Results/Analysis: Did our original leafs match the sequence we received?

Sample 1 was a match and was also closely related to Celery apiaceae which isn't the vegetable celery, but a common weed.

This result is not too surprising because we collected the sample from a bush on the Grant High School campus. Not that we are botany experts by any means but we believe that the soil near grant high school is probably not maintained, thus giving an opportunity for weeds to invade.

Key:
gb|FJ395559|hedera_helix: Hedera helix
1ML_JJ_RP_RS-F: Sample 1

Sample 1 Tree

Sample 2 was a match and ironically was related to another type of Ivy: Poision Ivy-Anacardiaceae which didn't relate to our sample of Ivy very well.

It was almost obvious that this sample was going to be an ivy variant. It showed similar characteristics to all common ivy plants and was found clinging onto the fence at the Grant High School Baseball field. Seeing that the menacing poison ivy is a close relative shows us how close the ivy family is as a whole.

Key:
gb|DQ978421|acer_palmatum: Acer palmatum
2ML_JJ_RP_RS-F: Sample 2

Sample 2 Tree

Sample 3 also matched and was what we hypothesized: closely related to wheat.

Our basis for hypothesizing that our sample was somewhat related to wheat was due to the buds attached to the stem of the plant. Knowing that the flowering part of wheat was similar bud arrangement we knew that they would be related.

Key:
gb|HQ600445|bromus_inermis: Bromus inermis
3ML_JJ_RP_RS-F: Sample 3

Sample 3 Tree

Matches: according to DNAsubway.org

Sample 1 which we hypothesized to be a species of ivy, was in fact Hedera helix (Common Ivy or English Ivy) The leaf in the image bellow perfectly matches what our original leaf had looked like.

Sample 1 Result

 

 Sample 2 was hypothesized to be a leaf from a native deciduous plant, but we we're quite sure of anything more specific. BLASTN told us that our sample 2 was a leaf from a Japanese Maple, but the images that were provided looked nothing like the leaf we had at the beginning of our experiment. The second match that the site gave us was Acer spicatum which once we researched that species, found that it closer resembled our original leaf.

 

 

Sample 2 (Incorrect Match)

 

Sample 2 (Correct Match)

 Sample 3 was thought to be a type of weed and possibly resemble wheat. The images provided from the site didn't appear to be a perfect match, but after some more research we are confident that the Bromus inermis was the species of leaf we had used for the experiment.


Sample 3 Result

 

Team Agreement:

Our group - Aaron Everly, Elle McRae, Emma Wienmann, and Madeline Williams - are testing 3 types of leaves from the Grant High School Campus and determining their specific species. Over the course of the experiment here is the participation that we all contributed each day:

May 22nd, Wednesday

All of us collected plant samples around Grant and began the process of extracting the DNA from each sample. Aaron created a blog and began updating it with images from the day and wrote out our procedure. Madeline also stayed through all of lunch to finish extracting the DNA from our samples.

May 24th, Friday

Today we worked on our lab packet for this experiment; it was more of a learning day then any hands on work. We were a little rushed into the experiment before we really understood what we were doing; but today we learned all about why we did what we did, and what it meant.

May 29th, Wednesday

Madeline was gone but Elle, Emma and Aaron finished out the experiment and identified which tubes we had been using for our experiment so they could sent of to get sequenced.

June 3rd, Monday

In class we officially assigned a job to everyone; beforehand we had been doing whatever need to be done but not in an organized fashion. We agreed that Madeline would blog the team agreement and results, Emma would blog the background information on our three samples, and Aaron would blog the procedure, analysis of our results and design the blog to be more appealing.

June 5th, Wednesday
Elle had graduated and is no longer working on the experiment. As for the rest of the team, we got our sequence back online and all three of us spent the period finding out what species our sequences were and analyzing the results. We also began working on more blog posts.

June 7th, Friday

Figured out that we had the wrong DNA that got mixed with another class period's group so once we found our real data, we were able to more accurately analyze our data. We spent the period working on the blog and making sure all of us knew what we had to do over the weekend to finish the blog.

Overall our team worked together really well and we all felt like the jobs were split equally among us. After all our experiment turned out perfect and I can't imagine it would have if we had not worked together like we did.

If we had to be plants...

Madeline Williams (Pink Gerbera Daisey)
"They're just so happy looking!"

Aaron Everly (Pineapple Tree)
"They produce the most delicious succulent fruit in the world"

Emma Wienmann (Japanese Maple)
"They're beautiful, I don't know"

Ellie Mcrea (did not specify)

May 22, 2013

Today our experiment commenced after we collected three samples of leaves from trees and bushes surrounding grant high school. Our primary goal going forth is to identify each plant species.

Sample 1 Source
 Acer spicatum is a deciduous tree that can grow to approximately 10 meters in height (Source). Native to North America and found in woodland canopies, A. spicatum are dispersed by insects. Known more commonly as the Mountain Maple, this tree is unable to grow in the shade and prefers well-drained soil with acidic or neutral pH (Source). They are part of the Aceraceae family and have medicinal properties.

Sample 2 Source
Bromus inermis, more commonly known as smooth bromegrass, is an invasive, perennial grass that has made an extensive, negative impact on growth of native plants in North America by slowing their growth and increasing extinction (Source). B. inermis uses different dispersal methods including, growing rhizomes, dispersing their seeds in the wind and using animals. The stems are smooth and freestanding, usually reaching 1.5 meters in height. The leaf blades are smooth, flat and 15-40cm long, and  are greyish blue on the top side and green on the bottom. 

Sample 3 Source
Hedera helix is an invasive species of ivy native to Europe and Western Asia. H. helix, or English Ivy, grows to a height of between 20 and 80 feet. English Ivy is a vigorous, fast-growing, evergreen, woody perennial that is primarily grown as a climbing vine or trailing ground cover (Source). Over time, it may spread to as much as 100 feet in length. The leaves are typically dark green with whitish vains, waxy and somewhat leathery, with a measure of 3-4 inches across (Source).

After gathering, certain samples were smashed into a substance that we could accurately test.

Smashing Process 

We extracted a smaller portion of a sample for testing

Once the samples were in a testable size and form we added 100 microliters of nuclei lysis solution to the tube to then later be incubated at 65 degrees celsius.