I. Introduction and Progress: A major goal of the ND INBRE in the current funding cycle was to establish bioinformatics expertise to serve the ND INBRE partners. In the early funding cycles of BRIN and INBRE, the ND INBRE bioinformatics program focused on the introduction and improvement of the electronic library resources that would be necessary to serve biomedical research in ND. At this early juncture in the program, there was both limited internet access and electronic library resources in ND. As detailed in the previous competing renewal, this goal was successfully accomplished by ND INBRE and all INBRE partners now have electronic access to the UNO Library system. Due to these advances, a major goal of the ND INBRE in the current grant cycle was to establish the foundation for the development of bioinformatics in ND through recruitment and development of bioinformatics faculty. In the current funding cycle, the ND INBRE challenged both Research Intensive Universities in ND to participate with the ND INBRE to develop a Bioinformatics Core to serve the educational and research needs of our partners throughout the state. As part of this challenge, the ND INBRE committed $125,000 a year to each RIU to assist each in joining the ND INBRE in this important endeavor of infrastructure building and a central goal of the IDeA program. The Dean of the SMHS took full advantage of this opportunity. Foremost, Dr. Wynne provided a state? supported FTE for the initial recruitment of the first bioinformatics faculty member at the UNO SMHS. This allowed ND INBRE funds committed to this appointment to be used to support the development of the faculty member and the Bioinformatics Core facility. The UNO SMHS successfully recruited Dr. Ke Zhang into the Department of Pathology to supervise the ND INBRE Bioinformatics Core. Dr. Zhang and ND INBRE initially equipped the facility with a Dell PowerEdge R910 4U rack server that has four Intel Xeon X7550 CPUs and 512 GB RAM. This R910 server allows parallel computation of 64 processes simultaneously. To date, this server has enabled the core to fulfill most of the required tasks for bioinformatics research and education. The R910 is a single-node server and a major advantage of R910 is that it has a large shared memory (500 GB) that allows development of computational algorithms with a large data structure. This Dell R910 server is valuable and will remain a valuable part of the Bioinformatics Core. The R910 server will continue to be used for methodology development and student training. Due to the success of the ND INBRE Bioinformatics Core, this server was becoming a limiting factor for meeting the computational requirements for the fast-growing area of genomic data-sets. As a result, the ND INBRE in early 2013, in combination with other internal resources of the PI at the UNO SMHS, purchased a cluster server in order to meet the computational challenges in the Bioinformatics Core. The cluster server will be used for computationally intensive tasks such as processing next generation sequencing data. The Summary Configuration of the cluster server is: 16 Compute Nodes, 2 Intel MIC chips, Gigabit Networking, and Rack with Power Distribution. Additional information on specifics is available below and on the ND INBRE website under Bioinformatics. The support of a major portion of Dr. Zhang's salary by the Dean of the SMHS also allowed important ND INBRE resources to be re-deployed to support the research and core duties of Dr. Zhang. These resources were used by Dr. Zhang to employ on average 3 computer science undergraduates and 2 computer science graduate students to support core function. In addition to employment, many students are pursuing research projects with Dr. Zhang. The SMHS and the Department of Pathology have provided Dr. Zhang 450 sq. ft. of space to support his undergraduate and graduate personnel. Each student has independent desk space that is equipped with a Dell computer and required software. The impact of this support is effectively illustrated by the numerous publications and presentations produced by Dr. Zhang since his arrival at UNO SMHS. These resources also supported his scholarly activity and service requirements necessary to compete effectively on the academic tenure track. Dr. Zhang is also a participant on a new R01 award in excess of $1.2 million. As detailed in the progress report, UNO SMHS institutional support to the Bioinformatics Core by Dr. Wynne, the Dean of the SMHS and Vice President for Health Affairs, will exceed $900,000 over the current 5year funding cycle. This is a return of over 100% of the direct investment of funds by the ND INBRE.
| Chauhan, Arun; Sun, Yuyang; Sukumaran, Pramod et al. (2018) M1 Macrophage Polarization Is Dependent on TRPC1-Mediated Calcium Entry. iScience 8:85-102 |
| Sukumaran, Pramod; Sun, Yuyang; Antonson, Neil et al. (2018) Dopaminergic neurotoxins induce cell death by attenuating NF-?B-mediated regulation of TRPC1 expression and autophagy. FASEB J 32:1640-1652 |
| Hovde, Moriah J; Larson, Garret H; Vaughan, Roxanne A et al. (2018) Model systems for analysis of dopamine transporter function and regulation. Neurochem Int : |
| Steffan, J J; Brevik, E C; Burgess, L C et al. (2018) The effect of soil on human health: an overview. Eur J Soil Sci 69:159-171 |
| Shabani, Shkelzen; Schmidt, Bryan; Ghimire, Bikalpa et al. (2018) Depression-like symptoms of withdrawal in a genetic mouse model of binge methamphetamine intake. Genes Brain Behav :e12533 |
| Jondle, Christopher N; Gupta, Kuldeep; Mishra, Bibhuti B et al. (2018) Klebsiella pneumoniae infection of murine neutrophils impairs their efferocytic clearance by modulating cell death machinery. PLoS Pathog 14:e1007338 |
| Basson, Marc D; Wang, Qinggang; Chaturvedi, Lakshmi S et al. (2018) Schlafen 12 Interaction with SerpinB12 and Deubiquitylases Drives Human Enterocyte Differentiation. Cell Physiol Biochem 48:1274-1290 |
| Selya, Arielle S; Thapa, Sunita; Mehta, Gaurav (2018) Earlier smoking after waking and the risk of asthma: a cross-sectional study using NHANES data. BMC Pulm Med 18:102 |
| Sun, Yuyang; Sukumaran, Pramod; Selvaraj, Senthil et al. (2018) TRPM2 Promotes Neurotoxin MPP+/MPTP-Induced Cell Death. Mol Neurobiol 55:409-420 |
| Claw, Katrina G; Anderson, Matthew Z; Begay, Rene L et al. (2018) A framework for enhancing ethical genomic research with Indigenous communities. Nat Commun 9:2957 |
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