Unit 10 Reflection

This unit focused on physiology, or how different systems in the human body are structured and how they work. We first started by learning about a major process in the body, homeostasis. Homeostasis is the body's ability to maintain an inner balance. We learned about two types of feedback loops: positive feedback loops (moving in one direction towards one extreme) and negative feedback loops (moving back and forth around a set point.) Certain examples of homeostasis are how the body tries to maintain a certain level of blood glucose and how it tries to stay around a set temperature.

We studied the major characteristics of the circulatory and respiratory systems, and how they work in conjunction. We breathe in oxygen, and it travels down into our lungs. As we inhale, the alveoli (tiny sacs in the lungs) expand and gas exchange happens between the alveoli and the capillaries. The oxygen goes into the blood and the pulmonary vein brings back oxygen-rich blood to the heart. It goes through the left atrium, then the left ventricle, which goes through the aorta to the body. Deoxygenated blood comes back from the body through the superior or the inferior vena cava, it then goes through the right atrium, right ventricle, and the pulmonary artery carries it to the lungs. The cycle repeats.

We studied the two parts of the nervous system: the central nervous system and the peripheral nervous system. The CNS includes the brain, the brain stem, and the spinal cord, and it has four parts: the cerebrum, the diencephalon, cerebellum, and the brain stem. Neurons are cells that have three parts: the cell body, the dendrites, and the axon. The stimulus starts at the dendrite, which travels the length of the neuron to the axon terminal and passes between neurons through the synapse. 

The endocrine system produces and regulates hormones. The hypothalamus links the endocrine system to the nervous system. The pituitary gland is often called the master gland and controls the other endocrine glands. Some other glands that produce hormones are the thyroid gland, the parathyroid, and the adrenal gland. 

In the digestive system, food is broken down mechanically and chemically at all stages of digestion. Food travels down the esophagus and into the stomach. The small intestine absorbs most nutrients, and and solid wastes and water are eliminated in the large intestine. 

I want to learn more about the physiology of the different systems in the body, and learn about the ones we didn't cover in this unit. 

This is my last blog post this year, and doing this blog has been a great learning experience.  I'm really proud of all the unit reflections, and another project I am really proud of is my Genetics Infographic, because we worked on it for a long time and I think it gets the information across in a visually appealing way. 

I've grown as a student since August, and reflecting on every unit (such as the Unit 6 Reflection), and writing conclusions and using pictures to reflect on labs has been a great part of the process.

Pig Dissection Lab

This lab was the most unique lab we have done throughout biology this year: we dissected a fetal pig in order to better understand its anatomy and physiology, as its systems are very similar to our own human systems in the body. We identified certain external structures, such as its wrists and shoulders, and pointed out their functions. In the digestive system, we were able to observe where the esophagus and the stomach were located, and we noticed the pancreas and liver as well. There were many differences in appearance between all of the organs, especially the large intestine and the small intestine. This helped us understand how food moves through the digestive system. We learned that the diaphragm separates the abdominal cavity from the thoracic cavity, and it puts pressure on the lungs which makes us breathe. We saw where the larynx, the trachea, and the lungs were located. We saw many veins and arteries in the circulatory system, and we saw the pig's four chambers of the heart. We also observed other organs, such as the spleen, the kidneys, and the thyroid gland. The dissection was very helpful in understanding really where everything was in the body and how the systems worked, and it was an enriching learning experience.



Here is our video tutorial of the pig dissection:

https://www.youtube.com/watch?v=s_tTXnivR1s

* The spleen has many different functions, but one of them is to filter blood in the immune system. 

20 Time Final Post

For my 20 time project, (See 20 Time Individual Reflection) I did a survey to measure people's awareness of certain risk factors for diabetes and heart disease. I particularly focused my survey on the South Asian population. My main product was the results/data and new information I collected after doing the survey. Below are the data in graphs of 2 sample questions out of the 30 total questions I asked. 

I asked people to rate their overall stress levels on a scale of 1-10. 

A question I asked about Triglycerides 

In order to share our findings during the process of the 20 time project, we gave a TED style talk to the class. Here is the video of my TED Talk:

The TED Talk was a really new and interesting experience for me. I had practiced beforehand and I felt that I gave a presentation that got across all the information that I wanted to share with the audience. However, my presentation was slightly overtime, and in general, while I was preparing for the talk, I found it to be a challenge to cut down all the information into 5 minutes. My public speaking skills and confidence to speak in public has definitely increased a lot through doing this TED talk. I can build on the 20 time project experience as well as the experience of transforming all the information into the most pieces to share with others. 

20 Time Individual Reflection

For my 20 time project, I chose to do a study that explores some of the risk factors and parameters that are important in diabetes, insulin resistance, and heart disease in South Asians. I created a survey and I gave it to a small sample of the community so that I could try and determine the common risk factors, and more importantly, the level of awareness in a sample of the South Asian community.

I formed my questionnaire after reading the book The South Asian Health Solution, which was my initial inspiration for doing this project. I was intrigued by the fact that South Asians are at higher risk for diabetes and heart disease, and I wondered why that was and wanted look further into it. My focus was for the study was to see how aware most people were, and also to determine the prevalent risk factors.

My first steps were to research the topic, and I started by reading about 3/4 of the book The South Asian Health Solution. I used this resource, along with a couple others, to create my survey. I am happy with the major risk factors that the survey addressed, and how I formulated it to specifically measure how aware people were.

I then sent it to roughly 20 people, and analyzed some of the trends and patterns I saw. If I had more time on the project, I definitely would increase my sample size significantly to make the study more accurate. I divided my time slightly unevenly between the research and actually administering the questionnaire, and this is something I would change could I do the project over again. However, I learnt a huge amount from all the research I did on the topic, as well as creating and looking at the results from the survey.

I would love to continue giving the survey to more people; the results are fascinating, and tell me a lot about the awareness of risk factors for diabetes and heart disease in my immediate community. An immediate goal for me would be to continue raising more awareness of this topic as well, and share what I learned from my research with others.

Unit 9 Reflection

This unit was called "What on Earth Evolved", and we delved deeper into each kingdom and looked at the characteristics that define each group of organisms. Scientists have classified approximately 1.2 million species, but 8.7 million species are still unclassified. A Swedish botanist named Carolus Linneaus developed the 7 levels of organization that we use today; he formed scientific names in binomial nomenclature form. Phylogeny is the evolutionary history and relationships of species. A cladogram shows species' evolutionary relationships, and there is a common ancestor where branches meet. As we saw in Your Inner Fish, humans and fish have a common ancestor (See "My Inner Fish"). There are seven taxonomic levels: kingdom, phylum, class, order, family, genus, and species.

The 5 kingdoms within eukarya are: monera (prokaryotes), protista, plantae, fungi, and animalia. After the discovery of archae, which were found to be very genetically different from bacteria, the 3 Domain System was developed. The 3 Domains are Eukarya, Archaea, and Bacteria. Archaea challenge what we think of as required to live, and they live near hydrothermal vents, digestive tracts of animals, marshes, etc. In the bacteria kingdom, actinomycetes produce antibiotics, symbiotic bacteria live in guts to help with digestion (fix nitrogen), and cyanobacteria are photosynthetic.

We classify bacteria by their shape, cell wall composition, and the way that they obtain energy. Bacteria can be cocci, bacilli, and spirals. The gram stain has a crystal violet dye which will either bond with the peptidoglycan (gram-positive), or not (gram-negative). Bacteria can be chemoheterotrophs (bacteria which take in organic molecules), photoautotrophs (use light to convert H20 and CO2 into glucose), or chemoautotrophs (use energy from chemical reactions). They are very important in decomposition, and as nitrogen fixers. Viruses are not cells, but instead cores of DNA or RNA surrounded by a protein coat, or capsid. There are two types of viruses: lytic viruses and lysogenic viruses.

Fungi is a unique kingdom, with different characteristics from plants. Their cell walls are made of chitin, and they absorb their food through hyphae. Some types of fungi include sac fungi, club fungi (mushrooms), bread molds. Some of plants' major phyla are bryophyta (mosses), pterophyta (ferns), gymnosperms, angiosperms (flowering plants). Angiosperms can be monocots (have a single seed leaf), and dicots (have two seed leaves).

In animals, there are two types of symmetry: bilateral and radial. Some phylums of invertebrates are cnidaria, porifera (sponges), molluska. Arthropods, crustaceans, and insects are also invertebrates.

A sponge, part of the phylum Porifera

In the phylum chordata, which is mostly vertebrates, there are 7 classes of vertebrates: agnatha, condricthyes, osteicthyes, amphibia, and the amniotes reptilia, aves, and mammalia. Reptiles and amphibians have 3 chambers in their hearts, while birds and mammals have 4. They can be either ectothermic (cold-blooded) or endothermic (warm-blooded).


Here is my "What on Earth Evolved Presentation"


In this unit, we each chose an organism to present about and research in depth, and we had to give a 4-8 minute presentation to the class. I had researched the topic and practiced the presentation, so I felt as if I knew the subject well. Since I practiced before presenting, my nerves went away as soon as I started presenting, and I learned that this is a way to be more confident that works for me. In the future, I would include additional interesting facts and pictures as well.

"My Inner Fish"

One of the main themes in the two episodes "Your Inner Fish" and "Your Inner Reptile" is that humans and fish have a shared ancestry, and humans and reptiles are actually closely related. There is a lot of concrete evidence in fossils and embryos to support this.

In the initial stages, a human embryo and and fish embryo look very similar because of the common Hox genes, which suggest common ancestry. Other evidence for common ancestry includes some structures that humans and fish both have today: bony skeletons, backbones and skulls, and shared basic brain anatomy.
The Sonic Hedgehog gene sends out the organizing signal; it tells cells to do different things, and creates the array of digits on the hand. Hair, which is a defining characteristic of mammals today, may have first evolved in our small mammalian ancestors as a sensory organ or a tool to help keep warm.

Another example of humans' relation to reptiles is their hearing anatomy. Mammals have an acute sense of hearing because they have 3 bones in their middle ear which form a lever system, while reptiles only have 1 bone in their middle ear. Scientists think that two jaw bones in reptiles got smaller, moved further up the jaw, and evolved to have a new purpose in the ear in mammals.

Human and fish embryos look very similar initially because of Hox genes, indicating a common ancestry

20 time update: Surveying

During the past couple weeks, I have finished creating my questionnaire that I am using to determine whether people are at risk for diabetes and heart disease. I have also interviewed 3 people using this questionnaire, and I think that it is proving reasonably effective.

My questionnaire originally contained quite specific numbers to determine whether a person was at risk for diabetes or heart disease. However, as I did my first interview, I realized that the majority of people don't know their exact test results, and at most they will remember whether it was in the low, normal, or high range. I shifted my questionnaire slightly to measure people's awareness of their own risk factors. I also used their answers of results being in the low, normal, or high range to determine their level of risk.

My next steps are to continue giving the questionnaire to more people; the more people I include in my study, the more accurate it will be.

Invertebrate of Your Choice: Jellyfish

Jellyfish are invertebrates, and belong to the phylum Cnidaria. They are the oldest existing animals that have specialized tissue. Jellyfish are medusas (non-polyps). They are part of the scyphozoans class of Cnidaria. Jellyfish are found in every ocean, and are about 500 to 700 million years old. Jellyfish are the oldest animal to have multiple organs. They cannot see, but some do have ocelli, which allows them to detect light. Jellyfish come in a very wide variety of sizes, which can range from 1 mm in height to about 2 meters in height. They don't have a central nervous system, a digestive system, a respiratory or a circulatory system. They obtain their oxygen instead by diffusion through their skin.

Source: Wikipedia

Moon jellyfish 

Creating the Questionnaire

In the past two weeks, I've started creating my questionnaire for my 20-time project. I finished reading The South Asian Health Solution and I am much better educated about my topic now. I will be doing a study that will look at how South Asians are at high risk for diabetes and heart disease. Using the study to determine what each individual's risk factors are, I would like to help people who are at risk for diabetes and heart disease make lifestyle changes so that they can prevent this from happening.

My questionnaire so far has tried to address people's family history, amount of exercise, diet, amount of sleep per night, and certain levels, such as triglycerides, HDL, blood pressure, that should ideally be around a certain number.

My next steps are to continue writing my questionnaire, and I will start surveying people as soon as possible.

Unit 8 Reflection

This unit was about evolution; we looked at how populations evolve and how life on Earth originated. Evolution happens because genetic variation exists in populations. Variation is due to sexual reproduction, meiosis, and crossing over which happens during meiosis. Humans breed animals for both work purposes and for food, and this is called artificial selection. They select individuals with the trait they want and only mate individuals with this trait. A selection process also occurs in nature, natural selection. Nature favors certain phenotypes which are advantageous for survival and these individuals have a better chance of surviving, reproducing, and passing on their genes. The population evolves to look like these "winners", which was one of Darwin's conclusion about the evolution of populations. This principle was illustrated in The Hunger Games Lab where each there were three phenotypes, and the ones that were better for picking up enough food survived, and those who couldn't gather sufficient food fast enough died and didn't pass on their genes. The initial population in this lab did evolve, as we could see by the change in allele frequency.

Allele frequency change in the Hunger Games Lab

We can tell if a population evolved by looking at if the allele frequency has changed. Allele frequency is how common an allele is in a population. Natural selection can favor one extreme phenotype, in which case the normal distribution bell curve will shift towards that extreme. This is called directional selection. In stabilizing selection, nature favors the intermediate phenotype, and in disruptive selection, nature favors both extreme phenotypes. Disruptive selection can lead to speciation, where two new species arise from one. They are considered two new species if they can no longer mate with each other. Speciation occurs when groups are reproductively isolated, either geographically, behaviorally, or temporally.

http://www.bio.miami.edu/dana/pix/selection_modes.jpg

Evidence of evolution can be seen in many ways, from the analogous and homologous structures in organisms to embryology to vestigial structures, which are evolutionary left-overs. These all indicate a common ancestry. Scientists use fossils as evolutionary evidence as well, although fossil evidence can be biased because organisms which have shells or bones fossilize the best. Earth's history, which is 4.6 billion years long, is divided into 4 eras (precambrian, paleozoic, mesozoic, and cenozoic), which are further divided into periods.

I am curious to learn more about the ways that current populations in the world are changing now.
I am working to become more assertive in group settings (rather than passive or aggressive). I am doing this by voicing my opinions, but also coming up with compromises and incorporating others' opinions as well.

Geologic Timeline Reflection

In this assignment, we made a timeline of Earth's history to better understand when and how some major events happened on our planet. We used a strip 10 meters long to represent the 4.6 billion years of Earth's history, where 1 million years was represented by 2 mm. One very significant major event is the creation of Earth itself, which happened 4.6 billion years ago. Nothing as we know it would exist if this collision did not happen to form our planet. The increase of oxygen in the atmosphere and organisms which use oxygen for life processes which happened in the Ordovician is an important event in Earth's history. This laid the foundation for processes such as photosynthesis and respiration, which are essential. The majority of organisms today are descended from these first organisms. The extinction of the dinosaurs was a very significant event in Earth's history as well. It happened during the Mesozoic Era and gave way for mammals to dominate. This paved a path for humans and other mammals to come into existence because the dinosaurs were very dominant at the time and the smaller mammals stood no chance.

In our scale, 1 million years was represented by 2 mm. It was surprising for how much of Earth's history there was no life. Being able to see this visually represented really put so much of history into perspective for me. Before doing this timeline, I knew that the Precambrian Era was 88% of Earth's history but when we scaled our timeline accordingly, I began to really understand how significant a part of history this is.

Humans have made up such a small part of Earth's history, and it is surprising how much they have changed the planet in such an relatively insignificant amount of time. Humans are now the dominant species, but have been around for not even a speck in terms of geologic time.

One question I have is, how significantly have humans changed the planet in relatively small time that they have occupied it?

Hunger Games Lab Analysis

1. In this lab, we simulated a population of organisms competing for survival. We wanted to model the process of natural selection. There were 3 phenotypes for picking up food in our environment: stumpys (AA), knucklers (Aa), and pinchers (aa). Corks represented food, and the food was scattered around a field. The organisms had 30 seconds to gather as much food as they could, and they had to get a certain amount in order to mate and reproduce.

2. Pinchers were the best phenotype at gathering food, because they got to pick up food with their thumb and their index finger, which was the easiest to get as much food as possible.

3. We found that the population did evolve, and the changed allele frequency is evidence for that. In the initial population, the frequency of the "A" allele was 52% and the frequency of the "a" allele was 48%. After 8 generations, the "A" allele frequency was 41% and the "a" allele frequency was 59%.

4. The genotypes and phenotypes that each organism was "born with" was completely random, the scattering of food throughout the field was random.

5. If the food supply was smaller than it was, there would have been more competition within the population for food. In this situation, the more aggressive organisms would have obtained more food regardless of their food-gathering phenotype. If there was a larger food supply, those organisms who weren't as aggressive would have a more equal chance. This parallels what happens in nature when food is scarce.

6. The results would probably have been significantly different if there was no incomplete dominance with the knucklers. The "A" allele would probably have been completely wiped out, because the stumpys' phenotype was the most difficult for gathering food.

7. In natural selection, nature "favors" individuals who have the best traits. The population evolves to look like these individuals.

8. At times when the food supply was clumped, some individuals developed aggressiveness in order to gather enough food and survive. There are many behaviors similar to this in nature, when an animal is more skilled at gathering food fast, or running from a predator. Individuals needed a place to store their food after they picked it up, and those with bigger pockets often had an advantage. In nature, certain animals will have certain genetic advantages like this over other organisms. The individuals with these strategies' phenotypes would have been more common in the population, which affects the allele frequency.

9. In nature, natural selection acts on and favors certain phenotypes, not genotypes. Populations as a whole will evolve, but not individuals.

10. One question I still have from this lab is: in nature, how much of an organism's chance of survival has to do with it's genes and how much has to do with it's learned skill set?

Beginning Research

During the past two weeks, I have begun to research my topic, which centers around risk factors for diabetes and heart disease in South Asians. I am currently reading a book for my research called The South Asian Health Solution. It is written by Ronesh Sinha M.D., an internal medicine specialist, who has noticed that South Asians are one of the groups that are at highest risk for diabetes and heart disease, and he states that overall, this is due to a set of high-risk genes coupled with poor lifestyle choices.

I read about the processes of inflammation and insulin resistance. Insulin is a hormone that carries glucose to your cells. The author likens insulin resistance to a train station, where insulin is the train ticket, glucose molecules are the passengers, the conductor is the insulin receptor, and and the train represents a muscle cell. Insulin resistance happens when the insulin receptors won't let in the glucose molecules, and therefore they remain in the bloodstream, increasing a person's blood sugar levels.

This is one of the key topics in the book, and I think the rest of the research will progress much faster now that I have the basics down. With a little bit more research, I think I will soon be ready to start creating my questionnaire.

Bird Beak Lab

Part 1: Analysis
In the bird beak lab, we came to the same conclusion as Darwin did: individuals who have "better" traits, or traits that are more suited to the environment, leave behind more offspring. We simulated 4 different types of birds' beaks with a spoon, a binder clip, a pair of tweezers, and a pair of scissors. The goal was for each bird to pick up as many pieces of "food" (rubber bands, macaroni, toothpicks, paper clips). We saw evidence that individuals with better traits leave more offspring when the tweezers-beaked bird had a total of 18 chicks, the highest among all other birds. A possible explanation for this could be that their beaks were more adept at picking up food. Another of Darwin's conclusions was shown true in our lab: the fact that populations gradually start to look more like the "winners", or individuals with the better traits. The tweezers chicks made up 37% of the population. An explanation for this is that the tweezers chicks collected more food and had more offspring.


Conclusion:
In this lab, we asked the question: if natural selection occurs in a population, how do changes in selective pressures affect the evolution of that species?  We also simulated a drought in this lab, where the drought wiped out all the seed pods (toothpicks). The toothpicks were removed from the birds' supply of food. Theoretically, this would affect only the birds who relied on the seed pods as a source of food. We found an increase in the tweezers chicks' population and the spoon chicks' population, who did not rely on the seed pods as a staple source of food. The scissors chicks' population stayed constant. This data support our claim because the birds did not rely much on the toothpicks for food, therefore the drought did not affect them much.

When we simulated the seed pod drought, our data somewhat contradicted the expected results. We hypothesized that the binder clip chicks' population would increase or stay constant, since it was the only type of bird that had never consumed the seed pods. Instead, the binder clip chicks' population decreased. This was probably due to an error. The binder clip required the user to apply a decent amount of pressure in order to operate it and pick up the food. When doing the back to back trials, using the binder clip became tiring. This error caused the population to decrease, instead of staying the same or increasing. In the lab as a whole, each bird beak was operated by a different student, and each student would have a different skill level in terms of picking up the food. This might have caused certain populations to be too high or too low. Due to these errors, in future experiments I would recommend students switching "bird beaks" in order to make the lab more objective and maybe finding an alternative for the binder clip, because of the finger pressure that is needed to use it.

This lab was done to demonstrate the concept of natural selection, and how every population will have winners and losers. From this lab I learned how natural selection would works in an ecosystem, and I now understand the concept better. Based on my experience from this lab, I can better understand why certain traits are more dominant in certain populations.

Intro to my 20-Time Project: Risk Factors for Diabetes and Heart Disease

The 20-time project, also called a passion project, refers to the idea that we get to use 20% of class time to work on a project of our interest. Every Monday, in class, this semester we will be working on a project of our choice and reflecting on our progress every other week.
In a nutshell, my project centers around exploring risk factors for diabetes and heart disease in South Asians.
My essential question for this project is this: what are some of the most prevalent risk factors for diabetes and heart disease in South Asians, and how aware are people about their risk factors? I will conduct a study, and using a questionnaire I will gather data at the end of the study that will give me an idea of how what people's risk factors are in my immediate community. One of my long-term goals for my 20-time project are to determine the general level of awareness in the South Asian community, and to make others aware of this too, so that if a person is at risk for diabetes or heart disease, they can make lifestyle changes as soon as possible.
Doing research and subsequently creating the questionnaire for my study will take some time, but I hope to get these steps underway as quickly as possible. The next steps in my project will be to gather data; I will meet with many people and ask them these questions. I think my study will be more accurate if I include as many people in my sample as possible. I can measure weekly progress by the number of new people I've interviewed, or the amount of research that I have done.

Unit 7 Reflection

This unit was about ecology, or the "study of house." We started off the unit by looking at how big ideas in biology, homeostasis, equilibrium, and interdependence are shown in nature. Environments are in best condition when they are in balance, or in homeostasis. Interdependence is also key theme in ecology because  living things are very dependent on each other for survival. We learnt about habitats vs. niches.  A habitat is the location where the organism lives, and includes all aspects of that area (abiotic and biotic factors). A niche includes all factors that a species needs to survive. I think that this was a weak area for me, and I still don't completely understand the difference between a habitat and a niche, but I think looking at more examples of this in nature will help me. There are 6 levels of organization on the earth: organism, population, community, ecosystem, biome, biosphere.

In an ecosystem, there are both producers (autotrophs) and consumers (heterotrophs). There are 5 trophic levels in an ecosystem: primary producers, primary consumers, secondary consumers, tertiary consumers, and quaternary consumers. A food chain shows how the different organisms get their energy, but doesn't account for the fact that usually an organism eats more than one other organism. A food web is a more accurate depiction. In a ecosystem, the producers at the bottom of the food web have the highest biomass (a method of measuring energy in calories or Joules), and the top-level consumers have the lowest biomass. This is because, at each level, 90% of the energy is lost as waste, and only 10% is retained. This is known as the 10% rule. I felt that trophic levels and energy transfer was one of my strengths.

We also learnt about the factors that can affect a population's growth. These include immigration, emigration, births, deaths, disease, predators, limited supply of abiotic factors, and population density and dispersion. All populations reach a carrying capacity (K), which is the maximum population that an environment can support. I thought that I understood this topic well. 

After a disturbance in an ecosystem, such as a fire, something called ecological succession results, which is the sequence of ecosystem changes that follow a disturbance. If soil remains after the disturbance, the type of succession is known as secondary succession. If there is no soil, it is called primary succession. 

A diagram of secondary succession 

Loss of species has shown to be tightly correlated with human population growth. Therefore, many species have gone extinct because of humans' behavior. 4 major threats to species' extinction are: habitat loss, introduced species by humans, overexploitation, and climate change. 

During this unit, we watched Bag It!, which explained why plastic bags and bottles are having a very negative impact of the environment. This is an issue that interested me, and I would like to learn more about it. 

We also did a conservation biologist project, where we researched an ecosystem (The Great Barrier Reef) and found out some of the threats facing the ecosystem. As a group, we brainstormed possible solutions to these threats. I learnt a lot from doing this project. Our group was able to collaborate effectively because we listened to each other's ideas and divided up the workload. We created a vodcast in which we taught what the Great Barrier reef looks like in balance, and how it is threatened. 

Unit 6 Reflection

This unit focused on the field of biotechnology, which is the use and manipulation of living things and their parts for human benefit. There are 4 main applications of biotech: industrial and environmental, agricultural, medical/ pharmaceutical, and diagnostic research. In the industrial and environmental field, fermentation as well as biofuels (using cellulase to break down cellulose into simple sugars as well as fermentation to produce alcohol for the fuel). Medical and pharmaceutical biotechnology includes gene therapy--both germ line gene therapy and somatic gene therapy. Gene therapy is inserting a copy of a healthy gene into a person who has a defective copy of that gene. An example of agricultural biotechnology is classical breeding, where individuals with a certain desired trait are bred several times. GMO, or transgenic organisms, have had recombinant DNA inserted into them. I felt that I understood this overview of biotechnology fairly well. There are also certain ethical questions that are asked of the field of biotechnology, called bioethical questions. Bioethics is the study of decision-making as it applies to certain advances in biology and medicine.

One technology in the field of biotech is recombinant DNA (rDNA). It is taking DNA from one organism and inserting it into another. The first step in this is to identify the gene of interest and the location and the sequence. Restriction enzymes are very specific enzymes which cut DNA whenever they read a specific sequence. They make a jagged cut and create two "sticky ends" that can bond with other DNA. Plasmids, which are circular DNA in bacteria, are naturally resistant to a certain antibiotic. I felt that this topic was one of my strengths, especially after doing the recombinant DNA lab, where we modeled inserting the insulin gene into a plasmid that was resistant to tetracycline, and only the bacteria with the plasmid would survive.

Model of recombinant plasmid

Another technology of biotech is PCR (Polymerase Chain Reaction), which is a procedure that creates millions of copies of a sequence of DNA so that that sequence can be analyzed. The DNA is denatured with heat, primers are annealed to the single-stranded DNA above and below the gene, DNA Polymerase are extended, and the process is repeated. Gel electrophoresis uses electricity to separate DNA fragments based on size, since the larger fragments travel more slowly than the smaller fragments. 

In the pGLO lab , we added a plasmid which contained GFP (Glowing Fluorescent Protein) to E.coli. There were 4 plates: -pGLO LB, -pGLO LB/amp, +pGLO LB/amp, and +pGLO amp/ara. The bacteria on the -pGLO plate formed a carpet of colonies. The -pGLO LB/amp plate had no growth. The +pGLO LB/amp plate had roughly 130 colonies, and the +pGLO LB/amp/ara had 150 colonies and glowed green under UV light. This lab helped me understand the process We also did the candy electrophoresis lab, where we put four reference dyes (Blue 1, Red 40, Yellow 6, Yellow 5) into four wells. Then we extracted dyes off of candies, such as purple skittles, blue m&m's, red skittles...etc and inserted them into remaining wells. We were able to compare the size of the fragments and identify if any of the reference dyes were present in the candies. From this lab, I was able to better understand how gel electrophoresis works and how to analyze the results. 

Candy Electrophoresis Lab 

I want to learn more about gene therapy and the advances in this technology that are being made today that are getting us closer to the "GATTACA" world. I also wonder about the ethical questions that go along with so many of these advances in gene therapy. 

This year, one of my new year's goals was to actively take charge of learning in biology by participating in class and acknowledging what I don't understand of the material. I am definitely putting more thought into writing relate and reviews and I am also including diagrams in my vodcast notes to help me understand the material better. My next steps are to think about what I don't understand and ask specific questions. 

pGLO Lab

1. Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB carpet tan tan - pGLO LB/amp none none none + pGLO LB/amp 130 tan tan + pGLO LB/amp/ara 150 tan green ** In our actual results, the -pGLO LB was accidentally plated on the plate labeled -pGLO LB/amp and the -pGLO LB/amp was plated on the plate labeled -pGLO LB.

2. The transformed bacteria now glow green under UV light because they have GFP (Glowing Fluorescent Protein). They also have resistance to ampicillin. 

3. The carpet of bacteria on the -pGLO LB plate indicates that there were hundreds of bacteria in the 100 uL which reproduced to create thousands.  

4. Arabinose is a sugar that gives bacteria the ability to glow under UV light. The plates which did not have arabinose did not glow under UV light. 

5. If the GFP gene is attached to a protein inside a cell, it can act as a microscope and allow the inside of a cell to be seen. Also, GFP is an indicator of activity inside the cell, especially protein activity. It can monitor gene expression. 

6. Bacteria can be genetically engineered to mass produce a protein product such as insulin, which is very useful in the medical field. 

+pGLO LB/amp/ara plate: bacteria which contain GFP

Candy Electrophoresis Lab

1. Some of our samples produced different color bands than the reference dyes. Some of the shades of the blue and the yellow were slightly different shades than the reference dyes. This could be because some of the candies have other ingredients in their coloring other than just the reference dyes, possibly some natural dyes.

2. Betanin (beetroot red) would probably migrate in a similar way to Blue 1. This is due to the fact that they are larger fragments, and the larger ones move more slowly through the gel than smaller molecules. Citrus red 2 would move in a similar way to Red 40 because they are of similar length.

3. Dog food manufactures might use artificial colors in dog food because it makes the food more appealing to the consumer, or the owner who is purchasing the dog food. Even though the food without the artificial dyes would taste the same, it looks less visually appealing and may dissuade owners from buying it.

5. The size of the fragment of the dye controls how far the dyes migrate away from their well. Also, the positive electrical current attracts the polar fragments and urges them to migrate through the gel.

6.  The positive electric current helps attract the dyes and move them through the gel.

7. The molecules of similar size will travel in groups and the larger molecules will not move as far through the gel as the smaller molecules. Therefore, the results will show which fragments are the smallest and the largest.

8. The molecules that weigh 600 daltons will be the farthest away from their starting point, the 1000 dalton molecules will be the next farthest away, then the 2000 dalton molecules, then the 5000 dalton molecules.

Recombinant DNA Lab: Thinking Like a Biotechnician

In this lab, we wanted to better understand the techniques of recombinant DNA technology and how bacteria can be used to mass produce a protein product, such as insulin for diabetics. We were given paper strips of cell DNA that had to be attached end to end in order to build a model. We also created a plasmid, which is circular DNA that is found in bacteria. Plasmids are naturally resistant to a certain antibiotic; in our case, the plasmid was naturally resistant to the antibiotic tetracycline. 

During the process of transformation, restriction enzymes cut DNA whenever they recognize a specific sequence. It cuts above and below the gene of interest (insulin gene) to "cut out" the gene to be placed into the plasmid. Usually a restriction enzyme makes a jagged cut, creating "sticky ends" which can bond with other DNA. The restriction enzyme also recognizes the same sequence of DNA on the plasmid. In our lab, we used the enzyme Hpa II because the sequence it recognizes matched base pairs on the DNA and one the plasmid and because its restriction site was close to the insulin gene. It cuts the DNA at two sites (above and below the gene) and it cuts the plasmid once (this is where the gene will be inserted. If an enzyme was to cut the plasmid in two places instead of one, part of the plasmid would be removed before the gene was inserted. Now, the enzyme ligase is added, which reattaches sticky ends. At this point, a recombinant plasmid has been created.

Next, you would put the bacteria in a petri dish containing the antibiotic that the plasmid is naturally resistant to. In our case, this would be tetracycline. We wouldn't use any other antibiotic because the plasmid will not be resistant to those. This would test whether the host cells have taken in the plasmid. Only cells with the plasmid will survive. When the bacteria containing the plasmid reproduce, they will begin to produce the gene product (insulin).

This process is vital in our everyday lives for mass producing a protein product that will be useful to us, especially something as important as insulin, which can be used to treat a diabetic patient. Recombinant DNA technologies could also be used for delaying food expiration and making it last longer, as well as resistance to pesticides. 

New Year's Goals

This year, I will actively take charge of learning in biology and by participating in class acknowledging what I don't understand of the material. My action plan to achieve this goal is to take time and put thought into writing the relate and reviews at the end of each vodcast. I will ask specific questions in class based on what topics I didn't understand from the previous night's vodcast.

This year, as a student in general, I will pay closer attention in class and do extra practice on difficult topics before a test. My action plan is to do homework or practice problems carefully and use it to determine my grasp of the topic. I will then go back after the unit is finished and redo problems that I got wrong or that were difficult. I think this will be a good way to study for tests.