Performing Department
(N/A)
Non Technical Summary
This 'Facility and Equipment' project proposal will focus on strengthening capabilities in high-resolution micro-imagery and next generation DNA sequencing to enhance research education documenting the taxonomic and genetic diversity of tropical and agricultural crops, invasive weeds, and native plant species in Guam and the Western Pacific. The project supports two Project Need Areas of RIIA/AGFEI FY2023: (a) Scientific Instrumentation for the improvement of research understanding and progress and (b) Student Experiential Learning for student participation with faculty on applied research projects. Our proposed project aims to acquire new, state-of-the-art technology in micro-imagery and next-generation DNA sequencing with the primary objective of broadening research and experiential learning opportunities for undergraduate and graduate students at the University of Guam (UOG). To improve capabilities in micro-imagery, we seek to acquire a high-resolution stereo microscope system with advanced imaging software. To enhance capabilities in next generation DNA sequencing, we seek to acquire a next-generation nanopore DNA sequencing device and other genetics and molecular biology equipment, including a deep freezer, tabletop centrifuge, bead mill, and thermocycler. Plant scientists in the Agriculture and Life Sciences Division and from the UOG Herbarium/Biology department will collaborate as a team to secure these up-to-date instruments to solve research questions in horticulture, plant taxonomy, and agroecology and to provide students more comprehensive learning experiences utilizing new technology. This project also opens the possibility for partnerships and other collaborative projects within UOG and with other insular institutions facing similar barriers in research and instruction.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Goals / Objectives
The University of Guam (UOG) is a land-grant university in the Western Pacific. the Agriculture and Life Science (ALS) Division of the College of Natural and Applied Sciences (CNAS) at UOG leads teaching, extension, and research program in agriculture, food, natural resources, and human nutrition. At the horticulture laboratories (PD, Marutani; co-PDs, McConnell and Fernandez) of the ALS Division, current research focuses on the classification of heirloom or landraces of food crops for local agriculture, the taxonomic identification of novel, invasive weeds for developing pest management strategies, and genetic studies on native plants for establishing a plant extinction prevention program in Guam and Micronesia. At the Plant Herbarium (co-PD, Xiao) of UOG, several collaborations are being undertaken both locally and globally to document and preserve plant specimens distributed throughout Guam and other Micronesian islands. Given the dynamic situation of plant research in Guam and premier research status of the University, it remains pivotal for UOG to continue the taxonomic documentation of local agricultural crops, novel weedy species, and native plants while integrating modern technologies that will keep plant research for the region updated. Despite the need for plant research in Guam and Micronesia, UOG faces several challenges in obsolete equipment, outdated protocol, and the lack of specialized instruments, especially in the key areas of advanced microscopic image analyses and next-generation DNA sequencing. This overall lack in research infrastructure has hindered progress in research and education on the taxonomic and genetic diversity of tropical and subtropical agricultural crops, invasive weeds, and native plant species in Guam. The goal of the project is acquisition of up-to-date research instruments which will provide PDs the opportunity to conduct competitive research in the areas of plant taxonomy and genetics and to provide students more experiential learning experiences in the plant sciences. We request the acquisition of new, state-of-the-art instruments in the key areas of (a) Micro-imagery research and (b) Next-generation DNA sequencing research in plants, fungi, and other microorganisms.The proposed project has two objectives:Objective 1. Acquire a high-resolution stereo microscope system with advanced imaging software to enhance research and instruction capabilities in plant taxonomy, horticulture, and agroecology.Objective 2. Acquire next-generation DNA sequencing technology and other genetics and molecular biology equipment to enhance research and instruction capabilities in plant taxonomy, horticulture, and agroecology.To enhance (a) Micro-imagery research, we plan on purchasing a high-resolution Nikon SMZ25 Research Stereo Microscope system to develop high-resolution imagery of vegetative and floral features for the taxonomic description of local food crop cultivars, invasive species, and native plants in Guam. This stereomicroscope will enable better inspection and description of biological specimens at its high magnification and resolution. This high-resolution imaging system will ultimately enhance existing education and research at the University by offering a more integrative view of biological systems down to the microscopic level to undergraduate and graduate students in the College of Natural and Applied Sciences at UOG.To improve (b) Next-generation DNA sequencing research, we plan on purchasing five different instruments including an ultra-low deep freezer, a bead mill, a refrigerated tabletop centrifuge, a PCR thermocycler, and an Oxford Nanopore MinION Mk1C. The system that will be developed from the requested equipment will allow for rapid species identification of agricultural crops, invasive species, native plants, pests and pathogens through DNA barcoding and sequencing. In addition, this widely accessible third-generation DNA sequencing technology will allow for more comprehensive lab experiences in genetics and molecular biology to university students and research interns through a complete overview of the research process from sample collection and extraction to DNA sequencing and sequence analyses. Four other instruments, the standard ultra-low deep freezer, bead mill, refrigerated tabletop centrifuge, and PCR thermocycler will provide a basis for supporting and optimizing the processing of genetic material for sequencing analyses. The Thermo Scientific TSX Series Ultra-Low Freezer will serve the primary purpose of preserving the biological structure of plant specimens and chemical structure of plant DNA extractions. This deep freezer will especially be helpful given the hot, humid environment of Guam that makes plant and DNA preservation challenging. The QIAGEN TissueLyser II bead mill will provide for thorough and rapid disruption of plant material during DNA extraction to improve DNA yield for downstream applications such as DNA purification and amplification. This instrument will aid in optimizing genetics studies involving large sample sizes and/or tedious purification protocol given how procedures are automated for reproducible, high-quality results. The bead mill will also allow genetics studies to bypass expensive, commercial DNA extraction kits that sometimes yield poor quality DNA at low concentrations. The refrigerated high-speed Eppendorf Centrifuge 5910 Ri will serve the primary purpose of high throughput recovery and purification of plant DNA samples for subsequent amplification and analysis. This instrument will be helpful in optimizing genetics studies involving large sample sizes and/or tedious purification protocol. The Applied Biosystems VeritiPro Thermal Cycler will mainly be used to amplify plant DNA samples via polymerase chain reaction (PCR) for subsequent applications including next-generation nanopore amplicon sequencing, ensuring adequate quantities of DNA for analyses. This instrument also features "better-than-gradient" technology, improving temperature control for primer annealing in especially difficult DNA samplesFor the Project Need Area of (b) Student Experiential Learning, we will encourage undergraduate and graduate students to tackle research questions taking advantage of these newly acquired instruments. The ALS program has realized several institutional challenges to providing students with adequate research experiences including the lack of specialized instruments, broken/irreparable equipment, and outdated protocol especially in rapidly advancing areas in microscopy and genetics. At the University, lab equipment for agriculture and biology student studies is often limited to existing equipment purchased by individual faculty using their grants. By securing new equipment, we will be able to recruit more undergraduate and graduate students who will engage in in plant taxonomy, horticulture, agroecology, and other food and agricultural sciences. Through these experiential learning opportunities, students will develop scientific and professional competencies that will enable them to solve complex problems in the context of real-world situations which is even more so important given the dynamic state of plant research in Guam and the Western Pacific. Through this project proposal, our overall goal is to better support student needs by enhancing research infrastructure with new equipment and instruments for the University especially in the main areas of (1) microscopy (2) genetics in agriculture to better fulfill the ALS division's overall goal of providing a comprehensive understanding of agriculture.
Project Methods
PD (Marutani) and co-PD (Fernandez) will acquire items in the proposal using the best available delivery methods and vendors from the US mainland or local distributors in Guam to best satisfy the proposed project's objectives. Dr. Xiao (Plant Biologist, Curator at UOG Herbarium) and Dr. McConnell (Horticulturist and Scientific Photographer) will install the equipment in the horticulture and plant laboratories at UOG. To enhance (a) Micro-imagery research, we plan on purchasing a high-resolution Nikon SMZ25 Research Stereo Microscope system to develop high-resolution imagery of vegetative and floral features for the taxonomic description of local food crop cultivars, invasive species, and native plants in Guam. This stereomicroscope will enable better inspection and description of biological specimens at its high magnification and resolution. This instrument will support existing projects by allowing for fine-scale taxonomic description of external plant tissues and structures and also systematic identification of insect, mites, fungi, and other plant pathogens and diseases affective local agricultural crops and native plants. This high-resolution imaging system will ultimately enhance existing education and research at the University by offering a more integrative view of biological systems down to the microscopic level to undergraduate and graduate students in the College of Natural and Applied Sciences at UOG. To improve (b) Next-generation DNA sequencing research, we plan on purchasing five different instruments including an ultra-low deep freezer, a bead mill, a refrigerated tabletop centrifuge, a PCR thermocycler, and an Oxford Nanopore MinION Mk1C. The system that will be developed from the requested equipment will allow for rapid species identification of agricultural crops, invasive species, native plants, pests and pathogens through DNA barcoding and sequencing. The Oxford Nanopore MinION Mk1C is a fully integrated system designed to produce short-reads of RNA/DNA to whole genome sequencing in real time either in the lab or field. The Oxford Nanopore system will mainly be used for studies genotyping local food crop cultivars, novel weedy species, and native plants when morphological-based methods prove difficult. Targeted amplicon sequencing using the Oxford Nanopore will be carried out using common DNA barcodes that allow for species identification within certain taxonomic groups including the internal transcribed spacer (ITS) region of the small-subunit ribosomal RNA (rRNA) in plants and fungal systems, the rbcL and matK genes of chloroplasts for plants, and the mitochondrial cytochrome c oxidase (COX I) gene for insects and other pests. Given how genetic sequencing for UOG is often allocated to off-island commercial sequencing companies, this third-generation sequencing technology will allow the University to expand its capabilities in genetics and molecular biology research. Such technology will allow for rapid, high-throughput species identification of weeds, crops, and native plants by cutting lead times and costs associated with sequencing by a third-party. In addition to the Oxford Nanopore MinION Mk1C, the standard ultra-low deep freezer, bead mill, refrigerated tabletop centrifuge, and PCR thermocycler will provide a basis for supporting and optimizing the processing of genetic material for sequencing analyses. The Thermo Scientific TSX Series Ultra-Low Freezer will serve the primary purpose of preserving the biological structure of plant specimens and chemical structure of plant DNA extractions. This deep freezer will especially be helpful given the hot, humid environment of Guam that makes plant and DNA preservation challenging. The QIAGEN TissueLyser II bead mill will provide for thorough and rapid disruption of plant material during DNA extraction to improve DNA yield for downstream applications such as DNA purification and amplification. This instrument will aid in optimizing genetics studies involving large sample sizes and/or tedious purification protocol given how procedures are automated for reproducible, high-quality results. The bead mill will also allow genetics studies to bypass expensive, commercial DNA extraction kits that sometimes yield poor quality DNA at low concentrations. The refrigerated high-speed Eppendorf Centrifuge 5910 Ri will serve the primary purpose of high throughput recovery and purification of plant DNA samples for subsequent amplification and analysis. This instrument will be helpful in optimizing genetics studies involving large sample sizes and/or tedious purification protocol. The Applied Biosystems VeritiPro Thermal Cycler will mainly be used to amplify plant DNA samples via polymerase chain reaction (PCR) for subsequent applications including next-generation nanopore amplicon sequencing, ensuring adequate quantities of DNA for analyses. This instrument also features "better-than-gradient" technology, improving temperature control for primer annealing in especially difficult DNA samplesAll PDs will conduct their "active" research and advise undergraduate students in special research projects and graduate students in theses focused on micro-imagery analysis, genetics, and taxonomy in plants. Research students will also be recruited either as winter/summer break trainees, those registering in special courses, or those pursuing MS degree in SAFNR or Biology. PD (Marutani) will announce these student opportunities after discussion with co-PDs.