BISC209/S12: Assignment 209 BIOLOG: Difference between revisions
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Turn in, at the beginning of Lab 5, a partial results narrative with tables/figures from the data collected for your your community metabolic diversity testing (carbon source utilization) and for co-operative behavior shown in exo-enzyme prevalence assays.<BR> | Turn in, at the beginning of Lab 5, a partial results narrative with tables/figures from the data collected for your your community metabolic diversity testing (carbon source utilization) and for co-operative behavior shown in exo-enzyme prevalence assays.<BR> | ||
'''What to do with the DATA you have collected | '''What to do with the DATA you have collected from your community exo-enzyme assays?'''<BR> | ||
One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community work as a community: implying that individuals in this community must co-operate as well as compete for a viable niche. There is evidence that shows that soil community members are not unaware of the other microbes they live among. There are mechanisms to regulate growth of the community based on quorum signaling among members. 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. To provide evidence for such metabolic diversity and for this kind of co-operative behavior, 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 prevalences and think about what differences might mean. A discussion of what differences might mean to the community or might say about the community would have to be conjecture on your part; therefore, that discussion should not be in this results narrative. Save it for the discussion section of your final paper when you can augment your conjectures with outside evidence from other studies. The results narrative should be limited to conclusions that can be made to our experimental questions from the data you collected and present in accompanying figures/tables. You can make some conclusions about metabolic diversity and co-operative behavior | One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community work as a community: implying that individuals in this community must co-operate as well as compete for a viable niche. There is evidence that shows that soil community members are not unaware of the other microbes they live among. There are mechanisms to regulate growth of the community based on quorum signaling among members. 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. To provide evidence for such metabolic diversity and for this kind of co-operative behavior, 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 prevalences and think about what differences might mean. Would it be best to show these prevalence data in a table or in graphic form? Would photos of the assay plates be useful or TMI? The goal is to provide visual information that allows your reader to see and compare the relevant processed data and understand the evidence for the conclusion(s) you describe in the narrative. A discussion of what differences might mean to the community or might say about the community would have to be conjecture on your part; therefore, that discussion should not be in this results narrative. Save it for the discussion section of your final paper when you can augment your conjectures with outside evidence from other studies. The results narrative should be limited to conclusions that can be made to our experimental questions from the data you collected and present in accompanying figures/tables. You can make some conclusions about one soil community from this evidence about metabolic diversity and co-operative behavior using these exozyme prevalence data, but the place to apply these conclusions more broadly is not here in results. <BR> | ||
'''What to do with the DATA you have collected (A<sub>590nm</sub>) from your BIOLOG™ plate?'''<BR> | '''What to do with the DATA you have collected and processed (A<sub>590nm</sub>) from your BIOLOG™ plate?'''<BR> | ||
Another way of measuring community metabolic diversity was in establishing a quantitative measurement of % carbon source utilization by exposing your soil extract to a variety of carbon sources. There were 31 carbon sources tested on your 96 well plate (remember there were replicates and controls)? Is this number likely to comprise the full range carbon sources found in the habitat from which your soil community came? No, but the assay tests for wide variety of metabolic machinery needed to process a broad range of substrates. Therefore, the value obtained from this assay is evidence for answering one of your basic questions. <BR> | |||
'''Showing Carbon source utilization patterning:'''<BR> | '''Showing Carbon source utilization patterning:'''<BR> | ||
Because | 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. You could plot on the y axis the A<sub>590nm</sub>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 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? | ||
<BR><BR> | <BR><BR> | ||
In addition to your figures | In addition to your table/figures, this assignment requires a narrative that should be written using the general results section structure described in [[BISC209:Assignment_209_Lab3 | Lab 3 Assignment: Colony Count vs. Direct Count Enumeration]]. | ||
Latest revision as of 12:15, 18 January 2012
Assignment 4: Community Metabolic Diversity & Prevalence of Starch & Cellulose Digestors & Phosphate Users
Turn in, at the beginning of Lab 5, a partial results narrative with tables/figures from the data collected for your your community metabolic diversity testing (carbon source utilization) and for co-operative behavior shown in exo-enzyme prevalence assays.
What to do with the DATA you have collected from your community exo-enzyme assays?
One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community work as a community: implying that individuals in this community must co-operate as well as compete for a viable niche. There is evidence that shows that soil community members are not unaware of the other microbes they live among. There are mechanisms to regulate growth of the community based on quorum signaling among members. 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. To provide evidence for such metabolic diversity and for this kind of co-operative behavior, 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 prevalences and think about what differences might mean. Would it be best to show these prevalence data in a table or in graphic form? Would photos of the assay plates be useful or TMI? The goal is to provide visual information that allows your reader to see and compare the relevant processed data and understand the evidence for the conclusion(s) you describe in the narrative. A discussion of what differences might mean to the community or might say about the community would have to be conjecture on your part; therefore, that discussion should not be in this results narrative. Save it for the discussion section of your final paper when you can augment your conjectures with outside evidence from other studies. The results narrative should be limited to conclusions that can be made to our experimental questions from the data you collected and present in accompanying figures/tables. You can make some conclusions about one soil community from this evidence about metabolic diversity and co-operative behavior using these exozyme prevalence data, but the place to apply these conclusions more broadly is not here in results.
What to do with the DATA you have collected and processed (A590nm) from your BIOLOG™ plate?
Another way of measuring community metabolic diversity was in establishing a quantitative measurement of % carbon source utilization by exposing your soil extract to a variety of carbon sources. There were 31 carbon sources tested on your 96 well plate (remember there were replicates and controls)? Is this number likely to comprise the full range carbon sources found in the habitat from which your soil community came? No, but the assay tests for wide variety of metabolic machinery needed to process a broad range of substrates. Therefore, the value obtained from this assay is evidence for answering one of your basic questions.
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. You could plot on the y axis the A590nmabsorbance 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 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?
In addition to your table/figures, this assignment requires a narrative that should be written using the general results section structure described in Lab 3 Assignment: Colony Count vs. Direct Count Enumeration.
