Identifying Essential Genes

 Part 1: Introduction
 The analysis of the human genome was first called pointless and a "waste of time" by critics, but as research has been performed and the genome has been collected, we have found many ways of applying our genetic sequences to very significant life scenarios. The human genome has been used to identify disease-causing genes, develop pharmaceuticals for diseases, study evolutionary patterns across species, track generational genetic lineage among humans, identify gene functions, and figure out how the genome works in general. In this lab, we'll use a small-scale simulation of a microarray to test 6 genes that are present in lung cells, and test for differences between these genes in healthy lung cells and cancerous lung cells.


 Part 2: Experiment

First we'll get our 2 slides. Each have 8 spots for aqueous solutions, though we'll only use 6, since we're only testing for 6 genes. We'll put 20 microliters of each gene sequence on a corresponding spot-- gene 1 on spot 1, gene 2 on spot 2, etc. Then we'll put 20 microliters of a cDNA solution, made with cDNA from each lung tissue sample, on each spot. After about a minute, we'll observe the spots for our results. Blue dots will represent a gene expressed in only the healthy lung sample, pink dots will represent a gene expressed only in the cancerous lung sample, clear dots will represent that the gene isn't in either, and purple will represent that the gene is represented in both.

  Part 3: Discussion
We found that the genes expressed in the lung cancer cells (pink) were C4BPA, SIAT9, and partially ODC1. Genes expressed in the healthy lung cells (blue) were partially ODC1, FGG, and CYP24. ODC1 was expressed in both, so it was normal in both samples; it's possible that it's a gene that synthesizes proteins for the lungs. HBG1 was expressed in neither sample. It codes for hemoglobin, which is in blood, which is not specifically directed or produced in the lungs. C4BPA or SIAT9 may be responsible for the cancer in the lung cells, as they are not present in healthy ones, but are present in the cancerous cells.
Some possible sources of error could have been contamination between specimens, dirty slides, incorrect measurements, or user error in placing genes in correct spots.

DNA Fingerprinting - Identification of the Future

 Part 1: Introduction 
DNA, the code of our lives, can now be extracted from animal cells and read like a personal ID card. This is a recent breakthrough that has been revolutionizing the scientific community. It's most commonly known as the main identification method in forensics, to find the truth of the locations of certain people at certain times. It has also been used in food identification, to find out if certain meats are actually pure meat of that type, or if something different is mixed in, and if the food is an endangered species. Also with animals, seeing the genetic code of certain species can determine whether the species are related or not. DNA testing has also cleared falsely convicted criminals of charges, and even saved falsely accused people from death row. DNA is also used to identify corpses if their teeth or fingerprints are compromised, or if only parts of the body remain. DNA testing is the light of truth where before there was none.
In this lab, we'll be comparing DNA samples to simulated criminals' DNA to find the perpetrator. This specific method is used in forensics, but slight variations of it apply to all the uses of DNA above.

  Part 2: Experiment
For the procedure, we'll have 6 tubes-- 1 of the "crime scene" DNA, and 1 for each of the 5 suspects. We'll add a restriction enzyme to each one to break apart the DNA at very specific places. We'll then put the tubes in a microcentrifuge to make sure the solution is mixed well. Then we'll put the tubes in a waterbath at 37C overnight. The next day, we'll place them in an ice block. Then we'll put the tubes in the microcentrifuge again to collect all the liquid at the bottom of the tube. Then we'll add loading dye to each tube so we can see approximately where the DNA is, and the dye also keeps the DNA sample in the wells of the gel. After putting in the dye we'll mix it in the microcentrifuge again. Then we put one sample in each lane of the agarose gel, which is inside the electrophoresis apparatus, and use a DNA size marker control for the first lane. Then we'll do the electrophoresis process. After that we'll take out the gel and put it in a staining tray, then put DNA stain in the tray (enough to cover the gel.) The next day, we'll look at the gel and record our results.

 Part 3: Discussion
 We found the perpetrator to be Katie, because the pattern made by her DNA matched the pattern of the crime scene DNA. One possible source of error could have been contamination, crossover of DNA solution in the gel, mislabeling a tube, or hearing another group's results.

Biofuels - Making Something Useful Out of Green Waste

Part 1: Introduction  

Biofuels have long been a topic of interest, though much more lately as we entered the "green" trend. As global warming becomes apparent, and as the price of gas rises, more and more people are looking to buy alternative cars, and alternative sources of energy to power their appliances. This demand for green technology has scientists scrambling to find an efficient way to recycle energy that won't harm the environment. Biofuels are usually combustible fuels that are made from biomass. They can be made by adding enzymes to plant material to break them down and release the energy stored inside them.
In this lab, we'll be making a biofuel out of cellulose by adding enzymes, and we'll measure how much fuel is made at several time intervals. My hypothesis is that there will be more indication of fuel as time progresses. We'll have tubes of non-enzyme solutions as controls.

Part 2: Experiment

 First, we'll get 7 vials, and label each one: Start, End, E1, E2, E3, E4, and E5. We'll put 500 microliters of stop solution into each one. Then we'll label one 15 ml conical tube "Enzyme Reaction" and the other "Control." Next we'll put 2 ml of 1.5 mM substrate into the "Enzyme Reaction" tube, then 1 ml of the same solution into the "Control" tube. Then we'll label two DPTP's, one "E" for Enzyme, and one "C" for Control.

After preparation, the reaction starts. We use the "C" pipet and put 500 microliters of buffer into the Control tube and mix gently, then we'll remove 500 microliters of the solution and put it into the "Start" vial. Then we'll take the "E" pipet and put 1 ml of enzyme into the Enzyme Reaction tube, and gently mix, then start our timer. At several time stops-- 1 min, 2 min, 4 min, 6 min, and 8 min-- we'll remove 500 microliters of the Enzyme Reaction tube and add it to each vial (e.g. at 1 min, 500 microliters into E1. at 2 min, 500 microliters into E2. etc). After these are all done, we'll use the "C" pipet and take out 500 microliters from the Control tube and put it in the "End" vial. Then we'll wash everything out.

The next day, we'll get a mushroom, measure out 1 g of it, put it into a mortar, add 2 ml of extraction buffer, and make mush with the pestle. Then we'll strain out the solid particles and put the juice in a 1.5 ml microcentrifuge tube. We'll put 500 microliters of stop solution into each of 6 vials (now clean). Then we'll label a 15 ml tube as the type of mushroom, and then put 3 ml of substrate into the tube. Next, we'll put 250 microliters of the mushroom juice into the tube of substrate, and start the timer. At the same time intervals as last time, we'll take out 500 microliters of mushroom extract/substrate mixture from the reaction tube and add it to each of only 5 vials. Then we'll add 500 microliters of extraction buffer to vial 6, and then add one drop of mushroom juice to it. Then we'll analyze the results.

Part 3: Discussion
 
In each tube through the experiment, each one got progressively more yellow in the slightest bit. It was extremely hard to notice. I had thought it would be a more apparent change.
I can't think of any possible sources of error, except for the tubes being possibly not all the way washed out, and the samples not being pure, as we didn't measure out the supply tubes; only the test ones.

Extracting Our Own DNA - And Wearing It

Part 1: Introduction  
 
DNA is a long, double-stranded helix nucleic acid contained in the nucleus of all animal cells. Its purpose is to store all the genetic information of the organism. DNA is comprised of nucleotides, which are simple molecules formed by 3 substances: a sugar (ribose or deoxyribose), a phosphate, and 1 of 4 nitrogenous bases (adenine, thymene, cytosene, guanine.) These bases are what code the genetic information used to determine almost all of the organism's characteristics. The correct formation and function of DNA is incredibly important for any organism, as a flaw can prove deadly. Genetic disfunctions can kill an organism before it has time to develop.


In this lab, we will be precipitating our own DNA. Precipitating DNA can be used by scientists and chemists to research genetics, practice cloning, test for traits or the probability of developing diseases, and also match DNA for forensics.

First we chew our cheeks to loosen cheek cells, then we swish around salene solution in our mouths. Then we spit the solution in a test tube. Next we add lysis buffer, which is a detergent, which breaks open the cell and nuclear membranes. This is required to access the DNA. Next we add protease, an enzyme that breaks down proteins. This is used because DNA is wrapped around proteins called histones, which let the DNA coil many, many times to reduce its size drastically. Removing these histones makes the DNA form into one large thread. The protease also breaks down unwanted molecules, like mitochondria, endoplasmic reticulum, and the golgi apparatus. Protease also destroys DNase, which is an enzyme that destroys DNA. If we want to collect the DNA, we want it to not be destroyed. Next we put the test tube in a water bath at 50 degrees Celcius, which catalyzes the reaction, mainly by helping the lysis buffer. Also many other bacteria will be killed at this temperature, and the growth of E. coli was slowed drastically.

Next we add cold ethanol, which cools the solution, which speeds the precipitation of DNA. After giving the DNA a few minutes to precipitate, we extract it from the solution with a pipette. We then put the DNA in a small container that is also a necklace piece, so we can have our own DNA in a super cool necklace.

Using Bacteria For Good - Koch's Postulates In Action

Part 1: Introduction

Bacteria are the most successful lifeforms on earth. They are found everywhere on the planet, even inside other living things. The initial reaction to this fact is disgust, because everyone thinks of bacteria as infections or as parasites. But the reality is quite the opposite-- only a few of the many types of bacteria are capable of causing disease, and many even help us. In this lab we will have a hands-on experiment with bacteria and see for ourselves how it can help us, in this case by turning milk into yogurt. The framework of this lab will be done by Koch's postulates, a series of tests and observations that will determine if a microorganism is responsible for a certain condition in another organism. This method is used by many biologists and scientists today for the same purpose (but with cases more complex than yogurt.)

In this lab we'll be using several different materials and instruments:

Materials

• milk
• yogurt
• ampicillin
• E. coli

Instruments

• test tubes
• inoculation loops
• agar plates

We will label 4 tubes: 1. Negative control (just milk), 2. Positive control (just yogurt), 3. Yogurt + ampicillin, 4. E. coli. We'll add 10 µl of ampicillin to tube 3, using sterile technique by minimizing potential of contamination during transfer. Next we'll dip an inoculation loop into some yogurt, and swirl the loop into tube 2. Then we'll use the same loop to dip in the yogurt again, and swirl in tube 3. With a new loop, we'll get some E. coli and put it into the yogurt in tube 4. Then we'll put them all in the mixer, and then in the waterbath.


Part 2: Experiment




Part 3: Discussion
After 24 hours, These were the results for each tube:

• 1. negative control (milk): white; gooey/gelatinous; smelled horrible, like sour milk and mold. pH of 7.
• 2. positive control (yogurt): slightly off-white; liquidy, milky; smelled like normal yogurt. pH of 4.
• 3. yogurt + ampicillin: slightly off-white; milky; smelled like old yogurt. pH of 6.
• 4. milk + E. coli: slightly off-white; liquidy; smelled like normal yogurt. pH of 4. 
• *. control yogurt (from cup, not in waterbath): white; gelatinous; smelled like yogurt. pH of 7.

 These data show that the negative control of normal milk turned sour without doing anything special to it, except for putting it in the waterbath. The positive control of yogurt turned liquidy in the waterbath, which shows that heat of the waterbath counteracts the bacteria and turns the yogurt to a milky texture. This was supposed to turn to all yogurt, but we probably didn't give it enough time. The yogurt with ampicillin shows that the antibiotic killed the active cultures in the yogurt, so the milk remained milk. It had a slightly sour smell to it which means that the milk had soured.The milk and E. coli had nothing special happen to it, because the E. coli had no effect on the milk. This is because not all types of bacteria turn milk into yogurt.

This lab shows that with some yogurt, you can turn milk into more yogurt. It also shows that not all bacteria curdles milk, and antibiotics can kill yogurt cultures. It also shows that milk sours when it's not kept cold, or if it stays around for too long. 

Some possible sources of error are:

• Test tube material-- could have skewed the observed color of the subject. May have been responsible for the slightly off-white appearance.
• Nothing is "sterile." Different types of bacteria could have gotten into any test tube through the air. This is unavoidable.
• We didn't set the waterbath temperature, so we don't know if it was right or not. We assumed it was right.
• 24 hours might not have been long enough to get the full effect of curdling.