This grant seeks funding to purchase a nanodrop UV-Vis spectrophotometer machine for classroom use in biology and AP biology courses at NTHS. A UV-Vis spectrophotometer passes specific wavelengths of light through a micro volume sample (1-2 microliters) to detect the presence of nucleic acids (DNA) and allow their quantification. Specifically it allows scientists to measure the precise amount of DNA extracted from samples for use in downstream applications like PCR and DNA sequencing.
This instrument is vital to modern DNA based molecular biology as it allows students to accurately calibrate and set up reactions using DNA they previously extracted from live samples. This is particularly important for setting up DNA sequencing reactions. The main goal of this grant is to allow students to be able to participate in molecular biology experiments that require novel DNA sequencing. Specifically NTHS, and NTHS students have been named as collaborators on a recently funded NSF grant to do just that.
NTHS biology, through Dr. Steakley has already been funded as a broader impacts collaborator on an NSF grant, NSF proposal #2145811, “Cytonuclear stoichiometry of heterotrophic plants”. This grant was prepared by Joel Sharborough (NTHS class of 2007) who is now a professor at New Mexico Technical University and studies genome evolution through the use of DNA sequencing and bioinformatics. Specifically this grant proposes to perform sequencing the genomes of the non-photosynthetic parasitic plants pinedrop and snowflower (collected from the Tahoe basin, live and in person in NTHS AP biology courses). These are plants that no longer perform photosynthesis, and instead are parasites of other plants in their ecosystems to get nutrients. Thus, there are many interesting questions to ask about what changes that has caused in their now unused chloroplast genomes. It is a fascinating example of how evolution might be able to change populations that enter new niches and abandoned old ones.
This project will be the first time these species have been fully DNA sequenced. NTHS students would get to participate in being the first to examine this new sequence data, and could theoretically become authors on the publication describing this data. The NSF grant described above has already allocated $5000 of funding for the sequencing reagents and sequencing machine costs. The dramatic decrease in sequencing cost will allow us a mostly complete genome sequence using new sequencing technology called nanopore sequencing (described here: How nanopore sequencing works). This level, and depth of sequencing for this low cost has only become possible in the last few years.
But, in order to answer those questions and get the sequence data we must first extract DNA from these plants and prepare samples for sequencing at NTHS. NTHS already possess the basic lab supplies (pipets, centrifuges (Excellence in Education 2018-2019 grant cycle), gel electrophoresis equipment, PCR machine (Excellence in Education 2017-2018 grant cycle), DNA extraction reagents to perform much of the required steps in this grant on site. But we specifically lack the ability to precisely quantify the amount of extracted DNA to put into the reactions that will enter the sequencing pipeline. The alternative option is to Fed-Ex the samples on ice back and forth to NM-Tech university, which is possible, but obviously not ideal and removes the students from a vital hand-on portion of the sample preparation.
A UV-Vis spectrophotometer is a standard part of a modern biology laboratory to quantify DNA samples and allows scientists to complete a number of modern molecular biology protocols. Having access to this will allow teachers to complete relevant and engaging labs with classes. Examples include: preparing samples of DNA from supermarket bought fish to determine if the label matches the actual species, preparing samples for DNA sequencing of bacteria from Lake Tahoe water samples to potentially identify new bacteria present in the lake, creating DNA samples to use in bacterial transformation activities to creating glowing bacteria, or research project to quantify mushroom cellulase activity from Spring and Fall mushrooms of the Sierra Nevada Mountains (for which AP Biology classes (supported by previous Excellence in Education grant purchases of spectrophotometers) this year have already collected some exciting preliminary data), among others. This tools will allow science students at NTHS to get real world experience using professional level equipment and doing modern, interesting molecular biology experiments. This is a tremendous help because students are able to contextualize and apply the scientific concepts they are studying in their courses with their own hands. With the transition to the Next Generation Science Standards (NGSS) this is now the expectation and the purchase of this tool will allow NTHS students to keep up with the now increasingly rigorous standards. As the district broadly transitions to NGSS science instruction, students students will need to engage with tools and labs like these in order to build the 21st century skills. This skills are paramount for success in future science careers, and success on upcoming NGSS-aligned science assessments.
It is possible to share the text of the entire NSF grant, however, it contains proprietary information from the Sharbrough lab that is not publicly available. So, if it is requested, grant committee members must agree to keep it confidential and not share methods or pre-publication data outside of the panel. Please e-mail me directly at dsteakley@ttusd.org and I can share the NSF grant materials.