ʻĀina-Informatics: Project Ideation

Students are passionate about a range of questions, but only a subset of those issues might be addressed using genetics or genomics. In the high school lab, where equipment and time are common limitations, most but not all of the questions that you can feasibly address with students using genetic techniques fall into a few basic categories.

QUESTION TYPES AND TECHNIQUES

Each question type uses a general set of techniques that students and lab can be outfitted to utilize. Use the chart below to determine which techniques you will need to support the questions your students are interested in. To explore specific examples of each question type that local teachers have been asking along with their classes, click through the icons on the image below the chart.

COST CONSIDERATIONS

The cost of DNA projects can add up quickly, but there are ways to get the most out of your grant funds. Most techniques involve one or two high cost items that can make or break a project. Planning ahead, resource sharing with ʻĀina-Informatics Network teachers and utilizing our equipment and reagent libraries are ways to defray the costs of pricier products.

EQUIPMENT

For lab equipment, ʻĀina-Informatics uses a suite of (relatively) affordable, well-designed MiniOne products - from micropipettes to thermocyclers - in our mobile lab. For example, their gel electrophoresis system replaces the need for external power sources and gel documentation systems, and is a fraction of the price of a lab grade unit. A good ballpark figure for outfitting a typical classroom would be between $4,000-6,000 depending on class size and packages deals available.

One of the main workhorses in the genetics lab that you may not be able to source at a discount is a tabletop centrifuge. Many DNA extraction protocols require centrifugation speeds in excess of 10k rpm, so your average microcentrifuge will not be sufficient. You can expect adequate models to cost $2,000-3,000, but you only need one.

DNA EXTRACTION AND PCR

There are many ways to extract DNA from biological samples, from basic boiling methods to fancy kits. For most PCR projects, the purity and yield of DNA extraction methods is less important than for sequencing projects. Tissues such as bacterial cells, plant leaves, fish fins and more can be extracted on the cheap using home brewed or commercial “hotshot” methods that don’t require filter columns.

For sequencing projects, high quality DNA is needed in order to yield the best results. Balancing cost with time and expediency, ʻĀina-Informatics has had good success using Qiagen kits for a variety of animal tissues, OPS kits for plant tissues, and stool kits for soil samples.

The main cost of PCR is the Taq polymerase used during amplification. Since PCR routines can be highly specific to a study, it is best to investigate which Taq products have been used in reported studies relating to your project. ʻĀina-Informatics has found that Bioline produces a generic Taq pre-mix that works well across a number of systems. MiniOne also supplies Taq products at very competitive prices. Shipping to Hawaiʻi can be very expensive, so sticking with a single supplier and grouping orders can often net the best savings.

SEQUENCING PROJECTS

There are really only two sequencing platforms that are relatively accessible to the high school classroom: Sanger sequencing (which is outsourced) and MinION sequencing (done within the classroom). For Sanger sequencing, ʻĀina-Informatics uses services such as Laragen to obtain sequence data at approximately $5-7 per sequence. On Oʻahu, UH Mānoa has a Sanger sequencing service that can be cheaper (about $3 per sequence).

Setting up the MinION sequencing platform for your classroom is a commitment. There are startup costs to consider, but cost-saving measures such as multiplexing (running multiple samples on the same flow cell) can bring the price per sample down considerably.