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$335 of $335 raised!
$335 of $335 raised!
1st Cut Biotech Video.mp4Intro
Intro
Our project, titled "Genus Russula Identification and Phylogenetic Delimitation by Means of DNA Barcoding," aims to sequence and analyze the phylogenetic differences of fungi in the genus Russula. In Colorado, the genus Russula acts as an ecological regulator of other plants in the ecosystem, also known as an ectomycorrhiza, by breaking down nutrients in the soil near trees. This role is of vast importance in any semi-arid ecosystem such as ours as it allows trees to absorb nutrients and then output oxygen. However, Russula are largely undocumented with DNA barcodes. This research is of vast importance to further research looking toward the goal of conservation and analysis of biodiversity. In addition, our analysis of the sequences will allow us to create a phylogenetic tree, which will contribute to specific knowledge of Colorado biodiversity.
This project aims to complete two goals. First, this work will help to expand the Colorado Mycoflora Project's database, which aims to catalogue and DNA barcode all plant and animal species in the Rocky Mountain area. Currently, there aren't many DNA barcodes that exist for the genus Russula, so by producing more barcodes the databases will be expanded, allowing for more scientists to quickly and accurately identify the species using DNA barcoding. Secondly, we plan to create a phylogenetic tree of Russula to better understand the relationships between the species of the genus.
Process
Process
This project will be completed in three major steps from start to finish with several smaller steps within the main three. The first step will be sample collection and prep so that the samples are ready for DNA extraction. We will be doing our own collection hikes where we will find, photograph, and document the samples. In addition, we will be using samples that have already been collected and phenotypically identified from the Colorado Mycoflora Project. Although some of the samples already have been identified down to the species levels, many of them do not have a DNA barcode linked to the species. The collections will take four or five days over a two-week period.
To the right is a picture of Camden and Jason documenting a sample on our team's first collection hike. We are using a DSLR camera to take high quality pictures of several parts of the mushrooms so that they can be identified later if needed.
The final step in this project will be sending the samples off to be sequenced. We will be sending the samples to the Colorado Mycoflora Project where they will provide the funding and send the samples to ELIM Biopharmaceuticals. They will read the DNA sequence and create a barcode that shows the sequence of bases in the DNA. We will have a unique sequence of A's, T's, C's, and G's that will allow us to determine the species of the fungus.
The next major step is to extract and amplify the DNA. We will be using an Omega Biotek ENZA Fungal DNA extraction kit to extract and purify the DNA. Next, the ITS gene will be amplified using a PCR thermocycler . This means that we will be making copies of the ITS gene to be used for sequencing. After the DNA is amplified we will make sure that the amplification is successful by using gel electrophloresis. If the amplification was successful, then each of the samples will show a thick band of DNA so we know that the samples are ready for sequencing.
To the left is a picture of the Colorado Mycoflora Project's lab where we got our first 24 samples.
Mentors
Mentors
Damon Tighe
Damon Tighe
Damon Tighe is a scientist who has worked on the Human Genome Project, which worked to sequence the entire human genome. He currently works for Bio Rad designing curriculum and training educators in the Western United States in biotechnology.
Dr. Andrew Wilson
Dr. Andrew Wilson
Dr. Andrew Wilson is an assistant curator at the Sam Mitchel Herbarium. He works to document macro fungi in the Southern Rocky Mountains. He focuses on studying their taxonomy and creating DNA barcodes for the fungi to understand their biogeographic history and evolutionary ecology.
What We Need
What We Need
This project will require several important supplies and without them, we won't be able to complete the work. First, we will need two Omega Biotek ENZA Fungal DNA extraction kits. These kits will allow us to efficiently and effectively extract and purify the DNA from the collected samples. Next we will need primers to amplify, or make copies of the DNA. We need ITSf and ITS4 primers to make copies of the forward and reverse sequence of the ITS gene. In addition, we need to purchase DNA polymerase which is used to actually make the copies of the DNA. Finally, we need 2% agarose gels which will be used to make sure the DNA amplification was successful. The samples will be placed in the gels and compared to previously successful samples to make sure that PCR was successful in making copies of the DNA.
Fortunately, we are receiving some help to pay for many of these materials. We would like to thank the Colorado Mycoflora Project for agreeing to pay for the cost of sequencing for all of the samples that they have collected. We would also like to thank Omega Biotek for offering us a buy-one-get-one free deal on the DNA extraction kits, which will save us $119.
In total, all of these supplies will cost $350.00 to purchase, and we need your help to raise these funds.
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