Source: SOUTH DAKOTA STATE UNIVERSITY submitted to NRP
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
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1006915
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Jul 3, 2015
Project End Date
Jun 30, 2020
Grant Year
(N/A)
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 Functional Genomics Core Facility (FGCF) has sought to focus on supporting instrumentation for techniques that cannot easily be shipped out. The Functional Genomics Core Facility (FGCF) has been providing equipment and technical support to researchers for the past 10 years. In order to guaranteed support for the next 5-10 years, organizational and financial challenges must be stabilized. Equipment purchase and maintenance costs are beyond the control of the institutions, 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 cores 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 1) core personnel and 2) to help cover the costs for service contracts on some of the more expensive equipment. Because these 2 permanent costs are the most critical and difficult to sustain, the requested support for this proposal will focus on these 2 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
60%
Applied
20%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2017299104060%
3047299104010%
3117299104030%
Knowledge Area
311 - Animal Diseases; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 304 - Animal Genome;

Subject Of Investigation
7299 - Research equipment and methods, general/other;

Field Of Science
1040 - Molecular biology;
Goals / Objectives
The overall goal of this project is the same as the mission of the 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 (at a minimum cost) 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 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 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;Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques;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.
Project Methods
This project will focus on the 5 listed objectives, and therefore, the project methods will service these objectives.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 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 a specialized company 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 affordable to encourage optimal usage. Historically, most of the active FGCF users have been from the College of Agriculture and Biological Sciences; attempts will be made to expand usage among researchers from other colleges, especially the College of Pharmacy and College of Arts and Science. 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 external companies in the region.Provide individual and group training and technical support to functional genomics researchersThe individual and group training and technical support provided to functional genomics researchers and potential users will include the following general topics: a) the various applications for each of the instruments in the FGCF, b) how to properly use each instrument in order 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 multiple user training sessions include: teaching lab courses through the FGCF, clustering multiple individuals for common training whenever possible, and facilitating workshop training through the various instrument companies. Use of training videos and web-based support are currently being explored.Encourage and facilitate PIs to continually incorporate the newest molecular techniques into their grant proposals and research programsBy helping PIs to 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 when they arrive at SDSU, 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 Drought Center, we have recently 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 areas that the FGCF lack experience with. As the recipients grow in their knowledge of that particular area, they are expected to be 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.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 PIs, and because research programs must have 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.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 07/03/15 to 06/30/20

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. 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 Qubit 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. 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. 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? Nothing Reported

Impacts
What was accomplished under these goals? The 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. Objective 1. Provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost. (ongoing) During the past five years the Functional Genomics Core Facility (FGCF) has provided research support to 79 principle investigator's laboratories with 511 registered users from 13 different departments and three centers. The FGCF also served researchers from USD, DSU, and regional biological industries (GlycoScience Research, Research Technology Innovation, Medgene, and Prairie Aquatech). The FGCF personnel provided numerous tours to visitors from local high schools, faculty from other universities, members of agricultureal organizations and industries in the USA, as well as international visitors. The FGCF currently has 258 registered users with 45 newly added during 10/01/19 - 06/30/20. The registered users include faculty, professional staff, visiting scholars, post-doctoral students, 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. FGCF expanded its users throughout the entire SDSU campus, Dakota State University, and the private sectors. 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 Qubit 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. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques. FGCF personnel have submitted proposals to the NSF MRI program in 2018, 2019, and 2020. The 2019 review panel provided an "OUTSTANDING" rating, but declined for not having preliminary data collected from the requested equipment. The revised proposal was submitted to the NSF MRI Program with the addition of preliminary data collected from the requested equipment in Jan., 2020. 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. Facilitate interdisciplinary collaborative research within the fields of biomolecular science. 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 examples, FGCF personnel: 1) helped several students/post-docs in multiple laboratories to assess nitrogen fixation using GC-MS coupled with acetylene reduction assay; 2) helped several students/post-docs in Sandeep Kumar's laboratory to quantify enzyme activity using the Synergy plate reader, a faster and more efficient method than using the cuvette-type spectrophotometer; 3) bridged a collaborative research project on "Characterizing the surface sugars of Anabaena Cylindrica" among the following laboratories: Drs. MB Hildreth and R Zhou (Biology and Microbiology); 4) bridged a collaborative research project on "identifying the cyanobacterial species in soil" among the laboratories of Drs. L Xu (Department of Natural Resource Management), S Kumar (Department of Plant Science), and R Zhou (Department of Biology and Microbiology). Objective 5. Encourage greater organization and cooperation among the University core facilities. 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 instances, the SDSU Genomics Sequencing Facility offers next-generation sequencing services using the Illumina NextSeq 500 and MiSeq platforms, while the FGCF has QuantStudio 6 Flex Real-Time PCR System for quantitatively analyzing the abundance of RNA (cDNA). Using the combination of both technologies, investigators collect differential gene expression profile through next-generation sequencing and confirm them by qPCR as secondary evidence using the QuantStudio 6 Flex Real-Time PCR System. Furthermore, the FGCF has excellent microscopic systems for high quality data collection and BioSNTR has a high-throughput imaging system that is very useful for screening. FGCF personnel recommended to the users that they can use the ImageXpress Micro XLS Widefield High-Content Analysis System in BioSNTR to do initial screening to narrow down the most important findings, and then focus the selected samples for more comprehensive analysis using the FGCF's FV1200 Confocal microscope.

Publications

  • 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: 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: 2019 Citation: Sarkar, A., B.M. Kobylkevich, D.M. Graham, M.A. Messerli. 2019. Electromigration of cell surface macromolecules in DC electric fields during cell polarization and galvanotaxis. J Theor Biol. 478:58-73. doi: 10.1016/j.jtbi.2019.06.015. Epub 2019 Jun 15. PMID: 31211960.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Mehta, D.S., L.E. Metzger, A.N. Hassan, B.K. Nelson, H.A. Patel. 2019. The ability of spore formers to degrade milk proteins, fat, phospholipids, common stabilizers, and exopolysaccharides. J Dairy Sci. 12:10799-10813. doi: 10.3168/jds.2019-16623. Epub 2019 Sep 11. PMID: 31521346.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sampson, A., B.G. Peterson, K.W. Tan, S.H. Iram. 2019. Doxorubicin as a fluorescent reporter identifies novel MRP1 (ABCC1) inhibitors missed by calcein-based high content screening of anticancer agents. Biomed Pharmacother. 2019 118:109289. doi: 10.1016/j.biopha.2019.109289.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Abbas, M., S. Alzarea, R.L. Papke, S. Rahman. 2019. The ?7 nicotinic acetylcholine receptor positive allosteric modulator prevents lipopolysaccharide-induced allodynia, hyperalgesia and TNF-? in the hippocampus in mice. Pharmacol Rep. 71(6):1168-1176. doi: 10.1016/j.pharep.2019.07.001.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yu, J., R. Liu, B. Zhou, T.W. Chou, E. Ghedin, Z. Sheng, R. Gao, S.L. Zhai, D. Wang, F. Li. 2019. Development and characterization of a reverse-genetics system for influenza D virus. J Virol. 93(21):e01186-19. doi: 10.1128/JVI.01186-19. PMID: 31413133; PMCID: PMC6803281.
  • 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
  • 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: 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: 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: 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: 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


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:The activities generated through this project will be particularly useful for SDSU research faculty studying genes and gene function, but it will also benefit any researcher that needs to use any of the instruments housed in the FGCF. More than 85% of the active users have been from the College of Natural Science and the College of Agriculture, Food & 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 the microscopes and microtomes present in the FGCF. 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 profile using QS6 qPCR 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. 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 activitie 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. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques. 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. 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? The 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. 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 currently has 222 registered users with 49 newly added during 10/01/18 - 09/30/19. The registered users include faculty, professional staff, Visiting Scholars, Post-doctoral students, 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. FGCF expanded its users throughout the entire SDSU campus, Dakota State University, and the private sectors. There were 131 Pharos active users during the period of 10/01/18 - 09/30/19 with a total of 4,189 login usages. The total usage hours of the nine Pharos controlled instruments increased 7.1% from 2,376.1 (10/01/17 - 09/30/18) to 2,545.3 hours (10/01/18 - 09/30/19), and the income was also increase from $20,368 (10/01/17 - 09/30/18) to $28,584 (10/01/18 - 09/30/19). There were 306 and 525 hours on Odyssey Fc and Confocal Microscopic Systems, significantly increased compared to the 175 and 342 hours usages during 10/01/17 - 09/30/18, respectively. 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. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques. (ongoing) FGCF personnel re-submitted (Feb., 2019) 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, but declined for not having preliminary data collected from the requested equipment. FGCF personnel and Co-PIs/participants are designing the experiments and planning to collect data at the University of Iowa Protein and crystallography Facility for the NSF MRI proposal revision and re-submission on Jan., 2020. Objective 4. 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 Sandeep Kumar's laboratory to quantify enzyme activity using the Synergy plate reader, a faster and more efficient method than using the cuvette-type spectrophotometer. 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, the SDSU Genomics Sequencing Facility offers next-generation sequencing services using the Illumina NextSeq 500 and MiSeq platforms, while the FGCF has QuantStudio 6 Flex Real-Time PCR System for quantatively analyzing the abundance of RNA (cDNA). Using the combination of both technologies, investigators collect differential gene expression profile through next-generation sequencing and confirm them by qPCR as secondary evidence using the QuantStudio 6 Flex Real-Time PCR System.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Jaaf S, Rosa F, Moridi M, Osorio JS, Lohakare J, Trevisi E, Filley S, Cherian G, Estill CT, Bionaz M. 2019. 2,4-Thiazolidinedione in Well-Fed Lactating Dairy Goats: I. Effect on Adiposity and Milk Fat Synthesis. Vet Sci. May 17;6(2). pii: E45. doi: 10.3390/vetsci6020045. PubMed PMID: 31108904; PubMed Central PMCID: PMC6632146.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Mahnashi M, Elgazwi SM, Ahmed MS, Halaweish FT. 2019. Cucurbitacins inspired organic synthesis: Potential dual inhibitors targeting EGFR - MAPK pathway. Eur J Med Chem. Jul 1;173:294-304. doi: 10.1016/j.ejmech.2019.04.018. Epub 2019 Apr 16. PubMed PMID: 31022583.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Pandey K, Zhong S, Diel DG, Hou Y, Wang Q, Nelson E, Wang X. 2019. GTPase-activating protein-binding protein 1 (G3BP1) plays an antiviral role against porcine epidemic diarrhea virus. Vet Microbiol. Sep; 236:108392. doi: 10.1016/j.vetmic.2019.108392. Epub 2019 Aug 19. PubMed PMID: 31500725.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Abbas I, Hildreth M. 2019. Egg autofluorescence and options for detecting peanut agglutinin binding for the identification of Haemonchus contortus eggs in fecal samples. Vet Parasitol. Mar;267:69-74. doi: 10.1016/j.vetpar.2019.01.009. Epub 2019 Feb 16. PubMed PMID: 30878089.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Alqahtani Y, Wang S, Najmi A, Huang Y, Guan X. 2019. Thiol-specific fluorogenic agent for live cell non-protein thiol imaging in lysosomes. Anal Bioanal Chem. Sep; 411(24):6463-6473. doi: 10.1007/s00216-019-02026-3. Epub 2019 Aug 26.PubMed PMID: 31448387; PubMed Central PMCID: PMC6760846.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yu J, Liu R, Zhou B, Chou TW, Ghedin E, Sheng Z, Gao R, Zhai SL, Wang D, Li F. 2019. Development and characterization of a reverse-genetics system for influenza D virus. J Virol. Oct 15;93(21). pii: e01186-19. doi: 10.1128/JVI.01186-19. Print 2019 Nov 1. PubMed PMID: 31413133.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Pipatpongpinyo W, Korkmaz U, Wu H, Kena A, Ye H, Feng J, Gu XY. 2019. Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice. Heredity (Edinb). Aug 7. doi: 10.1038/s41437-019-0253-8. [Epub ahead of print] PubMed PMID: 31391557.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Neupane S, Mathew FM, Varenhorst AJ, Nepal MP. 2019. Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean. Sci Data. Jul 24;6(1):133. doi: 10.1038/s41597-019-0140-4. PubMed PMID: 31341170; PubMed Central PMCID: PMC6656750.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Senevirathne ND, Anderson JL, Metzger L. 2019. Growth performance, nutrient utilization, and health of dairy calves supplemented with condensed whey solubles. J Dairy Sci. Sep;102(9):8108-8119. doi:10.3168/jds.2019-16314.Epub 2019 Jul 10. PubMed PMID: 31301825.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sarkar A, Kobylkevich BM, Graham DM, Messerli MA. Electromigration of cell surface macromolecules in DC electric fields during cell polarization and galvanotaxis. J Theor Biol. Oct 7;478:58-73. doi:10.1016/j.jtbi.2019.06.015. Epub 2019 Jun 15. PubMed PMID: 31211960.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Rosa F, Moridi M, Osorio JS, Lohakare J, Trevisi E, Filley S, Estill C, Bionaz M. 2019. 2,4-Thiazolidinedione in well-fed lactating dairy goats: II. Response to intra-mammary infection. Vet Sci. Jun 5;6(2). pii: E52. doi: 10.3390/vetsci6020052. PubMed PMID: 31195666; PubMed Central PMCID: PMC6632143.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Uprety T, Spurlin BB, Antony L, Sreenivasan C, Young A, Li F, Hildreth MB, Kaushik RS. 2019. Development and characterization of a stable bovine intestinal sub-epithelial myofibroblast cell line from ileum of a young calf. In Vitro Cell Dev Biol Anim. Aug;55(7):533-547. doi: 10.1007/s11626-019-00365-0. Epub 2019 Jun 10. PubMed PMID: 31183683.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Neupane S, Varenhorst AJ, Nepal MP. 2019. Transcriptome profiling of induced susceptibility effects on soybean-soybean aphid (Hemiptera: Aphididae) interaction. BMC Res Notes. Jun 10;12(1):325. doi: 10.1186/s13104-019-4372-3. PubMed PMID: 31182145; PubMed Central PMCID: PMC6558899.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Rosa F, Osorio JS. 2019. Short communication: Comparative gene expression analysis on the enrichment of polymorphonuclear leukocytes and gastrointestinal epithelial cells in fecal RNA from nondiarrheic neonatal dairy calves. J Dairy Sci. Aug;102(8):7464-7468. doi: 10.3168/jds.2018-16074. Epub 2019 Jun 6. PubMed PMID: 31178184.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Alzarea S, Rahman S. 2019. Alpha-7 nicotinic receptor allosteric modulator PNU120596 prevents lipopolysaccharide-induced anxiety, cognitive deficit and depression-like behaviors in mice. Behav Brain Res. Jul 2;366:19-28. doi: 10.1016/j.bbr.2019.03.019. Epub 2019 Mar 12. PubMed PMID: 30877025
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ma A, Qiu Y, Raihan T, Paudel B, Dahal S, Zhuang Y, Galla A, Auger D, Yen Y. 2019. The genetics and genome-wide screening of regrowth loci, a key component of perennialism in Zea diploperennis. G3 (Bethesda). May 7;9(5):1393-1403. doi: 10.1534/g3.118.200977. PubMed PMID: 30808689; PubMed Central PMCID: PMC6505134.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Guo A, Durymanov M, Permyakova A, Sene S, Serre C, Reineke J. 2019. Metal organic framework (MOF) particles as potential bacteria-mimicking delivery systems for infectious diseases: Characterization and cellular internalization in alveolar macrophages. Pharm Res. Feb 21;36(4):53. doi: 10.1007/s11095-019-2589-4. PubMed PMID: 30790066
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Katwal P, Thomas M, Uprety T, Hildreth MB, Kaushik RS. 2019. Development and biochemical and immunological characterization of early passage and immortalized bovine intestinal epithelial cell lines from the ileum of a young calf. Cytotechnology. Feb;71(1):127-148. doi: 10.1007/s10616-018-0272-y. Epub 2019 Jan 1. PubMed PMID: 30600465; PubMed Central PMCID: PMC6368510.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Durymanov M, Kroll C, Permyakova A, O'Neill E, Sulaiman R, Person M, Reineke J. 2019. Subcutaneous inoculation of 3D pancreatic cancer spheroids results in development of reproducible stroma-rich tumors. Transl Oncol. Jan;12(1):180-189. doi: 10.1016/j.tranon.2018.10.003. Epub 2018 Oct 25. PubMed PMID: 30554606; PubMed Central PMCID: PMC6295361
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Qiu Y, Tian S, Gu L, Hildreth M, Zhou R. 2019. Identification of surface polysaccharides in akinetes, heterocysts and vegetative cells of Anabaena cylindrica using fluorescein-labeled lectins. Arch Microbiol. Jan;201(1):17-25. doi: 10.1007/s00203-018-1565-4. Epub 2018 Sep 1. PubMed PMID: 30173343
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Neupane A, Feng C, Feng J, Kafle A, B�cking H, Lee Marzano SY. 2018. Metatranscriptomic analysis and in silico approach identified mycoviruses in the arbuscular mycorrhizal fungus Rhizophagus spp. Viruses. Dec 12;10(12). pii: E707. doi: 10.3390/v10120707. PubMed PMID: 30545059; PubMed Central PMCID: PMC6316171
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sreenivasan CC, Thomas M, Antony L, Wormstadt T, Hildreth MB, Wang D, Hause B, Francis DH, Li F, Kaushik RS. 2019. Development and characterization of swine primary respiratory epithelial cells and their susceptibility to infection by four influenza virus types. Virology. Feb;528:152-163. doi: 10.1016/j.virol.2018.12.016. Epub 2019 Jan 5. PubMed PMID: 30616205; PubMed Central PMCID: PMC6401229.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Damodaran S, Dubois A, Xie J, Ma Q, Hindi� V, Subramanian S. 2019. GmZPR3d interacts with GmHD-ZIP III proteins and regulates soybean root and nodule vascular development. Int J Mol Sci. Feb 14;20(4). pii: E827. doi: 10.3390/ijms20040827. PubMed PMID: 30769886; PubMed Central PMCID: PMC6412583
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Khadka VS, Vaughn K, Xie J, Swaminathan P, Ma Q, Cramer GR, Fennell AY. 2019. Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.). BMC Plant Biol. Feb 13;19(1):72. doi: 10.1186/s12870-019-1664-7. PubMed PMID: 30760212; PubMed Central PMCID: PMC6375209.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Neupane S, Schweitzer SE, Neupane A, Andersen EJ, Fennell A, Zhou R, Nepal MP. 2019. Identification and characterization of mitogen-activated protein kinase (MAPK) genes in sunflower (Helianthus annuus L.). plants (Basel). Jan 22;8(2). pii: E28. doi: 10.3390/plants8020028. PubMed PMID: 30678298; PubMed Central PMCID: PMC6409774
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gu XY, Pipatpongpinyo W, Zhang L, Zhou Y, Ye H, Feng J. 2018. Two contrasting patterns and underlying genes for co-adaptation of seed dormancy and flowering time in rice. Sci Rep. Nov 14;8(1):16813. doi: 10.1038/s41598-018-34850-5. PubMed PMID: 30429528; PubMed Central PMCID: PMC6235893
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gibbons J, Gu L, Zhu H, Gibbons W, Zhou R. 2018. Identification of two genes required for heptadecane production in a N(2)-fixing cyanobacterium Anabaena sp. strain PCC 7120. AMB Express. Oct 13;8(1):167. doi:10.1186/s13568-018-0700-6. PubMed PMID: 30317393; PubMed Central PMCID: PMC6186262
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kesharwani SS, Ahmad R, Bakkari MA, Rajput MKS, Dachineni R, Valiveti CK, Kapur S, Jayarama Bhat G, Singh AB, Tummala H. 2018. Site-directed non-covalent polymer-drug complexes for inflammatory bowel disease (IBD): Formulation development, characterization and pharmacological evaluation. J Control Release. Nov 28;290:165-179. doi:10.1016/j.jconrel.2018.08.004. Epub 2018 Aug 21. PubMed PMID: 30142410.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:The activities generated through this planned project will be particularly useful for SDSU research faculty studying genes and gene function, but it will also benefit any researcher that needs to use any of the instruments housed in the FGCF. More than 85% of the active users have been from the College of Natural Science and the Colleges of Agriculture, Food & Environmental Sciences. While this group 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 sector. 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 the microscopes and microtomes present in the FGCF. 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. 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. 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. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques. To facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques, I'm 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. 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? The 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. 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 currently has 403 registered users with 71 newly added during 10/01/17 - 09/30/18. The registered users include faculty, professional staffs, Visiting Scholars, Post-doctoral, 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. FGCF expanded its users throughout the entire SDSU campus, Dakota State University, and the private sectors. There were 135 Pharos active users during the period of 10/01/17 - 09/30/18 with a total of 3613 login usages. The total usage hours of the nine Pharos controlled instruments increased from 1880.3 (10/01/16 - 09/30/17) to 2376.1 hours (10/01/16 - 09/30/17), but the income was similar at approximately $20,300. The ABI 7900HT was replaced by the QuantStudio 6 Flex Real-Time PCR System (it installed in June, 2017, we provided training and allow the users to familiar with the instrument and software for 4.5 months free). There were 130 runs on QuantStudio 6 Flex Real-Time PCR System, a 24% decrease compared to the usage during (10/01/16 - 09/30/17). Moreover, the newly purchased Odyssey Fc (capable of quantify DNA, RNA, and protein gel images, as well as Western Blotting data analysis) had 615 usages for a total 175.6 hours. 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 and ABS 705) and an upper-level undergraduate course (MICR 438L). Objective 3. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques. (ongoing) FGCF organized Biacore Technical Seminar "Uses of Surface Plasmon Resonance Technology in Biomedical Research" (January 9th, 2018); FGCF personnel submitted 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" to the NSF MRI Program (Declined); FGCF personnel submitted revised letters of intent 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", which was selected to be one of SDSU's applications to the NSF MRI Program. Objective 4. Facilitate interdisciplinary collaborative research within the fields of biomolecular science. (ongoing) FGCF personnel gave 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 Sandeep Kumar's laboratory to quantify enzyme activity using the Synergy plate reader, a faster and more efficient method than using the cuvette-type spectrophotometer. 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, SDSU Genomics Sequencing Facility offer next-generation sequencing services using Illumina NextSeq 500 and MiSeq platforms, while the FGCF has QuantStudio 6 Flex Real-Time PCR System for quantatively analyzing the abundance of RNA (cDNA). Using the combination of both technologies, investigators collect differential gene expression profile through next-generation sequencing and confirm them by qPCR as secondary evidence using QuantStudio 6 Flex Real-Time PCR System.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Scott BL, Sochacki KA, Low-Nam ST, Bailey EM, Luu Q, Hor A, Dickey AM, Smith S, Kerkvliet JG, Taraska JW, Hoppe AD. Membrane bending occurs at all stages of clathrin-coat assembly and defines endocytic dynamics. Nat Commun. 2018 Jan 29;9(1):419. doi: 10.1038/s41467-018-02818-8. PubMed PMID: 29379015; PubMed Central PMCID: PMC5789089.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Arroyo JM, Hosseini A, Zhou Z, Alharthi A, Trevisi E, Osorio JS, Loor JJ. Reticulo-rumen mass, epithelium gene expression, and systemic biomarkers of metabolism and inflammation in Holstein dairy cows fed a high-energy diet. J Dairy Sci. 2017 Nov;100(11):9352-9360. doi: 10.3168/jds.2017-12866.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Han LQ, Zhou Z, Ma Y, Batistel F, Osorio JS, Loor JJ. Phosphorylation of nuclear factor erythroid 2-like 2 (NFE2L2) in mammary tissue of Holstein cows during the periparturient period is associated with mRNA abundance of antioxidant gene networks. J Dairy Sci. 2018 Jul;101(7):6511-6522.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gibbons J, Gu L, Zhu H, Gibbons W, Zhou R. Identification of two genes required for heptadecane production in a N(2)-fixing cyanobacterium Anabaena sp. strain PCC 7120. AMB Express. 2018 Oct 13;8(1):167. doi: 10.1186/s13568-018-0700-6.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Qiu Y, Tian S, Gu L, Hildreth M, Zhou R. Identification of surface polysaccharides in akinetes, heterocysts and vegetative cells of Anabaena cylindrica using fluorescein-labeled lectins. Arch Microbiol. 2018 Sep 1. doi: 10.1007/s00203-018-1565-4
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Davis JK, Vincent GP, Hildreth MB, Kightlinger L, Carlson C, Wimberly MC. Improving the prediction of arbovirus outbreaks: A comparison of climate-driven models for West Nile virus in an endemic region of the United States. Acta Trop. 2018 Sep;185:242-250. doi: 10.1016/j.actatropica.2018.04.028.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wang Z, Huang B, Thomas M, Sreenivasan CC, Sheng Z, Yu J, Hause BM, Wang D, Francis DH, Kaushik RS, Li F. Detailed mapping of the linear B Cell epitopes of the hemagglutinin (HA) protein of swine influenza virus. Virology. 2018 Sep;522:131-137. doi: 10.1016/j.virol.2018.07.013.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Xu Y, Wu Y, Wu J. Capturing pair-wise epistatic effects associated with three agronomic traits in barley. Genetica. 2018 Apr;146(2):161-170. doi: 10.1007/s10709-018-0008-0.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mochama P, Jadhav P, Neupane A, Lee Marzano SY. Mycoviruses as Triggers and Targets of RNA Silencing in White Mold Fungus Sclerotinia sclerotiorum. Viruses. 2018 Apr 22;10(4). pii: E214. doi: 10.3390/v10040214.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Morarie-Kane SE, Smirnova NP, Hansen TR, Mediger J, Braun L, Chase C. Fetal Hepatic Response to Bovine Viral Diarrhea Virus Infection in Utero. Pathogens. 2018 Jun 6;7(2). pii: E54. doi: 10.3390/pathogens7020054.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Damodaran S, Westfall CS, Kisely BA, Jez JM, Subramanian S. Nodule-Enriched GRETCHEN HAGEN 3 Enzymes Have Distinct Substrate Specificities and Are Important for Proper Soybean Nodule Development. Int J Mol Sci. 2017 Nov 28;18(12). pii: E2547. doi: 10.3390/ijms18122547.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Thomas M, Pierson M, Uprety T, Zhu L, Ran Z, Sreenivasan CC, Wang D, Hause B, Francis DH, Li F, Kaushik RS. Comparison of Porcine Airway and Intestinal Epithelial Cell Lines for the Susceptibility and Expression of Pattern Recognition Receptors upon Influenza Virus Infection. Viruses. 2018 Jun 7;10(6). pii: E312. doi: 10.3390/v10060312.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Sreenivasan CC, Jandhyala SS, Luo S, Hause BM, Thomas M, Knudsen DEB, Leslie-Steen P, Clement T, Reedy SE, Chambers TM, Christopher-Hennings J, Nelson E, Wang D, Kaushik RS, Li F. Phylogenetic Analysis and Characterization of a Sporadic Isolate of Equine Influenza A H3N8 from an Unvaccinated Horse in 2015. Viruses. 2018 Jan 11;10(1). pii: E31. doi: 10.3390/v10010031.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Alzarea S, Rahman S. Effects of alpha-7 nicotinic allosteric modulator PNU 120596 on depressive-like behavior after lipopolysaccharide administration in mice. Prog Neuropsychopharmacol Biol Psychiatry. 2018 Aug 30;86:218-228. doi: 10.1016/j.pnpbp.2018.05.018.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhai SL, Zhou X, Zhang H, Hause BM, Lin T, Liu R, Chen QL, Wei WK, Lv DH, Wen XH, Li F, Wang D. Comparative epidemiology of porcine circovirus type 3 in pigs with different clinical presentations. Virol J. 2017 Nov 13;14(1):222. doi: 10.1186/s12985-017-0892-4.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Eldakak M, Das A, Zhuang Y, Rohila JS, Glover K, Yen Y. A Quantitative Proteomics View on the Function of Qfhb1, a Major QTL for Fusarium Head Blight Resistance in Wheat. Pathogens. 2018 Jun 22;7(3). pii: E58. doi: 10.3390/pathogens7030058.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The target audience include faculty, visiting scientists, post-docs, graduate students and undergraduates. The main focus of our efforts is to support the research efforts of these various groups. We also support teaching activities through our involvement in graduate lab courses (e.g. BIOL 645L and ABS 705) and specific lab exercises within more general undergraduate courses (e.g. MICR 438). The FGCF also provides tours of the facility to various community groups, including visiting scientists, invited speakers, faculty candidates, alumni on campus, high school teachers/students, andstudents from Dakota State University. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project provided the following opportunities for training and professional development: (1) Attend the Agilent LC/MS MassHunter User Meeting. April 5th, 2017 Minneapolis, MN. (2) FGCF personnel organized a Technique Seminar/Demo on "Octet® Systems entitled "Label Free Applications with Octet: Simple Bio-Layer Interferometry Dip and Read Technology" Presented by Salim and Morgan from fortéBIO on May 7th, 2017. About 40 faculty, postdocs, graduate and undergraduate students attended. (3) FGCF personnel received comprehensive training on operation and maintenance of QuantStudio 6 Flex Real-Time PCR System. (4) FGCF personnel provided four hands-on group training sections on operating and data analysis using the QuantStudio 6 Flex Real-Time PCR System. 5) FGCF personnel showed the cutting-edge technologies for a variety of the audiences, including 60 students from SDSU General Biology-Honors (BIOL 151/L instructed by Madhav Nepal) class and approximately 40 Biology students from Dakota State University (instructed by Patrick Videau). How have the results been disseminated to communities of interest?During fall 2016, Biol 645L (Microimaging Techniques Laboratory, 20 graduate students enrolled) offered by the Department of Biology & Microbiologyused the microscopes and microtomesin the FGCF. Micro 438L-Molecular & Microbial Genetics Lab (10 undergraduates enrolled) and MICR 332L-Microbial PhysiologyLabused FGCF instruments. Similarly, in spring 2016, ABS 705-Research Methodology (12 graduate students enrolled)usedthe instruments in the FGCF with personnelin the FGCF and Biology and Microbiology. What do you plan to do during the next reporting period to accomplish the goals?Objective1. Provide guaranteed 24/7 access to "cutting-edge" research equipment necessary for functional genomics research at the lowest possible cost Continue to servethe faculty, visiting scientists, post-docs, graduate students and undergraduates at SDSU and other institutions in South Dakota. In addition, we will work hard for our Pharos reservation system and update the FGCF webpage. Objective2. Provide individual and group training and technical support to functional genomics researchers Continue to provide individual and group training and technical support on the following equipment: FV1200 confocal; BX53; IX70; and SZX16 fluorescent microscopies; Li-Cor Odyssey Infrared Gel Imaging system premiumand Odyssey Fc system; BioTek Synergy 2 microplate reader; Nanodrop ND-2000 Spectrophotometer; Bio-Rad ChemiDoc XRS; Quibit 3.0 fluorometer; QuantStudio 6 Flex Real-Time PCR System; Agilent Bioanalyzer; GCMS 5975 diffusion system; and LC 1220 system, as well as cryotome and microtomes. Objective3. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques FGCF personnel will continually look for opportunities to facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques Objective4. Facilitate interdisciplinary collaborative research within the fields of biomolecular science FGCF personnel will continually look for opportunities to facilitate collaborative research among its members. Objective5. Encourage greater organization and cooperation among the university core facilities FGCF personnel will collect equipment information on all the biological-type multiuser facilities on the SDSU campus and encourage greater visibility and cooperation among these 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 (on-going) The Functional Genomics Core Facility currently has 332 registered users with 65 newly added during 10/01/16 - 09/30/17. FGCFexpandedits users throughout the entire SDSU campus, Dakota State University, and the private sectors. Approximately 85% of the active users are from the College of Agriculture and Biological Sciences. There were 129 Pharos active users during the period of 10/01/16 - 09/30/17 with a total of 2868 usages. The total usage hours of the nine pharos controlled instruments decreased from 2209.5(12/18/15 - 09/30/16) to 1880.3 hours (10/01/16 - 09/30/17) and last year's total income was approximately $20,000 (10/01/16 - 09/30/17). The ABI 7900HT and Nanodrop showed multiple problems and several on-site services were requested for ABI 7900HT repair. Consequently,usageon ABI 7900HT was decreased significantly from 828.9 (12/18/15 - 09/30/16)to 490.9 hours (10/01/16 - 09/30/17). We have replaced both machines by QuantStudio 6 Flex Real-Time PCR System and Nanodrop ND-2000 Spectrophotometer respectively. We also added capacity through the acquisition of Quibit 3.0 fluorometer. Objective 2: Provide individual and group training and technical support to functional genomics researchers (ongoing) FGCF personnel has provided numerous individual and group training sessionsto the registered users on the FV1200 confocal; BX53; IX70; and SZX16 fluorescent microscopies; Li-Cor Odyssey Infrared Gel Imaging system premiumand Odyssey Fc system; BioTek Synergy 2 microplate reader; Nanodrop ND-1000 and Nanodrop ND -2000 Spectrophotometers; Bio-Rad ChemiDoc XRS; ABI 7900HT sequence detection system, QuantStudio 6 Flex Real-Time PCR System, and Quibit 3.0 fluorometer from Thermo Fisher Scientific; Agilent Bioanalyzer; GCMS 5975 diffusion system; and LC 1220 system, as well as training for tissue preparation with cryotome 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 and ABS 705) and an upper-level undergraduate course (MICR 438L). Objective 3:Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques (on-going) The Functional Genomics Core Facility acquired 1) Quibit 3.0 fluorometer; 2) QuantStudio 6 Flex Real-Time PCR System to replace the ABI 7900HT system; and 3) Nanodrop ND-2000 Spectrophotometer to replace ND-1000, with helpfrom the departments of Dairy Science, Biology & Microbiology, and South Dakota Agricultural Experiment Station. QuantStudio 6 Flex Real-Time PCR System is capable of multiplexing 4 targets with 96- and 384-well high-throughput capacity. FGCF personnel submittedletters of intent 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", which has been selected to be one of SDSU's applications to the NSF MRI Program. Objective 4:Facilitate interdisciplinary collaborative research within the fields of biomolecular science (ongoing) FGCF personnel gave 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 bridgedacollaborative researchproject on "Characterizing the surface sugars of Anabaena Cylindrica"among the following laboratories: Drs. MB Hildreth and R Zhou (Biology and Microbiology). 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, SDSU Genomics Sequencing Facility offer next-generation sequencing services using Illumina NextSeq 500 and MiSeq platforms, while the FGCF has QuantStudio 6 Flex Real-Time PCR System for quantification of DNA or RNA. Using the combination of both technologies, investigators identified multiple genome deletions through next-generation sequencing and revealed different editing ratios for different targets using QuantStudio 6 System.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dahal B, NandaKafle G, Perkins L, Br�zel VS. 2017. Diversity of free-Living nitrogen fixing Streptomyces in soils of the badlands of South Dakota. Microbiol Res. 195:31-39
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Li W, Challa GS, Zhu H, Wei W. Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes. G3 (Bethesda) 6(12):3837-3847
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Van Noort A, Nelsen A, Pillatzki AE, Diel DG, Li F, Nelson E, Wang X.2017. Intranasal immunization of pigs with porcine reproductive and respiratory syndrome virus-like particles plus 2, 3-cGAMP VacciGrade" adjuvant exacerbates viremia after virus challenge. Virol J. 14(1):76.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bauermann FV, Joshi LR, Mohr KA, Kutish GF, Meier P, Chase C, Christopher-Hennings J, Diel DG. 2017. A novel bovine papillomavirus type in the genus Dyokappapapillomavirus. Arch Virol. 2017 Jun 14. doi: 10.1007/s00705-017-3443-9. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Alsayari A, Kopel L, Ahmed MS, Pay A, Carlson T, Halaweish FT. 2017. Design, synthesis, and biological evaluation of steroidal analogs as estrogenic/anti-estrogenic agents. Steroids.118:32-40
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Alsharif FM, Dave K, Samy AM, Saleh KI, Amin MA, Perumal O. 2017. Influence of Hydroalcoholic Vehicle on In Vitro Transport of 4-Hydroxy Tamoxifen Through the Mammary Papilla (Nipple). AAPS PharmSciTech. 18(4):1366-1373
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Newkirk SJ, Lee S, Grandi FC, Gaysinskaya V, Rosser JM, Vanden Berg N, Hogarth CA, Marchetto MCN, Muotri AR, Griswold MD, Ye P, Bortvin A, Gage FH, Boeke JD, An W. 2017. Intact piRNA pathway prevents L1 mobilization in male meiosis. Proc Natl Acad Sci U S A. 114(28):E5635-E5644
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Yang Y, Guan X. 2017. Non-protein thiol imaging and quantification in live cells with a novel benzofurazan sulfide triphenylphosphonium fluorogenic compound. Anal Bioanal Chem. 409(13):3417-3427


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:The target audience include faculty, visiting scientists, post-docs, graduate students and undergraduates. The main focus of our efforts is to support the research efforts of these various groups, but we also support teaching activities through our involvement in graduate lab courses (e.g. BIOL 645L and ABS 705) and specific lab exercises within more general undergraduate courses (e.g. MICR 438). The FGCF also provides tours of the facility to various community groups, including visiting scientists, invited speakers, faculty candidates, alumni, and even high school teachers/students. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project provided the following opportunities for training and professional development: (1) Provided funding support to FGCF personnel to attend"Genomics of Energy & Environment Meeting" March 21 - 24, 2016 in Walnut Creek, CA. (2) The FGCF personnel organized a Technique Seminar and Demonstration on "Odyssey Fc Dual-Mode imaging System for accurate, reproducible Western blots and DNA gels" by Jim Rau and Jason Bader on May 3rd, 2016. About 25 faculty, postdocs, graduate and undergraduate students attended. (3) FGCF personnel received comprehensive training on Odyssey Fc system by Todd Holt (Li-Cor Technical Support Scientist). (4) FGCF personnel provided four hands-on group training sections on imaging and data analysis using the Odyssey Fc system. How have the results been disseminated to communities of interest?During fall 2015, Biol 645L (Microimaging Techniques Laboratory, 30 graduate students enrolled) offered by the Department of Biology & Microbiologyused the microscopes and microtomesin the FGCF. Micro 438L-Molecular & Microbial Genetics Lab (two sections with total 16 undergraduates enrolled) and MICR 332L-Microbial PhysiologyLabused FGCF instruments. Similarly, in spring 2016, ABS 705-Research Methodology (11 graduate students enrolled)usedthe instruments in the FGCF instructed by personnelin the FGCF and Biology and Microbiology Department. 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 sever the faculty, visiting scientists, post-docs, graduate students and undergraduates at SDSU and other institutions in South Dakota. In addition, we will work hard to updateour Pharos reservation system and update the FGCF webpage. Objective 2. Provide individual and group training and technical support to functional genomics researchers Continue to provide individual and group training and technical support on the following equipment: FV1200 confocal; BX53; IX70; and SZX16 fluorescent microscopies; Li-Cor Odyssey Infrared Gel Imaging system premiumand Odyssey Fc system; BioTek Synergy 2 microplate reader; Nanodrop ND-1000 Spectrophotometer; Bio-Rad ChemiDoc XRS; ABI 7900HT sequence detection system; Agilent Bioanalyzer; GCMS 5975 diffusion system; and LC 1220 system, as well as cryotome and microtomes. Objective 3. Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques FGCF personnel will continually look for opportunities to facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques Objective 4. Facilitate interdisciplinary collaborative research within the fields of biomolecular science FGCF personnel will continually look for opportunities to facilitate collaborative research among its members. Objective 5. Encourage greater organization and cooperation among the university core facilities FGCF personnel will collect equipment information on all the biological-type multiuser facilities on the SDSU campus and encourage greater visibility and cooperation among these 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 The Functional Genomics Core Facility currently has 267 registered users with 67 newly added during 10/01/15 - 09/30/16. More than 85% of the active users are from the College of Agriculture and Biological Sciences. FGCF furtherexpandedits users throughout the entire SDSU campus and into the private sectors. Although FGCF registered user number was similar to last year, the usage incomewas increased from $17,408.05(10/01/14 - 09/30/15) to $24,739.51 (10/01/15 - 09/30/16) and the maintanence costs were similar (~18,000). Objective 2: Provide individual and group training and technical support to functional genomics researchers FGCF personnel have provided numerous individual and group training to the registered users on the FV1200 confocal; BX53; IX70; and SZX16 fluorescent microscopies; Li-Cor Odyssey Infrared Gel Imaging system premiumand Odyssey Fc system; BioTek Synergy 2 microplate reader; Nanodrop ND-1000 Spectrophotometer; Bio-Rad ChemiDoc XRS; ABI 7900HT sequence detection system; Agilent Bioanalyzer; GCMS 5975 diffusion system; and LC 1220 system, as well as training for tissue preparation with cryotome and microtomes. In particular, FGCF personnel havebeen involved in teaching and demonstration of the modern technologies and operation procedures on various equipment during graduate level courses (Biol 645L and ABS 705) and upper-level undergraduate course (MICR 438L). Objective 3:Facilitate modern and advanced biological research by promoting the newest molecular and imaging techniques With the help of the "Science Undergraduate Research Grant" from the LI-COR, the Functional Genomics Core Facility, and the Biology & Microbiology department at SDSU, we acquired the Li-Cor ODYSSEY Fc SYSTEM designed to capture the most accurate Western blot data, including consistent ECL data or two-color multiplex detection using near-infrared fluorescence. The Odyssey Fc is also capable of documenting EtBr stained DNA gels with the additional 600 nm channel and Coomassie stained protein gels with the 700 nm channel. FGCF personnel developed an acetylene reduction assay using the GC-MS purchased from Dr. Ruanbao Zhou's DOT grant. Several laboratories used this technique for their projects, including Rajesh Chintala in Dr. T Schumacher's labin Plant Science Department [Mollinedo J, Schumacher TE, and Chintala R (2016) Biochar effects on phenotypic characteristics of "wild" and "sickle" Medicago truncatula genotypes. Plant and Soil 400:1-14];TyrelDeutscher's thesis in Dr. N Reese's labin Biology & MicrobiologyDepartment; Huilan Zhu and ChuckHalfmann_Dr. R Zhou's labin Biology & MicrobiologyDepartment (manuscripts in preparation). FGCF personnel draftedletters of intent for NSF MRI on acquisition of Atomic Force Microscopy, withfaculty from the Department of Pharmaceutical Sciences (Drs. O Perumal and W An), the Department of Electrical Engineering and Computer Science (Dr. Q Qiao), and the Department of Biology and Microbiology (Drs. X Wang, H Bucking, and R Zhou). Objective 4:Facilitate interdisciplinary collaborative research within the fields of biomolecular science FGCF personnel gave 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 bridged a collaborative researchproject on "identifying the cyanobacterial species in soil" among the following laboratories: Drs. L Xu (Department of Natural Resource Management), S Kumar (Department ofPlant Science), and R Zhou (Department ofBiology and Microbiology). Objective 5:Encourage greater organization and cooperation among the University core facilities. FGCF personnel are trying to 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, FGCF has excellent microscopic systems for high quality data collection and BioSNTR has a high-throughput imaging system that is very useful for screening. FGCF personnel recommended to the users that they use thehigh-throughput imaging system in BioSNTRto do initial screening to narrow down the most important findings, and then focus the selected samples for more comprehensive analysis using the FGCF's FV1200 Confocal microscope.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tylor J. Johnson, Charles Halfmann, Jacob D. Zahler, Ruanbao Zhou, William R Gibbons (2016) Increasing the tolerance of filamentous cyanobacteria to next-generation biofuels via directed evolution. Algal Research 18:250256
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tylor J. Johnson, Arash Jahandideh, Isabel C. Isaac, Emily L. Baldwin, Kasiviswanathan Muthukumarappan, Ruanbao Zhou, William R. Gibbons (2016) Determining the optimal nitrogen source for large-scale cultivation of filamentous cyanobacteria. J Appl Phycol DOI 10.1007/s10811-016-0923-3
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tylor J. Johnson, Jacob D. Zahler, Emily L. Baldwin, Ruanbao Zhou, William R. Gibbons (2016) Optimizing cyanobacteria growth conditions in a sealed environment to enable chemical inhibition tests with volatile chemicals. Journal of Microbiological Methods 126:5459
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Eljaki AA, Al Kappany YM, Grosz DD, Smart AJ, Hildreth MB (2016) Molecular survey of trichostrongyle nematodes in a Bison bison herd experiencing clinical parasitism, and effects of avermectin treatment. Vet Parasitol. 227:48-55.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu B, Zhang H, Zhou C, Li G, Fennell A, Wang G, Kang Y, Liu Q, Ma Q. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes. BMC Genomics 17:578. doi: 10.1186/s12864-016-2982-x.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Alsharif FM, Dave K, Samy AM, Saleh KI, Amin MA, Perumal O. Influence of Hydroalcoholic Vehicle on In Vitro Transport of 4-Hydroxy Tamoxifen Through the Mammary Papilla (Nipple). AAPS PharmSciTech. 2016 Aug 9. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang X, Zhao S, B�cking H. Arbuscular mycorrhizal growth responses are fungal specific but do not differ between soybean genotypes with different phosphate efficiency. Ann Bot. 118(1):11-21. doi: 10.1093/aob/mcw074
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Joshi LR, Mohr KA, Clement T, Hain KS, Myers B, Yaros J, Nelson EA, Christopher-Hennings J, Gava D, Schaefer R, Caron L, Dee S, Diel DG. Detection of the Emerging Picornavirus Senecavirus A in Pigs, Mice, and Houseflies. J Clin Microbiol 54(6):1536-45. doi: 10.1128/JCM.03390-15
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang X, Zhang H, Abel AM, Nelson E. Protein kinase R (PKR) plays a pro-viral role in porcine reproductive and respiratory syndrome virus (PRRSV) replication by modulating viral gene transcription. Arch Virol 161(2):327-33. doi: 10.1007/s00705-015-2671-0.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sreenivasan C, Thomas M, Sheng Z, Hause BM, Collin EA, Knudsen DE, Pillatzki A, Nelson E, Wang D, Kaushik RS, Li F (2015) Replication and Transmission of the Novel Bovine Influenza D Virus in a Guinea Pig Model. J Virol. 89(23):11990-2001. doi: 10.1128/JVI.01630-15.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mollinedo J, Schumacher TE, and Chintala R (2016) Biochar effects on phenotypic characteristics of wild and sickle Medicago truncatula genotypes. Plant and Soil 400:114


Progress 07/03/15 to 09/30/15

Outputs
Target Audience: The primary target audience includes: faculty members, postdoctoral fellows, graduate students and undergraduate students at SDSU. There were total 31 active principle investigator's laboratories 214 registered users from 10 different departments and three centers. The FGCF also served the researchers from USDA and regional biological industries (Medgene and Prairie Aquatech). The FGCF Personnelprovided numerous tours to visitors from local high schools, faculty from other universities, members of Ag organizations and industries in the USA, as well as international visitors. The FGCF governing body currently consists of eleven-member governing committee. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Group and individual trainings were given by the facility personnel from the experimental design, instrument operation, data acquisition, to data interpretation on the following equipments: 1) ABI 7900HT Sequencing Detection System; 2) BioTek Synergy 2 Multimode Detector; 3) LI-COR Odyssey Infrared Gel Imaging System; 4) Chemidoc XRS Imaging Station; 5) Nanodrop ND-1000 Spectrophotometer; f) ABI 9700 Thermocycler; 6) ABI Veriti Thermocycler; 7) Olympus Fluoview FV1200 Laser Scanning Confocal Microscope; 8) Olympus BX53 Upright Compound Microscope; 9) Olympus IX70 Inverted-Microscope; 10) Olympus SZX16 Epi-Fluorescent Stereo Microscope; 11) PALM MicroBeam Laser Micro-Dissection System; and 12) Agilent GC-MS system. FGCF personnel also provided major laboratory support for a graduate-level Microimaging Biol645 (30 students) and Research Methodology ABS 705 (12 students) courses. Occasional support was also given to an undergraduate-level molecular techniques Micro438L course (16 students). In addition to training and supporting the operation of the various instruments, FGCF personnel consulted on various projects and supported grant applications. Data generated at this facility was incorporated into at least 15 peer review publications and several new extramural funding applications (Senthil Subramanian: USDA; Ruanbao Zhou: USDA; Dan Wang: USDA). How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? During Jan. 1stto April 17th2015, we had used two different tracking systems (Pharos for the general lab and Idea Elan for the microscopic lab due to the Pharos couldn't support 64 bit computer). Then SDSU updated the Pharos system to 64 bit, so we decided to let our Idea Elan contract run out and return to the Pharos system. We got the Pharos system back up running again and everything was working well until this month the server running Pharos crashed. With this crash, we not only lost the ability to track usage for a period of time, we also lost the past 8 months of usage billing data, estimated about $9,000 revenue for the either pharos controlled instruments. From Dec 2014 to April 2015, the average usage was 11.22 h/day among the following nine software tracked instruments (Chemidoc, Nanodrop, Odyssey, Synergy 2, ABI 7900HT, BX53, IX70, SZX16, and Confocal FV1200). We noticed that the usage among the microscopes was increased significantly during the past 8 months. Moreover, the usage of the non-pharos instrument (Agilent LC1220 HPLC System and Agilent GCMS 5975 Diffusion System) was increased dramatically, particularly for Agilent GCMS after the FGCF personnel successfully developed a method for ethylene detection/quantification on GC-MS system. Data generated from the GCMS have produced one journal article [Mollinedo J, Schumacher TE, Chintala R (2015) Biochar effects on phenotypic characteristics of "wild" and "sickle" Medicago truncatula genotypes.Plant and Soil.] and one conference poster [Deutscher T, Brözel VS, Henry L, and Reese RN (2015) NITROGEN FIXING ENDOPHYTES OF A NON-NODULE FORMING LEGUME.South Dakota Academy of Science 100thannual meeting. Oacoma, SD April 11, 2015].

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Johnson TJ, Hildreth MB, Gu L, Zhou R, Gibbons WR. Testing a dual-fluorescence assay to monitor the viability of filamentous cyanobacteria. J Microbiol Methods. 113:57-64
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chen K, Xu X, Gu L, Hildreth M, Zhou R. Simultaneous gene inactivation and promoter reporting in cyanobacteria. Appl Microbiol Biotechnol. 99(4):1779-93.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Xu X, Gu L, He P, Zhou R. Characterization of five putative aspartate aminotransferase genes in the N2-fixing heterocystous cyanobacterium Anabaena sp. strain PCC 7120. Microbiology. 161(6):1219-30.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mollinedo J, Schumacher TE, Chintala R. Biochar effects on phenotypic characteristics of wild and sickle Medicago truncatula genotypes. Plant and Soil. DIO: 10.1007%2Fs11104-015-2708-x
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mensah JA, Koch AM, Antunes PM, Kiers ET, Hart M, B�cking H. High functional diversity within species of arbuscular mycorrhizal fungi is associated with differences in phosphate and nitrogen uptake and fungal phosphate metabolism. Mycorrhiza. 25(7):533-46.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sreenivasan C, Thomas M, Sheng Z, Hause BM, Collin EA, Knudsen DE, Pillatzki A, Nelson E, Wang D, Kaushik RS, Li F. Replication and Transmission of the Novel Bovine Influenza D Virus in a Guinea Pig Model. J Virol. 89(23):11990-2001.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wang X, Zhang H, Abel AM, Nelson E. Protein kinase R (PKR) plays a pro-viral role in porcine reproductive and respiratory syndrome virus (PRRSV) replication by modulating viral gene transcription. Arch Virol.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nizampatnam NR, Schreier SJ, Damodaran S, Adhikari S, Subramanian S. microRNA160 dictates stage-specific auxin and cytokinin sensitivities and directs soybean nodule development. Plant J. 84(1):140-53
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: White LJ, Jothibasu K, Reese RN, Br�zel VS, Subramanian S. Spatio Temporal influence of Isoflavonoids on Bacterial Diversity in the Soybean Rhizosphere. Mol Plant Microbe Interact. 28(1):22-9
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ye H, Feng J, Zhang L, Zhang J, Mispan MS, Cao Z, Beighley DH, Yang J, Gu XY. Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice. Plant Physiol. 169(3):2152-65
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Rettedal EA, Br�zel VS. Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H(2) (18) O. Microbiologyopen.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Venuganti VV, Saraswathy M, Dwivedi C, Kaushik RS, Perumal OP. Topical gene silencing by iontophoretic delivery of an antisense oligonucleotide-dendrimer nanocomplex: the proof of concept in a skin cancer mouse model. Nanoscale. 7(9):3903-14
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Deutscher T, Br�zel VS, Henry L, and Reese RN. NITROGEN FIXING ENDOPHYTES OF A NON-NODULE FORMING LEGUME. South Dakota Academy of Science 100th annual meeting. Oacoma, SD April 11, 2015
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Quast M, Sreenivasan C, Sexton G, Nedland H, Singrey A, Fawcett L, Miller G, Lauer D, Voss S, Pollock S, Cunha CW, Christopher-Hennings J, Nelson E, Li F. Serological evidence for the presence of influenza D virus in small ruminants. Vet Microbiol. 180(3-4):281-5.