Educator Profiles
If you've done one or more rounds of teaching Nanopore at the secondary or undergraduate level, please share your profile to highlight your work and connect with this growing community!
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Karen Barnard-Kubow
: James Madison University
: Harrisonburg, Virginia, United States
: Undergraduates
: email
: plants (chloroplast genome sequencing), also some 16s metabarcoding
: Experienced with Nanopore
About Karen
Classroom research question(s)
We run a module in our core Genetics lab (10 lab sections of 24 students) asking if structural variation in the chloroplast genome of Campanula americana is related to strength of cytonuclear genetic incompatibility. The focus of the 2-week module is to introduce students to the concepts of speciation, reproductive isolation, and genetic incompatibility, as well as chloroplast function and structure, and long-read next generation sequencing, with a focus on Nanopore sequencing.
Using Nanopore in the classroom
The module utilizes the plant species, Campanula americana, which exhibits cytonuclear incompatibility in the form of hybrid seedlings exhibiting chlorosis (reduced chlorophyll production) leading to yellow or white seedlings. The week before the module starts each group plants hybrid seeds from a different cross, which they will score for strength of incompatibility once the plants germinate by scoring their phenotype (green=no incompatibility, yellow=moderate incompatibility, while=strong incompatibility). We start the first week with an introductory presentation about the project and Minion sequencing. The students then interact with used flow cells, where each student practices priming and loading a used flow cell with water. The students then do a trial run-through of the bioinformatic analysis pipeline which is carried out in Google Colab, so all students can run the pipeline on their own computers. The following week, students use the bioinformatics pipeline to analyze Minion sequence data and assemble the chloroplast genome of one of the parents of their seedlings. In the pipeline they check the quality of the reads using Nanoplot, assemble the chloroplast genome using Flye, visualize the assembly using Bandage, and annotate it using GeSeq. They then get the genome assembly for the second parent of their hybrid seeds from another group and align the two assemblies and score structural variation between the two chloroplast genomes using Assemblytics. Then we combine data across all eight groups and make a graph with number of structural variants on the x and strength of genetic incompatibility on the y, to ask if there is a relationship between extent of structural variation between chloroplast genomes and strength of genetic incompatibility.
URLs
https://github.com/kbkubow/NanoporePlastidAssemblyModule/tree/main -
Yokshitha Bathula
: HudsonAlpha Institute for Biotechnology
: Huntsville, Alabama, United States
: High school
: email
: eDNA
: Some experience with Nanopore
About Yokshitha
Educational Goal
Exploring bacterial biodiversity and antibiotic resistance across different soil ecosystems.
Using Nanopore in the classroom
We use Nanopore sequencing as part of a semester-long independent project with high school students. The students extract eDNA from soil samples and perform 16S sequencing. They use the results from the EPI2ME workflow to do a comparative study of bacterial diversity and look for antibiotic-resistance genes that align with the microbial lab results.
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Anna Feitzinger
: Cold Spring Harbor Laboratory, DNA Learning Center
: Brooklyn, New York, United States
: Support for all educators, High school, Undergraduates
: email
: plants, bacteria, eDNA, human
: Experienced with Nanopore
About Name
Educational Goal
One research question we ask is how does human activity impact the local waterways of NYC?
Using Nanopore in the classroom
I teach a semester long college course in which students explore the biodiversity and water quality of local waterways in New York City with a focus on eDNA. In addition, I work with high school students, introducing them to genomics and bioinformatics during summer workshops.
URLs
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Bob Kuhn
: FCS Innovation Academy STEM High School
: Georgia, United States
: High school
: Reach me on Slack
: 16S DNA Barcoding, Phage Genomes
: Getting started with Nanopore
About Bob
Classroom research question(s)
How do bacterial abundance and assemblages change across environments and scales?
Using Nanopore in the classroom
We have used Nanopore 16S barcoding to investigate simple variable differences such as bean beetles dosed with probiotics, salamander species skin swabs, different vegetables in kimchi, and bacterial profiles in Georgia lakes. We also hope to begin bacteriophage genome sequencing in fall 2025 as part of our phage discovery program.
URLs
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Sylvia Franke McDevitt
: Skidmore College
: Saratoga Springs, NY, United States
: Undergraduates
: email
: 16S barcoding
: Some experience using Nanopore
About Sylvia
Educational Goal
We are analyzing microbial communities from a variety of sources to answer questions like changes in the microbiome of mice, impact of heavy metal contamination in soil, or bacteria in sourdough.
Using Nanopore in the classroom
In my research we are looking at the microbial communities of creek sediments near old manufacturing sites, which have historically released heavy metals. Additionally we are analyzing fecal samples of mice with and without zinc supplement. The latter project is being done both in my research group as well as in my upper-level class. In my intermediate level General Microbiology students are proposing their own research question comparing microbial communities using the 16S Barcoding workflow.
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James Melton
: Spelman College
: Atlanta, Georgia, United States
: Undergraduates
: email
: Bacteriophage
: Experienced with Nanopore
About James
Educational Goal
This research is conducted as a part of the SEA-PHAGES (Science Education Alliance- Phage Hunters Advancing Genomics and Evolutionary Sciences) program to isolate and characterize phages from soil.
Using Nanopore in the classroom
In the classroom, we perform whole genome sequencing of Arthrobacter globiformis and Gordonia rubripertincta phages. Approximately ten students isolate a phage from soil and gain hands-on experience with Nanopore sequencing and bioinformatics.
URLs
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Fernando Nieto
: State University of New York, Old Westbury
: New York, United States
: High school, Undergraduates
: email
: Bacteriophages, and 16S/18S metabarcoding.
: Some experience with Nanopore
About Fernando
Educational Goal
We are interested in understanding microbial diversity and microbiome change patterns in the environment and in humans.
Using Nanopore in the classroom
We are using Nanopore sequencing for sequencing bacteriophage genomes isolated by students from soil samples as part of the SEA-PHAGES program. We are also trying for the first time to use ONT for 16S and 18S sequencing to analyze environmental and human oral microbiome. These activities are integrated as CUREs into our undergraduate biology courses that are part of the major, i.e. ecology and microbial ecology. HS students are also involved as part of of their participation in the Science Technology Entry Program (STEP) funded by NYSED.
URLs
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Robyn P
: Bridgewater College
: Virginia, United States
: Undergraduates
: email
: amphibians
: Getting started with Nanopore
About Robyn
Educational Goal
Looking at vernal pool use by amphibians breeding in Virginia.
Using Nanopore in the classroom
I am hoping my department will purchase an MinIonMk1D unit. I am working with the microbiologist on 16S sequences from environmental samples, and I am interested in metagenomic samples of eDNA from vernal pools.
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Jonathan Pugh
: Oxford Nanopore Technologies
: Oxford, United Kingdom
: Support for all educators
: email
: Experienced with Nanopore
About Jon
Educational Goal
I facilitate educators to do more of their great work, and collaborate with key organisations to utilise existing networks of educators
Using Nanopore in the classroom
Here to facilitate, collaborate, champion, and protect!
URLs
Publications
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Jason Williams
: Cold Spring Harbor Laboratory, DNA Learning Center
: Cold Spring Harbor, New York, United States
: Support for all educators, High school, Undergraduates
: email
: Plant and microbial DNA, DNA Barcoding
: Experienced with Nanopore
About Jason
Educational Goal
Develop resources that allow faculty to bring Nanopore into the classroom.
Using Nanopore in the classroom
As the lead PI for the project, Jason was the first to introduce Nanopore sequencing at the DNA Learning Center in 2014 as a potential activity for our students. Since then, it has been a long journey of technological and curricular development to bring this technology into the hands of educators across the country and around the world.
URLs
Publications
- This eBook!
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Miguel Urdaneta
: University of Puerto Rico, RÃo Piedras Campus
: San Juan, Puerto Rico, United States
: Undergraduates
: email
: Insects: Diaprepes abbreviatus, Apis mellifera / DNA Barcoding / 16S / Ligation-based Amplicons
: Experienced with Nanopore
About Miguel
Educational Goal
Antibiotic-resistance patterns in gut-microbes of insects and their potential role as probiotics and regulators of the gut-brain axis. Potential pathogens variations on Puerto Rico honey bees Apis mellifera.
Using Nanopore in the classroom
In our undergraduate Applied Microbiology laboratory, we have been used the Nanopore 16S Barcoding and the Ligation-based Amplicon Barcoding protocols to investigate the bacterial diversity on the Caribbean pest insect Diaprepes abbreviatus and in the honeybees Apis mellifera.