BISC209: Lab8: Difference between revisions
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You spent many weeks just trying to coax some of these bacteria to grow outside of their soil habitat. You spent additional time separating them from other members of their community. Both of these tasks were difficult. Why did we do all that when we know that these bacteria exist naturally, quite happily, as part of a large diverse community? Well, most importantly, we needed to get the bacteria isolated to pure culture to be able to send off unique 16S rRNA genes for DNA sequencing identification. Unlike sending our soil genomic DNA to find out the diversity of the bacteria in the soil community (culturable or unculturable), we wanted, in this case, to know the species id of each of the bacteria we cultured and studied so that we could ''name'' the bacteria we characterized with our biochemical and physical tests. The other main reason that we did all the morphologic, physical and biochemical tests on pure cultures was to acquire evidence to answer our main question about roles and relationships of particular microbes in their community. If you found out that one or more of your bacteria secret an antibiotic, what does that tell you about at least one of its roles in the community and in the larger world? If you found out that you have cellulolytic or nitrogen fixing bacteria in your community or that they are highly motile, you have other evidence to write an interesting discussion about their possible roles. You will not write a discussion section for this assignment but a good results section is crafted to lead into the points you want to make in your discussion. The results section will not try to assign roles or relationships but will point out relevant test findings and observations that allow you to make those inferences in your discussion. <BR><BR> | You spent many weeks just trying to coax some of these bacteria to grow outside of their soil habitat. You spent additional time separating them from other members of their community. Both of these tasks were difficult. Why did we do all that when we know that these bacteria exist naturally, quite happily, as part of a large diverse community? Well, most importantly, we needed to get the bacteria isolated to pure culture to be able to send off unique 16S rRNA genes for DNA sequencing identification. Unlike sending our soil genomic DNA to find out the diversity of the bacteria in the soil community (culturable or unculturable), we wanted, in this case, to know the species id of each of the bacteria we cultured and studied so that we could ''name'' the bacteria we characterized with our biochemical and physical tests. The other main reason that we did all the morphologic, physical and biochemical tests on pure cultures was to acquire evidence to answer our main question about roles and relationships of particular microbes in their community. If you found out that one or more of your bacteria secret an antibiotic, what does that tell you about at least one of its roles in the community and in the larger world? If you found out that you have cellulolytic or nitrogen fixing bacteria in your community or that they are highly motile, you have other evidence to write an interesting discussion about their possible roles. You will not write a discussion section for this assignment but a good results section is crafted to lead into the points you want to make in your discussion. The results section will not try to assign roles or relationships but will point out relevant test findings and observations that allow you to make those inferences in your discussion. <BR><BR> | ||
Remember that any results section should start out with a restatement of the experimental goals of this part of the paper: "In order to find out ....". Then it recaps BRIEFLY a summary of what you did, but DOES NOT, repeat the whole materials and methods section | Remember that any results section should start out with a restatement of the experimental goals of this part of the paper: "In order to find out ....". Then it recaps BRIEFLY a summary of what you did, but DOES NOT, repeat the whole materials and methods section. The results narrative does not start describing the data until it frames for the reader how the results you describe were obtained and why. The most important findings are found in two forms in the results section: in a narrative description that introduces all figures and tables, and in those visual representations of data, the figures or tables. There is extensive information about how to write a results section in the Guidelines to Science Writing in the [[BISC209/S10:Resources | Resources]] section of the wiki. Remember that you are preparing your reader for your discussion section. Make sure to limit or omit describing results that aren't pertinent to your discussion of the diversity, roles and relationships of bacteria in a particular soil community. | ||
<BR><BR> | <BR><BR> | ||
You will probably not get the sequencing results back until next week. Nevertheless, you can write this results analysis without the complete id of your bacteria. You may, for this assignment, refer to your bacteria by their preliminary group name or by a code name that you will go back and edit later when you know the genus and species names after analyzing your sequencing results. | You will probably not get the sequencing results back until next week. Nevertheless, you can write this results analysis without the complete id of your bacteria. You may, for this assignment, refer to your bacteria by their preliminary group name or by a code name that you will go back and edit later when you know the genus and species names after analyzing your sequencing results. | ||
Revision as of 20:31, 17 January 2010
Lab Practical
Today you will have a lab practical exam designed to assess your mastery of basic tools, techniques, and theoretical information on which the field of microbiology is based.
Culturable Bacteria Identification continued
Read last weeks tests, Continue with new tests, add motility and other stains (if useful and not completed yet)
Assignment
Results section with figures/tables:
Identification of Culturable Soil Bacteria by Physical and Metabolic Characteristics
You will write part of the results section for your final paper as a graded assignment to turn in at the beginning of Lab 9. You have worked hard this semester to isolate and identify a few of the thousands of microbes that contribute to the soil community of your habitat. You used DNA sequencing of the 16S rRNA gene to identify your bacteria, as well as traditional culture and isolation methods, combined with biochemical and physical tests, to obtain morphologic and metabolic characterizations of a few of these bacteria. Now it's time to start the synthesis of all those results into a cogent and clear analysis of the evidence that answers, or sheds some light on, our original experimental question: What are the roles and the functional and phylogenetic relationships among soil bacteria in their community?
You spent many weeks just trying to coax some of these bacteria to grow outside of their soil habitat. You spent additional time separating them from other members of their community. Both of these tasks were difficult. Why did we do all that when we know that these bacteria exist naturally, quite happily, as part of a large diverse community? Well, most importantly, we needed to get the bacteria isolated to pure culture to be able to send off unique 16S rRNA genes for DNA sequencing identification. Unlike sending our soil genomic DNA to find out the diversity of the bacteria in the soil community (culturable or unculturable), we wanted, in this case, to know the species id of each of the bacteria we cultured and studied so that we could name the bacteria we characterized with our biochemical and physical tests. The other main reason that we did all the morphologic, physical and biochemical tests on pure cultures was to acquire evidence to answer our main question about roles and relationships of particular microbes in their community. If you found out that one or more of your bacteria secret an antibiotic, what does that tell you about at least one of its roles in the community and in the larger world? If you found out that you have cellulolytic or nitrogen fixing bacteria in your community or that they are highly motile, you have other evidence to write an interesting discussion about their possible roles. You will not write a discussion section for this assignment but a good results section is crafted to lead into the points you want to make in your discussion. The results section will not try to assign roles or relationships but will point out relevant test findings and observations that allow you to make those inferences in your discussion.
Remember that any results section should start out with a restatement of the experimental goals of this part of the paper: "In order to find out ....". Then it recaps BRIEFLY a summary of what you did, but DOES NOT, repeat the whole materials and methods section. The results narrative does not start describing the data until it frames for the reader how the results you describe were obtained and why. The most important findings are found in two forms in the results section: in a narrative description that introduces all figures and tables, and in those visual representations of data, the figures or tables. There is extensive information about how to write a results section in the Guidelines to Science Writing in the Resources section of the wiki. Remember that you are preparing your reader for your discussion section. Make sure to limit or omit describing results that aren't pertinent to your discussion of the diversity, roles and relationships of bacteria in a particular soil community.
You will probably not get the sequencing results back until next week. Nevertheless, you can write this results analysis without the complete id of your bacteria. You may, for this assignment, refer to your bacteria by their preliminary group name or by a code name that you will go back and edit later when you know the genus and species names after analyzing your sequencing results.
Links to Labs
Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12
