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Molecular NYC Research Overview

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

Fall Semester Syllabus - Field Ecology

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?

  • 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
  • Field Notebook for all 4 days at Inwood Hill Park
  • Soil Analysis
  • Water Quality Analysis
  • Species Identification
  • Species Preservation
3. CREATE Method How can we find, read and understand scientific articles?
  • reading articles
  • finding journal articles
  • citing articles
  • CREATE Notebook for 2 articles (New York City biodiversity and article of choice)
4. DNA Extraction How can we extract DNA from our samples?
  • dirty prep DNA extraction
  • lab report write up/ scientific method
  • Lab notebook with 2 DNA Extraction protocols
  • Lab report
5. Final Report How can we combine everything we have learned this fall into a final paper?
  • background paper on urban ecology, Inwood Hill Park and your species
  • Methods Section (study site, field methods, DNA extraction)
  • Results of Soil analysis, water analysis, species identification, DNA extraction
  • 10 page paper

 

Spring Semester Syllabus – Molecular Ecology 

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 How does DNA barcoding identify a species? Lecture, Reading, Discussion Notes and discussion participation
2. DNA Barcoding Article How can DNA barcoding support traditional morphological species identification? CREATE DNA Barcoding Article, Pros and cons of DNA Barcoding CREATE Notebook, One page Pros and Cons list for DNA Barcoding using evidence from the readings
3. Collection, identification and observation of samples How can individuals of the same species vary in a population? Identify your specimens, observe your specimens, drawings and descriptions of individuals 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? Lecture, Tour of the lab, making solutions/dilution, pipieting,  
6. DNA Extraction of Samples How is DNA extracted from individual specimens? Lecture, DNA extraction using Qiagen DNeasy DNA extraction kit  
7. Primer Selection How are primers selected for PCR? Lecture, primer search  
8. Sample PCR How can sample DNA be amplified using PCR? Lecture, PCR using Qiagen PCR kit  
9. Gel Electrophoresis How can we confirm if PCR was successful using gel electrophoresis? Lecture, Pour an agarose gel, prepare sample for gel electrophoresis, load gel, run gel, stain/destain gel, visualize gel (take picture) analyze gel  
10. DNA Sequencing How are DNA samples sequenced? Lecture on DNA sequencing, field trip to sequencing lab, computer simulation  
11. Proposal Development/Literature Review How can we ask a new research question using DNA barcoding techniques? Search google scholar for primary literature on DNA barcoding, Find 5 articles, print articles, CREATE articles, develop new research question  
12. DNA Barcode Analysis 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.

 

Course Themes/Goals

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. 

 

Return to course introduction page.