Fall

Urban Ecology 

Inwood Hill Park Ecosystem Study 
 CREATE Method for reading primary literature 
 DNA Extraction 
 Fall Final Report 
Spring

Introduction to Molecular Ecology 

DNA Barcoding

The goal of the fall semester is to introduce students to the ecology of New York City through a study of Inwood Hill Park, as well as research methods used in the field for studying ecosystems. In addition, students will learn the CREATE method for reading scientific papers and write a final report on their Fall Semester work.
Topic Essential Question Learning Activities Assignments
1. Introduction to Urban
Ecology
Why are urban ecosystems important and how can we study them?
Manahatta Project
-
Manahatta Ted Talk Notes
Reading/Discussion on Urban Ecosystems
2. Inwood Hill Park Ecosystem
Study
How can we learn about urban ecology and field research at Inwood Hill Park?
3. CREATE Method How can we find, read and understand scientific articles?
GPS coordinates/mapping
- Soil pH, texture, moisture, nutrients
Water Quality - DO, nutrients, pH
Collecting and preserving samples of invertebrates and plants
Identifying species using dichotomous keys and field guides
track traps for small mammals
reading articles
finding journal articles
citing articles
Field Notebook for all 4 days at Inwood Hill
Park
Soil Analysis
Water Quality Analysis
Species Identification
Species Preservation
CREATE Notebook for 2 articles (New York
City biodiversity and article of choice)

4. DNA Extraction
5. Final Report
How can we extract DNA from our samples?
How can we combine everything we have learned this fall into a final paper?
dirty prep DNA extraction
lab report write up/ scientific method
Lab notebook with 2 DNA Extraction protocols
Lab report
background paper on urban ecology, Inwood Hill - 10 page paper
Park and your species
Methods Section (study site, field methods, DNA extraction)
Results of Soil analysis, water analysis, species identification, DNA extraction
The goal of the spring semester is to introduce students to biotechnology techniques through literature that focuses on ecological questions and molecular lab activities.
Topic Essential Question Learning Activities Assignments
1. Introduction to DNA
Barcoding
2. DNA Barcoding Article
How does DNA barcoding identify a species?
How can DNA barcoding support traditional morphological species identification?
3. Collection, identification and How can individuals of the same species observation of samples vary in a population?
Lecture, Reading, Discussion
CREATE DNA Barcoding Article, Pros and cons of
DNA Barcoding
Identify your specimens, observe your specimens, drawings and descriptions of individuals
Notes and discussion participation
CREATE Notebook, One page Pros and Cons list for DNA Barcoding using evidence from the readings
Sample ID, observations and drawings of individuals with a labeling system
4. Preservation and documentation of samples
How do specimens need to be preserved for use in the lab?
Lecture, sample preservation and documentation
5. Introduction to lab technique
How is the molecular laboratory set up and what is the function of all of the equipment?
6. DNA Extraction of Samples How is DNA extracted from individual specimens?
7. Primer Selection How are primers selected for PCR?
8. Sample PCR
9. Gel Electrophoresis
Lecture, Tour of the lab, making solutions/dilution, pipieting,
Lecture, DNA extraction using Qiagen DNeasy DNA extraction kit
Lecture, primer search
How can sample DNA be amplified using
PCR?
Lecture, PCR using Qiagen PCR kit
How can we confirm if PCR was successful Lecture, Pour an agarose gel, prepare sample for using gel electrophoresis? gel electrophoresis, load gel, run gel, stain/destain gel, visualize gel (take picture) analyze gel

10. DNA Sequencing
11. Proposal
Development/Literature
Review
12. DNA Barcode Analysis
How are DNA samples sequenced? Lecture on DNA sequencing, field trip to sequencing lab, computer simulation
Search google scholar for primary literature on How can we ask a new research question using DNA barcoding techniques? DNA barcoding, Find 5 articles, print articles,
CREATE articles, develop new research question
How are samples related to one another and the BOLD database?
Lecture on bioinformatics, Compare DNA samples from sequencing to the Barcode of Life Database
(BOLD), interpret your results
Write a full report including background, methods, results and conclusions for one of your sample organisms.
Research Literacy

Locate printed and online articles from the professional scientific literature

Read and interpret data in the professional scientific literature

Write a review of scientific literature in the area of interest

Critically assess relevance and procedures of primary research
Experimental Design

Develop a research plan in the area of interest

Identify and develop testable hypotheses

Understand the significance of relevant variables, controls, materials, and overall experimental design

Explain and perform analytical procedures in the area of interest
Data Collection/Analysis

Apply appropriate laboratory techniques to data collection in the area of interest

Summarize and present data in an appropriate format using statistical software such as Excel


Interpret and evaluate data as supporting or refuting the hypothesis proposed
Maintain organized lab/field notebook
Sharing Results

Write, present and publicly defend a research proposal

Summarize key points of research concisely and clearly using PowerPoint software

Prepare a research poster to be displayed in a public presentation

Write a final research proposal/report
Relevance and Impact of Research

Connect primary research to everyday problem solving

Evaluate the ethical implications of research and acknowledge limitations of research


View problems using a whole system approach that incorporates various fields of inquiry

Apply critical thinking skills outside of the classroom.