Hopkinton students study bioinformatics

Published: 06-05-2023 3:00 PM

Bioinformatics is an interdisciplinary field where computer programs are used to analyze immense amounts of complex biological data. The Human Genome Project is one example. Other initiatives include identifying unknown species by collecting DNA from a specimen, amplifying select marker genes using the polymerase chain reaction, sequencing these amplified products, and comparing the sequence reads from a sample against a universal database to enable identification.

Through these activities, students at Hopkinton High School are engaging in collecting and analyzing data precisely and accurately, critical thinking, problem solving, and so much more.

The goal is to participate in a pilot program as citizen scientists who contribute to a collaborative project with the Lake Sunapee Protective Association. With the help of Dr. Geoff Cook and others from New England College as well as the staff at LSPA, students will be collecting water samples from the lake to isolate environmental DNA from the water. The collected DNA will then be used to identify what invasive species are present in the lake; monitor bacterial communities, and potentially track fish populations. Hopefully no invasive species will be found, but if they are then LSPA will now be aware and can make plans to manage the situation.

As practice, students collected bacterial cells from various school surfaces and cultured them on standard growth agar in Petri dishes. Results were surprising in that cell phones were cleaner than expected while less surprising results included more bacteria found on water bottle mouth pieces and staircase railings. Students practiced micropipetting technique with a focus on accurate and precise data collection as well as learning how to use a common scientific tool/equipment. DNA was extracted from the bacterial cultures grown on the Petri dishes.

In May, students piloted a citizen scientist data collection project with Dr. Cook (NEC) and Dr. Elizabeth Harper and others from LSPA. The focus is on using eDNA found in water samples from the lake to determine if invasive species are present, track bacterial communities over time and space, and possibly monitor fish populations. In addition, students learned about the health of the watershed by studying cyanobacteria and macroinvertebrate populations in Lake Sunapee.

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