The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

Subscribe to this blog

Sign up for email notifications

UCLA Undergraduates Barcode California’s DNA

We are happy to post this news report from Maura Palacios Mejia, HHMI Postdoctoral Scholar, UCLA. As described below, her curriculum draws on training and resources from our colleagues at DNA Learning Center, Cold Spring Harbor Laboratory–nice work!

The Class

Science is making sense of the world around us. I set out to use the process of scientific discovery to teach my 42 mostly first year students at UCLA. The class, California’s DNA: A Field Course, meets for 50 minutes a week and aims to introduce students to a variety of life science disciplines e.g. ecology, microbiology, genetics, etc.) with a twist of environmental DNA (DNA that organisms shed into the environment). The class has a strong field component, where each Saturday, we have a 2-5 hour field trip to a new ecosystem; salt-marsh, chaparral, forest, where students learn about the natural history from scientists with a variety of expertise (undergraduate students, biologists, soil scientists, etc.), jobs (reserve managers, museum curators, etc.), and backgrounds.

Students carrying out a field study at Arroyo Seco. Photos courtesy of Audra Huffmeyer.

The DNA Barcoding Project

This past summer I attended a Barcoding Educator workshop, an effort between James Madison University and Cold Spring Harbor Laboratory (CSHL), to train and expand DNA barcoding (the use of a single region of DNA to identify a species as simple as scanning a supermarket barcode) to other institutions across the nation. I chose to focus our DNA Barcoding Project at a location in our backyard, Arroyo Seco, an urban stream that flows into the L.A. River. The students were tasked to collect one insect with the use of a D-net, sweep net, or trapping them in a collection tube. We also set up a Malaise trap in the event a student was unable to collect a sample. In addition, students made observations using the iNaturalist application, an easy tool to create unique class specific projects (https://www.inaturalist.org/projects/eeb-87-california-s-dna-a-field-course). In groups students also collected water quality data and sediment environmental DNA samples. To our surprise, this hidden gem harbored high levels of biodiversity which included chorus frogs, salamanders, dragonflies, wolf spiders, and even horses!

With the insect samples collected and preserved in 70% ethanol, Kiumars Edelati, the course learning assistant and Caroline Schreck, a volunteer undergraduate research assistant took on the tasks of photographing each individual, extracting DNA, running PCRs, and running gels (methods in https://dnabarcoding101.org/lab/index.html). The samples were then sent out for sequencing and we obtained results the very next day, thanks to the support of Bruce Nash at CSHL!

Undergraduate students who assisted in processing samples and developing tutorial.

Biodiversity Literacy in Undergraduate Education 

During this time, I was also a participant of the Biodiversity Literacy in Undergraduate Education (BLUE) network Faculty Mentoring Program, where I was meeting weekly with faculty from 3 other campuses. The goal of the program is to develop teaching modules that help students gain scientific skills and critical thinking that can be publicly shared. Every week we had a small goal, e.g. learning objectives, where we would obtain feedback and have a small discussion. I was able to observe how each member incorporated and implemented modules, particularly the Data is the New Science. I found an excellent opportunity to merge the DNA barcoding project  and the use of biodiversity databases.

The faculty participants of the Biodiversity Literacy in Undergraduate Education network.

The Implementation

With the assistance of our team, we processed the sequences in DNA Subway and put together a step by step tutorial and worksheet for students to work through during class. We set up the classroom with two projectors, one with the tutorial and the other for the demo. Each student received a unique insect sequence from the samples from the Arroyo Seco to explore and, as a class, we moved through database by database. This included submitting their new found discovery of identifying their organism, submitting an image, and the sequences into the BOLD student portal.

This was an excellent exercise tying together their experience in the field with scientific discovery and the efforts of each student in making scientific contributions.

Students in the classroom carrying out computational analyses for the Insect DNA Barcoding Project. Photos courtesy of Kiumars Edelati.

https://lh3.googleusercontent.com/c9AcCfpTqKJR0eR7fKwjk-sVaor7aeDzTMuA2evu_7zULqzGIwoX_AqBmXxLPt_ljOpmgsjVX3FR6RQyCPx1Y7K39UqWDM8wtxysjzIAg7lVWmgNYIYD4pptnDynP2eGhhpImxwt
BOLD student portal submissions for the Insect Barcoding Project for our course.

This entry was posted on Saturday, December 14th, 2019 at 10:14 pm and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

Comments are closed.

Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.