Bacterial ID Lab
Completing this virtual lab and answering the following questions helps meet Standard 3: Lab Skills.
First, go to:
(works best in FIrefox, not Safari browser)
In this virtual lab you will assume the role of a lab technician in a modern molecular biology laboratory. As such, you are responsible for providing lab results to medical doctors for use in diagnosing their patients. Be sure to follow the steps of the procedure in order and to make use of the notes on the right side of the computer screen. As you work through the lab, answer the following questions:
As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?
I am trying to determine whether the new sequence bears a significant degree of similarity (or homology) to another known sequence.
How did you prepare the DNA to be used in this investigation?
We prepared negative and positive control reactions. Instead of the sample DNA, the positive control reaction contains positive control DNA.
Describe how PCR is used to make copies of DNA sequences. Use the animation and notebook entries in the PCR Amplification step to guide your answer. Note that you may replay the animation as needed.
Double-stranded DNA is “unzipped” with an enzyme to start the process. In PCR, single-stranded DNA is made by heating up a fragment to a certain temperature. Then it is cooled down so that the primers bind to the original DNA strands. Repeating this process over again many times you will end up with millions of DNA strands..
Summarize the technique used to purify the PCR product.
Once the PCR product is in the gel, you can cut out the stuff corresponding to the PCR product and isolate the DNA from the gel. Microfilters to filter the DNA from the PCR tube without running a gel. Microfilters can filter out all he of unneeded things in the PCR and it becomes purified.
What is produced during the sequencing prep PCR run? Use the animation and notebook as needed in thinking through your answer.
16s rDNA, is produced during the sequencing prep in the PCR run.
Describe how the automatic sequencer determines the sequences of the PCR products.
The automatic sequencer determines the sequence of the PCR by a method called Gel electrophoresis this is to separate molecules based on differences in size. The sequencer used in this lab has a thin capillary tube attached at one end to a syringe mechanism that contains a buffer solution. The tube is filled with the buffer solution and the other end inserted into one of the tubes containing the DNA pieces. Then, an electric current is applied so that the end of the tube in contact with the DNA has a negative charge and the syringe end a positive charge. Since DNA molecules are negatively charged, they start to move through the tube toward the positively charged syringe end, with the smaller pieces moving faster than the larger ones. Near the syringe end, the capillary tube passes through a laser beam that excites the fluorescent markers, and optical detectors detect the color of the fluorescence.
What does BLAST stand for?
Basic Local Alignment Search Tool
What conclusions did you make using the results of the BLAST search? Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?
Using the BLAST search I figured that the DNA samples match exactly and that the patient did have a disease.
