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)? An opportunity for NYC high school students “to do science” and compete for $20,000 in prizes. A chance to explore the living environment in NYC. A way to take part in a global effort to identify all living organisms.
What is DNA barcoding and why is it important?
ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG Organism is sampled DNA is extracted “Barcode” amplified Sequenced DNA is compared with a barcode database How DNA barcoding works
Issue #1: No one knows how many species there are.
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
Currently between 1.5 and 2 million species are described/known This number may represent as little as a third 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.
Classical taxonomy may call one species what it is actually many…
Issue #4: Education lacks opportunities to engage students in their own learning
DNA Barcoding is engaging in and outside of the classroom, and directs curiosity to opportunities for practical inquiry…
Kate Stoeckle August 23, 2008
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 open to NYC high school students enrolled in grades 9–12. Student teams consist of either 9 th /10 th graders or 11 th /12 th graders. Team members do not have to be from the same school. Teams of 2–4 students must be sponsored by a qualifying teacher who has completed a six-hour training session with the DNALC (see next slide). Sponsors do not have to be from the same school as any of the students on their team.
How does a sponsor qualify? Only science teachers currently employed by a private or public secondary school in NYC’s five boroughs can sponsor a team. A sponsor commits to overseeing her/his student team. Sponsors can work with up to five (5) student teams. Each team can have a maximum of four (4) students. Prospective sponsors must participate in a six-hour training workshop A $150 stipend is available for teachers participating in the training. Training events will be held at the Harlem DNA Lab on either - Saturday, April 2, :00am-3:00pm, or - Saturday, April 30, :00am-3:00pm, or - Saturday, May 14, :00am-3:00pm, or - Saturday, June 4, :00am-3:00pm. Prospective sponsors must r.s.v.p. on the UBP website for a training session.
What will sponsor training entail? 1.Background information on DNA barcoding. 2.Project and lab safety training. 3.Training in all lab and bioinformatics procedures required to conduct DNA barcoding, including: 1.DNA extraction from plant and animal tissues and food sources; 2.PCR amplification of DNA barcodes; 3.Agarose gel electrophoresis; 4.Submitting DNA barcodes to sequencing facilities; 5.Analyzing DNA barcode sequences. 4.Assistance with proposal ideas and outlines
2. Student teams must submit a research/project proposal
Proposals will be accepted during one of two submission periods June 1-15, 2011 (Round I) October 1-15, 2011 (Round II)
Proposals must be submitted online at the UBP website
A research question can be about any living thing in NYC or about non-living things (foods or other products) that have DNA. Are there invasive or non-native plants in my local park? What are the most popular types of flowers in NYC? 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? How many species of butterfly migrate through NYC? What kind of research questions are acceptable? Examples for research questions:
1.An introduction to the question, describing why your question is original, creative, and relevant. You should also have references to previous research, such as examples of DNA barcoding used to answer a similar question or examples relating to research on the specific organisms. 2.Explain the goal of your project, and what you plan to achieve. 3.Methods, including how samples will be collected and processed. 4.Safety and legality concerns, such as how any necessary permission will be secured. 5.Brief biographies of each team member. Proposals will include, amongst other things:
3. If a proposal is accepted, the team becomes part of the UBP and 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
Teams whose proposal is accepted will have access to the materials needed for the DNA barcoding component of their project: 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
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
Teams will have access to online tools to analyze their results
***Demo Blue Line*** at
Every participating team will also be assigned a scientific mentor Mentors will be drawn from NYC research institutions and will help with technical issues
4. Finish your research, and present it at the UBP symposium in Spring 2012
Summary Details 1.Form a team of 2-4 NYC high school students and a qualifying science teacher (sponsor). 2.Develop a project proposal. 3.Go to and submit your proposal online by one of two deadlines. 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.
Follow us Online twitter.com/urbanbarcode Latest news and announcements posted first to: