Difference between revisions of "20.109(S16): Protein engineering summary"
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===Revision submission: <font color = red>March 28th</font color>=== | ===Revision submission: <font color = red>March 28th</font color>=== | ||
| − | Your | + | Your Protein engineering summary revision is '''due by 5 pm''' on <font color = red> Monday, March 28th</font color>. |
| − | You will then have the opportunity to revise your report for up to a one and one-third letter grade improvement. In other words, a C can be revised up to a B+, a C+ to an A-, a B- to an A, etc | + | You will then have the opportunity to revise your report for up to a one and one-third letter grade improvement. In other words, a C can be revised up to a B+, a C+ to an A-, a B- to an A, etc. |
'''For your final report, all changes need to be in a different colored font so the improvements you made are clear'''. You should also include a cover letter with your final draft that explains how you addressed the concerns raised (e.g. "paragraph x was completely rewritten to better explain….” or “Results for the agarose gel analysis were clarified by …."). You will receive additional comments and your final grade on the assignment by Tuesday, April 12th. | '''For your final report, all changes need to be in a different colored font so the improvements you made are clear'''. You should also include a cover letter with your final draft that explains how you addressed the concerns raised (e.g. "paragraph x was completely rewritten to better explain….” or “Results for the agarose gel analysis were clarified by …."). You will receive additional comments and your final grade on the assignment by Tuesday, April 12th. | ||
| Line 43: | Line 43: | ||
*'''Second page: Abstract''' | *'''Second page: Abstract''' | ||
*'''Body''': 8-12 pages (not including Title and Abstract pages). Recommended section lengths (including both text and figures): | *'''Body''': 8-12 pages (not including Title and Abstract pages). Recommended section lengths (including both text and figures): | ||
| − | **'''Background''': 2 slides | + | **'''Background and Motivation''': 2 slides |
| − | ***Contents of Background: The majority of this section will be bulleted text. Include schematic figures when appropriate. | + | ***Contents of Background and Motivation: The majority of this section will be bulleted text. Include schematic figures when appropriate. |
**'''Results and Interpretation''': 5-8 slides | **'''Results and Interpretation''': 5-8 slides | ||
| − | ***Contents of a Results | + | ***Contents of a Results and Interpretation slide: Top half: figure(s) with caption(s). Bottom half: bullet points that present and interpret the data. (Remember that captions should not contain interpretation.) |
***Figure presentation: In published research figures are rarely a full page in size; rather each plot is usually only 3 inches x 3 inches. | ***Figure presentation: In published research figures are rarely a full page in size; rather each plot is usually only 3 inches x 3 inches. | ||
***Present you Results and Interpretation such that the figure, caption, and interpretation bullet points '''all fit on a single slide'''. Remember that when you shrink a figure, you must make sure it remains legible. | ***Present you Results and Interpretation such that the figure, caption, and interpretation bullet points '''all fit on a single slide'''. Remember that when you shrink a figure, you must make sure it remains legible. | ||
| − | **'''Implications | + | **'''Implications and Future Work''': 1-2 slides |
***Contents of Implications and Future Work: This section will be bulleted text. | ***Contents of Implications and Future Work: This section will be bulleted text. | ||
| Line 57: | Line 57: | ||
A few prompts to get you started are below, but note that this list is not exhaustive and also that several elements could reasonably be included in more than one section. In addition, this is not a checklist of what should be in your summary. Think about which elements are most appropriate in answering your research question. | A few prompts to get you started are below, but note that this list is not exhaustive and also that several elements could reasonably be included in more than one section. In addition, this is not a checklist of what should be in your summary. Think about which elements are most appropriate in answering your research question. | ||
| − | === | + | ===Title and Abstract=== |
| − | + | Please review the Title and Abstract [[Media:20.109 Workshop 2 - Abstract draft worksheet.docx| worksheet]] and [[Media:Abstract and Title rubric.xlsx| rubric]] from the BE Communications Lab workshop. | |
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| − | === | + | ===Background and Motivation: potential topics and figures=== |
| + | *''Topic'': Introduce and discuss the importance of calcium signaling. | ||
| + | *''Topic'': Describe the mechanism by which IPC measures calcium concentration. | ||
| + | *'''Figure''': IPC conformation with and without bound calcium ions. | ||
| + | *''Topic'': What is your experimental question? How will you answer this question? | ||
| + | *'''Schematic''': Experimental approach. | ||
| + | **You may prepare something similar to the schematic from the lecture notes, but should NOT copy and insert it directly. Be sure your figure is tailored specifically to this assignment and audience. What steps can be cut or added? How can you highlight the key steps? | ||
| + | *''Topic'': Why is it useful to generate new calcium sensors? | ||
| − | + | ===Results and Interpretation: potential topics and figures=== | |
| − | + | Figures and topics are listed below according to the two major phases of your experiment. Within each phase, you should look for sub-groupings of interest, rather than treat each piece of data in isolation. In other words, try to both interpret and communicate outcomes holistically. | |
| − | + | Keep in mind that you described the detailed methods in a separate homework assignment and it does not need to be included in this report. Therefore, figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the names of the diagnostic enzymes, experimental techniques, or assays. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
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| − | ==== | + | ====System construction: generating and verifying mutant IPC gene==== |
| + | *''Topic'': Confirmation of pRSET-IPC template. | ||
| + | *'''Figure''': Gel electrophoresis of confirmation digests. | ||
| + | *''Topic'': Describe your mutagenesis strategy. | ||
| + | **Include your logic for selecting which residue to mutate. | ||
| + | *'''Schematic''': Residue within WT IPC that was mutated. | ||
| + | *''Topic'': Apparent success of SDM in altering IPC sequence. | ||
| + | *'''Figure''': Sequencing results of SDM product. | ||
| + | *''Topic'': Apparent success of protein induction and purification. | ||
| + | **Be sure to discuss the controls when interpreting the data. | ||
| + | *'''Figure''': Polyacrylamide gel of induced cell samples and purified protein. | ||
| + | *'''Figure''': MicroBCA assay values. | ||
| − | *'''Schematic''': | + | ====Titration assay==== |
| − | ** | + | *'''Schematic''': Experimental approach. |
| − | *''Topic'': | + | **Do not include minor details that are not necessary to understand the experiment (e.g. an image of the plate map). |
| − | *'' | + | *''Topic'': Affinity and cooperativity of your IPC mutant. |
| − | *'' | + | *'''Figure''': Plots showing WT and mutant IPC titration curves. |
| − | ** | + | *''Topic'': Differences in data using each MATLAB analysis method. |
| − | *'''Figure''': | + | **Be sure to give an explanation for any differences by including details on how the data were generated by MATLAB. |
| − | *'' | + | *'''Figure''': Table with affinity and cooperativity values generated by each MATLAB analysis method. |
| − | ** | + | *''Topic'': Assess affinity and cooperativity of 2-3 mutant IPCs. |
| − | * | + | **Do not randomly choose mutations for this comparison. Think about how to construct a cohesive story by supplementing your data with additional results from your classmates. A random collection of IPC mutants in your results section will not be scored highly. |
| − | *''Topic'': | + | *'''Figure''': Plots showing titration curves of relevant IPC proteins. |
| − | + | *''Topic'': What do the residual plots tell you about your data? | |
| − | * | + | *'''Figure''': Residual plots of relevant IPC proteins. |
| − | + | ||
| − | + | ||
| − | ===Implications and | + | ===Implications and Future Work: potential topics=== |
| − | *''Topic'': Based on the results, whether they matched your expectations or not, what experiments might you recommend next? Follow-up experiments could distinguish between competing explanations of a given outcome or broaden the sample set for a question you already asked, to give just two examples. | + | *''Topic'': Did your results match your expectations? |
| + | **If no, provide a putative explanation. If yes, how can you further test if your hypothesis is correct? | ||
| + | *''Topic'': Based on the results, whether they matched your expectations or not, what experiments might you recommend next? | ||
| + | **Follow-up experiments could distinguish between competing explanations of a given outcome or broaden the sample set for a question you already asked, to give just two examples. | ||
*''Topic'': How might this assay be improved? | *''Topic'': How might this assay be improved? | ||
| − | *''Topic'': How might this assay be used as a research tool? in the clinic? in | + | *''Topic'': How might this assay be used as a research tool? in the clinic? in industry? |
| − | + | ||
Latest revision as of 20:18, 29 February 2016
Contents
Overview
The culminating assignment for Module 1 will consist of two elements: an abstract that succinctly describes your protein engineering investigation, and a thorough summary of your data in figures and supporting text – including context for understanding the work’s broader implications.
The figure format is similar to that of a scientific journal article, but the traditional Results and Discussion sections found in journal articles are to be condensed into succinct bullet point form accompanying each figure. The purpose of this assignment is to prepare you to write a full journal article at the end of Module 2 by encouraging you to practice writing concisely using bullet points.
The target audience for this report is a scientifically literate reader who is unfamiliar with your specific field. Thus, you can assume rapid comprehension – but not a priori knowledge – of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.
Logistics
You will complete this assignment with your partner. Be sure to review the 20.109 statement on collaboration and integrity as you proceed.
Method of submission
Please submit your completed summary via email to Dr. Lyell (nllyell@mit.edu) with filename TeamColor_LabSection_Mod1.ppt (for example, Rainbow_TR_Mod1.ppt).
Be sure to review the class late policy (link) as well as the further clarification below.
Draft submission: March 12th
Your DNA engineering summary is due by 5 pm on Saturday, March 12th.
Dr. Lyell will comment on your submission and assign it a grade. The BE Communication Instructor, Dr. Chien, will provide feedback about abstract structure and comprehensibility -- she will also assign the grade for the Abstract portion of the assignment. You will receive all comments on Thursday, March 17th.
Revision submission: March 28th
Your Protein engineering summary revision is due by 5 pm on Monday, March 28th.
You will then have the opportunity to revise your report for up to a one and one-third letter grade improvement. In other words, a C can be revised up to a B+, a C+ to an A-, a B- to an A, etc.
For your final report, all changes need to be in a different colored font so the improvements you made are clear. You should also include a cover letter with your final draft that explains how you addressed the concerns raised (e.g. "paragraph x was completely rewritten to better explain….” or “Results for the agarose gel analysis were clarified by …."). You will receive additional comments and your final grade on the assignment by Tuesday, April 12th.
Guidelines on formatting and length
See example of appropriate format here. Create your report as a series of PowerPoint slides. This will allow you to create figures that are representative of those found in the literature (i.e. sized appropriately with sub-panels if necessary).
- Layout: Portrait, not landscape.
- Font: Arial 14pt for text; Arial 12pt for figure captions.
- Text should be written as bullet points, not full sentences and paragraphs.
- First page: Title and Author information (section/color/names)
- Second page: Abstract
- Body: 8-12 pages (not including Title and Abstract pages). Recommended section lengths (including both text and figures):
- Background and Motivation: 2 slides
- Contents of Background and Motivation: The majority of this section will be bulleted text. Include schematic figures when appropriate.
- Results and Interpretation: 5-8 slides
- Contents of a Results and Interpretation slide: Top half: figure(s) with caption(s). Bottom half: bullet points that present and interpret the data. (Remember that captions should not contain interpretation.)
- Figure presentation: In published research figures are rarely a full page in size; rather each plot is usually only 3 inches x 3 inches.
- Present you Results and Interpretation such that the figure, caption, and interpretation bullet points all fit on a single slide. Remember that when you shrink a figure, you must make sure it remains legible.
- Implications and Future Work: 1-2 slides
- Contents of Implications and Future Work: This section will be bulleted text.
- Background and Motivation: 2 slides
Content guidelines
Begin by reading the general guidelines for scientific writing. In particular, the sections on Title, Abstract, Figures, and Holistic View of Data are particularly applicable to this assignment.
A few prompts to get you started are below, but note that this list is not exhaustive and also that several elements could reasonably be included in more than one section. In addition, this is not a checklist of what should be in your summary. Think about which elements are most appropriate in answering your research question.
Title and Abstract
Please review the Title and Abstract worksheet and rubric from the BE Communications Lab workshop.
Background and Motivation: potential topics and figures
- Topic: Introduce and discuss the importance of calcium signaling.
- Topic: Describe the mechanism by which IPC measures calcium concentration.
- Figure: IPC conformation with and without bound calcium ions.
- Topic: What is your experimental question? How will you answer this question?
- Schematic: Experimental approach.
- You may prepare something similar to the schematic from the lecture notes, but should NOT copy and insert it directly. Be sure your figure is tailored specifically to this assignment and audience. What steps can be cut or added? How can you highlight the key steps?
- Topic: Why is it useful to generate new calcium sensors?
Results and Interpretation: potential topics and figures
Figures and topics are listed below according to the two major phases of your experiment. Within each phase, you should look for sub-groupings of interest, rather than treat each piece of data in isolation. In other words, try to both interpret and communicate outcomes holistically.
Keep in mind that you described the detailed methods in a separate homework assignment and it does not need to be included in this report. Therefore, figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the names of the diagnostic enzymes, experimental techniques, or assays.
System construction: generating and verifying mutant IPC gene
- Topic: Confirmation of pRSET-IPC template.
- Figure: Gel electrophoresis of confirmation digests.
- Topic: Describe your mutagenesis strategy.
- Include your logic for selecting which residue to mutate.
- Schematic: Residue within WT IPC that was mutated.
- Topic: Apparent success of SDM in altering IPC sequence.
- Figure: Sequencing results of SDM product.
- Topic: Apparent success of protein induction and purification.
- Be sure to discuss the controls when interpreting the data.
- Figure: Polyacrylamide gel of induced cell samples and purified protein.
- Figure: MicroBCA assay values.
Titration assay
- Schematic: Experimental approach.
- Do not include minor details that are not necessary to understand the experiment (e.g. an image of the plate map).
- Topic: Affinity and cooperativity of your IPC mutant.
- Figure: Plots showing WT and mutant IPC titration curves.
- Topic: Differences in data using each MATLAB analysis method.
- Be sure to give an explanation for any differences by including details on how the data were generated by MATLAB.
- Figure: Table with affinity and cooperativity values generated by each MATLAB analysis method.
- Topic: Assess affinity and cooperativity of 2-3 mutant IPCs.
- Do not randomly choose mutations for this comparison. Think about how to construct a cohesive story by supplementing your data with additional results from your classmates. A random collection of IPC mutants in your results section will not be scored highly.
- Figure: Plots showing titration curves of relevant IPC proteins.
- Topic: What do the residual plots tell you about your data?
- Figure: Residual plots of relevant IPC proteins.
Implications and Future Work: potential topics
- Topic: Did your results match your expectations?
- If no, provide a putative explanation. If yes, how can you further test if your hypothesis is correct?
- Topic: Based on the results, whether they matched your expectations or not, what experiments might you recommend next?
- Follow-up experiments could distinguish between competing explanations of a given outcome or broaden the sample set for a question you already asked, to give just two examples.
- Topic: How might this assay be improved?
- Topic: How might this assay be used as a research tool? in the clinic? in industry?
