LAB 10: Data Analysis & Final Paper & Presentation Workshop I
We will learn how to use the RDB (ribosomal data base, a public data base provided by Michigan State University) to analyze your sequencing results. Lab to be held in a computer classroom (TBA). Make sure you have signed up for an account on the RDB and received a username and password before you come to lab. Link to the RDB:
Click on myRDP (orange sidebar on the left of the screen).
Click on "Not a user? Sign up!" and this will take you to a registration screen. Fill out the information required and then check your email. You will be sent a password. Go back to the myRDP site and login with your email and this password. It will then prompt you to change that password to something you can remember.
WRITE THIS DOWN! Don't lose your password!
In LAB 11 we will not have a formal lab. Instead, We will have another Science Writing & Presentation Workshop to prepare you for writing up your semester long investigation as an original research report (NOT AS A TRADITIONAL LAB REPORT!!) and to help you and your teammates (soil sampling groups) prepare an oral group presentation in Lab 12. If we haven't already brainstormed some potential topics for you to choose for the oral presentation we will meet pre or post the RDB Data Analysis today. Some suggestions and things to think about in choosing your topic are found in Lab12
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 Procaryotesand/or Bergey's Manual 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.
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