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Molecular NYC

    Molecular NYC: A Study of Biodiversity in Urban Environments

Course Description:

At the High School for Environmental Studies, students will research, design and implement a DNA barcoding project to identify and catalog the biodiversity of New York City. The class stresses inquiry, field and lab data collection, writing, researching and presentation skills before moving into teaching advanced molecular biology techniques. DNA barcoding is a new and efficient way of identifying animals and plants based on small fragments of DNA. Students will work in small groups to identify a plant or invertebrate species of interest. They will collect samples from all over New York City, extract the DNA from their samples, develop novel polymerase chain reaction (PCR) protocols to amplify the specific barcode region for their organism, send samples out for sequencing, perform comparative analysis using bioinformatics tools, and build a website to publicize their work. Throughout this process, students will develop a range of skills from traditional morphology identification to advanced molecular techniques while documenting biodiversity and answering ecological questions in their city.

This course is designed as a multi year - Authentic Research Module (ARM) that should be used as a foundation for a stand alone science research course for secondary science classrooms

Course Goals: Students will be able to:

Content:

Students will collect, preserve and identify species from specific taxa, research and develop protocols to extract DNA, run PCR analysis, and analyze DNA barcode sequences.  Through the New York City Biodiversity DNA Barcoding Project, students will begin to catalog the diversity of species in New York City as well as identify any new sub-species that may exist.  Students will share this work with the larger scientfic community through the develpment of a database that will document the collection and identification process. They will also share their protocols as well as pictures and DNA sequences for specific taxonomic groups.  Throughout the entire project, students will develop research skills including reading primary literature, data collection, and analysis skills.  This will occurr through the experimental protocols developed to extract DNA, develop primers, run PCR analysis, and gel electrophoresis, and technical skills through the develpment of a website and database.

 

Skills:

Perfom basic ecological protocols to analyze soil, water, and air quality from urban parks.  Students will be able to make inferences about the health and biodiversity of a park.  Appropriately collect invertabrates from local parks for use in DNA barcoding.  Extract DNA from insects, amplify DNA fragments, and analyze the DNA sequences.  Determine genetic relationships between individuals and potentially identify new sub species or unknow invasive species.

Research Objectives:

1. Catalog biodiversity in NYC

2. Identify new sub-specis of insects or plants

3. Spread of invasive species into NYC

4. Genetic variation within NYC populations

Reasearch Examples:
-Natural Transgenesis in Honey Bees (Apis Mellifers)
-Estimating and Identifying Species of Slow Loris in Southeast Asia
-Biodiversity of bed bugs in NYC
-Endangered Meats in Ethnic Food Markets

Course Outline:

Freshman Year: Inwood Hill Park Ecosystem Study (includes 4 Saturday field trips), DNA extraction of samples collected at Inwood Hill Park, How to search for and understand scientific articles

Sophomore Year: During the fall semester sophomores will present their research plan, collect data for a pilot study of their research projects, and write up a final paper of their research. If ready, sophomores will submit their research plans to the New York City Science and Engineering Fair (NYCSEF) for the December deadline. During the spring semester sophomore research students will modify their research projects and either develop a new project or modify their original project based on their fall pilot study.

Junior Year: During the fall semester, juniors will present their research plan, collect data for their research projects, and write up a final paper of their research.  If ready, juniors will submit their research plans to the New York City Science and Engineering Fair (NYCSEF) for the December deadline.  During the spring semester junior research students will modify their research projects and either develop a new project or modify their original project based on their fall study.  Juniors will also prepare submissions to the Intel Science Talent Search.

Senior Year: Senior research students will work towards submitting projects to the following competitions: Siemens, Intel Science Talent Search, NYCSEF, New York Ciy Urban Barcoding Project, Junior Science and Humanities Symposium, AMNH Young Naturalists. During Spring semester, seniors will complete their research experience working with younger students on developing their project proposals,  data collection, writing research papers or preparing presentations.