The Esteemed Life and Times of SASHIMI: A Modern Glimpse at Sushi in Today's Culture

Introduction

a. Background
This lab focuses on the use of Proteomics to determine the evolution of certain organisms. The Study of evolution includes both genomics and proteomics. Genomics is the study of genes and genomes, and proteomics is the study of proteins. Proteomics is specifically focused on studying the structures and functions of proteins, as well as inclyuding the study of protein functions, protein-protein interactions, cellular locations, expression levels, and posttranslational modification of proteins. Charles Darwin created the "Theory of Natural Selection". This theory states that there are more organisms brought into the environment than can be supported by the environment. Organisms engage in survival of the fittest.

b. Purpose
In this lab, we are attempting to compare fish and determine which are more similar to eachother. We will take a sample of their muscle tissue and compare them through gel electrophoresis. According to proteomics, the more similar the bands are from gel electrophoresis, the more related the organisms are to eachother.

c. Process
First, we will grind up and denature the muscle proteins, Actin and Myosin. Then, we will run the samples on argarose gel. The results will let us know which fish and other organisms are more similar to eachother and related.

d. Hypothesis

To Gene or Not to Gene: That is the Question

a. Background

DNA testing exposes a certain DNA sequence out of a genome, and this can be helpful to identify certain disease carrying genes. The genome is our hereditary code and it conists of every gene in our body. The genes code for all of our characteristics and traits, including physical and some mental qualities. Molecular Biology is the study of our genes and the molecular details that maintain the flow of genetic information changing from DNA==> RNA==> proteins. PCR has allowed the process of DNA sequencing, and it is a process that amplifies a section of DNA. PCR has changed genetic research in many ways, such as: gene mapping; cloning; DNA sequencing; and gene detection.

b. Purpose

The purpose of this lab is to uncover whether or not a gene is "turned on" in somebody's DNA. Specifically for our lab and the gene that we are isolating, the gene would be interesting to study for migration patterns and evolution. If we  used other genes, such as Huntingtons Disease, we would be able to see if someone carries the gene in their genetic makeup.

c. Procedure

This lab is a 3 day process. On Day 1 we will extract DNA from our cheek cells. By biting the inside of our lip lightly, the membrane will break up. Then, the gene is put into a vile and it is put into a warm water bath. The temperature should be set at 95 degrees celsius. Then, the instagene matrix beads are added. This is to insure that DNAse is killed. On Day 2 of the lab, we will undergo PCR. The steps of PCR are: The DNA strand is denatured at 94 degrees C; then the anneal primers are set to 60 degrees C; then the primer attaches and so does the Taq polymerase, and the temperature is set to 72 degrees; then the cycle is repeated 40 times. For the ingredients, the primer targets the "disease gene". There are 2 versions of this gene, the long and the short. Together, they are heterozygous. On Day 3, we put the DNA fragments through gel electrophoresis and view the results.

d. :((( MADDY HAS THE DISEASE!!!! NOOOOOOOO!!!!!!!!!We are all very sad about this. She was in row 6 for gel electrophoresis and her results showed up to have the gene. The rest of us didn't have this gene, but that doesn't mean that we weren't carriers for the gene.

e. Our sources of error for this lab could have been to suck up all the matrix beads. Also, it could have been possible that our cheek cells were not loosened enough so we wouldn't have had a big enough sample to run in the gel electrophoresis.

GMO:OMG

Background
GMOs are genetically modified organisms. They are used to make organisms resistant to something. For example, genetic modification can make plants resistant to cold weather or resistant to certain bacteria. GMOs are made by looking at a GOI (gene of interest) and a Ti Plasmid. A Ti Plasmid is tumor inducing. The gene of interest is put into Agrobacteria, and then the agrobacteria is put into a plant cell.
The plant cell is then put into the plant, creating a GM plant. Through PCR (DNA polymerase chain reaction), DNA is copied. The primer allows specific genes to be targeted, specifically the Ti plasmid. 85% of all GM foods have a Ti Plasmid. Also, nucleotides and DNA are necessary for PCR to take place. The GM controversy is over the fact that humans do not really know what the effect of altered organisms will have. GM foods are not labeled in stores, so buyers are unaware of when they are purchasing GM foods. There could be potential health problems in the future from GM products.

Purpose
In this lab we are going to extract genomic DNA from food samples. On the second day we are going to run PCR reactions to amplify GMO and natural plant sequences from DNA. On the third day of the lab we will run the DNA through gel electrophoresis. We will be able to see which foods contain GMOs, and if the food that we eat on a daily basis is genetically modified. In the real world, people will be able to test foods for GMOs



Procedure

On the first day we will start DNA extraction. Using a mortar and pestle, we will break open the cell wall. Then, the cell and nuclear membrane will break up once it is put in a 99 degree Celsius water bath. However, we will encounter a problem! If we break open the membrane, DNAse will encounter DNA. DNAse is an enzyme that kills DNA, so in order to avoid this deathly encounter between the DNA and enzyme, we will put in Instagene matrix beads. These beads kill enzymes. On day two of the lab, we will start PCR. There are two primers necessary for PCR, Plant DNA and GM DNA. Plant DNA is the control because it is in every plant. PCR produces a large amount of DNA from a starting material. The steps of PCR are: Place the tube into a MyCyler thermal cycler to go through temperature cycling, heat the sample to 94 degrees Celsius for the denaturation step. The next step is the Annealing step, and the thermal cycler cools to 59 degrees Celsius. The last step is the extension step, and the thermal cy cler heats up to 72 degrees Celsius. The temperature cycle= denaturation step+annealing step+extension step. On Day three of the lab, we are going to run the DNA fragments through gel electrophoresis on agarose gel.

 Hypothesis
My hypothesis is that our strawberries will be proven to be genetically modified. However, I have heard that it is very important to buy organic strawberries because their thin skin can absorb pesticides easily.

GFP Jellyfish

a. Background
In this lab we are going to use the procedure known as genetic transformation. A gene is a piece of DNA that gives instructions for a protein, and a protein gives an organism a trait. Genetic transformation means the change caused by genes. It is done by the insertion of a gene into an organism in order to alter the original trait of the organism. This technique can be used in the agricultural industry, bioremediation, mediine, and other aspects of biotechnology. The gene that we will be using codes for Green Fluorescent Protein (GFP). Bioiluminescent jellyfish are the real source for this gene. The Proten causes jellyfish to glow in the dark with a bright green color.

b. Purpose

c. Process

d. Results/analysis