Educator Training

We offer up-to-date teacher training through biology workshops and development for teachers in genetics and biotechnology. With federal and private foundation funding, we offer these free workshops to high school and college educators, especially those in the areas of genetics, biology, genomics, and bioinformatics.

DNA Barcoding and Metabarcoding for CURES Workshops

Funded by the NSF Improving Undergraduate STEM Education Initiative

The Cold Spring Harbor Laboratory DNA Learning Center (DNALC), in collaboration with New York City College of Technology (City Tech), Bowie State University (BSU), and James Madison University (JMU), is offering two five-day workshops on DNA barcoding or metabarcoding in course-based undergraduate research experiences (CUREs). Applicants to these free workshops should be undergraduate teaching faculty with a sincere desire to involve students in authentic research projects, especially in CUREs for students in introductory courses.


DNA Barcoding Workshop

2021 Virtual Workshop
June 7, 9, 11, 14, 16, 2021, 1:00–4:00 p.m. EDT

  • Monday, June 7: Intro and Sample collections
  • Wednesday, June 9: Pipetting, Extraction, PCR
  • Friday, June 11: Gels and Sequencing
  • Monday, June 14: DNA subway (can be swapped with w/Wed if sequences get held up)
  • Wednesday, June 16: Implementations, other resources, and exit survey

Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a “DNA barcode” is a unique pattern of DNA sequence that identifies each living thing. DNA barcoding provides a powerful way for biology faculty to lead CUREs, which have been shown to increase student retention and success when provided early in undergraduate programs. Barcoding integrates ideas from molecular biology, genetics, bioinformatics, ecology, and biodiversity—while at the same time providing the flexibility to address a variety of student-driven questions. Barcoding can be mastered in a relatively short time, allowing students to generate new data and reach a satisfying research endpoint within a single course. Furthermore, undergraduate students often have limited patience for bioinformatics, and DNA barcoding provides a wet-lab or field-based “hook” to increase engagement. Bioinformatics analysis of DNA barcodes generated via Sanger sequencing are conducted in the user-friendly DNA Subway Blue Line, an open-access, browser-based pipeline.

DNA Metabarcoding Workshop

2021 Virtual Workshop
June 21, 23, 25 & August 3, 5, 2021

  • Week 1, June 21–25:
    Monday (1:00–3:00 p.m. EDT), Wednesday, Friday, 1:00–4:00 p.m. EDT
  • 6 week recess for participant sample collection, processing, & sequencing
  • Week 2, August 3–5:
    Tuesday, Thursday, 1:00–4:00 p.m. EDT

Rather than analyzing one DNA barcode at a time, metabarcoding leverages next generation sequencing (NGS) to analyze thousands of DNA barcodes from complex mixtures of DNA—representing microbes (microbiomes) or environmental DNA (eDNA). Moving from DNA barcoding to metabarcoding perfectly embodies the conceptual transition from single gene to massively parallel genome analysis, introducing students to NGS analysis and data science. A single lane of an NGS machine can accommodate hundreds of student metabarcoding samples. Similar to DNA barcoding, metabarcoding draws on techniques from molecular biology, genetics, bioinformatics, ecology, and biodiversity. Bioinformatics analysis of metabarcoding NGS data are conducted in the recently developed DNA Subway Purple Line, a browser-based pipeline incorporating QIIME2, a research-grade metabarcoding platform.

 


Workshop participants learn all the biochemical and bioinformatics techniques required to implement DNA barcoding or metabarcoding, including the use of the DNALC’s sequence analysis tools. Workshop seminars introduce key concepts (“big ideas”), CURE development, management and evaluation, data science, methods to work with diverse student populations, workforce development, and details about the project. Seminars include insights from project Co-PIs, including DNALC’s experts; faculty leading JMU’s curriculum, which engages 800 students and 20 instructors in DNA barcoding each semester; and City Tech and Bowie State faculty who lead DNA barcoding and metabarcoding with diverse student populations. The competencies required for bioinformatics, genome science, and biological data sciences are also presented.

Faculty who complete the workshops receive travel support, a stipend, and have year-round mentoring and support from project Co-PIs as they implement barcoding CUREs. Those implementing CUREs receive free reagents and DNA sequencing for student research. DNA barcoding workshop participants from the previous year are eligible to attend metabarcoding workshops—any remaining spots will be filled competitively. Select faculty will be invited to mentor other faculty, building a network of educators implementing DNA barcoding CUREs.

Faculty are asked to participate in a series of evaluation activities throughout the project, beginning with workshop evaluation. Faculty who go on to implement CUREs are enrolled in additional evaluation activities centered on their experiences as well as those of their students. Select schools will be asked to participate in additional longitudinal evaluation of students.

  • Virtual DNA Barcoding Workshop
    June 7, 9, 11, 14, 16, 2021
  • Virtual DNA Metabarcoding Workshop
    June 21, 23, 25, & Aug 3, 5, 2021
  • Audience: Undergraduate Faculty

Apply

Past Event

InnovATE BIO National Biotechnology Education Center and Cold Spring Harbor Laborator
invite you to a mini-symposium

Agricultural Biotechnology: Emerging Technologies and Insights

Thursday, January 28, 2021
1:00 – 4:00 pm EST

High school and college faculty and students are welcome to attend this free webinar.
Registration is required.

Symposium sessions

1:00 pm EST

Agricultural Genomics: The Rise of Genomes

Doreen Ware

Doreen Ware, Ph.D.

Molecular Biologist, USDA Agricultural Research Service and Adjunct Professor, Cold Spring Harbor Laboratory, New York

Breeding for 2050 and beyond will require designing plants for new environments and preparing them for new diseases, while they are still offshore. Key to this effort will be access to high-quality genomes and annotations for agricultural species and their pests. The genomes of many plants have been sequenced over the past decade, but these are usually limited to one reference assembly. The available genomes are often fragmented and missing complex repeat regions—and so lack sufficient high-level representation of genes and functional variation within a species. We are now entering an era where genome assemblies are reaching a theoretical maximum of contiguity and completeness—at ~0.1% the cost of 10 years ago. This provides an unprecedented opportunity to access genomic information to dissect complex agronomic traits and to provide insights into species evolution.

Doreen Ware is recognized as a leader in plant genomics and bioinformatics. Over the last several years her laboratory has contributed to collaborative projects supporting genomics-enabled science with a focus on understanding plant genome architecture and its impact on complex traits—including grain yield, response to nitrogen, and disease resistance. Dr. Ware’s group has contributed to the development of reference genome resources for rice, maize, sorghum and grape, as well as Cyberinfrastructure projects to support access and integration of genome-scale data. Dr. Ware serves in several leadership positions within the plant science community and was acting Chief Scientific Information Officer for USDA Agricultural Research Service (ARS) from 2014-2017.

2:00 pm EST

Emerging Trends in Agricultural Diagnostics

Zach Bateson

Zach Bateson, Ph.D.

Research Scientist,
National Agricultural Genotyping Center, Fargo, ND

Pests and pathogens account for up to 30% of the annual losses in food crops worldwide. All agricultural commodities are negatively impacted by pests, either directly in the field or indirectly through the supply chain. Molecular diagnostics to identify and manage threats in agriculture lag behind diagnostic applications in the medical sciences, despite deep connections between agriculture and human health. In this webinar, I describe the diagnostic biotechnology used at the National Agricultural Genotyping Center (NAGC) and how diagnostic data provide insights into emerging threats across the agricultural community. Specifically, I discuss research underway at NAGC that helps: 1) identify drivers of colony losses impacting the honeybee industry, 2) quickly detect herbicide resistant weeds, and 3) measure environmental pathogen densities to develop predictive models for crop diseases. While the research is diverse in scope, the diagnostic methods take advantage of a commonality across all pests and pathogens—the genetic code.

Trained as a population geneticist, Zack Bateson has used bioinformatics and molecular diagnostics for the last 15 years to investigate issues in conservation genetics and agriculture. Dr. Bateson is currently lead research scientist at the National Agricultural Genotyping Center (NAGC), a not-for-profit, ISO-accredited testing facility. At NAGC, he and colleagues develop molecular-based tests to rapidly identify pathogens and pests that threaten crops and livestock around the United States. NAGC is also the primary testing facility for the National Predictive Modeling Tool Initiative, a new USDA ARS collaborative project that aims to help farmers predict disease outbreaks. Dr. Bateson is a part-time instructor at North Dakota State University in Fargo.

3:00 pm EST

Clones, Carbon and Climate Change: The Epigenetics of Oil Production

Rob Martienssen

Rob Martienssen, Ph.D.

Professor,
Cold Spring Harbor Laboratory, NY

The African oil palm is the most efficient oil bearing crop, but demand for edible oils and biofuels, combined with sustainability concerns over dwindling rainforest reserves, has led to intense pressure to improve oil palm yield. The fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield—and has largely halted efforts to clone elite hybrids for oil production. Using epigenome wide association studies, we found that loss of methylation of a LINE retrotransposon related to rice Karma predicts mantled fruit. Identifying “bad Karma” in cloned plantlets allows growers to cull mantled palms before they reach the field. Since many palms in a given plantation are low-yielding, the broad introduction of high-performing clones promises to reduce the land needed to meet world requirements for palm oil.

Rob Martienssen studies epigenetic mechanisms that shape and regulate the genome, and their impact on transposable elements, first discovered by Barbara McClintock at Cold Spring Harbor Laboratory. These mechanisms underlie clonal propagation of oil palm, with implications for rain forest conservation, and of aquatic plants, including the humble duckweed, that are being engineered in the Martienssen lab for biofuel production and carbon sequestration. The link between epigenetics and RNA interference was named “Breakthrough of the Year” by Science magazine in 2002. Dr. Martienssen joined the faculty at Cold Spring Harbor in 1989. He is a Fellow of the Royal Society and a Howard Hughes Medical Institute Investigator. He was awarded the McClintock Prize in 2018 and the Darwin Medal in 2020.

PAST EVENT

Genetics and Biotechnology Teacher Training Workshops

This program is designed to enable teachers to deliver hands-on, inquiry-based experiments in genetics and biotechnology. 8th–12th grade teachers will be trained to implement lab activities that complement the New York State Life Science, Living Environment, and AP® Biology curricula.

Workshops will provide in-depth demonstrations of labs that target key concepts in genetics and biotechnology, instruction on lab planning and preparation, and classroom implementation. Upon completion, participants will be invited for a follow-up workshop in the fall to become eligible to rent DNALC Footlocker Kits for each lab containing equipment and consumables for up to four classes.

Teachers may register for individual sessions or a series. Virtual sessions will run from 1:00 pm – 3:00 pm. A certificate of completion will be provided for each session; the DNALC is a New York State CTLE certfied provider of Professional Development.

Bacterial Transformation and Protein Isolation

This experiment illustrates the direct link between an organism's genetic complement (genotype) and its observable characteristics (phenotype). In this lab, E.coli cells are engineered with genes for antibiotic resistance and bioluminescence. Following overnight incubation, transformed bacteria are compared to unexposed bacteria for their ability to grow in the presence of ampicillin and fluoresce. Green Fluorescent Protein (GFP) is then isolated and purified from transformed cells, illustrating how many biotech products such as insulin are produced.

DNA Restriction Analysis

DNA restriction analysis is at the heart of recombinant-DNA technology.  The ability to cut DNA predictably and precisely enables scientists to manipulate and recombine DNA molecules at will. This laboratory introduces the genotypic analysis of DNA using restriction enzymes and gel electrophoresis. In this experiment, samples of DNA from bacteriophage Lambda are cut with two different restriction enzymes, EcoRI and HindIII. The DNA is electrophoresed to produce a “fingerprint” of the restriction digest, which is then used to identify a third “mystery” enzyme.

PCR & Human DNA Variation, Part I: Human DNA Fingerprint - Genotyping a “Jumping Gene”

This experiment examines an ancient DNA polymorphism called a transposon, or “jumping gene,” on chromosome 16. Mimicking forensic DNA fingerprinting and genetic diagnosis, participants prepare a sample of their own DNA from cells obtained by saline mouthwash, and PCR is used to amplify polymorphic DNA fragments. After gel electrophoresis, molecular genotypes are scored, and class data is used to explore population genetics, Hardy-Weinberg equilibrium, and theories of human evolution.

PCR & Human DNA Variation, Part II: Human Mitochondrial Sequencing

This experiment examines Single Nucleotide Polymorphisms (SNPs) in the human mitochondrial genome. Students amplify a small region of their own mitochondrial DNA and use the product as a template for DNA cycle sequencing. The participants obtain their "finished" sequence and perform computer analysis of the data using the DNALC's online bioinformatics tools Sequence Server and DNA Subway. Bioinformatic analysis of mitochondrial sequences is used to explore human evolution and migration, and to produce phylogenetic trees using both ancient and modern human mitochondrial DNA sequences.

New Virtual Workshop Training Schedule

PCR and Human DNA Variation: DNA Isolation

(this “pre-class” session will allow participants to isolate their own DNA to be used in the PCR and Human DNA Variation sessions the following week. Materials will be shipped to registrants a week in advance.)

Monday, August 24, 2020
Bacterial Transformation, Part I Tuesday, August 25, 2020
Bacterial Transformation, Part II Wednesday, August 26, 2020
DNA Restriction Analysis, Part I Thursday, August 27, 2020
DNA Restriction Analysis, Part II Friday, August 28, 2020
PCR & Human DNA Variation: DNA Fingerprint, Part I Monday, August 31, 2020
PCR & Human DNA Variation: DNA Fingerprint, Part II Tuesday, Sept. 1, 2020
PCR & Human DNA Variation: Mitochondrial Sequencing, Part I Wednesday, Sept 2, 2020
PCR & Human DNA Variation: Mitochondrial Sequencing, Part II Thursday, Sept. 3, 2020

More lab info and downloads under High School Field Trips

  • All sessions will take place from 1:00 pm – 3:00 pm
  • Each lab will be presented over two sessions.
  • Pre-Class session for DNA isolation is suggested for participation in PCR and Human DNA Variation session the following week
  • For NY metro area 8th–12th grade teachers
  • Register for individual sessions or a series
  • Certificate of completion issued for each session

PAST EVENT

DNA Barcoding Teacher Training Workshops

The Urban Barcode Project (UBP) is a science program spanning the five boroughs of New York City and the surrounding metropolitan area. Just as a unique pattern of bars in a universal product code (UPC) identifies each item for sale in a store, a DNA barcode is a DNA sequence that uniquely identifies each species of living thing.

Trained teachers will be eligible to assemble student research teams in grades 9 to 12 and submit an original research proposal using our proposal submission guidelines. Teams with accepted proposals will receive supplies, equipment, and scientific support needed to conduct experiments during the school year. Results will be shared at an annual symposium.

June 29 – July 2, 2020 Harlem DNA Lab
2351 First Avenue at 120th Street, East Harlem, New York 10035
July 6 – 9, 2020 Regeneron DNA Learning Center
1 Rockwood Road, Sleepy Hollow, New York 10591

Virtual Workshop:
NEW SCHEDULE: June 29–July 3 & July 6–10
Week 1, June 29–July 3: Monday, Wednesday, Thursday 9:00 a.m.–12:00 p.m. EDT
Week 2, July 6–10: Monday, Wednesday, Friday 9:00 a.m.–12:00 p.m. EDT

Learn More about UBP and apply

  • Week 1, June 29–July 3: Monday, Wednesday, Thursday 9:00 a.m.–12:00 p.m. EDT
  • Week 2, July 6–10: Monday, Wednesday, Friday 9:00 a.m.–12:00 p.m. EDT
  • For NY metro area high school teachers

Sites of Major DNALC Faculty Workshops, 1985-present

This map shows the locations of the DNALC's faculty workshops taught over more that thirty years.

Open the map key map key to show/hide the years in groups of three. Click the check boxes to show or hide the years. Click the dots for information on host institution, year, and instructional level of participating faculty. Map can be opened full screen in a separate browser window by clicking the full screen icon at the upper-right.