BISC209/S12: Lab10

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In LAB 11 we will have another Data Analysis/Science Writing & Presentation Workshop to continue preparing you to write your semester long investigation as an original research report and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. Some suggestions and things to think about in choosing the topic for your group presentation are found in [[BISC209/S12: Lab12 | Lab12 ]].<br>
In LAB 11 we will have another Data Analysis/Science Writing & Presentation Workshop to continue preparing you to write your semester long investigation as an original research report and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. Some suggestions and things to think about in choosing the topic for your group presentation are found in [[BISC209/S12: Lab12 | Lab12 ]].<br>
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(If your group's gene sequencing didn't work well, omit the exercise described in this paragraph.)If your soil sample's 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on your cultured isolates. This analysis should identify your cultured soil community members. Do these bacteria belong to the genus or family you expected from the morphologic and metabolic information you have gathered? You can use Wellesley's electronic version of ''The Procaryotes'' found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=title%3a%28the+prokaryotes%29&sortorder=asc&Content+Type=Reference+Works] and/or ''Bergey's Manual''found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=Bergey%27s+Manuals] to look up the bacteria identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses of your isolates.Do you have evidence for phylogenetic diversity as different form of richness in the community? Create a phylogenetic tree of your community members and selected non-members to try to determine evolutionary relatedness among your cultured isolates. Keep in mind that if you find broad phylogenetic diversity it is significant and can be used as evidence for another kind of richness in your microbial soil community. However, if all your cultured isolates belong to closely related clads, it does NOT mean that your soil community is ''not'' phylogenetically diverse. Why? Bring these table/figures, including a phylogenetic tree to Lab 11. We will workshop your figures and talk about our findings and discuss how they might be used in your final paper.<BR>
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(If your group's gene sequencing didn't work well, omit the exercise described in this paragraph.)If your soil sample's 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on the cultured isolates from your soil sample. This analysis should identify them as much as possible (from the 16s rRNA gene sequence comparisons done using the RDP data base or from an NCBI BLAST. Do your isolated bacteria belong to the genus or family you expected from the morphologic and metabolic information you have saw in your test results? You can use Wellesley's electronic version of ''The Procaryotes'' found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=title%3a%28the+prokaryotes%29&sortorder=asc&Content+Type=Reference+Works] and/or ''Bergey's Manual''found at [http://0-www.springerlink.com.luna.wellesley.edu/content/?k=Bergey%27s+Manuals] to look up more information on the isolates identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses. Do you have evidence for phylogenetic diversity in your soil sample? (This is a different form of richness in the community.) Create a phylogenetic tree of your soil sample's community members (using a variety of non-members as reference points to try to determine evolutionary relatedness among your soil sample's cultured isolates. Keep in mind that if you find broad phylogenetic diversity it is significant and can be used as evidence for another kind of richness in your microbial soil community. However, if all your cultured isolates belong to closely related clads, it does NOT mean that your soil community is ''not'' phylogenetically diverse. Why? Bring these table/figures, including a phylogenetic tree to Lab 11. We will workshop your figures and talk about our findings and discuss how they might be used in your final paper.<BR>
Your research report on your semester project is due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai by that time. The electronic copy is required ''in addition'' to a required hard copy that must be submitted to your instructor per her instructions. <BR><BR>
Your research report on your semester project is due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai by that time. The electronic copy is required ''in addition'' to a required hard copy that must be submitted to your instructor per her instructions. <BR><BR>

Revision as of 13:35, 15 March 2012

Wellesley College-BISC 209 Microbiology -Spring 2012

LAB 10: Data Analysis & Final Paper & Presentation Workshop I

This lab (and the next will) be devoted to instructor designed workshop activities to help prepare you to write your final paper and to give you time to work with your group on a presentation that you will give in Lab 12.

Assignment

In LAB 11 we will have another Data Analysis/Science Writing & Presentation Workshop to continue preparing you to write your semester long investigation as an original research report and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. Some suggestions and things to think about in choosing the topic for your group presentation are found in Lab12 .

(If your group's gene sequencing didn't work well, omit the exercise described in this paragraph.)If your soil sample's 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on the cultured isolates from your soil sample. This analysis should identify them as much as possible (from the 16s rRNA gene sequence comparisons done using the RDP data base or from an NCBI BLAST. Do your isolated bacteria belong to the genus or family you expected from the morphologic and metabolic information you have saw in your test results? You can use Wellesley's electronic version of The Procaryotes found at [1] and/or Bergey's Manualfound at [2] to look up more information on the isolates identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses. Do you have evidence for phylogenetic diversity in your soil sample? (This is a different form of richness in the community.) Create a phylogenetic tree of your soil sample's community members (using a variety of non-members as reference points to try to determine evolutionary relatedness among your soil sample's cultured isolates. Keep in mind that if you find broad phylogenetic diversity it is significant and can be used as evidence for another kind of richness in your microbial soil community. However, if all your cultured isolates belong to closely related clads, it does NOT mean that your soil community is not phylogenetically diverse. Why? Bring these table/figures, including a phylogenetic tree to Lab 11. We will workshop your figures and talk about our findings and discuss how they might be used in your final paper.

Your research report on your semester project is due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai by that time. The electronic copy is required in addition to a required hard copy that must be submitted to your instructor per her instructions.

More information about the final paper can be found at: Assignment: Assignment: Final Paper. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site.

Discard and clean up any remaining tests and cultures on your isolates. Note that there are 5 bonus points awarded for perfect clean-up. Your instructor will explain the "rules" for obtaining these bonus points.

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

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