Sunday, June 9, 2013

Our Team




Taylor Debnam is from Portland, Oregon. She enjoys reading, music, drawing and exploring. She is an aspiring political science major and social advocate. Taylor also loves mini m&ms and writing.

This is Coyla Munson, she is from Portland, Oregon. She loves the outdoors, and enjoys hiking and reading her favorite books, The Plague and The Hot Zone. She is an aspiring scientist as well as a visual artist. Coyla also loves to write poetry and yoga. 

















Litopenaeus vannamie

Litopenaeus vannamie is also known as the white-leg shrimp, farm and caught in the Pacific Ocean in the Americas. This shrimp is commonly used for food, caught wild on the coast of Mexico and farm raised in the Americas.

This specific type of white shrimp is approved by the FDA, and should be the kind of white shrimp offered in stores.

Pacific Shrimp:
Shrimp found in the Pacific do not grow as fast because of the colder temperatures of the water. These Pacific shrimp are often caught at smaller sizes, and because they live in colder waters there is not many nutrients which makes it harder for larger shrimp populations to grow. Because of this most, Pacific shrimp are farmed. This means that they have a controlled diet and live in confined quarters, the system of fisheries allow the shrimp size and taste to be more consistent, than shrimp that are caught in the wild. This type of Pacific White Shrimp is often used for salads.

Mexico Shrimp:
While shrimp found on the coast of Mexico are usually caught wild. The warm waters provide a better environment for shrimp. The shrimp have a more diverse diet therefore the flavors of the shrimp are less predictable and grow larger. The shrimp also live in a larger environment than a farm so they are able to swim more and build more muscle which equates to a more firm and tasty shrimp.


For more information on our white shrimp, Google it, or check out some of our sources listed below.

http://en.wikipedia.org/wiki/Whiteleg_shrimp

http://www.fao.org/fishery/culturedspecies/Litopenaeus_vannamei/en

http://www.thekitchn.com/whats-the-difference-white-bro-1-149543



Friday, June 7, 2013

How we got down and jiggy with our shrimps' DNA sequence

After an unfortunate run in with some apple samples, Taylor, Chelsea and I found a redeeming second chance for our experiment, shrimp.

Our lovely shrimp came from Fred Meyers, a trusted local grocery store chain in Portland.

In our first sample we have the farm raised white shrimp, our second is white Mexican shrimp that were wild caught, and our third sample is of the farm raised white shrimp marketed separately for its slightly larger size.

We took small tissue samples from the shrimps we had and processed them to attain a specific DNA sequence which would allow us to bar-code the shrimp and match them to their proper species. After we extract the DNA from the tissue samples our processed shrimp are sent off to the east coast to Gene Wiz for the nucleotide sequences. Then we take the nucleotide sequences and enter them into BLAST, a database for DNA segments of specific species of organisms all across the world.


How we extract our DNA from the shrimp is a very long, tedious process with many technicalities.


First we crush our small samples of tissue, which were about half the size of a pencil eraser, with a plastic pestle in a tube with nuclei lysis. Nuclei lysis is necessary to break down the nucleus of the tissue cells to free the DNA, and we incubated the solution in a water bath at 65 degrees Celsius for optimal results.



To make sure the what we will be amplifying is only DNA, we added RNAse to the solution to break down any RNA within our samples (and we incubated our samples at 37 degrees Celsius for the enzyme to be properly utilized).

In order to isolate our DNA we mixed some protein precipitation solution to our tubes. The proteins condensed and separated from the DNA. Then the samples were put through the vortex for about five seconds to separate the DNA from the rest of the tissue cell matter we were using. The samples were then separated into the surpernatant, DNA in the liquid matter, and the  pellet on the bottom, the rest of the undesired cell matter.



The supernatant was then transferred into a new tube, and the tubes with the pellets were discarded. Isopropanol was also added to the new tubes to precipitate the DNA and the samples were also centrifuged for one minute to create a DNA pellet.



The pellet of DNA was saved as the supernatant (liquid) was removed and ethonol was added to the solution. Ethonol was used to futher refine the purity of our DNA, we were careful not to disturb the pellet so we flicked the bottom of the tube. Thesample was centurifuged once and the supernatant and ethonol were removed.

The samples air-dried for about fifteen minutes before we added the DNA rehydrant to them. The extracted DNA was then refrigerated overnight, and hence forth kept at cold temperatures in order to prevent damage.

In order to make sure we had adequate DNA and to amplify a code within the DNA, we then used PCR. We added an insect/animal primer COI which copied the coded sequence of the shrimp DNA. Then some of the amplified DNA of each sample was placed into a DNA gel and underwent electrophoresis. In electrophoresis, DNA is magnetized to a positive charge on the opposite end and the negatively charged end of the DNA gel, done with a battery, caused the amplified pieces to travel in a visible line from one end to another. PCR will show whether or not there was any DNA in the samples because evenly sized pieces of thousands of DNA strands will form a visible line to the naked eye.

In our results of PCR it was not important that if the DNA traveled really far, but if the DNA showed up at all. In our first sample of farm raised shrimp, and in our third sample of the large farm raised shrimp the DNA was visible. We then sent off our samples to the east coast to attain the codes of the DNA samples for processing.

Once we attained our sequences a few days later, we utilized the DNA subway and BLAST databases to see if Fred Meyer's white shrimp was properly labeled and we created a philogenic tree to support our primer and the credibility of good ole' Freddys.



Shrimp Sequencing Results Sample 1



Shrimp Sequencing Results Sample 2


Shrimp Sample Results Sample 3


Checkout this video!

http://www.youtube.com/watch?feature=player_detailpage&v=5JyTCySI2cg

Our little shrimp in action in a farm.

I wonder where the shrimp are farmed and if it would be better to get the wild caught shrimp.

Phiologenic Tree


To amplify the coded sequence of DNA in our sample we used a primer of insects and animals. Primers replicate a sequence of DNA of the organism and thus amplifies the unique genetic code of the organism. Because shrimp can be classified as an anthropoid, we used the insect and animal primer.

Below is a photogenic tree of possible connections between the shrimp and supports whether or not our samples match the DNA code of white shrimp. The numbers of each branch are how sure the relationship is according to the DNA database BLAST and DNA subway.

As displayed below, the shrimp, identified below the tree, shrimp are distantly related to insects. The insect primer works because fish appear to be 'cousins' of the shrimp, and the primer would most likely heed false results. As you can see the types of fish are more closely related to grasshoppers. The insects share common ancestors with the shrimp.

Litopenaeus vannei is the coded white shrimp of the system, matching to our samples. Although the samples seem to be loosely connected with each other, they remain connected with the white shrimp. This supports that Fred Meyers most likely using properly labeled shrimp.
20CM_TPD_CU-F: Sample One, the white shrimp farm grown from Fred Meyer

21CM_TPD_CU-F:Sample Two, white shrimp wild caught in the Gulf of Mexico from Fred Meyer

22CM_TPD_CU-F:Sample Three, large white shrimp farm grown from Fred Meyer

gb/AY781297: Litopenaeus vannei, the white shrimp

May 22, 2013: Day One

We attained our samples of the Fred Meyer Shrimp and extracted DNA from three different kinds of shrimp sold there. We had the wild caught Pacific white shrimp from Mexico and we had farm grown white shrimp and we had some large white shrimp that were farm grown.

We had to go through the procedure to extract the DNA twice. The first time we confused the supernatant and pellet of the DNA and the tissue matter, so we had mush as a product the first time around. So I, Coyla, stayed back to repeat the first portion of the lab once more.

 Long story short, we took our time getting cozy with our anthropoid friends and very tentative of our procedure.
Smaller farm grown shrimp. Sample one.
Mexico wild caught shrimp. Sample 2. 
Larger farm grown shrimp. Sample 3. 


May 24, 2013 Day Two

We  preformed PCR with our samples, yielding great success with our first and third sample. We will be sending in all the amplified shrimp DNA with the hopes of having enough viable data for an answer to our inquiry.

May 29, 2013 Day Three

Today we will be seeing the if the results indicated by PCR are accurate. Our samples will be going through electrophoris, visually indicating if we have any DNA from our second attempt with our procedure. Samples one ant three seem to have the most promise, however we will also be sending in sample two for sequencing.

Although sample two may not have shown DNA the sample could still be coded. We could not complete the suggested 30 minutes of electrophorisis for our samples and due to time restraints we could not go through the process once more.

All we can do now is keep our fingers crossed.

May 31, 2013 Day Four and June 4, 2013 Day Five

We sent in our samples for DNA sequencing!



Our DNA available and after sequencing and using the DNA Subway and BLAST, Fred Meyers has been found credible!

Ideally, we there would need to repeat the process with many many more shrimp to ensure support and accuracy in the possible solution of the inquiry.

http://25.media.tumblr.com/tumblr_m2ssrpSV8z1qmr54yo1_500.jpg

To Conclude

We will need to ideally do more testing, however, so far Fred Meyers remains an accredited source for your anthropoidic needs!

Inquiry:

Background:
In this lab we will be identifying shrimp samples collected from the local Fred Meyer on Hawthorne and 33rd. Fred Meyer has an almost spotless reputation, before and after it was bought out by Kroger in 1998. Our experiment idea derived from the recent attention sushi restaurants have gotten from the media after mis labeling their sushi. They often include seafood delicacies in their menus but after closer research they are actually using common, basic seafood. This is a problem because they are ripping off the consumer and dishonesty in the food industry is a major issue. We wanted to see if this practice occurs in Fred Meyer grocery stores.
http://www.nytimes.com/flashtalking/ftlocal.html

Question:
Is Fred Meyer shrimp labeled correctly?

Hypothesis:
Fred Meyer has a very good reputation for honesty with their consumer, so we assume that the shrimp is labeled correctly. And most dishonesty with fish occur in restaurants, not grocery stores.

( http://www.masonrypromotion.com/projectFocus/fredMeyer.html)

It is a lot harder for larger corporations such as Kroger and Wal-Mart to mislabel and make mistakes or even try to lie to the consumer. Since they operate on such a large scale, there are more people to check products before they are sold to the consumer.


(http://smartgrowthusa.files.wordpress.com/2010/08/kroegerfredmeyeroverlap.gif)