Annotation of Five Genes in the DNA Mismatch Repair Pathway of Kytococcus Sedentarius

Annotation of Five Genes in DNA Mismatch Repair Pathway of Kytococcus Sedentarius Joseph M. Gawron, Rama Dey-Rao, Ph.D., Stephen T. Koury, Ph.D. Department of Biotechnical and Clinical Laboratory Sciences, School of Medicine and Biomedical Sciences, State University of New York University at Buffalo, 26 Cary Hall, 3435 Main Street, Buffalo, NY 14214 Background information: Kytococcus sedentarius is an opportunistic pathogen that can survive on and inside humans. Understanding the genetics of this organism and its biologic pathways can lead to better treatments in addition to possible uses of the gene protein products it produces. Purpose: The purpose of this study was to use in silico gene annotation to characterize five genes in the DNA mismatch repair pathway of K. sedentarius. Methods: This study used the IMG-ACT website to record data in a digital notebook. The gene details page was accessed for basic information on each gene. Databases such as BLAST, CDD, TIGRFAM, PDB, PSORT-B, MetaCyc, and Prosite were used to collect qualitative and quantitative data for the five genes, including similar genes in other organisms, functional families, crystal structures, localization, and the presence of necessary functional residues. Websites like Phylogeny.fr, Pfam, KEGG, TMHMM, SignalP, Web Logo, and Phobius were used to generate diagrams that used in the analysis. Conclusions: The proposed annotations for all five genes were confirmed. The genes were found to be phylogenetically conserved between K. sedentarius and multiple orthologs. Keywords: Gene annotation, Kytococcus sedentarius, DNA mismatch repair, BLAST, orthologs, horizontal gene transfer, DNA sequence conservatio

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With nearly 15 million people that live within 250 miles of Kansas City, the demand for local food is increasing. Local beginning farmers in the region want to reach an emerging wholesale market. However, selling directly to consumers demands different skills than the wholesale market requires. There are many educational programs offered in the region that are focused on direct to consumer sales. Unfortunately, there is a gap in educational programs that are offered to support beginning farmers that wish to expand into wholesale markets. In 2018, the Beginning Farmer Wholesale Project was started within the Growing Growers Kansas City program in congruence with the overall mission to improve the skills and livelihoods of the region’s growers. The project offers support and training to beginning farmers as they begin to navigate new market opportunities. It provides on-farm technical assistance, mentorship, opportunities to connect to wholesale buyers, a workshop series, a manual and an extensive foodshed GIS map. The ongoing project has seen several contributions to improving farmer access to wholesale markets. As of 2020, six workshops have been conducted that have covered a variety of farm production and marketing skills. Six farmer mentees have enrolled in the mentor program which enlists nine farmer mentors from across the region. Over twenty farmers have utilized the technical assistance service on their Kansas and Missouri farm operations and the farmer buyer matching program has resulted in thirteen beginning farmers gaining access to new markets. The project highlights the value of collaboration among organizations and the importance of offering multiple farmer services in order to improve wholesale access