Virtual Genetics Labs

[Sean Nash]

Visit this excellent genetics resource from the University of Utah.

After viewing these prerequisite animated tutorials:
BUILD A DNA MOLECULE
TRANSCRIBE AND TRANSLATE A GENE
WHAT MAKES A FIREFLY GLOW?
...to get a feel for the animations on the site, chose two of the following "virtual labs" for a deeper look:

DNA EXTRACTION

GEL ELECTROPHORESIS

POLYMERASE CHAIN REACTION

DNA MICROARRAY

For each one of the two you select, return here and post three things you learned from the virtual lab. Remember, these can be things from concrete facts, to wider insights into the entire process of the way this impacts some other aspect of life. A response including all of these "levels" of understanding would be even better.

Also, for each of the two you select, post one unanswered question you had after completing the lab. This should be something that wasn't clear by the end of the experience, or perhaps even a larger question that goes one step beyond the lab in some way. The cool challenge in the end is that you must also answer your question and cite (preferably by linking if it is an online source) the resource(s) used to draw your conclusion.

Have fun... I am anxious to see the array of things you gained from the experience as well as what you thought of beyond the screen.

[kristen sheehan]

Well I have to say that these labs were amazing!!

This is what I learned from the DNA extraction:

1. That there are thousand of cells lost in your mouth a day

2. Alcohol and ethanol are used in DNA extraction. I had no idea on that one!

3. I put two and two together and figured out what lysis solution does. It makes the cells burt, which is what the word lyse means, to burst! :-)

This is what I learned from the DNA microarray:

1. That there are five types of cells in the human body: skin, muscle, pancreatic islet, erythroblasts and melanocytes.

2. Different types of genes are turned on and off in different types of cells

3. DNA microarray can tell the different types of genes for two different types of cells. I had no idea there was such a thing to do that.

My question is who actually invented the human genome?

James D. Watson came up with the idea to make it. But no credit is given to one particular person for coming up with it.

[Ryne Relford]

The first virtual lab I did was PCR. 1)The first thing that I learned was that the purpose of PCR is to make DNA copies, but surprisingly not very little DNA is needed to make these copies.2) PCR works by heating and cooling the solution over and over so PCR tubes are designed for even heat distribution, and a double helix DNA separates at 95 degrees celsius into two single stranded DNA molecules.3) PCR is used to diagnose diseases, identify bacteria and viruses, match criminal to crime scenes, at the same timing being cost efficient.

The second virtual lab I did was DNA Extraction.1) We need cells because cells contain a nucleus and within the nucleus is about two meters of DNA.2) Scientists isolate DNA for genetic testing, body identification and analysis of forensic evidence.3)DNA extraction is typically the first step in a longer laboratory process. DNA first needs to be purified away from proteins and other cellular contaminants.

My questions were who created or discovered PCR? And What are the odds that two random people could have the same DNA and have lawyers and juries in courts always felt comfortable using DNA information?

The answers: Kary Mullis 1984, and was later awarded the nobel prize in chemistry for his work. And The actual probability that 2 random persons have the same DNA is only 1 in 3 trillion.In the early days of the use of genetic fingerprinting as criminal evidence, juries were often swayed by spurious statistical arguments by defense lawyers along these lines: given a match that had a 1 in 5 million probability of occurring by chance, the lawyer would argue that this meant that in a country of say 60 million people there were 12 people who would also match the profile. This was then translated to a 1 in 12 chance of the suspect being the guilty one. This argument is not sound unless the suspect was drawn at random from the population of the country. In fact, a jury should consider how likely it is that an individual matching the genetic profile would also have been a suspect in the case for other reasons. Another spurious statistical argument is based on the false assumption that a 1 in 5 million probability of a match automatically translates into a 1 in 5 million probability of guilt and is known as the prosecutor's fallacy.

I found both of the answers to my questions at http://www.wikipedia.org/. I found the first answer at http://en.wikipedia.org/wiki/PCR and I found the second answer at http://en.wikipedia.org/wiki/DNA_profiling.

[Chris Michaels]

my first experiment was the DNA MICROARRY

What i learned was:
1. That genes can be turned off and on to make that particular cell
2.Cancerous gene can effect the growth not just make the cell stop
3.Healthy cells and Cancerous cells look the same underneath a microscope, this is why you need a DNA Microarry

My Question was how much does the microarry and all supplies costv in total?

Explained by http://www.microarrayworld.com/ the supplies and the study cost atleast 100,000 dollars to the lab.

My second experiment was the PCR experiment.

what i learned was:

1.That genomes are made of 3,000,000,000 chemical base pairs.
2.100,000,000,000 copies of the DNA can be made in less than a matter of hours.
3.PCR can be conducted with a smaple of DNA as small as 1 peice of hair.

My question is who found the PCR lab?

Stated by http://en.wikipedia.org/wiki/PCR the founder of the lab was Kary Mullis and assigned to Cetus Corporation, where Mullis worked when he invented the technique in 1983

[Erin McAndrews]

The first virtual lab I did was DNA Extraction.
Things I learned:
1) I didn't realize that you could actually see DNA from the naked eye, at all.
2) Extracing DNA from inside of your cheek, is actually a simple process and doesn't require much equipment.
3) Scientists isolate DNA for genetic testing, body identification, and analysis of forensic evidence.

Question: How long does it take to do this lab in real life?
Answer: To do this in real life it only takes around 15 minutes!

The seond virtual lab I did was DNA Microarray.
Things I learned:
1) Genomics is a way to study many genes all at once using the DNA Microarray.
2) Every cell in our body carries each of our 20,000 or so genes, but some genes are turned "on" and some are turned "off". You can determine if it's turned "on" by if it's expressing the gene by producing mRNA.
3) By isolating the mRNA you can determine which genes are being expressed. mRNA is isolated from the tRNA and rRNA by washing the RNA samples over columns filled with small beads that will only bind to RNA strands that have a poly-a tail. The tRNA and the rRNA just wash away.

Question:When were DNA microarry's first developed?
Answer: The first microarray was published in 1997 with a complete eukaryotic genome.

[Kaylee Burris]

The first lab I did was DNA extraction and I wish there would have been more because it was fun.
1) You lose thousands of cells in your mouth, it seems weird, where do they go? -I understand now that you lose them very often with like food and stuff.
2) Lysis solution makes the cells burst and the DNA can come out.
3)Salt of all things is involved in DNA extraction, I would have never guessed that, it pretty much completes the separation of DNA from proteins.

The second lab I did was PCR, I didnt know temperature affected DNA this much.
1) This makes 100 billion identical copies of DNA in a hour, that is faster than any machine.
2) You have to add nucleotides to the solution, I didnt know you could just add that stuff.
3) When you heat up the DNA to 95 degrees celcius it starts to separate at that temperature.

Now my question is: Is DNA a testing 100% positive or are they sometimes unsure?
I didn't find a site just about DNA testing, but reading about this type of DNA testing was interesting. Not all forms of testing can me completly accurate but it can get really close.

[Rachel Huntsman]

DNA Extraction:
-We lose thousands of cells from our mouths everyday. This seems like a lot, but it makes sense since we eat and drink throughout the day. It's not any different than losing skin cells I guess.
-Chromosomes can be broken down very far, they are extremely complex. I knew this, but didn't really comprehend all the smaller pieces a chromosome could be broken down into.
-It seems like such a simple process to extract DNA, but it is actually used for very important reasons, such as identifying a body.

Question: Who discovered DNA?
Answer: Friedrich Miescher in 1869

DNA Microarray:
-Humans have 20,000 genes.
-Cancer can be described as: a disease of "genes gone bad".
-Color blind people cannot read the microarray because the colors used to depict cancerous and healthy cells are red and green, so those colors can be changed to show up in yellow and blue.
-Very "cool" sound effects accompany this process. =)

Question: How long does the microarray process take?
Answer: Anywhere from two to four weeks.

[ricky maddox]

The first experiment I did was the DNA Extraction lab. The first thing I learned was that like many other things in science the word Lysis has a Latin base. I also found out that they put salt into the compound to help it clot, is that like what happens to cause high blood pressure? Finally I discovered that when you use a centrifuge you have to balance it out with water. So this brings up my question, what happens when you don't balance a centrifuge? Apparently the people at Discovery Chanel have a few scenarios you might find interesting : ).

The next lab I did was the PCR test, or the POLYMERASE CHAIN REACTION. Now this one I found very interesting because I learned that it can make 100 billion copies of a certain gene in just 30 cycles. Also I thought it was prety cool that it has to go threw so many temp changes before it will happen properly. Finally i thought it was awsome that it only take a couple of Hours to get billions of copies of the same gene, amazing. My question on this one is who developed the process? PCR was invented by Kary Mullis. At the time he thought up PCR in 1983. You can check out the full article here.

[Korby Trautman]

Here is what I learned...
DNA MICROARRAY...
1. Cells use the two-step process of transcription and translation to read each gene and produce the string of amino acids that makes up a protein.
2. Oligo-dT Beads are used as a filter
3. Only organic solvents are used to separate the RNA from everything else.
QUESTION????
What types of organic solvents are used in order to break down the cells?
ANSWER!!!!!
Chloroform is primarily used, due to it's chemical characteristics.
GEL ELECTROPHORESIS
1. The gel acts as a small filter to sort out the different lengths.
2. Electricity pushes the DNA through the Gel
3. Agarose is made from seaweed and is very similar to gelatin.
QUESTION????
Why do DNA strands of different lengths need to be sorted.
ANSWER!!!!
The strands are separated in different lengths to build a DNA Ladder

[Zachery Langdon]

DNA Extraction
FACTS:
• Scientists isolate DNA for genetic testing, body identification, analysis of forensic evidence and much more.
• Skin on the inside of the mouth loses thousands of cells every day.
• The Lysis solution causes the cell to burst open and release there DNA. It also cuts the histones to free the DNA.
Question:
• Who invented genetic testing?
Answer: (I could not find who invented genetic testing, but here is the next best thing.) Gregor Johann Mendel
Achieved info from: Student Handbook 2 Including Young Reader’s Companion
Published by R. R. Bowker
Copyright 1993 by Carruth and Ehrlich Books, Inc.

Gel Electrophoresis
Facts:
• Scientists use Gel Electrophoresis to sort DNA strands by length.
• By adding an electrical current you can make the DNA move.
• Short strands of DNA move more quickly through the gel than do larger strands do, that’s how they separate.
Question:
• Why is the DNA repelled from the negative charge and attracted to the positive charge.
Answer: The phosphate groups in the DNA backbone carry negatively-charged oxygen’s- giving a DNA molecule an overall negative- charged DNA moves towards the positive pole of the electrophoresis chamber
Achieved info from dnalc.org

I really liked the Lean Genetics site, it had all the information you'd ever need...Well ... about genetics.

[Tori Scott]

*PCR
-The polymerase chain reaction can generate 100 billion identical copies of a specific DNA sequence in a matter of hours
-Primers- short pieces of DNA that are made in a lab. Primers are used for copying very specific DNA. Almost no chance primers will target wrong sites.
-1 primer attaches to the top strand at one end of your segment and the other primer attaches to the bottom
*Question- I understand what PCR can do and the process used, but what exactly is it used for?
*Answer- PCR is a proven quick reliable method for detecting all manner of mutations associated with genetic diseases
*Source- http://www.accessexcellence.org

[Chelsie]

These labs were pretty cool.....

DNA Extraction

3 Things I learned are...

1. DNA neeeds to first be purified away from any protiens and other cellular contaminants.
2. The skin in our mouth loses thousands of cells everyday.
3. Detergent in the solution lysis disrupts the cell membrane and nuclear envelope causing thecells to burst open and release their DNA.

One question I still have is...
Why is DNA extractions taken from the inside of your mouth? Can other things like hair be used?
Answer: You use your mouth because it is the most accurate. One website said existing animal hair DNA-extraction methods have shown a relatively low sucess rate or even failed if adherent roots were absent.
source: linkinghub.elsvier.com

PCR Virutual Lab

3 Things I learned are...

1. The human genome is made up of 3 billion cehmical base pairs.
2. The polymerase chain reaction can generate 100 billion identical copies of specific DNA sequence in matter of hours.
3.PCR stans for polymerase chain reaction.

One question I still have is...
What does the word genome mean?
All of the DNA that a person possesses. The human genome is made up of all of the DNA in our chromosomes as well as that in our mitochondria.
Source: http://www.medterms.com/script/main/art.asp?articlekey=3818

[Taylor Snider]

These labs were pretty awesome. I liked the animations and how they explained what was going on in the lab.
From the DNA Microarray i learned that it lets you see all of the genes at the same time. I also learned that the strands of DNA are longer than RNA molecules. Finally i learned what hybridization is. It's two complementary DNA strands from different sources can pair with another. The question i had was "How long does it take to make a microarrary?"