BISC209/S11: Lab9
LAB 9: Data Analysis Lab
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:
[ http://rdp.cme.msu.edu/index.jsp]
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 10 you will have a lab practical exam. See the Assignment section below for tips for how to prepare for this assessment.
In LAB 11 we will not have a formal lab. Instead, you and your teammates (soil sampling groups) will present a "virtual poster". At the end of the Data Analysis lab today, we will brainstorm some potential topics for you to choose for this oral presentation. Some suggestions and things to think about in choosing your topic are found in Lab11
.
Assignment
Study for your Lab Practical.
In Lab 10 you will have a LAB PRACTICAL, an exam that tests your ability to function as a microbiologist in the lab. There will be two main categories of assessment: testing practical skills such as your ability to perform crucial techniques (aseptic transfer, streaking for isolation, performing a Gram stain, micropipetting, etc.) and testing for your understanding of the biological basis behind the work that you've done this semester. For example, you assess the OF-glucose test for yellow or blue color in certain regions or tubes to distinguish facultative fermentors of glucose from bacteria that have only an aerobic pathway for catabolism of glucose or no way to break down that nutrient; you also learn from that test whether or not the bacteria can catabolize peptone. What the practical will assess on the OF-glucose test is not that you can perform the test without access to the directions, but that you understand how to evaluate the results in terms of the general biological mechanism of the test (pH change) and the metabolic capabilities implied from the results (such as my description of glucose and peptone catabolism above). Another example: we might give you a starch plate flooded with iodine and ask you which, if any, of the bacteria forming colonies on this plate are capable of digesting starch and/or what is the ingredient in the medium that allows this evaluation?
Wondering how to study? A lot of what we will evaluate you on, you already know how to do in your sleep, such as streaking for isolation using proper technique. You do not have to memorize the procedures in the wiki. You will have access to the directions that are printed in the wiki for performing techniques, such as Gram staining; however, you will not have access to how to read those tests or to the theoretical background information about those tests, such as the cell structural differences that the Gram stain uses as its differentiating principle. You should know that sort of information by studying the background information and protocols found in the Protocols section of the wiki for all the work that have you performed this semester. The protocols in the wiki that describe tests that you have not done are NOT included in the practical. However, even if you didn't do or get a positive test from those tests performed on your isolates, you should know how to evaluate the tests we all set up, such as the SIMS medium, eg. how to recognize a positive vs. a negative.
Don't forget that understanding of the molecular tools we used for culture independent 16srRNA analysis and what we can learn from sequencing this gene ARE practical material. Your homework assignment for last week should be a good study guide for that material as is all of the background information in the wiki in LABS 1-8 and in the general information page for our project in the main menu.
Continue to wind down and finalize the classification of your culturable isolates. Start discarding your cultures.
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
