So, a while ago we had this dude that came into our class to talk about the growing problem of animal overpopulation in the Valley. He showed us that after only a few generations of cats, 2 cats will soon become over 300 cats!! That's insane. So, to include us in his research, we have to do an indexing project. It's the easiest homework I've ever gotten in my life. Basically, we take a 30 minute walk, and count the animals. We were asked to count all feral dogs, owned dogs, and any cats, as well as any other animals we encounter. The company will then collect this data and use the information to determine if spaying and neutering animals helps the abandoned animals numbers. This is actually a pretty cool and effective way to count these animals.
I have two walks down and two walks to go. On my first walk I only saw a few animals but on my second walk I saw a lot more dogs, cats, and SQUIRRELS!!!
This activity is probably the easiest homework assignment I've gotten in a long long time, and it forces me to get my exercise. (:
Thursday, April 28, 2011
Tuesday, April 26, 2011
Transformation Lab
Our group was amazing! It included me, Sierra, and Tyler. We worked really hard to focus and learn something about the pGLO gene(also known as jellyfish gene!!) By the way, jellyfish hurt, a lot!!
The PROCESS!!
1. label one closed test tube +pGLO and another -pGLO. Place in the foamy tubey thingy..
2. open tubes and use pipet to transfer 250ul of the CaCl2. Place on ice.
4. Use loop to pick up a single colony of bacteria from the starter plate. Get the +pGLO tube and immerse the loop into the transformation solution at the bottom of the tube. Spin the loop "washing machine" until the entire colony is dispersed. Place the tube back in the ice. Repeat with -pGLO with a new sterile loop.
5. Examine plasmid DNA with the UV lamp. Immerse new into plasmid DNA stocktube. Withdraw a loopful. Should be a film of plasmid across the ring, like you're about to blow a bubble. Mix loopful into the cell suspension of the +pGLO tube. Return it to the ice. Don't add plasmid DNA to the -pGLO tube.
6. Incubate tubes on ice for 10 minutes. Bottom of tubes should make contact with the ice.
7.Label four agar plates on the bottom as follows: one LB/amp plate label +pGLO; LB/amp/ara plate label -pGLO; LB/amp label -pGLO; and the LB plate -pGLO.
8. HEAT SHOCK!! Transfer both tubes into the water bath that's set at 42 degrees Celsius for exactly 50 seconds. (Push the tubes all the way down in the rack so the bottom of the tubes make contact with the water. Replace both tubes on ice immediately. Incubate in ice for 2 minutes.
9. Take off ice and open a tube. Use a new pipet to add 250 ul of LB nutrient broth to the tube and reclose it. Repeat with a new pipet to the other tube. Incubate at room temp for 10 minutes.
10. Tap closed tubes with finger to mix(or flick it). Use new sterile pipet for each tube, pipet 100ul of the transformationa nd control suspensions to appropriate plates.
11. Spread suspensions evenly with a sterile loop.
12. Stack of plates and tape them together, upside down. Put it in the Biology rooms' incubator overnight which is set at 37 degrees Celsius.
Review Answers:
Observations:
+pGLO; LB/amp: has the gene but it isn't "turned on". It has a medium to heavy population which is white and yellow. Our estimated count was 130. Transformation plates
+pGLO; LB/amp/ara: has the protein that is turned on, which makes it glow. It has a medium to heavy population that's yellow then a light white. Our estimated count is 149. Transformation plates
-pGLO; LB/amp: has no population and no bacteria!! Control Plates
-pGLO; LB: has a HEAVY bacterial lawn!!! Control Plates
Analysis:
Plasmid doesn't make a difference to the health.
Our goal is to see if it glows or doesn't glow
The amp kills unless a gene from the plasmid is LB/amp +/-
Definitions:
amp = antibiotic
ara = arabinose sugar (activates some genes)
The PROCESS!!
1. label one closed test tube +pGLO and another -pGLO. Place in the foamy tubey thingy..
2. open tubes and use pipet to transfer 250ul of the CaCl2. Place on ice.
4. Use loop to pick up a single colony of bacteria from the starter plate. Get the +pGLO tube and immerse the loop into the transformation solution at the bottom of the tube. Spin the loop "washing machine" until the entire colony is dispersed. Place the tube back in the ice. Repeat with -pGLO with a new sterile loop.
5. Examine plasmid DNA with the UV lamp. Immerse new into plasmid DNA stocktube. Withdraw a loopful. Should be a film of plasmid across the ring, like you're about to blow a bubble. Mix loopful into the cell suspension of the +pGLO tube. Return it to the ice. Don't add plasmid DNA to the -pGLO tube.
6. Incubate tubes on ice for 10 minutes. Bottom of tubes should make contact with the ice.
7.Label four agar plates on the bottom as follows: one LB/amp plate label +pGLO; LB/amp/ara plate label -pGLO; LB/amp label -pGLO; and the LB plate -pGLO.
8. HEAT SHOCK!! Transfer both tubes into the water bath that's set at 42 degrees Celsius for exactly 50 seconds. (Push the tubes all the way down in the rack so the bottom of the tubes make contact with the water. Replace both tubes on ice immediately. Incubate in ice for 2 minutes.
9. Take off ice and open a tube. Use a new pipet to add 250 ul of LB nutrient broth to the tube and reclose it. Repeat with a new pipet to the other tube. Incubate at room temp for 10 minutes.
10. Tap closed tubes with finger to mix(or flick it). Use new sterile pipet for each tube, pipet 100ul of the transformationa nd control suspensions to appropriate plates.
11. Spread suspensions evenly with a sterile loop.
12. Stack of plates and tape them together, upside down. Put it in the Biology rooms' incubator overnight which is set at 37 degrees Celsius.
Review Answers:
- I would expect to find bacteria on the LB plate because I never saw any plasmid.
- Genetically transformed bacterial cells would be located on the LB/amp/ara and LB+ plate. Because the antibiotic is selecting.
- LB/amp plates should be compared to determine any genetic transformation because it can be used as a control.
- The controls were: same bacteria, same temperature, and the same amount of bacteria. In this case the LB was the control.
Observations:
+pGLO; LB/amp: has the gene but it isn't "turned on". It has a medium to heavy population which is white and yellow. Our estimated count was 130. Transformation plates
+pGLO; LB/amp/ara: has the protein that is turned on, which makes it glow. It has a medium to heavy population that's yellow then a light white. Our estimated count is 149. Transformation plates
-pGLO; LB/amp: has no population and no bacteria!! Control Plates
-pGLO; LB: has a HEAVY bacterial lawn!!! Control Plates
Analysis:
Plasmid doesn't make a difference to the health.
Our goal is to see if it glows or doesn't glow
The amp kills unless a gene from the plasmid is LB/amp +/-
Definitions:
amp = antibiotic
ara = arabinose sugar (activates some genes)
Tuesday, April 5, 2011
GATTACA
Questions about GATTACA!
(I wasn't here for the second part of the movie. :[ )
1. The following terms were used in the movie. How do they
relate to the words we use: degenerate and invalid?
De-gene-erate
In-valid - an invalid in the movie meant that a person wasn't "perfect" They weren't created artificially through the country's program to make the perfect child.
Borrowed Ladder
2. Why do you think Vincent left his family, tearing his
picture out of the family photo, after winning the swimming race against his
brother?
I think he finally proved his point to his brother that he could do what he wanted even though he was an invalid, but after he accomplished that he felt that he could move on with his life and pursue the things he wanted to pursue, without his family.
3. Describe the relationship between Vincent and Anton.
Vincent and his brother, Anton were very competitive in the beginning of the movie, always trying to beat the other one in a competition or race. Anton was then the detective investigating Vincent's case.
4. When Jerome Morrow said to Vincent/Jerome, “They’re not
looking for you. When they look at you, they only see me,” what did he mean?
Can you find any parallels to this type of situation in real life?
5. Choose your favorite character from the film. Explain why
you choose that person. Would you want to be that person? Why? Why not?
7. The technology to do what was done in the movie is
definitely possible within the next fifty years. Do you think that Vincent’s
world could eventually happen in America? Why?
8. What do you think is wrong with the society portrayed in
"GATTACA"? What is right?
I don't think anything was right in that movie. I think the fact that the parents got to choose the baby was extremely wrong. The fact that they discriminated against the "invalid" or the unhealthy ones, in order to get a perfectly normal job was wrong. It seemed that if you weren't "valid" and had perfect health, history, etc you were basically an outcast because you could possibly have a .1% possibility of having a heart problem or something.
10. You and your spouse are having a child and are at the
Genetic Clinic pictured in the movie. What characteristics would you want for
your child and what would you ask to be excluded? Why would you make those
choices?
I wouldn't choose to have my child chosen from the Genetic Clinic. Basically because of my religion and believes that's not okay with me in any way. It's basically determining the future.
11. Picture yourself as either Vincent, Jerome, or Anton.
Would you have acted the same or done things differently if you were in the
same world as them?
12. How does the society in GATTACA resemble the type of
society America was during the height of the eugenics movement?
People were going crazy with "making their own personalized babies" just like in GATTACA. In GATTACA the clinic babies were the only babies thought acceptable, which was probably what some people thought during the eugenics movement.
I really enjoyed this movie. It taught me a lot about how America could possibly turn out if we keep digging for information or going against our beliefs to make our lives perfect. It's scary how close we could be to a world like this.
Sunday, April 3, 2011
PCR!!
If only it was PBR right? (: (Professional Bull Riding) but no. This is almost as interesting, without the screaming fans, angry animals, and cowboys.
I did an online Bacterial ID Lab that was intended to identify the bacterial sample given.
First of all you have to prepare the DNA sample that is to be used. This involves placing the bacterial colony in a microcentrifuge tube and inserting the digestive buffer. The tube has to sit for several hours until the sample is ready. Following that you have to heat-inactivate the digestive enzymes which will denature and inactivate them. Add counterbalance and spin down cellular debris for removal from the sample. Then the wanted DNA is supernatant. Transfer the supernatant to the PCR tube and the sample prep is complete!!
Next step is to use PCR to make copies of DNA sequences. To do this you have to add a PCR master mix solution to all of the tubes. To set up a positive control reaction, you have to add control dna to one tube. For negative reactions you must add de-ionized water to one tube. Then insert both of them into the PCR machine. The short strands are desired DNA strands from PCR thermal cycling process.
NEXT: Purify the PCR product. To do this you have to set up the microconcentrator column and add a buffer solution to the column, then add the PCR product to the column. Put the positive and negative controls on ice until needed again. Add counterbalance to the tube and put it in the centrifuge. After a while DNA is trapped into the column and you need to loosen it into a new tube. Invert the column into the new tube (turn it upside down) and add a buffer. Now put centrifuge assembly to collect DNA into a collection and wait patiently.
PCR sequencing prep is next. First you have to dillute the PCR product to increase the volume. Add distilled water to purify the PCR product. The green and blue strip tubes contain PCR reaction mixtures, so now you can add purifed PCR product to them. They are now ready for PCR amplification so put it in the PCR machine. The Sequencing prep is complete!
Second to last step is DNA Sequencing. You must load the auto sequencer and insert the tubes. In my case the first tube read tacggtagcgtaatgcc. And that completes the DNA sequencing event.
The last step is to analyze the sequence. Copy the output from the DNA sequencer and past it on the ncbi website. The ncbi website searches through it's massive database and eventually comes up with results. The bacteria was identified as bartonella henselae.
I did an online Bacterial ID Lab that was intended to identify the bacterial sample given.
First of all you have to prepare the DNA sample that is to be used. This involves placing the bacterial colony in a microcentrifuge tube and inserting the digestive buffer. The tube has to sit for several hours until the sample is ready. Following that you have to heat-inactivate the digestive enzymes which will denature and inactivate them. Add counterbalance and spin down cellular debris for removal from the sample. Then the wanted DNA is supernatant. Transfer the supernatant to the PCR tube and the sample prep is complete!!
Next step is to use PCR to make copies of DNA sequences. To do this you have to add a PCR master mix solution to all of the tubes. To set up a positive control reaction, you have to add control dna to one tube. For negative reactions you must add de-ionized water to one tube. Then insert both of them into the PCR machine. The short strands are desired DNA strands from PCR thermal cycling process.
NEXT: Purify the PCR product. To do this you have to set up the microconcentrator column and add a buffer solution to the column, then add the PCR product to the column. Put the positive and negative controls on ice until needed again. Add counterbalance to the tube and put it in the centrifuge. After a while DNA is trapped into the column and you need to loosen it into a new tube. Invert the column into the new tube (turn it upside down) and add a buffer. Now put centrifuge assembly to collect DNA into a collection and wait patiently.
PCR sequencing prep is next. First you have to dillute the PCR product to increase the volume. Add distilled water to purify the PCR product. The green and blue strip tubes contain PCR reaction mixtures, so now you can add purifed PCR product to them. They are now ready for PCR amplification so put it in the PCR machine. The Sequencing prep is complete!
Second to last step is DNA Sequencing. You must load the auto sequencer and insert the tubes. In my case the first tube read tacggtagcgtaatgcc. And that completes the DNA sequencing event.
The last step is to analyze the sequence. Copy the output from the DNA sequencer and past it on the ncbi website. The ncbi website searches through it's massive database and eventually comes up with results. The bacteria was identified as bartonella henselae.
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