Fantastic Feedback Loops

Homeostasis is defined as the tendency of the body to maintain a constant internal environment. The body manages itself by using feedback loops that make adjustments to different variables such as blood calcium levels, blood glucose levels, and metabolism. Without these feedback loops our bodies would not be able to function as there would be no balance.

Blood Calcium Levels:

     This feedback loop monitors our blood calcium levels. When there is too much calcium in our blood our Thyroid is alerted and releases calcitonin. Calcitonin is in charge of lowering our blood calcium level by reducing calcium uptake in the kidneys and depositing calcium in our bones. Doing so removes excess calcium from our blood and stores them away, hereby lowering our blood calcium levels to the norm.
     On the other hand, sometimes our blood calcium level is too low. When this occurs, our body is required to increase these levels by stimulating the Parathyroid to release PTH or  Parathyroid Hormone. PTH signals the bones the start releasing calcium, the kidneys and intestines to increase uptake of calcium through Vitamin D. Eventually our blood calcium level will increase to an acceptable level.


Blood Glucose Levels:

     Here is another feedback loop that helps sustain our body's blood glucose levels. When we have too much sugar in our body the Beta cells in our pancreas releases insulin.  The insulin stimulates our body cells to take up more glucose and our liver to store the excess as glycogen. As glucose is removed from our blood stream our blood glucose levels decrease to normal and the release of insulin diminishes.
     When our blood glucose level is too low the alpha cells in our pancreas release glucagon. Glucagon tells the liver to break down glycogen and release the glucose into the blood stream. Afterwards, blood glucose levels start to increase to a set point and the release of glucagon diminishes.

Metabolism:

     Our metabolism controls the nutrients and energy in our body. When our metabolism is working too much, Triiodothyronine (T3) and Thyroxine (T4) signal the hypothalamus and pituitary gland to stop producing TSH which, therefore, stops the production of T3 and T4. This brings our metabolism back into balance.
     However, when our metabolism is too low, our hypothalamus stimulates the release of TSH which tells the thyroid to start releasing T3 and T4. This affects the heart, liver, bones, and central nervous system activity. Our body will start to sweat and our heart rate will increase, thus restoring our metabolism to its norm.

Table 1: This table shows the relationship between temperature as it increases and the amount of oxygen gas produced by the liver enzymes.

Temperature of H2O2 (oC)	Starting Amount of Gas (mL)	Ending Amount of Gas (mL)	Net Amount of Gas (mL)
20	210	325	115
20	213	305	92
60	250	340	90
60	200	225	25
73	200	250	50
80	150	200	50
90	205	280	75

*Each reaction is timed for 90 seconds

Observations:

·         Bubbling

·         Erlenmeyer flask started fogging up

·         Paper discs turned white

·         H₂O₂ started to boil at 80^oC Resulting in Popping sounds

·         Smells “sour” and “funky”

It is Law

The second law of thermodynamics, also known as the law of entropy, states that order will always decrease and chaos will rise. Entropy can also be used as a unit of measure for energy that is no longer capable of affecting a closed system; closed system meaning a system that is not losing energy, nor gaining.

For example, friction in the atmosphere is produced by gas molecules colliding with one another as well as the Earth, thus creating disorderly energy. Another more practical example is ice melting into water. In order for this to occur, bonds between the water molecules must be altered; hence, order turning into chaos. An additional example is the decomposition reaction of hydrogen peroxide. When H2O2 decomposes, two other molecules produced: water and oxygen gas. To visualize entropy, let's picture a mug of hot coffee. You want to drink this coffee as soon as possible because you are incredibly tired and need to prepare for the long day of work ahead of you. You can either a) add cold cream to your coffee and wait 5 minutes or b) wait 5 minutes and then add cold cream. With a thorough understanding of the law of entropy, it would be most logical to wait 5 minutes first because the initial difference in temperature between the air and the coffee is greater, thus resulting in a higher rate of heat transfer. If you were to add cream at the beginning, the temperature would be a lot cooler and the difference would be a lot smaller, resulting in a slower rate of heat transfer. Overall, entropy is obeyed when there is a change of state, formation of energy, and/or the number of molecules.

Ironically, to achieve orderly energy, there must be disorder. Therefore, so long as the amount of orderly energy is less than the amount of disorderly energy, then the second law of thermodynamics stands true.

Sceyence Fear

1. Question
Why does the mouse with the mutated ACTM gene in T cells go blind? How can we prevent and cure the blindness?

2. Key words:
mouse
gene mutation
blindness
T cells
ACTM gene
abnormal eye structure
eye infection
medical treatment
human eye diseases

3. Relevant questions:
A mouse has many genes so why was the ACTM gene mutated?
Why should the blindness in mice be investigated?

How can we dissect and check the eyes of the mouse?
How can we prevent and cure blindness of mice or humans?

What is the structure of the normal eyes of mice and humans?
What are the possible reasons leading to blindness in mice and humans?

Where is the ACTM protein localized in T cells?
Where do T cells stay in the eyes of mice or humans?

When do the mutated mice go blind?
At what stage should mice with eye diseases be treated to prevent and/or cure blindness?

Who, in addition to people with serious diabetes, go blind?
Who among blind humans have, or may have, this mutated gene?

4. Three sources:
(1). Q liu and K. siminovitch, unpublished data
(2). Mallick, I (2007, August 13). T-cells - What are T-Cells?. About.com Leukemia and Lymphoma. Retrieved November 3, 2012, from http://lymphoma.about.com/od/glossary/g/tcells.htm
(3). EYE STRUCTURE AND FUNCTION. (n.d.) My Eye World. Retrieved November 3, 2012, from http://www.myeyeworld.com/files/eye_structure.htm

5. 3 equations:
(1). frequency of blind mice = (number of blind mice / total number of mice) x 100%
(2). frequency of T cells in an eye = (number of T cell in an eye / total number of cells in the eye) x 100%
(3). frequency of another kind of cell in an eye (B Cells) = (number of another kind of cell (B Cells) / total number of cells in an eye) x 100%

Control:
Wild Type Mouse without a mutated ACTM gene

Independent:
Mice with mutated ACTM gene

Dependent:
Blindness

To Hear or Not to Hear

Sound and Fury is a documentary directed by Josh Aronson. The film is about the Artinian family, all of whom have different views on the deaf society. Peter Artinian is deaf and has been "blessed" with an all deaf family of a wife and three kids. However, when his daughter, Heather, asks for a cochlear implant, Peter is at a loss for words. Chris Artinian, on the other hand, finds out that one of his newborn baby twins is deaf. The news completely devastates him and his wife, but when he discovers that a cochlear implant would allow his son to hear, he jumps at the opportunity. In Chris' eyes, being deaf is a huge disability, but to Peter, one couldn't possibly wish for more.

It's hard to determine who has the "correct mindset" here. Chris and his wife, Mari, don't know what it's like to be deaf. Mari has had some experience with deaf people since both her parents were deaf. But once she grew up, she wanted to get away from the deaf community as soon as possible. In her eyes, being deaf was a huge burden. That is why, when she found out that her son was deaf, she wanted him to get a cochlear implant right away. Yet, to Mari's parents, she was making a huge mistake. Mari's mother was definitely upset with Mari's decision. It was like she had completely turned her back on her family and the deaf community. You see, for most deaf people, being deaf was a gift. They did not see it as a disability but as a lifestyle. They were perfectly capable of leading successful lives which was why Chris' brother, Peter, loved his all deaf family. To him, his life and family were perfect. He had a job in New York, all his children attended school, and his wife took care of everything at home. This was no different from the life of a hearing person. But when Heather, Peter's 5 year old daughter, wants to hear "alarms ring, telephones, and all sorts of thing", Peter is taken back. Like any father, he wants whatever is best for his children, and to him, staying deaf was the way to go. However, Peter's parents, both of whom can hear, are telling Peter that they should go through with the cochlear implant. He is frustrated with his parents because he believes he knows what is in Heather's best interest and refuses to be criticized for it. So the million dollar question is, "To hear or not to hear?"

Let's think about it. What exactly is a disability? According to the Merriam-Webster Online Dictionary, a disability is the condition of being disabled or the limitation in the ability to pursue an occupation because of a physical or mental impairment. Looking back at Peter, was he limited in the ability to pursue an occupation because of a physical or mental impairment? I wouldn't say so. He has a job and is happy with his life. Mari's parents are both happy as well and have not been limited in any way. But to Chris and Mari, they see their son as being disabled with a lot of limits to come. They find it very hard to relate to deaf people because they have not experienced life without any sound, but from what they can imagine, it must be a very closed and muted world. They want their son to live like they do because they believe that their hearing life is best. We can see that the mentalities of the hearing and deaf people are completely different .

At the end of the day, the same question still arises. Should the deaf be allowed to hear? Should Heather be given the cochlear implant she desires so much? I would personally have to say yes, she deserves to have one. Peter is afraid that he will lose her daughter in the hearing world and that she'll forget all about the deaf culture. I highly doubt that will happen. Heather has already learned sign language and is able to communicate thoroughly with deaf people. It will be very hard for her to forget as well since she learned it at the age of 5, a very optimum time for learning languages in children. In addition, Heather will be able to translate for her parents in the future if they ever encounter a situation where communication is difficult. I honestly see no harm in giving Heather the ability to hear. The fortunate news is Heather eventually receives a cochlear implant at the age of 9. Ever since, Heather has been prospering well in school and has become assimilated with speech. I'm happy that she got her implant, but I feel like they did it a tad late. It's still evident that Heather needs some sort of speech therapy since she has a heavy accent which can be hard to understand. However, the point is, Heather is happy.

All in all, we can see that everyone has different views on life. What we might consider to be a disability, someone else might not. It's not our job to preach what we believe is correct. It's our job to do what we must do to make our lives better and let others do what they think will make their lives better.

Preventing Mutations...Au Naturel

Cells in our body are constantly busy with replicating DNA, transcribing mRNA, and producing proteins. With all of this happening again and again and again, the probability of errors, or better known as mutations, are quite high. To prevent these unwanted variations from happening, nature has developed its own defense mechanisms.

During the replication process, the parent DNA is copied into two daughter DNA molecules. Nature had to find an effective way to create exact duplicates of the DNA without risking exposure to mutations. This is why DNA is copied through the process of semi-conservative replication. Semi-conservative replication means inside every newly copied DNA molecule, exists one original strand from the parent DNA and one newly synthesized DNA strand. By having the original parent DNA as a template, the copied DNA molecules should technically be exactly the same by simply matching pyramidines and purines. As well, with every cell division, the ends of the chromosomes, called Telomeres, slowly deteriorate. This is because every time DNA is replicated, some genetic information is lost. Fortunately, the telomere contains no important genetic information, therefore there are no errors on the important parts of the DNA.

How exactly is the DNA copied? DNA is in the shape of a double helix. In order for replication to take place the DNA molecule must be unwound with the help of the Helicase enzyme. Then a second enzyme called the Single-Strand Binding Proteins help to keep the DNA strands unwound. Now most people would think that the Helicase enzyme would start to unzip the strands starting at one end, but that would jeopardize the DNA. With the one end exposed, the DNA would become susceptible to foreign invaders and could easily break and/or mutate. This is why nature decided to have DNA replicate in "bubbles". All along the parent DNA, there would be small sections of replication. The parent DNA wouldn't unwind all at once, therefore protecting the genetic information. Instead, it would unwind little by little; here and there. By doing this, there will be a lot of tension in the DNA molecule which is why Gyrase, another enzyme, helps to rid the DNA of its stiffness. As the DNA is copied, DNA Polymerase III, the enzyme that is in charge of elongating the daughter DNA, moves along the parent strand, expanding the bubble, until two bubbles meet, thus forming a bigger bubble. The process continues until there are no more bubbles; just two daughter DNA molecules.

DNA is not only replicated, but can also be transcribed into mRNA for protein production. Once RNA Polymerase II has finished transcribing the DNA, Pre-mRNA is made. Pre-mRNA cannot be translated into amino acids yet because it contains introns. Introns are useless pieces of genetic information that do not contribute to the creation of amino acids, at least not in this particular gene. Exons are the ones that contain the codes to make amino acids. However, introns do serve some purpose; they reduce the likelihood of mutations. If there is a strand of RNA that contains only exons and a foreign invader were to attack that RNA, a mutation on the important genetic information is inevitable. But if a foreign invader were to target a strand of RNA that contains introns and exons, then the introns reduce the probability of mutations only occurring on the exons. The introns are essentially taking the "blows" for the exons.

Eventually introns are removed from the Pre-mRNA with an enzyme called the Splicesosome or the snRNPs. Splicesosomes will cut away the introns and reconnect the exons. The way they do this is very unique. Rather than just slicing and gluing haphazardly, snRNPs loop the intron. By doing this, the two ends of the exons are brought very close together. The snRNPs quickly cut off the intron, which floats away, and combines the exons. The fact that the exons were already so close leaves little time and space for invaders to mess with the coding.

Introns aren't the only way nature protects the RNA. If an RNA strand were simply floating around, the two ends of the RNA would be at risk of being attacked by water. This is why nature added a G-Cap or 5'-Cap to the 5' side of the RNA and a Poly-A tail on the other. The G-Cap contains multiple Guanine molecules and does not actually code for anything. It also signals to the ribosome where to start. The Poly-A tail contains multiple Adenine nucleotides and does not code for anything either. But by having the two caps, the RNA is safe from water. It's like the RNA has two body guards.

After the Pre-mRNA has lost its introns, it is now ready to be dispatched from the nucleus. Once translation has started the ribosome converts the nucleotides, three at a time (codons), into amino acids. Most of the amino acids can be made from multiple different codons.

In the chart we can see that Glycine can be produced by a GGG, GGU, GGA, and GGC codon. Therefore, if a mutation were to occur on the third letter of the codon, the same amino acid would still be produced. If the mRNA codon was supposed to be AGU, but was, instead, mutated to become AGC, there are no worries because serotonin would still be produced nonetheless. This is known as the Wobble Effect.

Nature works in wondrous ways to preserve our identities. Had there been none of these defense tactics, our bodies would be severely mutated and we would not be able to survive. These are only some of the ways that nature protects our genetic information. We should not take nature's work for granted. Without it, there would be no life on Earth.

New Genetic Discoveries from labfest