THE SDSU FUNCTIONAL GENOMICS CORE FACILITY AND ITS SUPPORT OF AGRICULTURAL RESEARCH IN SOUTH DAKOTA

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: ACTIVE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1022863
• Project Start Date: Jul 1, 2020
• Project End Date: Jun 30, 2025
• Program Code: [(N/A)]- (N/A)

Recipient Organization
SOUTH DAKOTA STATE UNIVERSITY
PO BOX 2275A
BROOKINGS,SD 57007

Performing Department
Biology & Microbiology

Non Technical Summary
The primary purpose of this proposal is to seek financial support for a multiuse core facility at SDSU that provides access to expensive equipment and technical support to biomolecular researchers studying gene function in agriculturally-related biological systems. Modern molecular biology rests heavily on a plethora of high end techniques that require advanced and expensive instrumentation, expert operators, and in many cases constant use for fiscal sustainability. Some analyses can easily be performed on extracts and samples shipped to facilities off campus, while others require analysis using fresh samples in the hands of the investigators. Equipment core facilities have become an essential component to all research universities as a way to guarantee access to critical, ever-improving, expensive equipment at the lowest practical cost. Biomolecular studies involving gene function are among the most expensive research to conduct, and yet most major improvements to agricultural productivity are based upon these technologies.The FGCF has sought to focus on supporting instrumentation for sample analyses that cannot easily be shipped to other laboratories. The FGCF has been providing equipment and technical support to researchers for the past 15 years. To continue this effort over the next 5-10 years, organizational and financial challenges must be overcome. Equipment purchase and maintenance costs are beyond the control of the institution, but income that they generate is variable and dependent on usage. Core facilities generate their cost savings by maximizing the number of researchers using each instrument by centralizing availability, and by encouraging usage through technical support of each instrument. Yet, most university core facilities cannot cover their actual operating costs based only upon user fees, and therefore they must be subsidized at various levels. These subsidies are often used to stabilize salaries for core personnel and to help cover the costs for service contracts on some of the more expensive equipment. Because these permanent costs are the most critical and difficult to sustain, the requested support for this proposal will focus on these two needs while also seeking a more permanent solution. Attempts will be made to increase usage by expanding research productivity and funding success among the users. Efforts will also focus on generating federal instrumentation grants each year. Expected outputs include increased success in these areas of grant funding, and also in expanded usage among internal and external users.

Animal Health Component

20%

Research Effort Categories

Basic

30%

Applied

20%

Developmental

50%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
102	0199	1040	20%
201	1530	1040	50%
203	0410	1101	10%
206	0410	1040	10%
303	3299	1030	10%

Knowledge Area
303 - Genetic Improvement of Animals; 206 - Basic Plant Biology; 102 - Soil, Plant, Water, Nutrient Relationships; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
3299 - Poultry, general/other; 0199 - Soil and land, general; 1530 - Rice; 0410 - Air;

Field Of Science
1040 - Molecular biology; 1101 - Virology; 1030 - Cellular biology;

Keywords

core facility

genomics

genetic analysis

molecular biology

south dakota

Goals / Objectives
The overall goal of this project is the same as the mission of the Functional Genomics Core Facility (FGCF), which is to facilitate interdisciplinary gene function research and training in viral, bacterial, plant and animal systems. This is to be accomplished by providing researchers with: 1) access to the various expensive equipment needed for the advanced techniques used in functional genomics research, but which cannot be outsourced, 2) training and support on the optimal uses of these technologies, and 3) an opportunity to assist with and influence future purchases of functional genomics related equipment. To insure that this equipment and training will remain available to functional genomic researchers during the next 5-10 years, creative approaches toward greater financial sustainability must be further developed within this a multiuser core facility at SDSU by focusing on the following 5 objectives:Central Objectives: Provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost;Provide individual and group training and technical support to functional genomics researchers;Encourage and facilitate principal investigators to continually incorporate the newest molecular techniques into their grant proposals and research programs;Encourage and facilitate interdisciplinary collaborative research within the fields of biomolecular science;Encourage greater organization and cooperation among the University core facilities.These 5 objectives are based upon the 9 general approaches that university core facilities use to minimize the effects of financial challenges on the core and the researchers using it. The 9 approaches to financial challenges outlined by Haley (2011) include: 1) cutting services or raising rates; 2) growing institutional use of the core; 3) marketing services outside of the university to increase use; 4) managing equipment transactions more effectively; 5) managing start-up packages for new faculty more proactively; 6) exploring possible core consolidation or shut-down; 7) sharing core personnel and creating satellites; 8) developing inter-institutional core partnerships; and 9) crafting more disciplined core financial arrangements.

Project Methods
This project will focus on the 5 listed objectives, and therefore, the project methods will service these objectives.Objective 1: Provide guaranteed access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible costThe cutting-edge equipment supported through the FGCF includes instruments that are necessary for functional genomics research but are too expensive for researchers to own in their own laboratory. To provide guaranteed 24/7 access to sophisticated and expensive equipment, they must be covered under service contracts from the manufacturers or specialized companies capable of supplying these services. Use of this equipment will be available to all researchers on campus, and attempts will be made to keep user fees as low as possible to encourage optimal usage. Historically, most of the active FGCF users have been from the College of Natural Science and the College of Agriculture, Food and Environmental Sciences. Attempts will be made to expand usage among researchers from other colleges, especially the College of Pharmacy and College of Engineering. As usage increases across the campus, additional support from other colleges and the University will be sought. Expanded efforts will also be made to encourage FGCF usage by companies in the SDSU Innovation Center and companies throughout the region.Objective 2: Provide individual and group training and technical support to functional genomics researcherThe individual and group training and technical support provided to functional genomics users will include the following general topics: a) various applications for each instrument in the FGCF, b) how to properly use each instrument to gain the maximum amount of data while also preserving the quality of the instrument, and c) how to correctly interpret their results from each instrument. This training is the most important activity within the FGCF, but accomplishing this effectively is a huge challenge with the limited number of FGCF personnel and with many new users (i.e. graduate and undergraduate students) continually coming to the FGCF. In addition to graduate and undergraduate students, this training will be provided to faculty, visiting scientists, and post-docs. Therefore, efforts will focus on identifying better methods to provide training in more efficient ways. In addition to training individual users, approaches currently being used include: teaching lab courses through the FGCF, providing group training whenever possible, facilitating workshop training through the various instrument companies. Use of training videos and web-based support are currently being explored.Objective 3. Encourage and facilitate principal investigators to continually incorporate the newest molecular techniques into their grant proposals and research programsBy helping PIs continually incorporate the newest molecular techniques into their grant proposals and research programs, they will be able to remain more competitive for funding. This third objective is based upon the observation that many of our faculty are coming to SDSU with amazing, cutting-edge research techniques, but struggle to continue adopting new emerging techniques after being here for even a few years. Post-docs (and to a lesser degree PhD students) can help establish these new methods into a lab if the equipment is available. With support from the South Dakota Drought Center, we have established a FGCF User Award Program that provides funds to faculty, post-docs, and grad-students to cover user fees while they are gaining experience in specific FGCF areas. As the recipients grow in their knowledge of that particular area, they are expected to becoje a resource for other researchers interested in that technique. We also plan to become even more aggressive at inviting equipment companies to provide workshops on their new instruments as a way of driving new methods into SDSU.Furthermore, to facilitate modern and advanced biological research by promoting the newest molecular techniques, FGCF personnel submitted a proposal entitled "Molecular Interaction Research Opportunities Created by Biolayer Interferometry: Acquisition of a forteBIO Octet RED96 Biolayer Interferometry Instrument for Measuring Critical DNA-DNA, DNA-RNA, DNA/RNA-Protein and Protein-Protein Interactions" to the NSF MRI Program. The review panel provided an "OUTSTANDING" rating to the previous proposal submitted in Jan. 2019, but declined for not having preliminary data collected from the requested equipment. FGCF personnel and Co-PIs/participants designed several experiments and collected primary data by collaborating with Mr. Hui (Field Application Scientist Manager Americas at Pall ForteBio) for the NSF MRI proposal revision and re-submission in January 2020.Objective 4: Encourage and facilitate interdisciplinary collaborative research within the fields of biomolecular scienceBecause the sustainability of the FGCF is dependent on the grantmanship success of the SDSU principal investigators, and because research programs must be effective collaborating programs to be successful, the FGCF personnel will continually look for opportunities to facilitate collaborative research among its members. The FGCF is uniquely positioned to identify student, post-doc, and faculty users that are developing particular experience with specific techniques. These emerging techniques can often have applications for other researchers working with other ag-related biological systems. Personnel in the FGCF will foster these collaborations at the technique level. The FGCF Governing Committee is responsible for recommending and prioritizing the purchases of new equipment. These prioritizations are strongly related to the potential of each instrument to strengthen these collaborations.Objective 5: Encourage greater organization and cooperation among the University core facilitiesIn an attempt to improve University support and greater core efficiencies, the FGCF will identify all the biological-type multiuser facilities (both formal and informal) on the SDSU campus and encourage greater visibility and cooperation among these facilities. This cooperation may include issues such as approaches to management and marketing or ways that duplications can be minimized.

Progress 07/01/20 to 09/30/20

Outputs
Target Audience:The capabilities generated through this project will be particularly useful for SDSU research faculty studying genes and gene function, but will also benefit any researcher that needs to use any of the instruments housed in the Functional Genomics Core Facility (FGCF). More than 82% of the active users have been from the College of Natural Science and the College of Agriculture, Food and Environmental Sciences. While these groups will continue to be the focus, the FGCF would benefit financially by expanding its users throughout the entire SDSU campus, Dakota State University, and the private sectors. Each fall semester, approximately 15-20 graduate students take the Biol 645L Micro-Imaging course that is offered by the Department of Biology & Microbiology, but taught in the FGCF with its microscopes and microtomes. Likewise, each spring semester about 10-12 graduate students take the ABS 705 Research Methodology class, which is largely taught using the instruments in the FGCF by personnel in the FGCF and Biology and Microbiology Department. In addition, graduate students take the DS731 Laboratory Techniques in Dairy Science course that is offered by the Department of Dairy Science to study gene expression profiles using the QuantStudio 6 Flex Real-Time PCR system present in the FGCF. Lastly, at the undergraduate level, some of the labs for Micro 438L (Molecular & Microbial Genetics Lab) and MICR 332L (Microbial Physiology) are taught using FGCF instruments. With the recent acquisition of GS-MS and HPLC systems, we have also begun discussion of encouraging the development of a graduate-level chromatography lab course supported by the FGCF. In the past, researchers from other South Dakota campuses have also used the more specialized equipment, and we are encouraging a further expansion of this outreach. The affected researchers include faculty, visiting scientists, post-docs, graduate students, and undergraduates. The FGCF also provides tours of the facility to various community groups, alumni, and even high school students. All of the information and resources from the FGCF are available on the FGCF website (https://www.sdstate.edu/south-dakota-agricultural-experiment-station-sdsu/functional-genomics-core-facility). As additional training resources are produced, they will also be added to this site. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?As noted in Objective 2 above, FGCF personnel have provided numerous individual and group training sessions to the registered users on various types of equipment. How have the results been disseminated to communities of interest?Results have been disseminated through formal and informal training sessions, journal publications, conference presentations, and classroom activities. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost. Continue to provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost. Objective 2. Provide individual and group training and technical support to functional genomics researchers. Continue to provide individual and group training and technical support to functional genomics researchers. Objective 3. Encourage and facilitate principal investigators to continually incorporate the newest molecular techniques into their grant proposals and research programs. To facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques, we are going to submit to NSF MRI Program the revised full-proposal entitled "Molecular Interaction Research Opportunities Created by Biolayer Interferometry: Acquisition of a forteBIO Octet RED96 Biolayer Interferometry Instrument for Measuring Critical DNA-DNA, DNA-RNA, DNA/RNA-Protein and Protein-Protein Interactions." Objective 4. Encourage and facilitate interdisciplinary collaborative research within the fields of biomolecular science. Continue to facilitate interdisciplinary collaborative research within the fields of biomolecular science. Objective 5. Encourage greater organization and cooperation among the University core facilities. Continue to encourage greater organization and cooperation among the University core facilities.

Impacts
What was accomplished under these goals? Objective 1: Provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost (ongoing) The Functional Genomics Core Facility (FGCF) currently has 263 registered users with 45 newly added during 10/01/19 - 09/30/20. The registered users include faculty, professional staff, visiting scholars, post-doctoral students, and graduate and undergraduate students. Approximately 85% of the active users are from the College of Natural Sciences and the College of Agriculture, Food and Environmental Sciences. The FGCF expanded its users throughout the entire SDSU campus, Dakota State University, and the private sectors. Due to the COVID-19 pandemic, there were only 97 Pharos active users during the period of 10/01/19 - 09/30/20, with a total of 2673 login usages. The total usage hours of the nine Pharos controlled instruments decreased 52% from 2,545.3 hours (10/01/18 - 09/30/19) to 1220.7 hours (10/01/19 - 09/30/20), and income was also decrease from $28,584 (10/01/18 - 09/30/19) to $13,869 (10/01/19 - 09/30/20). Objective 2. Provide individual and group training and technical support to functional genomics researchers. (ongoing) FGCF personnel have provided numerous individual and group training sessions to the registered users on the FV1200 confocal, BX53, IX70, and SZX16 fluorescent microscopes; Li-Cor Odyssey Infrared Gel Imaging system premium and Odyssey Fc system; BioTek Synergy 2 microplate reader; Nanodrop ND -2000 Spectrophotometers; Bio-Rad ChemiDoc XRS; QuantStudio 6 Flex Real-Time PCR System, and Quibit 3.0 fluorometer from Thermo Fisher Scientific; GCMS 5975 diffusion system; and LC 1220 system. FGCF personnel have also provided training for tissue preparation with cryotomes and microtomes. In particular, FGCF personnel have been involved in teaching and demonstration of the modern technologies and operation procedures on various equipment during graduate level courses (Biol 645L Microimaging Techniques and ABS 705 Research Methodology) and an upper-level undergraduate course (MICR 438L Techniques in Molecular Biology Laboratory). Objective 3. Encourage and facilitate principal investigators to continually incorporate the newest molecular techniques into their grant proposals and research programs. (ongoing) FGCF personnel re-submitted (Jan., 2020) a proposal entitled "Molecular Interaction Research Opportunities Created by Biolayer Interferometry: Acquisition of a forteBIO Octet RED96 Biolayer Interferometry Instrument for Measuring Critical DNA-DNA, DNA-RNA, DNA/RNA-Protein and Protein-Protein Interactions" to the NSF MRI Program with the addition of preliminary data collected from the requested equipment. The review panel pointed out the weaknesses regarding the Management Plan. FGCF personnel and Co-PIs/Participants are going to address those problems and will submit for SDSU internal selection. Hopefully this proposal can be selected for re-submission to NSF MRI program in Jan., 2021. Objective 4. Encourage and facilitate interdisciplinary collaborative research within the fields of biomolecular science (ongoing) FGCF personnel provided useful suggestions on the technology/instrumentation for various projects and will continually look for opportunities to facilitate collaborative research among its members. For example, FGCF personnel helped several students/post-docs in multiple laboratories to assess nitrogen fixation using GC-MS coupled with acetylene reduction assay. Objective 5. Encourage greater organization and cooperation among the University core facilities. (ongoing) FGCF personnel collect equipment information on all the biological-type multiuser facilities (both formal and informal) on the SDSU campus and encourage greater visibility and cooperation among these facilities. For instance, Dr. Willand-Charnley laboratory in Chemistry & Biochemistry at SDSU offers cell sorting technology using a Flow Cytometer. Specific cell types can be collected by Flow Cytometry for further gene expression analyses, such as RNA-seq and/or quantitative PCR using the QuantStudio 6 Flex Real-Time PCR system in FGCF.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Sekaran, S., J.R. Loya, G.O. Abagandura, S. Subramanian, V. Owens, S. Kuma. 2020. Intercropping of kura clover (Trifolium ambiguum M. Bieb) with prairie cordgrass (Spartina pectinata link.) enhanced soil biochemical activities and microbial community structure. Applied Soil Ecology. 147,103427. doi.org/10.1016/j.apsoil.2019.103427
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Smita, S., J. Kiehne, S. Adhikari, E. Zeng, Q. Ma, S. Subramanian. 2020. Gene regulatory networks associated with lateral root and nodule development in soybean, in silico. Plants, 2(1) diaa002. doi.org/10.1093/insilicoplants/diaa002
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Omar, A.G., S. Udayakumar, S. Singh, J. Singh, M.A. Ibrahim, S. Subramanian, V. Owens, and S. Kumar. 2020. Intercropping kura clover with prairie cordgrass mitigates soil greenhouse gas fluxes. Scientific Reports (Nature Publisher Group). 10(1). DOI:10.1038/s41598-020-64182-2
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Venkateswarlu, S., A. Kommineni, C. Marella, K. Muthukumarappan, L.E. Metzger. 2020. Foam fractionation technology for enrichment and recovery of cheese whey proteins. Asian J Dairy Food Research. 9(3):187-194.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Andersen, E.J., M.P. Nepal, J.M. Purintun, D. Nelson, G. Mermigka, and P.F. Sarris. 2020. Wheat disease resistance genes and their diversification through integrated domain fusions. Front. Genet., 05. doi.org/10.3389/fgene.2020.00898
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Byamukama, E., C. Tande, M. Nampijja, F. Mathew, and B. Bleakley. 2020. First report of Xanthomonas vasicola pv. vasculorum, the causal agent of bacterial leaf streak of corn in South Dakota. Plant Disease. 104(6). doi.org/10.1094/PDIS-12-19-2650-PDN
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Baldwin, E., B. Karki, T. Johnson, J. Zahler, J. Gibbons, and W.R. Gibbons. 2020. Enhancing cellulase production in Aureobasidium pullulans by genome shuffling. Industrial Biotechnology. 16(4). doi.org/10.1089/ind.2018.0011
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelsalam, K., M. Rajput, G. Elmowalid, J. Sobraske, N. Thakur, H. Abdallah, A.A.H. Ali, C.C.L. Chase. 2020. The effect of bovine viral diarrhea virus (BVDV) strains and the corresponding infected-macrophages supernatant on macrophage inflammatory function and lymphocyte apoptosis. Viruses. 12(7): 701. doi: 10.3390/v12070701
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Gao, R., Z. Sheng, C.C. Sreenivasan, D. Wang, F. Li. 2020. Influenza A virus antibodies with antibody-dependent cellular cytotoxicity function. Viruses. 12(3): 276. doi: 10.3390/v12030276
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Sheng. Z., C. Huang, R. Liu, Y. Guo, Z. Ran, F. Li, D. Wang. 2020. Next-generation sequencing analysis of cellular response to influenza B virus infection. Viruses. 12(4): 383. doi: 10.3390/v12040383