Assignment Unit 9.3: Howard Hughes Medical Institute (HHMI)
Bacterial Identification Lab: This virtual lab uses various biotechnology techniques to identify different types of bacteria based on DNA sequences. Basic steps include DNA sample preparation, PCR amplification, PCR purification, sequence preparation, DNA sequencing, and sequence analysis.
HHMI BACTERIAL IDENTIFICATION LAB WORKSHEET
Introduction:
Go to http://www.hhmi.org/biointeractive/explore-virtual-labs. Scroll down and click on The Bacterial Identification Virtual Lab.
Complete Bacterial Identification Lab for Sample A (default sample in Lab)
Click to Enter the Lab. (Click the window on the left-hand side of the screen.) As you enter the lab, follow the instructions in the Lab Window on the left. Use the information in the Notebook Window on the right to answer the Discussion Questions.
Laboratory Steps:
1.    SAMPLE PREPARATION
2.    PCR AMPLIFICATION
Now run the PCR. Watch the virtual lab animation before proceeding to Part 3.
3.    PCR PURIFICATION
4.    SEQUENCING PREPARATION
Watch the virtual lab animation before proceeding to Part 5.
5.    DNA SEQUENCING
Watch the virtual lab animation before proceeding to Part 6.
6.    DNA SEQUENCE ANALYSIS
Click on the link that opens your unknown sequence. Copy and paste the sequence for further analysis.
A.    Copy sequence into a file for Homework Submission.
B.    Copy sequence into a BLAST search for identification.
Hints: Follow the steps listed on the page. Copy and Paste the DNA Sequence into the NCBI website (blast.ncbi.nlm.nih.gov). Put the sequence into the large box at the top of the BLAST

search page. Once your query sequence is entered click the BLAST tab. Be patient for BLAST data can take a while to search.
When the BLAST results appear, scroll down below the color key to the significant alignments and note your DNA Sequence Identity. Go back to the virtual lab window (left side) and follow the instructions to identify the DNA.
Discussion Questions:
1.    What is the overall purpose of this laboratory exercise?
2.    What are the basic steps involved in this bacterial identification lab?
3.    What is the DNA sequence that you determined? (copy nucleotide sequence)
4.    What is the scientific name of the bacteria you sequenced?
5.    After completing Bacterial Identification of Sample A, complete Bacterial Identification of 2 of the other 5 samples.
Write down:
Letter of the sample you choose DNA sequence you determined Scientific name of the bacteria