What Ava Marsh Knows About The Human Body

    The human body is a complicated and intricate thing.  There are many systems that interact with each other such as the nervous system, the digestive system, the respiration system, the reproductive system, and the excretory system.  Each of these systems work together to keep our body alive.
     The foundation of our body is bones.  Without them, we would be jello.  There are a lot of bones in our body.  Bones provide structure, and also protect certain organs.  On top of bones is muscle.  As shown in the diagram, there are different names for different muscles.  Muscles help our body move.  On top of muscle is skin.  Skin protects the body from pathogens and the outside environment.
    The brain is the control center of the body.  It sends and receives signals that control reactions, functions, and thoughts.  The brain also stores memories in these signals.  It controls all the organs, such as the heart, which pumps oxygenated blood through the body, the stomach and intestines which digest food, and the eyes which allow us to see.

     These organs are made up of things called cells.  Cells are the basic units of life, as shown in the picture.   There are many different types of cells in the human body that each serve a specific function, such as skin cells, brain cells, and liver cells.  Every cell in our body contains a nucleus that holds DNA.  DNA is a genetic code that carries instructions for basic life.  The DNA codes for protein synthesis. Proteins basically make up everything.
    Cells are made up of atoms grouped together to form different compounds and substances.  Over 75% of our body is H₂O.
   The cells in our bodies need certain things to survive and function properly.  That is why we need to eat, breath, and sleep.  Sleeping a very important process in which the cells in our body need to recharge.  Most of healing, growing, and regeneration happens when people sleep.  That is why it is important for adults to get eight hours per day.  Teenagers need even more sleep because they are growing and developing.  Most people fail at getting adequate sleep.

Genetic Traits

 In biology class we collected data of different genetic traits from our family members and classmates.  Then we compared our result to see if we could figure out our genotypes.  The genetic traits included tongue-rolling, attached or unattached ear lobe, hitch hiker's thumb, and widows peak.  After completing a survey on my immediate family members, I came up with these results:

  From an outside source I was able to find that tongue rolling is a dominant trait, unattached earlobes are dominant, straight thumbs are dominant, and widow's peaks are dominant.  Using this information it is possible to predict what my family's genotypes are.  Since tongue rolling is a dominant trait, and my mother, Pamela, cannot roll her tongue, she definitely has a homozygous recessive (tt) tongue-rolling gene. My father, Carl II, on the other hand, can roll his tongue, which opts for two possible options: he either has a homozygous dominant (TT) gene, or a heterozygous (Tt) gene.  Since all of Pamela's and Carl II's children can roll their tongues, it is quite probable that Carl II has indeed a homozygous dominant tongue-rolling gene, as this punnett square shows.

Attached vs. unattached earlobes seemed to be the most controversial survey taken, therefore the following results may lack accuracy.  Carl II, who has unattached earlobes, and Pamela, who has attached earlobes, produced three children with unattached earlobes and one child with attached earlobes.  Since unattached earlobes are the dominant trait, Pamela definitely has the homologous recessive genotype (ee).  Then we can predict that Carl has the heterozygous genotype, since most of his offspring have unattached earlobes, but one of them have attached.  

   As for hitch hikers thumb, I concluded that both my parents have the homozygous recessive gene (hh), as well as all of us offspring.  Straight thumbs are dominant, and therefore the offspring of a person who carried that gene would have a chance of having a straight thumb, even if the other parent was homozygous recessive.  Out of four kids all of us have hitch hiker's thumb, therefore having homozygous recessive hitch hiker thumb genes.  Although, there is still a chance that one of my parents are heterozygous.

   Widows peak is a dominant gene.  Carl II has a widow's peak, his wife does not, and neither do any of his children.  This means that Carl II probably has the heterozygous widow's peak gene (Ww) and Pamela has the homozygous recessive gene along with the rest of her children (ww).  

   Next I compared my findings with my class results.

What I found the most interesting about this was that the dominant traits are not always the most common.  For example, Widow's peak is a dominant gene, however less than half of our class have them.

Forensics

     Forensic science is any type of scientific tests or techniques used in the investigation of crimes.   Forensic scientists are the ones who provide the scientific proof to prove a criminal guilty or a person innocent in court.  Real forensics is a little bit different then the media portrays it to be in shows like Law and Order, CSI, or NCIS, but it is still very interesting.

   A variety of techniques and tests are used to provide evidence for a criminal investigation such as modern computer and clay facial reconstruction, DNA fingerprinting, autopsy techniques, forensic anthropology, and toxicology.  DNA fingerprinting is an especially useful part of this.
    As we all know, DNA is a sequence of nucleic acids that code for protein creation and basically are the directions for all living things.  No two people have the same DNA sequence, and scientists have found how to make a DNA profile of an individual in order to identify that person.  They scan 13 specific regions of DNA, which are called loci.  These locus points are different in every person, and the chance that two people will match at all thirteen sites is very small (1 in 400 trillion).
     When crime scene investigators find any type of evidence at a crime scene that can be tested for DNA, such as hair or blood, it is taken to a lab.  There the DNA is extracted by a chemical technique similar to that of the DNA necklace experiment our class conducted.  If this technique doesn't isolate enough DNA to analyze, scientists artificially increase the strand by adding DNA polymerase to the extracted DNA strand.  The polymerase catalyzes DNA synthesis, and the DNA strand is replicated, creating enough DNA for analysis.  Fluorescent molecules are attached to the certain parts of the DNA, and then the DNA is run through a DNA sequencing machine that makes the DNA fingerprint that can be compared.

      Nowadays scientists are working on isolating specific genes that code for specific things.  For example scientists are now able to identify the part of the DNA responsible for inherited traits.  This can make reveal the suspect's hair or skin color and help solve a crime.  In the future scientists will be able to figure out what height or race a person is.  They are even researching how to build a model of a suspect's face from DNA found in evidence, like a single drop of blood.  The possibilities are unknown, but DNA in forensics certainly helps solve a lot of crimes and bring justice to people.  For example, it helped identify bodies after 9/11.  For more information on that: http://www.terradaily.com/reports/Sept_11_Panel_Makes_Recommendations_For_DNABased_ID_After_Mass_Disasters.html
     There are some moral/ethical issues surrounding this topic.  CODIS, which is the COmbined DNA Index System, stores DNA fingerprints of DNA collected at crime scenes and of convicted offenders.  The privacy of this index is definitely a concern.  Usually once a sample is stored in the index it is never destroyed, so peoples' entire genetic makeups are up for grabs.  Genes can reveal many aspects about a person including susceptibility to particular diseases, legitimacy of birth, and maybe even behavioral aspects and sexual orientation. 
Sources:

http://library.thinkquest.org/04oct/00206/pti_dna_matching.htm

http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml#6

"Short Ecuadorians hold anti-aging secret"

    In this recent New York Times article, Jennifer Welsh discussed the discovery of a specific cancer and diabetes resisting gene that is found in Ecuadorians with Laron syndrome.  Laron syndrome happens when certain genes responsible for releasing growth hormones are mutated, stopping the production of the growth factor IGF1.  Although this causes dwarfism, studies have shown it also increases longevity and reduces the incidence of cancer and diabetes.  

    I find this research to be very uplifting and exciting.  I really hope that this can develop into something that can prevent cancer and diabetes in the future, because they are really horrible and should be eradicated.  Valtar Longo, the lead study author of the University of Southern California, says that he is planning to run clinical trials with these drugs.  I think this is a great idea but I also feel that the negatives of artificially altering the hormone levels in a person might out weigh the positives, especially if there are unknown side effects and such.  Doesn't a lack in IGF1 cause dwarfism and other complications?  I really like this research though it is very hopeful and interesting. 

Melanoma

           Melanoma is the sixth most common cancer in the US.  It is the deadliest of skin cancers, and causes 8,700 deaths in the US per year.  What’s even scarier is that Melanoma rates have been rising increasingly in the past 20 years, so melanoma prevention and medical research is very important.

            John Hunter first discovered melanoma in 1787.  He described the tumor he found as a “cancerous fungus” and put in the Hunterian Museum in Royal College of Surgeons in England.  It wasn’t until 1968 that the tumor was tested and found to be metastasized melanoma.  Melanoma was first recognized as an actual disease in 1806, by Rene Laenne.  Henry Lancaster made the connection between sunlight intensity and the development of melanoma in 1956.

            There are several types of melanoma.  The most common type is called Superficial Spreading Melanoma.  It usually occurs in Caucasians, and can be found in all body sites.  Superficial spreading melanoma produces lesions, usually flat and irregular in shape and color, with different shades of black and brown.  Nodular melanoma, which accounts for about 15% of melanoma cases, usually starts as a raised area that is dark blackish-blue or bluish-red.  Another type of melanoma is called Lentigo Maligna Melanoma.  It is most common in the elderly, and usually occurs in sun damaged skin on the face, neck, arms, hands, soles of the feet, or around the toenails.  Lentigo Maligna Melanoma is large, flat, and tan with areas of brown.  The least common form of melanoma, Acral Lentiginous Melanoma, usually occurs on the palms, soles, and under the nail.  It is more common in African Americans.  When melanoma occurs in the colored part of the eye, it is called Melanoma of the Eye, or Ocular Melanoma.

            Melanoma is directly linked to sun exposure and ultraviolet radiation. Older people are at a higher risk to develop melanoma, however the disease often affects young, otherwise healthy people.  Risk factors include having a fair complexion, living in a sunny climate or at a high altitude, long-term exposure to high levels of strong sunlight, one or more blistering sunburns during childhood, the use of tanning devices, family history of melanoma, being freckle-y or having multiple birthmarks, exposure to certain carcinogens such as arsenic, coal tar, and creosete, and a weakened immune system due to AIDS, leukemia, organ transplants, and various medications. 

            Melanoma develops when UVA and UVB radiation from sunlight causes certain mutations in the DNA of melanocytes, which are cells that produce melanin, a skin pigment responsible for skin and hair color.  These mutations cause errors in the matches of nucleic acids in the DNA strands, specifically the genes involved in cell growth: tumor suppressors and proto-oncognes. When these genes become deformed, they no longer function properly.  With mutated tumor suppressors, which are cells that prohibit cell division, and proto-oncognes, which are cells that speed up cell division, cancerous melanocytes virtually have no checkpoint system and divide abnormally fast, producing more cancerous melancytes that then divide and build up and create problems. 

            The progression of Melanoma is classified into stages.  Stage I is classified as Thin Melanoma of the Skin, and happens when cancerous melanocytes begin to accumulate.  These atypical melanocytes have mutated genes and produce abnormally large amounts of melanin, causing darker lesions to appear on the skin.  These lesions are usually asymmetrical, large, elevated, and have irregular borders and variations in color.  When Melanoma is caught in stage I, surgery is done to remove the lesion and patients usually survive, with a 90% survival rate.

            Stage II, which is medium or thick melanoma of the skin, is when mutated melanocytes begin to divide radically, causing the cancer to spread deeper into the skin.  Surgery is usually used to remove the lesion and surrounding area.  Samples of the nearby lymph nodes are also taken to make sure the melanoma has not progressed.  There is a 75% survival rate for stage II melanoma.

            When the melanoma has progressed to the lymph nodes, or moved a ways from the primary skin lesion, it is classified as stage III.  Stage III is harder to treat because the cancer has metastasized, and there is a 30%-60% survival rate depending on the extent of the disease.  Treatments include surgical removal of the lesions and affected lymph nodes, radiation, and high-dose interferon-alpha for a year.  The interferon boosts the immune system, which helps fight the cancer and prevents it from recurring. 

            When the melanoma spreads to distant sites in the body, for example organs or multiple lymph nodes, it is classified as stage IV melanoma.  Usually, surgery and radiation is used to remove the tumors, and systemic drugs, which are oral or IV drugs that go throughout the body, are administered.  Stage IV melanoma has a less than 10% survival rate, and there are no established treatments.  Most of the treatments and clinical trials such as interleukin-2, temozolomide, thalidomide, cisplatin-based chemotherapy, and biochemotherapy, which is cisplatin with or without other chemotherapy drugs, combined with interleukin-2 and interferon-alpha.  Other experimental treatments and include vaccines, new immunotherapy drugs, anti-angiogenic drugs, molecularly targeted small molecule drugs administered orally or intravenously, and bone marrow transplant from relatives. 

These treatments, among many others, are currently being researched to improve the survival rates of melanoma.  For the time being, the best way to survive melanoma is to prevent it by wearing sunscreen and watching skin for irregular freckles and moles. 

         Sources:

http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001853

http://www.oncolink.org/types/article.cfm?c=18&s=63&ss=861&id=9623

http://www.cancerquest.org/

http://www.medicinenet.com/biological_therapy/article.htm

http://www.mamashealth.com/cancer/melanoma.asp

http://www.sunislife.com/ART_sunscreenscancer2.html

http://www.malignant-melanoma.net/who-discovered-melanoma.php

http://www.melanomahopenetwork.org/Section.asp?SID=2200&N=Treatment%20Options

http://www.nature.com/nature/journal/v445/n7130/fig_tab/nature05661_F1.html

http://www.cancer.org/acs/groups/content/@nho/documents/document/acspc-024113.pdf

Light and Dark Reactions

     Plants and fungi do not eat other organisms to supply their energy.  Instead, they have evolved to use water, carbon dioxide, and sunlight in a process called photosynthesis to make their energy, as shown in picture of basic photosynthesis.  The basic equation of photosynthesis is 3 CO₂ + 3 H₂O --> C₃H₆O₃ + 3 O_3.  

     Photosynthesis happens in two major parts: the Light Reaction, and the Dark reaction.  The light reaction requires sunlight and involves the absorption of light energy, and the conversion of light energy into chemical energy.  The dark reaction, also known as the Calvin Cylce, does not require sunlight and is the process that takes the chemical energy and stores it in the form of usable glucose.

     Plant cells have chloroplasts in them (refer to picture), which consist of groups of stacked thylakoids surrounded by a membrane.  The space surrounding the thylakoids is called the stoma.  Embedded in the membrane of thylakoids is chlorophyll, a green pigment that absorbs light.  Chlorophylls form two types of clusters, called photosystems (PS) I and II. (shown in picture)

     When sunlight comes in contact with a plant, photons from the sunlight hit the chloroplast to start the light reaction.  Solar photons take only eight minutes to reach plants from the sun.  When electrons attached to a chlorophyll are stuck by a photon, they become excited.  These electrons are then so excited that they are transferred from one PS II to one PS I.  An electron transport system is formed between the photosystems, and more electrons are transferred.  Water is oxidized into O₂ and H⁺ in an enzyme by PS II.  Electrons are also formed in the oxidation that replace the electrons lost in the transferring of electrons.  The protons (H⁺) made in the oxidation process accumulate in the thylakoid space, making a difference in the concentration gradient.  When electrons reach PS I, NADP⁺ is reduced to NADPH, which is used later in the Calvin Cycle.  The difference in concentration gradients of protons causes potential energy to build up, and then protons are forced through the ATP synthase, which reduces ADP to ATP.

    The Calvin Cycle (shown in picture) uses the NADPH and the ATP created in the light reaction, along with some carbon dioxide to form sugars that the plant or fungi can use.  To start the calvin cycle, three carbon dioxides are combined with three 5-carbon sugars (RuBp) with the help of the catalyst rubisco, which immediately split into six molecules of a 3-carbon acid.  This first phase is known as Carbon Fixation.  Next, the six 3-carbon acids are rearranged with the energy from one ATP and one NADPH and creates G3P.  One G3P is half of a glucose.  Then, the remaining 5-carbon sugars are rearranged with the help of ATP to create more RuBp, which joins with other carbon dioxides to continue the Calvin Cycle.
     The rate of photosynthesis depends on light levels, water levels, nutrient levels, temperature, and carbon dioxide availability.

Extra Information:
http://www.johnkyrk.com/photosynthesis.html

Cellular Respiration

     In biology class Annie and I made a stop motion to show how cellular respiration works.  We used candy to represent different molecules.   Creating this project really helped me understand the confusing processes of cell respiration and also to learn all the details of it.  We had a lot of fun making this video and I hope you enjoy it!

Lionfish Invasive Species

     Recently, lion fish have invaded the florida keys and have been wrecking havoc there.  This prezi explains how the lion fish invaded, and also the extent of the damage they have caused.

     This video from the New York Times shows how some people are trying to put an end to this invasive species.


For more information:
http://www.miamiherald.com/2010/02/07/1468635/lionfish-invade-the-keys.html
http://www.usnews.com/science/articles/2010/04/23/lionfish-invasion-continuing-to-expand.html?s_cid=related-links:TOP

Krebs Cycle Explained

The Krebs Cycle is the second step in cellular respiration.  From one pyruvate, 3 CO2, 4 NADH, 1 FADH2, and 1 ATP are produced.  

Glycolysis Explained

This is a sketchfu showing how glycolysis works.  Glycolysis is the first step in cellular respiration, a decomposition pathway that provides all cells with energy.  Glycolysis requires one molecule of glucose and 2 molecules of ATP.  The outputs of Glycolysis are 2 pyruvates, a net gain of 2 ATP, and 2 NADH.

Caffeinated Alcoholic Drinks are Dangerous

     On November 17, 2010, the F.D.A. decided that caffeine is an illegal additive to alcoholic drinks.  The F.D.A. particularly condemned the drink Four Loko, a drink that is 12 percent alcohol by volume and has up to 156 milligrams of caffeine per can.  (equivalent to 4 shots of liquor and 3 cups of coffee)  The F.D.A. research over the past year has proven that people who drink these caffeinated alcoholic beverages are more likely to become intoxicated.  The caffeine masks the effects of alcohol, and leads people to "a state of wide-awake drunk".  This causes them to consume more alcohol without passing out, and do crazy things resulting in hazardous and life-threatening situations.
      Four Loko has caused several deaths in the past months.  Students at Ramapo College in Mahway, M.J., and Central Washington University in Ellensburg, Wash. who drank this beverage ended up in emergency rooms with high levels of alcohol poisoning.
     The F.D.A. issued warnings to fourteen major companies that produce these caffeinated alcoholic drinks, urging them to take their products off the shelves.  Many colleges have banned Four Loko.  A few states, including Michigan and Washington have also banned the drinks.  Other states are following them.



For more information:
http://www.hedgefundlive.com/blog/blackout-in-a-can
http://www.nytimes.com/2010/11/18/us/18drinks.html?ref=science
http://southfield.injuryboard.com/defective-and-dangerous-products/caffeinated-party-brew-banned-in-several-states.aspx?googleid=286270

Osmoregulation in Adelie Penguins

     Adelie Penguins (shown in video below) live in Antarctica, with no access to fresh water.  Their diet is largely made up of marine invertebrates, mostly krill.  Because these penguins require lower salt concentrations in their bodies than their surroundings, they need to regulate the levels of salt and water in their cells, or their osmotic concentration.  This is called osmoregulation.

       An Adelie penguin's salt levels are lower than that of its environment, and this causes a concentration gradient that favors the influx of salt.  They also must drink salt water to obtain the water they need.  In order to get rid of the extra salt, the penguins developed a mechanism called the salt gland.  The salt gland lies in the skull of the penguins.

     This picture from http://digimorph.org/specimens/Pygoscelis_adeliae/ shows where the salt glands are located in the skull of the Adelie Penguin.  Salt diffuses into blood cells, and salt ions (Na⁺ and Cl^-) in the blood are removed by the sodium transport mechanism (the sodium potassium pump).  These salt ions are moved to the salt glands where they are secreted into a highly concentrated salty solution and "sneezed out" by the penguins.
     Salt glands are also found in other marine birds, marine reptiles, and sharks.  Without them these organisms would not be able to drink saltwater without becoming dehydrated. 


Information from:
https://elibrary.unm.edu/sora/Auk/v114n03/p0488-p0495.pdf
http://www.cartage.org.lb/en/themes/sciences/zoology/animalphysiology/osmoregulation/osmoregulation.htm

Eukaryotic Cell Project

Chlamydia trachomatis

A jing on the bacteria that causes the STD Chlamydia:

Macromolecules Lab Reflection

     Yesterday during biology class we conducted a series of lab tests to find what macromolecules existed in different foods. Each lab partners were given either egg whites, egg yolks, potatoes, apples, onions, strawberries, or lemons, and were required to find if those foods contained protein, glucose, starch, and/or lipids.  We used different indicator tests to look for each macromolecule.  (shown in picutre) Some of the results were very unexpected and interesting.

     My lab partner was Shelby and we were assigned strawberry. (shown in picture) My prediction was that strawberry would contain glucose, but no protein, starch, or lipids. We tested for glucose by adding 3 mL of Benedict's solution to 5 mL of strawberry in a test tube, then we put the test tube in a beaker of boiling water and heated it. The pink/red strawberry changed to a bright orange color after five minutes. The color change indicated that the strawberry contained glucose. To test for starch, we added five drops of Lugol's iodine solution to 5 mL of strawberry. The strawberry did not turn black, and this meant that there was no starch in the strawberry. We tested for proteins by adding ten drops of Biuret solution to 5 mL of strawberry, and the pink/red strawberry changed to a brown color. This showed that the strawberry had proteins. For the final test, we rubbed strawberry on to a piece of brown paper to look for lipids. We let the paper dry over night, and no glossy finish or grease on the paper was visible, which meant that there were no lipids in strawberries.

     It was very interesting to see the other groups results. For example, I was surprised to see that lemon contained none of the four macromolecules we tested for. I was also surprised to see that the egg yolk and the egg whites didn't have protein in them but strawberry did.  However, experimental error could have occurred because the group could have had a problem, so its possible that the results aren't entirely accurate.  From this experiment I learned a lot about the different macromolecules that exists in different foods.  It was very interesting and fun.

 Picture #1 from: (http://media.photobucket.com/image/starch,%20glucose,%20lipids,%20proteins/veewhy_x3/Sept07/0919075.jpg)
Picture #2 from:
(http://art4linux.org/system/files/strawberry.jpg)

Proteins

A jing about proteins and their structure and functions:

Characteristic Properties of Water

     72% of earth is water, and living cells contain 70 - 80% water.  Obviously, it is a very important substance, and it has many unique, unusual, and amazing properties.

Polarity:
     Water is a polar covalent bond between one oxygen atom and two hydrogen atoms.  This means two hydrogen atoms decided to share their one electron each with an oxygen atom.  Since oxygen atoms are bigger, they pull the shared electrons (electrons = negative charge) closer to their nucleus, which contains neutrons as well as protons that have a positive charge. This makes the electron and negative charge farther away from its Hydrogen nucleus.  Because of this, the side of the water molecule with the hydrogen atoms has a slight positive charge, and the opposite side has a negative charge.

Solubility:  

     Because water has both a negative and a positive charge,  negatively and positively charged atoms are attracted to it and therefore many different things can dissolve in water, for example, sugar, ions, Na

+

.  This is why water is known as the universal solvent.  

Adhesion and Cohesion:
     Water sticks together, and that is why it forms droplets and puddles.  The negative side of a water molecule is attracted to the positive side of another molecule, and they stick together this way.  It is called a Hydrogen bond.

Density:
     The density water is 1g/ml.  Water in its solid form is less dense than water in its liquid for and therefore, it floats.  For example, icebergs float on the top of the ocean.  The reason why ice is less dense then water is because of the hydrogen bond is stronger, and the molecules are more dense and less stable in water in its liquid form.  The molecules in frozen water form a lattice formation, it is more stable and less dense, and therefore ice is lighter per ml than water.


Specific Heat:
     Specific Heat is the amount of energy necessary to raise one gram of a substance one degree celsius.  Water has a high specific heat because the molecules are bound together so tightly that it takes more energy to break them apart.  For example, when you boil water on a stove, it takes a while for the water to heat up, however the pot or thing that you are using to boil the water in gets hot very quickly.  This indicates that water takes a long time to heat up, and also it takes a long time to cool down.


Neutral pH:
     H₂O is constantly ionizing.  This means the water molecules are separating, creating ions OH^- and H⁺.   As they separate, the water molecules combine again, to form H₂O.  Because there is an equal amount of H⁺ and OH^- molecules in water, water is neither acidic or basic.  Therefore pure water is neutral and has a pH of 7.

Biology Class

     Biology is the study of life, and this year during biology I want to learn more about living things.  It fascinates me how separate cells react together to form an entire living being, how viruses can hijack cells to infect an organism and how scientists can create medicines and vaccines with the knowledge of biology.  Scientists can do amazing things to alter living things, by injecting things into their DNA and changing hormone levels and such, and my goal is to understand more of the science and technology that is involved.  I want to learn how scientists can do all those amazing things to prevent disease, and learn about genetics and evolution.
     Technology will definitely help me reach those goals, because there is so much information on the internet.  Web tools will make this goal more achievable, for example, the blogs will offer a new and interesting way for me to study biology and complete assignments, and to connect to other people and exchange ideas and knowledge.