Presentation on theme: "Supported by a grant from the Alfred P. Sloan Foundation."— Presentation transcript:
Supported by a grant from the Alfred P. Sloan Foundation
What is the Urban Barcode Project (UBP)? UBP is a way for NYC high school students to take part in a global effort to identify living things A chance to explore the living environment in NYC An opportunity to compete for $20,000 in prizes
What is DNA barcoding and why is it important?
ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG Organism is sampled DNA is extracted “Barcode” amplified DNA barcodes identify species Sequenced DNA creates a unique “barcode” for each species
How many species can you name? How many animals did you name? How many mammals? How many plants? How many insects? “Cat” Felis catus “Dog” Canis lupus familiaris “Oak Tree” Quercus alba “Shark” Ginglymostoma cirratum “Beetle” Popillia japonica
Issue #1: No one knows how many species there are.
Currently between 1.5 and 2 million species are described/known This number may represent as little as half of the true number of species Perhaps more than 1/3 of all species are threatened (IUCN Red list version ) VertebratesSpecies Mammals5,490 Birds9,998 Reptiles9,084 Amphibians6,433 Fishes31,300 Total62,305 InvertebratesSpecies Insects1,000,000 Mollusks85,00 Crustaceans47,000 Corals2,175 Arachnids102,248 Total (+others)1,305,250 PlantsSpecies Angiosperms281,821 Gymnosperms1,021 Ferns and Allies12,000 Mosses16,236 Algae10,134 Total321,212
Issue #2: T here is a lack of agreement of what “species” means.
Canis lupusCanis lupus (familiaris) Anas platyrhynchos Defining “species” is complex and depends on many factors: Interbreeding capabilities Morphological variation Ecological context Genetic similarities
Issue #3: Traditional taxonomic identification methods may be inadequate/too slow to capture vanishing biodiversity.
Classical taxonomy is difficult for non-experts to understand The body form ranges from hemispherical (e.g., Cleidostethus) to elongate oval (e.g., Clypastraea) to latridiid-like (e.g., Foadia). Corylophids are typically dull brown, but some species have contrasting yellowish-brown patches on the pronotum or elytra. The integument is often densely punctured and may be glabrous or bear short, fine recumbent setae. Most corylophid adults can be diagnosed using the following morphological features: Maxilla with single apical lobe; Mesotrochanter short and strongly oblique; Head usually covered by pronotum; Frontoclypeal suture absent; Antennae elongate with 3-segmented club; Procoxal cavities closed externally; Tarsal formula 4-4-4; Pygidium exposed Adding to the complexity: immature, damaged, or incomplete specimen may make identification impossible.
ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG Organism is sampled DNA is extracted “Barcode” amplified Sequenced DNA is compared with a barcode database How barcoding works
Why DNA barcoding works: genes with the right number of differences. matK rbcL CHLOROPLASTMITOCHONDRION CO1
Fail: Sequence is completely conserved, good for PCR, but uninformative as barcode Fail: Sequence shows no conservation, impossible for PCR, but good as barcode Win: Sequence shows ~70% conservation, good for PCR, good as barcode Why DNA barcoding works: differences allow identification
Issue #4: Education lacks opportunities to engage students in their own learning.
DNA barcoding is engaging in the classroom, and directs curiosity to opportunities for practical inquiry…
Kate Stoeckle August 23, 2008
Contributing to big science
How will UBP work?
1. Students will convene in teams and design projects that use DNA barcoding to answer a question
Who can enter the competition? Competition is open to NYC high school students enrolled in grades 9–12. Student teams consist of either 9th-10 th or 11th -12th graders. Team members do not have to be from the same school. Teams of 2–4 students must be sponsored by a qualifying science teacher or mentor. Sponsors do not have to be from the same school as any of the students.
How can a teacher sponsor qualify? Prospective sponsors must participate in a six-hour training conducted by the DNA Learning Center (DNALC) in its Harlem DNA Lab. (A $150 stipend is available for teachers participating in the training.) A teacher oversees his/her students’ project. Sponsors can work with up to five student teams. Student project proposals are only accepted if sponsor has completed the official DNALC training. Training can be taken at the Harlem DNA Lab or other locations. See UBP website for dates. Participants must register through the UBP website.
What will teacher training entail? 1.Background information on DNA barcoding. 2.Detailed hands on instruction on how to extract DNA, perform PCR, conduct agarose gel analysis, get DNA samples sequenced and analyze sequences. 3.Instruction in bioinformatics and the use of the sequence analysis platform DNA Subway. 4.Assistance with proposal ideas and outlines
Who can be a science mentor? Science mentors can be postdoctoral fellows, graduate students, undergraduate students under supervision (e.g. university professors), or research fellows working in a university or a research institution/organization. Each team will be provided with a mentor who acts as an advisor in monitoring the project’s progress. Mentors have the option of participating in a six-hour training conducted by the DNA Learning Center (DNALC) in its Harlem DNA Lab or at other locations. See UBP website for dates. (A $150 stipend is available for mentors participating in the training.) All participants must register through the UBP website.
2. Student teams will enter UBP by submitting a research/project proposal
Research questions can be about any living thing or about non-living things (foods or other products) that have DNA. Are there invasive (non-native) plants in my local park? What are the most popular types of flowers in my city? Do the teas I buy at my supermarket really contain the ingredients on the package? How many different living organisms can I find in an office building? What research questions could students ask? Examples:
Proposals are accepted during one of two submission windows June 1-15, 2011 (Round I) October 1-15, 2011 (Round II)
1.An introduction to the question, describing why your question is original, creative, and relevant. You should also have references to previous research, e.g. examples of DNA barcoding used to answer a similar question. 2.An explanation of the the goals of your project, and what you plan to achieve. 3.Methods, including how samples will be collected and processed. 4.Brief biographies and personal information for each team member. Proposals should include:
3. If a proposal is accepted the research can begin
Collect Samples (Leaves, Insects, Foods, etc. ) Collect Samples (Leaves, Insects, Foods, etc. ) Do DNA Barcoding Experiment Get Results and Make Conclusions Project Workflow
You will have access to all the materials you need for the DNA barcoding component of your experiment DNA extraction kit PCR machine and reagents DNA sequencing Bioinformatic tools (analysis of DNA sequence)
The DNA barcoding equipment is safe and easy to use, and the experiments can be done in a few hours depending on the number of samples
Materials and equipment are provided to participating teams: Either: by attending “Open Lab” days held in NYC at sites including: - Harlem DNA Lab - New York Academy of Sciences - American Museum of Natural History - The Rockefeller University - Others (TBA) Or: by borrowing it from the UBP.
You will have access to online tools to help you analyze your results
DNA Subway Blue Line
4. Finish your research, and present it at the UBP Symposium in Spring 2012
Summary 1.Form a team of 2-4 NYC high school students and a qualifying science teacher or mentor (sponsor). 2.Develop a project proposal. 3.Go to and submit your proposal online by the next deadline. 4.Proposals will be judged for originality, creativity, relevance, plausibility, and scientific merit. The top teams from each round of submissions will be invited to compete in the Urban Barcode Project. 5.Invited competitors must complete their projects by Spring 2012 and present their work at a project symposium.
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