BISC209/S13: Lab10: Difference between revisions
Tucker Crum (talk | contribs) (New page: {{Template:BISC209/S13}} <div style="padding: 10px; width: 720px; border: 5px solid #CC8099;"> ==LAB 10: Data Analysis & Final Paper & Presentation Workshop I== This lab (and the next wil...) |
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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? | (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? | ||
Your research report on your semester project is due in your lab instructor's office by 5pm on . 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 5pm on May 7 or May 8 . 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> | ||
More information about the final paper can be found at: | More information about the final paper can be found at: | ||
Assignment: [[BISC209/S13: Assignment_209_Lab10 | Assignment: Final Paper]]. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site. <br> | Assignment: [[BISC209/S13: Assignment_209_Lab10 | Assignment: Final Paper]]. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site. <br> | ||
Revision as of 05:47, 7 May 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
(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 Manual found 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?
Your research report on your semester project is due in your lab instructor's office by 5pm on May 7 or May 8 . 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
