BISC209/F13: Assignment 209 BIOLOG: Difference between revisions

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=='''Grading Rubric'''==
''' Rubric Results & Discussion Community Metabolic Profiling
– 20 points'''
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{| border="1"
|+
!  !! At or Above Standard !! Below Standard !! Possible<br>Points !! Points
Earned
|-
! Table(s)<br>&/or Figure(s)
| Table(s) and/or Figure(s) well designed to illustrate conclusions. Included all crucial information that allows the figure or table to make the main points visually and to “stand alone”: novice reader does not need to read the narrative  or the legend to see the data’s main meaning. All data adequately identified; correct units included; labeling appropriate.
|  Figure(s) or table(s) not well designed to illustrate main points visually, clearly, or in most direct and simple way or missing essential information needed for understanding.
| 5
| __/5
|-
! Legends
| Figure legend is below figure & includes a number. Table # & title is above table, legend info below. Tables numbered sequentially, independent of figure numbers. All legends include all essential information and no unnecessary detail about how data shown was generated. Figure or table title gives the main point of the figure or table. Body of legend does not summarize main conclusions or include other material more appropriate for the narrative data analysis. All data adequately identified and parameters, ambiguous symbols or terms defined.
| Missing figure or table#, title, or legend. Legend (or title) is in wrong place or does not include appropriate numbering. Missing information about how data was generated. Missing part or all of key to symbols/ colors or other ambiguous information. Missing part or all crucial information that helps the figure or table to “stand alone”. Legend includes unimportant detail or includes a summary of the findings that is more appropriate for the narrative portion of the data analysis.
| 2
| __/2
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! Narrative Data Analysis in Results
| Narrative is structured appropriately: begins with a concise description of topic, experimental goals and experimental design. Narrative references figures & tables directly and describes key findings accurately, concisely and clearly & includes only relevant information. Data analysis is thorough and leads incrementally & clearly to appropriate conclusions to experimental question and addresses topic’s goals. Conclusions, where possible, are clearly stated. Analysis is understandable to an audience unfamiliar with topic and principles used in the experimental design.
| Narrative doesn't begin with an appropriately concise description of the experimental goals and experimental design. Narrative omits key findings, describes the data inaccurately or unclearly, includes irrelevant information, or is repetitive. Narrative fails to give appropriate conclusions to the experimental questions or fails to show how the experimental data allow the conclusions. Specific figure and table numbers for data that support conclusions is not cited in the narrative. Data analysis requires background knowledge that general audience may not have. Conclusions missing.
| 5
| __/5
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! Discussion
|  Discussion begins with a short summary paragraph describing main findings in results with figure/table # references and includes context as to the main questions addressed. Discussion uses sufficient, appropriate, formally cited outside references in journal ‘’Cell’’ format to help reader understand how the results and conclusions from experimental evidence in this study fits into the body of knowledge of the topic to date. The significance of the findings in a broader context is addressed. Tools are evaluated, if appropriate. The discussion ends with a clear concluding paragraph.
|  Summary of experimental evidence from this study missing or is improperly positioned. Context (study goals) missing. Insufficient outside source support for a thorough understanding of how this study’s findings fit into the body of knowledge on the topic to date.  Discussion is not centered around this study’s findings. Concluding paragraph missing or inappropriate.
| 7
| __/7
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! References
|  All information that is not common knowledge is cited appropriately in journal ‘’Cell’’ format. 
|  Source information missing or not cited in format requested. Reference page not formatted properly in journal “Cell’’ style.  Inappropriate or insufficient references used to support or refute experimental findings.
| 1
| __/1
|-
! Total
|
|
| 20
| __/20
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|}
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Revision as of 05:48, 25 September 2013

Wellesley College- BISC209 Microbiology- Fall 2013

Assignment:Evidence for Functional Metabolic Diversity in a Soil Community

Due prior to Lab 5.

Your assignment is to create the results section (including a narrative and tables/figures from the data collected for your community functional metabolic diversity testing [carbon source utilization] and in exo-enzyme prevalence assays) and the discussion section of a scientific research report.

One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community each finds a niche to survive and thrive. Our working hypothesis is that the microbial population must be highly diverse, particularly functionally metabolically diverse. We propose that they work as a community-- co-operating as well as competing for resources and space. There is evidence that soil community members are not unaware of the other microbes they live among. There is also evidence that bacteria sometimes aid other members of the community by secreting digestive enzymes into the environment that digest or process nutrients into a form usable by themselves and by members of the community that lack the ability to process those nutrients without help. Altruistic intent is hard to establish, but the result of metabolic diversity in community level exoenzyme prevalence is a community benefit: a richer, more diverse community means that not every member has to have the all the metabolic machinery to break down the wide variety of nutrients that may be available.

How can you effectively present our evidence for functional metabolic diversity and co-operative behavior among the microbes in the soil community?

What to do with the DATA you have collected from your community exoenzyme assays?

  • Be sure you calculate the prevalence (the percentage of microbes that can process each of the nutrients for which we tested compared to the total number detected in your assays). Compare those prevelances and think about what differences might suggest or mean. What is the best way to show these prevalence data in a table or in graphic form? The goal is to provide visual information that allows your reader to visualize easily the relevant processed data and understand the evidence for the main conclusion(s) you make in the narrative.



What to do with the DATA you have collected and processed (A590nm) from your BIOLOG™ plate?

  • Measuring Community Metabolic diversity
    A quantitative measurement of metabolic diversity can be calculated from figuring out the proportion of carbon sources available (offered to your microbial community) that were useable by microbes in your soil. There were 31 carbon sources available on the 96 well plate (remember there were replicates and controls)? You calculated the proportion that were able to be used. Therefore, the closer the number is to 100%, (31) the more functionally diverse the community is. However, we are unlikely to have offered the community the full range of carbon sources found in your soil. That is a shortcoming in this measuring tool, but the 31 sources offered include a broad range of substrates. This assay is evidence for functional metabolic diversity but it has the shortcoming of not being a complete test.

  • Showing Carbon source utilization patterning:
    Because relative number of carbon sources used by a community does not provide information about the pattern of carbon substrates useable, you must think about a different way to display these complex data. For example, you could plot on the y axis the A590nm absorbance on the final day of testing or on the peak day of metabolic activity versus the 31 different carbon sources on the x axis. Should you arrange the substrates on the x axis in a different order than in the random order on the Biolog plate? Yes. What should be the criterion for an alternative organization? What arrangement of substrates would best show your reader your main point(s)? The main point you want to make from looking at the pattern of utilization is what? Note that there is no such thing as negative absorbance; therefore, any negative values should be graphed as zero. Are there other or better ways to organize and display these data to make your main point than the graph just described? What are your conclusions about soil community microbial metabolic diversity or about co-operation/competition? Your goal is to design a graph that visually shows those conclusions.

What is there to "discuss"
Coming up with a quantitative measurement of diversity as CMD as a number and inferring great or little functional metabolic diversity from that measurement is difficult without comparisions to other microbial communities and a plausible reason for diversity based on evidence. There are many other tools that we could have used to measure functional metabolic diversity. In your discussion use outside sources to strengthen your conclusions, validate your tools or the converse. Remember that the discussion can't leave your data behind after the initial summary paragraph but must always be centered around your findings and use outside sources as a comparison. Don't trash your tools but help your reader understand their limitations if that's important. Always end with a concluding paragraph that sums up where your findings fit in the body of knowledge on our question(s).

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