '''__/5'''
-	\|-
-	~~! '''Results'''~~
-	\| '''12.5-15 pts.''' Uses figures and tables formatted for maximum clarity and ease of interpretation. All figures & tables are numbered & have correctly formatted legends with appropriate information; all data is labeled. The text portion describes accurately, clearly, and succinctly the major findings & analyzes the data appropriately to show reader how conclusions are drawn.
-	\| '''0-12 pts.''' Not all key figures and/or tables included. Figures &/or tables are difficult to read or to interpret due to missing information and/or poor design. The text portion omits key findings, describes the data inaccurately or unclearly, includes irrelevant information, or is repetitive.
-	~~\| '''__/15'''~~
	\|-		\|-
	! '''Discussion'''		! '''Discussion'''
-	\| '''12.5-15 pts.''' ~~Discussion focuses on experimental data & refers to it directly by fig. or table number. Major findings from results are referenced appropriately.~~ Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings~~, background information~~ & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise	+	\| '''12.5-15 pts.''' Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise
-	\| '''0-12 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among ~~experimental~~ findings missing or incorrectly applied~~. Relationship between experimental findings, background information & relevant research missing or incorrectly interpreted~~. Conclusions incorrectly drawn, and/or not related to ~~larger significance~~. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	+	\| '''0-12 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among findings missing or incorrectly applied. Conclusions incorrectly drawn, and/or not related to question. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.
	\| '''__/15'''		\| '''__/15'''
	\|-		\|-
-	! '''~~References~~'''	+	! '''Outside Sources'''
	\| '''2 pt.''' Includes complete, properly formatted citation for each work cited in body of report. Cites all material used that is not commons knowledge. Uses an adequate number of reliable, appropriate sources including primary studies published in peer-reviewed journals.		\| '''2 pt.''' Includes complete, properly formatted citation for each work cited in body of report. Cites all material used that is not commons knowledge. Uses an adequate number of reliable, appropriate sources including primary studies published in peer-reviewed journals.
	\| '''0-1 pts.''' Does not include complete, properly formatted citations for all references, lists works not cited in report, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources, or fails to use an adequate number of primary studies from peer reviewed journals.		\| '''0-1 pts.''' Does not include complete, properly formatted citations for all references, lists works not cited in report, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources, or fails to use an adequate number of primary studies from peer reviewed journals.

Tucker Crum: /* Writing a Full Scientific Paper on Reverse Genetics Project 50 points */

2012-11-18T16:46:34Z

Writing a Full Scientific Paper on Reverse Genetics Project 50 points

←Older revision		Revision as of 16:46, 18 November 2012
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	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.

-	==~~Writing a Full Scientific Paper~~ on Reverse Genetics Project 50 points==	+	==Answering Each Question on the Reverse Genetics Project- 10 points each for total of 50 points==
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	Earned'''		Earned'''
	\|-		\|-
-	! '''~~Title~~'''	+	! '''Structure'''
-	\| '''1 pt.''' ~~Gives accurate & appropriate content~~ information to ~~reader, stressing answer to experimental questions over tools or techniques. Lists your lab partner(s) as second author(s)~~.	+	\| '''1 pt.''' Structure of the narrative presents information in a logical sequence. Refers to figures/tables by number in the narrative & inserts figures/tables into narrative appropriately.
-	\| '''0-0.5 pts.''' Did not ~~give enough content~~ information, or ~~too much, or inaccurate information.~~	+	\| '''0-0.5 pts.''' Did not impart information in a logical sequence.Did not reference figures/tables or insert them appropriately into the narrative
	Does not include authorship.		Does not include authorship.
	\| '''__/1'''		\| '''__/1'''
	\|-		\|-
-	! '''~~Abstract~~'''	+	! '''Figures/Tables'''
-	\| '''3-4 pts.''' ~~Concisely summarizes in appropriate format: topic, experimental questions,~~ general ~~methods, major~~ findings ~~(strongest evidence leading~~ to ~~conclusions)~~, ~~conclusions & implications of study~~.	+	\| '''3-4 pts.''' Figures/Tables are designed effectively to allow a general audience to visualize the most important findings and make the main message ease to grasp. Figure/Table titles include the main conclusion to be made from the data included. Figure/Table #, title and legend is formatted correctly.
-	\| '''0-3.5 pts.''' ~~Omits key information; includes tangential information; misinterprets information and~~/or ~~implications; uses incorrect format~~.	+	\| '''0-3.5 pts.''' Figures/Tables are poorly designed or don't include appropriate findings processed to be visualized effectively: it is difficult for a general audience to grasp the main message. Figure/Table titles are missing, too general or fail to include the main conclusion to be made from the data or findings shown. Figure/Table #, title and legend formatted incorrectly.
	\| '''_/4'''		\| '''_/4'''
	\|-		\|-

Tucker Crum: /* Final Assignment on the Reverse Genetics Project using RNAi 50pts */

2012-11-18T16:34:58Z

Final Assignment on the Reverse Genetics Project using RNAi 50pts

←Older revision		Revision as of 16:34, 18 November 2012
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-	1)'''Did we successfully silence or knockdown expression of ''lsy-2'' using RNAi?''' <BR>	+	1) '''Did we successfully silence or knockdown expression of ''lsy-2'' using RNAi?''' <BR>
	Use all the course data in total. Optionally, you could compare the compiled data to subsets (different lab sections or individual experiments) to see if there is consistency in experiments and between different IPTG inductions (lab days). If your conclusion is that we did not successfully downregulate or silence ''lsy-2'' or that you aren’t sure, please include a discussion of why RNAi, a highly touted tool for silencing gene expression, didn’t work in this context (using outside sources). Propose other specific experiments to resolve ambiguities, such as whether or not we are sure that our “treated” nematodes ingested ''lsy-2'' dsRNAi. This question’s answer will require a combination of Results and Discussion with a Literature Cited section in ''Genetics'' journal format.		Use all the course data in total. Optionally, you could compare the compiled data to subsets (different lab sections or individual experiments) to see if there is consistency in experiments and between different IPTG inductions (lab days). If your conclusion is that we did not successfully downregulate or silence ''lsy-2'' or that you aren’t sure, please include a discussion of why RNAi, a highly touted tool for silencing gene expression, didn’t work in this context (using outside sources). Propose other specific experiments to resolve ambiguities, such as whether or not we are sure that our “treated” nematodes ingested ''lsy-2'' dsRNAi. This question’s answer will require a combination of Results and Discussion with a Literature Cited section in ''Genetics'' journal format.

-	2)'''Is the ''C. elegans rrf-3'' mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the ''N2'' wild type strain?'''<BR>	+	2) '''Is the ''C. elegans rrf-3'' mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the ''N2'' wild type strain?'''<BR>
	Use the data from our experiments to answer this question, if possible, in terms of the ''lsy-2 gene'' and then use outside studies to either support or to call our study’s findings and conclusion into question considering the evidence to date on other ''C elegans genes'' or types of genes. Include an explanation of the proposed mechanism for RNAi enhancement in the ''rrf-3'' mutant strain. This question should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).		Use the data from our experiments to answer this question, if possible, in terms of the ''lsy-2 gene'' and then use outside studies to either support or to call our study’s findings and conclusion into question considering the evidence to date on other ''C elegans genes'' or types of genes. Include an explanation of the proposed mechanism for RNAi enhancement in the ''rrf-3'' mutant strain. This question should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).

-	3)'''Is ''lsy-2'' expression critical for proper asymmetric development of the left and right gustatory neurons (ASEL and ASER)?'''<BR>	+	3) '''Is ''lsy-2'' expression critical for proper asymmetric development of the left and right gustatory neurons (ASEL and ASER)?'''<BR>
	Use the data from our experiments to answer this question, if possible, and then use outside studies to either support your findings and conclusion or to call into question our study’s findings and your conclusion from these findings. Question#3 should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).		Use the data from our experiments to answer this question, if possible, and then use outside studies to either support your findings and conclusion or to call into question our study’s findings and your conclusion from these findings. Question#3 should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).

-	4)'''What is RNAi and how does in work in ''C. elegans''?'''<BR>	+	4) '''What is RNAi and how does in work in ''C. elegans''?'''<BR>
	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You need not reference your own study or your data. There must be a self-designed figure, which should be in the form of a schematic illustration of the sequence of steps from initiation to destruction of normal gene transcripts of a model gene. Grishok (2005) published a review paper that you can find in the Journal Articles folder in Sakai to look at an example of such a schematic, but keep in mind that this Grishok’s illustration is not up to date. We have learned a lot since 2005 and your figure must include what we think we know about how RNAi works in ''C. elegans'' in 2012.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You need not reference your own study or your data. There must be a self-designed figure, which should be in the form of a schematic illustration of the sequence of steps from initiation to destruction of normal gene transcripts of a model gene. Grishok (2005) published a review paper that you can find in the Journal Articles folder in Sakai to look at an example of such a schematic, but keep in mind that this Grishok’s illustration is not up to date. We have learned a lot since 2005 and your figure must include what we think we know about how RNAi works in ''C. elegans'' in 2012.

-	5)'''What are zinc finger transcription factors and how do they regulate gene expression?'''<BR>	+	5) '''What are zinc finger transcription factors and how do they regulate gene expression?'''<BR>
	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.

Tucker Crum: /* Final Assignment on the Reverse Genetics Project using RNAi 50pts */

2012-11-18T16:34:22Z

Final Assignment on the Reverse Genetics Project using RNAi 50pts

←Older revision		Revision as of 16:34, 18 November 2012
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	Please use the course data we have obtained from our reverse genetics investigation of the ''C. elegans'' ''lsy-2'' gene and outside sources to answer these questions fully! Include both a narrative AND at least one effective figure/table with a proper legend (10 points each). Remember that the proper conclusions can be more nuanced than yes or no. “It is unclear” or “it appears _____, but _____” may be the best answer to one or more of these questions using our experiments and our study’s data. For questions 1-3, begin with the structure you have learned for organizing a results narrative: in order to find out________(goal in this case is the question posed), we ______(brief explanation of the part of the experimental design that relates to the data you will use to answer that question). We found____________(specific findings or subsets of data comparisons that address this question), which indicates _________(conclusion that answers that question-- hedged as much as the conclusion needs to be from the evidence presented), because________ (analysis of the data to help reader understand how your data leads you to arrive at that conclusion). The rest of your answer to questions 1-3 should be in discussion format. You will put your findings together with related outside study methods and findings to bring your conclusions into context with the current state of understanding on these questions within the ''C. elegans'' genetics community. Questions 4 &5 will be answered in research review format (do not mention your study) using exclusively outside sources (include the most current available).		Please use the course data we have obtained from our reverse genetics investigation of the ''C. elegans'' ''lsy-2'' gene and outside sources to answer these questions fully! Include both a narrative AND at least one effective figure/table with a proper legend (10 points each). Remember that the proper conclusions can be more nuanced than yes or no. “It is unclear” or “it appears _____, but _____” may be the best answer to one or more of these questions using our experiments and our study’s data. For questions 1-3, begin with the structure you have learned for organizing a results narrative: in order to find out________(goal in this case is the question posed), we ______(brief explanation of the part of the experimental design that relates to the data you will use to answer that question). We found____________(specific findings or subsets of data comparisons that address this question), which indicates _________(conclusion that answers that question-- hedged as much as the conclusion needs to be from the evidence presented), because________ (analysis of the data to help reader understand how your data leads you to arrive at that conclusion). The rest of your answer to questions 1-3 should be in discussion format. You will put your findings together with related outside study methods and findings to bring your conclusions into context with the current state of understanding on these questions within the ''C. elegans'' genetics community. Questions 4 &5 will be answered in research review format (do not mention your study) using exclusively outside sources (include the most current available).

-	1) '''Did we successfully silence or knockdown expression of ''lsy-2'' using RNAi?'''	+
		+	1)'''Did we successfully silence or knockdown expression of ''lsy-2'' using RNAi?''' <BR>
	Use all the course data in total. Optionally, you could compare the compiled data to subsets (different lab sections or individual experiments) to see if there is consistency in experiments and between different IPTG inductions (lab days). If your conclusion is that we did not successfully downregulate or silence ''lsy-2'' or that you aren’t sure, please include a discussion of why RNAi, a highly touted tool for silencing gene expression, didn’t work in this context (using outside sources). Propose other specific experiments to resolve ambiguities, such as whether or not we are sure that our “treated” nematodes ingested ''lsy-2'' dsRNAi. This question’s answer will require a combination of Results and Discussion with a Literature Cited section in ''Genetics'' journal format.		Use all the course data in total. Optionally, you could compare the compiled data to subsets (different lab sections or individual experiments) to see if there is consistency in experiments and between different IPTG inductions (lab days). If your conclusion is that we did not successfully downregulate or silence ''lsy-2'' or that you aren’t sure, please include a discussion of why RNAi, a highly touted tool for silencing gene expression, didn’t work in this context (using outside sources). Propose other specific experiments to resolve ambiguities, such as whether or not we are sure that our “treated” nematodes ingested ''lsy-2'' dsRNAi. This question’s answer will require a combination of Results and Discussion with a Literature Cited section in ''Genetics'' journal format.

-	2) '''Is the ''C. elegans rrf-3'' mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the ''N2'' wild type strain?'''	+	2)'''Is the ''C. elegans rrf-3'' mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the ''N2'' wild type strain?'''<BR>
	Use the data from our experiments to answer this question, if possible, in terms of the ''lsy-2 gene'' and then use outside studies to either support or to call our study’s findings and conclusion into question considering the evidence to date on other ''C elegans genes'' or types of genes. Include an explanation of the proposed mechanism for RNAi enhancement in the ''rrf-3'' mutant strain. This question should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).		Use the data from our experiments to answer this question, if possible, in terms of the ''lsy-2 gene'' and then use outside studies to either support or to call our study’s findings and conclusion into question considering the evidence to date on other ''C elegans genes'' or types of genes. Include an explanation of the proposed mechanism for RNAi enhancement in the ''rrf-3'' mutant strain. This question should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).

-	3) Is ''lsy-2'' expression critical for proper asymmetric development of the left and right gustatory neurons (ASEL and ASER)?	+	3)'''Is ''lsy-2'' expression critical for proper asymmetric development of the left and right gustatory neurons (ASEL and ASER)?'''<BR>
	Use the data from our experiments to answer this question, if possible, and then use outside studies to either support your findings and conclusion or to call into question our study’s findings and your conclusion from these findings. Question#3 should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).		Use the data from our experiments to answer this question, if possible, and then use outside studies to either support your findings and conclusion or to call into question our study’s findings and your conclusion from these findings. Question#3 should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).

-	4) What is RNAi and how does in work in ''C. elegans''?	+	4)'''What is RNAi and how does in work in ''C. elegans''?'''<BR>
	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You need not reference your own study or your data. There must be a self-designed figure, which should be in the form of a schematic illustration of the sequence of steps from initiation to destruction of normal gene transcripts of a model gene. Grishok (2005) published a review paper that you can find in the Journal Articles folder in Sakai to look at an example of such a schematic, but keep in mind that this Grishok’s illustration is not up to date. We have learned a lot since 2005 and your figure must include what we think we know about how RNAi works in ''C. elegans'' in 2012.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You need not reference your own study or your data. There must be a self-designed figure, which should be in the form of a schematic illustration of the sequence of steps from initiation to destruction of normal gene transcripts of a model gene. Grishok (2005) published a review paper that you can find in the Journal Articles folder in Sakai to look at an example of such a schematic, but keep in mind that this Grishok’s illustration is not up to date. We have learned a lot since 2005 and your figure must include what we think we know about how RNAi works in ''C. elegans'' in 2012.

-	5) What are zinc finger transcription factors and how do they regulate gene expression?	+	5)'''What are zinc finger transcription factors and how do they regulate gene expression?'''<BR>
	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.		This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.

Tucker Crum: /* Scientific Research Report on Reverse Genetics Project using RNAi 50pts */

2012-11-18T16:32:31Z

Scientific Research Report on Reverse Genetics Project using RNAi 50pts

←Older revision		Revision as of 16:32, 18 November 2012
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	<div style="padding: 10px; width: 720px; border: 5px solid #2171B7;">		<div style="padding: 10px; width: 720px; border: 5px solid #2171B7;">

-	==~~Scientific Research Report~~ on Reverse Genetics Project using RNAi 50pts==	+	==Final Assignment on the Reverse Genetics Project using RNAi 50pts==
-	~~Write~~ a ~~full scientific research report~~ on your ~~Reverse Genetics Project~~. Use ~~other genetics studies published~~ in ~~high impact factor journals~~ such as ''Genetics'' or ''~~Cell~~'' as ~~models~~ for ~~how~~ to ~~structure~~ your ~~paper~~. ~~Use the journal~~ ''~~Genetics~~'' ~~for~~ reference ~~format~~. ~~Refer to~~ the ~~[[BISC219/F12:Resources]] section~~ of ~~this wiki~~ to ~~download~~ a ~~copy~~ of ~~"Guide~~ to ~~Scientific Writing~~ in ~~BISC219"~~. ~~There~~ are ~~appropriate~~ reference ~~articles available~~ in the ~~References section~~ of ~~your lab Sakai site~~.	+	'''Final Assignment Series 3 Reverse Genetics F12'''<BR>
		+	Please use the course data we have obtained from our reverse genetics investigation of the ''C. elegans'' ''lsy-2'' gene and outside sources to answer these questions fully! Include both a narrative AND at least one effective figure/table with a proper legend (10 points each). Remember that the proper conclusions can be more nuanced than yes or no. “It is unclear” or “it appears _____, but _____” may be the best answer to one or more of these questions using our experiments and our study’s data. For questions 1-3, begin with the structure you have learned for organizing a results narrative: in order to find out________(goal in this case is the question posed), we ______(brief explanation of the part of the experimental design that relates to the data you will use to answer that question). We found____________(specific findings or subsets of data comparisons that address this question), which indicates _________(conclusion that answers that question-- hedged as much as the conclusion needs to be from the evidence presented), because________ (analysis of the data to help reader understand how your data leads you to arrive at that conclusion). The rest of your answer to questions 1-3 should be in discussion format. You will put your findings together with related outside study methods and findings to bring your conclusions into context with the current state of understanding on these questions within the ''C. elegans'' genetics community. Questions 4 &5 will be answered in research review format (do not mention your study) using exclusively outside sources (include the most current available).
		+
		+	1) '''Did we successfully silence or knockdown expression of ''lsy-2'' using RNAi?'''
		+	Use all the course data in total. Optionally, you could compare the compiled data to subsets (different lab sections or individual experiments) to see if there is consistency in experiments and between different IPTG inductions (lab days). If your conclusion is that we did not successfully downregulate or silence ''lsy-2'' or that you aren’t sure, please include a discussion of why RNAi, a highly touted tool for silencing gene expression, didn’t work in this context (using outside sources). Propose other specific experiments to resolve ambiguities, such as whether or not we are sure that our “treated” nematodes ingested ''lsy-2'' dsRNAi. This question’s answer will require a combination of Results and Discussion with a Literature Cited section in ''Genetics'' journal format.
		+
		+	2) '''Is the ''C. elegans rrf-3'' mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the ''N2'' wild type strain?'''
		+	Use the data from our experiments to answer this question, if possible, in terms of the ''lsy-2 gene'' and then use outside studies to either support or to call our study’s findings and conclusion into question considering the evidence to date on other ''C elegans genes'' or types of genes. Include an explanation of the proposed mechanism for RNAi enhancement in the ''rrf-3'' mutant strain. This question should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).
		+
		+	3) Is ''lsy-2'' expression critical for proper asymmetric development of the left and right gustatory neurons (ASEL and ASER)?
		+	Use the data from our experiments to answer this question, if possible, and then use outside studies to either support your findings and conclusion or to call into question our study’s findings and your conclusion from these findings. Question#3 should be answered as a combination Results and Discussion with a separate Literature Cited section (not combined with earlier questions).
		+
		+	4) What is RNAi and how does in work in ''C. elegans''?
		+	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You need not reference your own study or your data. There must be a self-designed figure, which should be in the form of a schematic illustration of the sequence of steps from initiation to destruction of normal gene transcripts of a model gene. Grishok (2005) published a review paper that you can find in the Journal Articles folder in Sakai to look at an example of such a schematic, but keep in mind that this Grishok’s illustration is not up to date. We have learned a lot since 2005 and your figure must include what we think we know about how RNAi works in ''C. elegans'' in 2012.
		+
		+	5) What are zinc finger transcription factors and how do they regulate gene expression?
		+	This question requires a discussion/ research review type answer. Use outside sources and cite them properly. Include a separate Literature Cited page. You should not reference your own study or your data. Describe at least one example (other than the ''lsy-2'' gene product) of positive regulation and one of negative regulation. There must be a self-designed figure, which should be in the form of a schematic illustration, showing a positive regulatory pathway and a negative regulatory pathway that relies on this type of transcription factor.

	==Writing a Full Scientific Paper on Reverse Genetics Project 50 points==		==Writing a Full Scientific Paper on Reverse Genetics Project 50 points==

Tucker Crum: /* Writing a Full Scientific Paper on Reverse Genetics Project 50 points */

2012-10-26T12:57:53Z

Writing a Full Scientific Paper on Reverse Genetics Project 50 points

←Older revision		Revision as of 12:57, 26 October 2012
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	! '''Discussion'''		! '''Discussion'''
	\| '''12.5-15 pts.''' Discussion focuses on experimental data & refers to it directly by fig. or table number. Major findings from results are referenced appropriately. Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings, background information & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise		\| '''12.5-15 pts.''' Discussion focuses on experimental data & refers to it directly by fig. or table number. Major findings from results are referenced appropriately. Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings, background information & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise
-	\| '''0-~~9.5~~ pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among experimental findings missing or incorrectly applied. Relationship between experimental findings, background information & relevant research missing or incorrectly interpreted. Conclusions incorrectly drawn, and/or not related to larger significance. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	+	\| '''0-12 pts.''' Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among experimental findings missing or incorrectly applied. Relationship between experimental findings, background information & relevant research missing or incorrectly interpreted. Conclusions incorrectly drawn, and/or not related to larger significance. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.
	\| '''__/15'''		\| '''__/15'''
	\|-		\|-

Tucker Crum: /* Writing a Full Scientific Paper on Reverse Genetics Project 50 points */

2012-10-26T12:56:36Z

Writing a Full Scientific Paper on Reverse Genetics Project 50 points

←Older revision		Revision as of 12:56, 26 October 2012
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	\|-		\|-
	! '''Abstract'''		! '''Abstract'''
-	\| '''3.5-5 pts.''' Concisely summarizes in appropriate format: topic, experimental questions, general methods, major findings (strongest evidence leading to conclusions), conclusions & implications of study.	+	\| '''3-4 pts.''' Concisely summarizes in appropriate format: topic, experimental questions, general methods, major findings (strongest evidence leading to conclusions), conclusions & implications of study.
-	\| '''0-3 pts.''' Omits key information; includes tangential information; misinterprets information and/or implications; uses incorrect format.	+	\| '''0-3.5 pts.''' Omits key information; includes tangential information; misinterprets information and/or implications; uses incorrect format.
-	\| '''_/5'''	+	\| '''_/4'''
	\|-		\|-
	! Introduction		! Introduction
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	\|-		\|-
	! '''Materials<br> & Methods'''		! '''Materials<br> & Methods'''
-	\| '''2.5-4 pt.''' Procedures are accurately, clearly & succinctly described.	+	\| '''3.5-5 pt.''' Procedures are accurately, clearly & succinctly described.
-	\| '''0-2 pts.''' Procedures incorrectly or unclearly described or omitted; uses too much detail.	+	\| '''0-3 pts.''' Procedures incorrectly or unclearly described or omitted; uses too much detail.
-	\| '''__/4'''	+	\| '''__/5'''
	\|-		\|-
	! '''Results'''		! '''Results'''