BISC219/F12: Assignment Series3 Reverse Genetics Paper using RNAi

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Scientific Research Report on Reverse Genetics Project using RNAi 50pts)
(Final Assignment on the Reverse Genetics Project using RNAi 50pts)
Line 6: Line 6:
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.

Revision as of 11:34, 18 November 2012

Final Assignment on the Reverse Genetics Project using RNAi 50pts

Final Assignment Series 3 Reverse Genetics F12
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

Section At or Above Standard Below Standard Points

Earned

Title 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). 0-0.5 pts. Did not give enough content information, or too much, or inaccurate information.

Does not include authorship.

__/1
Abstract 3-4 pts. Concisely summarizes in appropriate format: topic, experimental questions, general methods, major findings (strongest evidence leading to conclusions), conclusions & implications of study. 0-3.5 pts. Omits key information; includes tangential information; misinterprets information and/or implications; uses incorrect format. _/4
Introduction 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 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. __/8
Materials
& Methods
3.5-5 pt. Procedures are accurately, clearly & succinctly described. 0-3 pts. Procedures incorrectly or unclearly described or omitted; uses too much detail. __/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 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 0-12 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
References 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. __/2
Total __/50



Personal tools