BISC209/S13: Lab10

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Assignment)
(Assignment)
Line 11: Line 11:
In class, we learned how to identify bacteria by 16s rRNA gene sequences.  (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?  
In class, we learned how to identify bacteria by 16s rRNA gene sequences.  (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?  
-
You can earn points by submitting a draft of your revised final paper in Lab 10.
+
'''You can earn points by submitting a draft of your revised final paper in Lab 10.'''
Your final 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>
Your final 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>

Revision as of 11:39, 30 January 2013

Wellesley College-BISC 209 Microbiology -Spring 2013

Lab 10 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. Please also submit a complete Rough Draft of your final paper.

Complete freezing, discarding and cleaning 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.

Assignment

In class, we learned how to identify bacteria by 16s rRNA gene sequences. (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?

You can earn points by submitting a draft of your revised final paper in Lab 10.

Your final 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: BISC209/S13: Assignment 209 Lab10. A grading rubric is posted to the Rubrics folder in the Resources section of your lab Sakai site.

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab 11

Personal tools