After doing genetic barcoding as a lab during AP biology class at Brunswick High School, we decided to take advantage of an extended learning opportunity (ELO) and continue the study of local organisms. We collected organisms from a nearby stream —Mare Brook—as part of a larger study of the environmental effects of the surrounding infrastructure.
Using the materials generously lent to us by Deborah Landry of iXplore, we were able to extract DNA from the organisms and send genetic material to Genewiz to be sequenced. This information will help compare two different species (silverfish and spider) from two different locations on the stream. Along with the thirteen samples that were barcoded within the AP biology class, these samples will contribute to a genetic database of barcoded organisms and species in Brunswick, as part of the Maine Barcode of Life project.
In the biology classroom, students learned more about biotechnology and bioinformatics and how it relates to the local species around them. The extended learning opportunity helped fuel our interest in genetics and environmental science and how they are related. Thank you to IDEXX Labs, Maine Community Foundation Rines-Thompson Fund, Thermo-Fisher Scientific and iXplore STEM for their generosity and making projects like this possible.
By Erin Coughlin and Alex Morse, Brunswick High School Class of 2019
“Orconectes virilis”, crayfish, with light- to olive-brown body color.
Kids are fascinated with what’s living beneath the water’s surface — oceans, rivers and lakes — spending endless hours exploring. Trying to identify creatures can be difficult as their features may vary with age, sex and even the environment. Experts rely on color and other traits to identify and classify organisms, but on occasion, species look so similar that even professionals can’t tell them apart. That’s why, as of 2013, scientists have included a new laboratory test to verify species identity, called DNA barcoding.
Gorham High School student loads an electrophoresis gel to analyze DNA.
Over the past year, Gorham, Westbrook, and Deering High School students used this technology to identify plants and animals collected from their regions. Each student extracted DNA from their specimen, used biotechnology to amplify and sequence a target gene, and then submitted the sequence to a genetic database for a comparison. This DNA barcode confirms the identity of the organism as well as evolutionary relationships to other species. The BoldSystems database stores more than 5 million barcodes from around the globe, including GPS coordinates and specimen images.
“Luxilus cornutus”, aka common shiner.
In the end, Maine students accurately identified many organisms from their regions and many contributed voucher (or reference) specimens to the genetic library of species living today (Maine Barcode of Life).
Imagine how useful this technique would have been to Charles Darwin as he examined the many varieties of beetles, birds, and barnacles!
Student examines neurons at the University of New England Imaging Core
“Wow!” is the first word uttered by those who see the complexity and beauty of neurons under the microscope. Students participating in the iXplore Summer Program had this opportunity at the University of New England’s Histology and Imaging Core. Here, students investigated the nervous system using a variety of histologic techniques. Students stained mouse brain tissue and found that neurons (black dots, below left) are clustered in symmetrical regions of the brain. Higher magnification showed neurons with long branching projections (dendrites and axons), which aid in communication between neurons.
Close up of neurons, mouse brain. [400X, Golgi stain. Peter Caradonna, UNE.]
Are all 75 million neurons in the mouse brain alike? To answer this question, students examined brains stained by immunohistochemistry, a method highlighting specific molecules, and concluded all neurons are not alike, since dopamine (a neurotransmitter, staining red) is produced in varying amounts in the brain (below).
Sagittal section of mouse brain. Nuclei (blue) and dopamine-making regions (red). [Tyrosine-Hydroxylase (TH), DAPI, 100X. P. Caradonna, UNE.]
Mouse brain tissue showing cell nuclei (blue) and dopamine-making neurons (red). [DAPI, TH, 400X. Peter Caradonna, UNE.]
Do neurons form patterns outside of the brain? Students looked at cornea slides stained for a neuron receptor called TRPV. This receptor was found on neurons throughout the cornea (green). With higher magnification, TRPV staining (red), shows neurons form a swirling pattern in the cornea. These receptors respond to injury — like a poke in the eye — and send signals to the tear ducts to produce tears.
Whole mouse cornea staining for TRPV1 (green), a heat and pain receptor. [Stitched, 100X, P. Caradonna, UNE.]
Mouse cornea TRPV1 pain and heat receptor staining (red). [200X, P. Caradonna, UNE.]
Deering High School students visit the Marine Science Center at the University of New England.
Engaging students in STEM can be challenging, especially with the limited resources of most classrooms. That’s why Karen Shibles, a Deering High School science teacher, took advantage of a unique opportunity offered by iXplore and enlisted her students in the “Maine Barcode of Life” (MBOL) project. This project focuses on biodiversity and genetics and connects students to the living world around them.
During the first phase of the project, students learned about marine organisms by visiting the University of New England’s (UNE) Marine Science Center. Dr. Markus Frederich and Dr. Deborah Landry gave the visitors a tour of the marine biology labs with expansive touch tanks. At first, the students were very apprehensive (even scared) about getting too close to live marine organisms, but with the help of UNE students, the high schoolers slowly began exploring the saltwater tanks and holding starfish, crabs, and urchins.
A skate startles a group of students.
Determining the exact species of fish, crab or sea star can be very difficult, even with a field guide, unless you’re experienced. This was especially true for the Deering students since most of them had never been to the ocean. During the second phase of the MBOL project, students learned how to use DNA barcoding, a powerful research method which can identify and classify any organism. So how does DNA barcoding work? First, students extract DNA from the organism through a series of steps using different chemicals and equipment. Second, students use biotechnology to amplify one universal gene and later obtain the DNA sequence or code. Third, students import the DNA code into the BOLDsystems website, which compares the code to all the other codes stored in the genetic database. Within seconds, BOLDsystems reports the species name and how it relates to all other species. In the end, Deering High School students learned about marine biodiversity, advanced their lab and analytical skills, and published 8 new species records. Thank you Deering High School for contributing to the Maine Barcode of Life!
“What can boring fish eggs teach us?” a 4th grader asked while looking at the motionless eggs at the bottom of the tank. “I thought you were bringing real fish into the classroom”.
“Just you wait!” I said hoping he would reconsider after watching the eggs transform over the next three months.
My goal, as STEM curriculum developer, was to bring into focus how organisms grow and develop. Studying Atlantic salmon, from eggs to fish, would provide a model for the study of life cycles, traits, behavior, natural selection, and the influence of the environment. The Yarmouth Elementary Salmon Hatchery offered a unique, hands-on experience for students and educators, who might otherwise never get up-close to such fascinating creatures that once lived abundantly in the nearby Royal River. Students also applied math skills when predicting “Hatch-Out” day and estimating the relative amounts of ocean, glacier, ground and fresh water on Earth.
After the students released the young salmon fry many miles upriver from Yarmouth, they asked new questions….Will they find enough food? Will they survive? Will they return to the Royal? Although I knew we couldn’t answer most of these questions, their experience clearly stimulated thinking beyond the classroom.
In the end, the 4th graders made keen observations, asked questions, tested predictions, and shared conclusions in conversations and writing about the growth and development of salmon. Their first hand experience observing, caring for, and learning about an endangered species, will likely make a lasting impression and potentially create a new generation of environmental stewards.
What a surprise to find a post about the Maine Barcode of Life (MBOL) project coming all the way from Canada! Dirk Steinke, a DNA barcoding expert from the Biodiversity Institute of Ontario at the University of Guelph writes a very complementary post about our work. iXplore launched MBOL in 2013 and recently, with a generous donation from the Maine Community Foundation Rine-Thompson fund, we will broaden student participation in Greater Portland, Maine. The grant provides the necessary funds to complete the “DNA Barcoding Foot Locker” containing equipment and supplies. The foot locker will travel to high schools to support student research during the academic year. Thanks for the shout out Dirk… and you’re right, we do like to have fun!
IXplore STEM was awarded a generous grant from the Rines-Thomson Fund of the Maine Community Foundation to broaden student participation in science, technology, engineering and math (STEM). This grant provides high school students (in the Greater Portland area) the opportunity to engage in modern scientific research using DNA barcoding and contribute to the Maine Barcode of Life project (MBOL 2015). Funds will go towards the purchase of equipment and supplies to create a “DNA Barcoding Footlocker”, which can travel from school to school for classroom research. IXplore STEM launched the Maine Barcode of Life project in 2013, which is a joint effort by Maine high schools and colleges to assess the biodiversity, distribution and abundance of Maine’s marine and land-based organisms and to build a genetic library of Maine species – past, present, and future.
Students use biotechnology in their research projects.
“Life science students and teachers will benefit from this project – using modern biotechnology and equipment that would otherwise not be available to them,” stated Karen Shibles, a Deering High School science teacher who completed training during an iXplore summer workshop. “I am convinced that such experiences will build the kind of 21st century STEM skills, knowledge and confidence that our students need.”
“Students investigate topics such as the effects of global warming on biodiversity, the presence of invasive species, and food fraud in markets and restaurants,” said Deborah Landry, Executive Director of iXplore STEM. “Students publish their results in BOLDsystems.org and build the genetic library of existing Maine species that can be used by scientists around the globe.”
The University of New England’s Marine Science Center will collaborate on the project and host classroom visits to collect specimens for student research.
Students and educators collect specimens for research while visiting the UNE Marine Science Center.
“This effective teaching tool not only offers an avenue for authentic classroom research, but it also prepares students for college level science,” commented Markus Frederich, a UNE professor of marine biology.
IXplore STEM partners with institutes of higher learning, businesses, and other nonprofits to develop programs that encourage students to pursue STEM degrees and promote STEM awareness in the community. To learn more about student and educator programs, visit www.ixplorestem.org.
The Maine Community Foundation is located in both Ellsworth and Portland and works with donors and other partners to improve the quality of life for all Maine people. Visit www.mainecf.org to learn more about the foundation.