Epigenetics

IDENTICAL TWINS: PINPOINTING ENVIRONMENTAL IMPACT ON THE EPIGENOME

1. Often, the physical characteristics of genetically identical twins become increasingly different as they age, even at the molecular level. Explain why this is so. (use the terms "environment" and "epigenome")
When twins are first born they are subject to the same environment. As they grow older they make different choices in how they eat and what environment they choose to grow up in. Their epigenome changes based on the signals received based on the environment they surround themselves with.

2. Name 3-4 environmental factors that influence the epigenome.
What you choose to eat, the kind of stress related to your work profession, and how often you exercise.

3. What is an imprinted gene?
a silenced copy of either mom or dad’s gene. Only one is used.


YOUR ENVIRONMENT, YOUR EPIGENOME
1. Discuss factors in your daily life (ie. Diet, exercise, stress etc.) that could be affecting your epigenome
The fact that I’m in DLC and not in regular classes could contribute the amount of stresss I feel on a daily basis. The way I eat and how much exercise certainly contributes to my epigenome. The friends I choose to hang out with can influence how much I feel depressed or elated.

LICK YOUR RATS

1. Explain how a high- nurturing mother rat shapes her pup's epigenome, and what that pup's response to stress will be.
They will be extremely relaxed. They will ease more quickly after a stressful situation.

2. In rats, does licking by the mother activate, or deactivate her pup's GR gene?
It activates the GR gene, and the amount that they lick their pup unwinds the GR genome to a certain amount.

3. Exp la in how cortisol and the GR protein work together in the brain to relax a rat pup. You may draw a diagram.
The cortisol acts as the signal to the GR to tell it to unwind. The more cortisol released, the more relaxed the GR genome becomes. The amount of GR protein in the hippocampus depends on whether the mother was a high nurturer or a low one. The cortisol is released into the brain. This usually happens during the fight or flight response. The cortisol bonds with the protein and sends calming signals to the GR. The more proteins the more signals.

4. The rat nurturing example shows us how parental behavior can shape the behavior of their offspring on a biochemical level. Relate this to humans and think about the personal and social implications. Record your thoughts.
If a mother neglects or ignores a child, then the child will be more likely to lead a stressful life and ignore its children. If the mother is highly attentive, then the child will probably live a relatively stress free life.

NUTRITION & THE EPIGENOME
1. Explain how the food we eat affects gene expression.
If our parents were healthy eaters, we are less likely to have a big chance of getting diabetes or diseases that result from poor diet. It is the same if your parents were poor eaters. You are more likely to get diabetes.

2. Can the diets of parents affect their offspring's epigenome?
Yes they can. Your parents can put you at risk for diabetes and heart disease.

EPIGENETICS & THE HUMAN BRAIN

1. How does Dietary methyl influence gene expression ?
Drugs can tell the body to produce more methyl. The more methyl, the less proteins produced. This can change you r gene expression greatly.

2. Why do Toxins affect gene methylation?
Toxins trigger changes in brain regions and even when the system is wiped clean the changes can continue to linger. These changes could possibly be passed on to the next generation.

Dogs Decoded 
Is domestication related to epigenetics?

I think that it does.

Notes
- They can read our emotions by scanning our faces starting on the left. They don’t do this with any other species.
- They have been man’s companions for a long time. Archaeological records say not that long ago (a few thousand years) that they became domesticated. Mitochondrial DNA says even longer.
- Humans can understand the different barks that dogs use. They know when the bark means anger and when it is begging etc.
- When humans pet dogs, both receive bursts of oxitosin, the same thing that happens when a mother breast feeds her baby (creates bond)
- From information found in mitochondrial DNA, we know that domesticated dogs descended from the gray wolf (closest match, which is extremely close).
- Dogs were probably a pivotal point for hunter-gatherers because we could now bring down bigger game, which meant more food, which meant population increase.
- Dogs respond to pointing and the direction that our eyes look. Our almond shape eyes expose the white sclera when we look to the side. Even puppies as old as six weeks respond to pointing. Even our closest relatives, the chimps, don’t respond to pointing. They just do whatever they want.
- Nurture v. Nature   Up bringing has little to do with domestication. Wolves and puppies were brought up in the same way, and the wolves didn’t listen to the owners, they did whatever they want.
- Silver foxes were bred. Only the tamest were allowed to breed. Over time they became affectionate to humans. Even newborns started to be less aggressive.
Along with the lost aggressiveness, They lost their silvery-black fur. They started turning white. Some retained their curly tails. Their limbs and tails became shorter. The babies had floppy ears for a longer amount of time. - They found that genetics had to do with aggressiveness. They also bred the most aggressive foxes. They stayed the same.
- Scientists found that the tamer foxes also had less adrenaline, which meant they were not as scared, so they were not aggressive.
- By doing brain scans they found that humans emotional part of the brain becomes active when looking at pictures of babies and dogs. Most of our dogs now have infantile features. This is probably because we are naturally protective of infants. We feel the need to nurture the dogs. Most dogs are chosen for their looks.
- Amazing border collie has over 300 “word” vocabulary. Can fetch toys by name. Can get scale models. She can fetch things from a picture. The picture represents the toy. This is amazing because most dogs can’t do this. 2-yr olds are just starting to learn to do that kind of a thing.

Households Acids and Bases

We were given the following household solutions and had to find their pH.
Vinegar
Ammonia
Lemon juice
Soft Drink (Coke)
Drain Cleaner
Detergent
Baking Soda
Milk

I made a hypothesis for each of what their pH would be.
Vinegar -Acid 3
Ammonia -Base 12
lemon juice -Acid 3
Soft drink -Acid 6
Drain Cleaner -Base 13
Detergent -Base 10
Baking soda -Base 8
Milk -Base 11

We used these materials to help find the pH
-computer
-vernier computer interface
-logger pro
-vernier pH sensor
-wash bottle
-distilled water
-stirring rod
-250 mL beaker
-sensor soaking solution
-household solutions
-8 small test tubes
-test tube rack
-blue litmus paper
-paper towel
-red cabbage juice
-graduated cylinder

We followed these procedures:
Obtain materials and put on the goggles. Remember not to drink or eat in the lab area. Label the test tubes from 1-8. In test tube one, put 3 mL of vinegar. As in the order above, pour 3 mL of the specified solution into the remaining test tubes. [As a note, the baking soda solution must be made with 20 mL of water and 1/2 a tablespoon of baking soda. Stir thoroughly.] Using the dropper, collect some of the solution in the dropper. Remove a slip of litmus paper and drop a few drops from the dropper onto the litmus paper. Compare the color to a pH scale and record the best estimate for the acidity or basicness of the solution. Clean the dropper before the next use. Repeat the test for the rest of the solutions. Don’t empty the solution, instead retrieve some cabbage juice. Pour 3 mL of the cabbage juice in each test tube, and in between record the acidity or basicness of the solution. Dump each of the test tubes contents when you are done. Refill the same liquid in the same container. Unpack the probe and connect to the computer via lab quest mini. Open the file called “21 Household Acids” from the Chemistry with Vernier folder. Remove the sensor from the storage solution, and don’t spill it. Rinse the tip of the sensor with distilled water and put it in the first test tube. When the number on the computer stabilizes record it on a chart. A good example of the chart can be found in the results section. Remove the sensor, and rinse with distilled water. Put it back in the storage solution, and then remove and rinse again with distilled water. Put in the next test tube and continue the pattern. When you are done, rinse the sensor in distilled water and put back in storage solution. Pack up your materials and dispose of solutions.


Some of the results we ended up with were different than our hypothesis, and some were the same. The following chart is our results.

Test tube	solutions	blue litmus paper	red cabbage juice	pH
1	Vinegar	Acid 2	Acid 2	2.64
2	Ammonia	Base 12	Acid 6.5	11.31
3	Lemon juice	Acid 2	Acid 2	3.27
4	Soft drink	Acid 3	Acid 3	2.97
5	Drain cleaner	Base8	Acid 5.5	12.69
6	Detergent	Base 10	Base 10	9.98
7	Baking Soda	Base 9	Base 8	7.91
8	Milk	Base 9	Base 9	6.57

This is a picture of the sensor in our 5th test tube.







This is a picture of us cleaning the sensor.


This is when we labeled the test tubes.

This is a shot of one of the pieces of litmus paper.


This table compares my hypothesis’ and my results.

Solution	Hypothesis	Result
Vinegar	Acid 3	2.64
Ammonia	Base 12	11.31
Lemon juice	Acid 3	3.27
Soft Drink	Acid 6	2.97
Drain Cleaner	Base 13	12.69
Detergent	Base 10	9.98
Baking Soda	Base 8	7.91
Milk	Base 11	6.57

Conclusion: I got the majority of my hypothesis’ confirmed. Some of them were complete opposites of the hypothesis, but most were extremely close to my guesses. I think that if we were to do this again we should have more items to test, even some tests that are harder.
We even had the chance to see that the pH of the storage solution for the pH sensor. It was acidic and turned our litmus paper red. When the probe was in it, it said that it had a pH of about 3.5. We should have more opportunities for testing the different materials.