ʻĀina-Informatics: Curriculum — ʻIolani Community Science

Our ‘Āina-Informatics lab curricula have been designed alongside and in response to our network of educators to introduce place-based content and practical skills acquisition for genetics and genomics. These labs can be conducted in sequence or as standalone modules, and can be framed in ways which complement different subject areas, from conservation to health to forensic science. For each lab, we recommend relevant bioethics activities that deepen students’ understanding of the social and ecological contexts of the technologies they are learning.

Our lab curriculum assumes that students have some basic proficiency in micropipetting. Micropipettes are included in our mobile lab, and we always conduct a hands-on training in pipette mechanics and proper technique prior to initiating any lab activities with students. LabXchange.org offers both an excellent video introduction to micropipetting as well as interactive online resources to learn more about pipettes and how they are used to transfer fluids in the lab.

GM Papaya Lab

Students supply papaya leaves from their yards for PCR screening of the CaMV1 transgene promoter in GM papaya.

LAB OVERVIEW

LEARNING OBJECTIVES:

Students will understand a generalized process for accessing information from DNA molecules
Explore foundational genetics lab techniques and equipment
Comprehend the mechanics, utility and impacts of GMOs

Crosscutting concepts: SI units, sexual reproduction in plants, organelles, cell division, chemical concentrations, electricity/electric charge

Lab techniques: DNA extraction, PCR, gel electrophoresis

Keywords: GMO, food safety, agriculture, environmental health

HANDOUT: GM PAPAYA LAB ROADMAP

Student GM papaya results mapped by sampling location.

UNIT 4: GM BIOETHICS IN HAWAIʻI

Basic: GMO Papaya Scenarios Activity

Digging Deeper: Maui County GMO Moratorium Bill Activity

Lava Cave Microbes Lab

Students use the MinION to sequence cultured microbial isolates from Hawaiʻi Island lava caves. This lab is designed to sequence three targets simultaneously on a standard MinION flow cell, but it can be modified to do a single genome or a duplex run. Flongle protocol coming soon.

LEARNING OBJECTIVES:

Students learn first, second and third generation sequencing techniques to connect genetics to genomics
Assemble a genome using basic online bioinformatics tools
Investigate what genomic data can reveal about an organism’s function or capabilities

Crosscutting concepts: DNA replication, gene expression, computer algorithms, taxonomy

Lab techniques: MinION sequencing, online bioinformatics

Keywords: Microbial biodiversity, early Earth, astrobiology, drug discovery, extremophile biology, quorum sensing

HANDOUT: MinION SEQUENCING LAB ROADMAP and TEACHER GUIDE

ACTIVITY: GENOME ASSEMBLY PUZZLE

UNIT 1: MinION SEQUENCING

Library prep protocol | MinION protocol

UNIT 2: WHOLE GENOME BIOINFORMATICS

Ulana | EDGE Bioinformatics | KBase

Additional lab content

Non-tuberculous Mycobacteria Lab

Students use the MinION to sequence NTM strains which have been collected from domestic and wild environments around Hawaiʻi. This lab is designed to sequence three targets simultaneously on a standard MinION flow cell, but it can be modified to do a single genome or a duplex run. Flongle protocol coming soon.

Lab techniques: MinION sequencing

Keywords: Public health, citizen science, microbial ecology

HANDOUT: MinION SEQUENCING LAB ROADMAP and TEACHER GUIDE

UNIT 1: MinION SEQUENCING

Lesson slides | Library prep protocol | MinION protocol | Flow cell washing protocol (optional)

ACTN3 “Speed Gene” Lab

Students use RFLP to genotype their own cheek cell DNA for ACTN3, also known as the “speed gene.”

LEARNING OBJECTIVES:

Students will understand a generalized process for genotyping human beings for a trait
Explore foundational genetics lab techniques and equipment
Draw connections between genotype and phenotype

Crosscutting concepts: SI units, human physiology, organelles, cell division, chemical concentrations, electricity/electric charge

Lab techniques: DNA extraction, PCR, restriction digest, gel electrophoresis

Keywords: Personal genetics, human health, forensics