A computational analysis of antisense off-targets in prokaryotic organisms
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2015-01-01
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© 2014 .The adoption of antisense gene silencing as a novel disinfectant for prokaryotic organisms is hindered by poor silencing efficiencies. Few studies have considered the effects of off-targets on silencing efficiencies, especially in prokaryotic organisms. In this computational study, a novel algorithm was developed that determined and sorted the number of off-targets as a function of alignment length in Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv. The mean number of off-targets per a single location was calculated to be 14.1. ±. 13.3 and 36.1. ±. 58.5 for the genomes of E. coli K-12 MG1655 and M. tuberculosis H37Rv, respectively. Furthermore, when the entire transcriptome was analyzed, it was found that there was no general gene location that could be targeted to minimize or maximize the number of off-targets. In an effort to determine the effects of off-targets on silencing efficiencies, previously published studies were used. Analyses with acpP, ino1, and marORAB revealed a statistically significant relationship between the number of short alignment length off-targets hybrids and the efficacy of the antisense gene silencing, suggesting that the minimization of off-targets may be beneficial for antisense gene silencing in prokaryotic organisms.
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Worley-Morse, Thomas O, and Claudia K Gunsch (2015). A computational analysis of antisense off-targets in prokaryotic organisms. Genomics, 105(2). pp. 123–130. 10.1016/j.ygeno.2014.11.010 Retrieved from https://hdl.handle.net/10161/11463.
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Claudia K. Gunsch
Claudia Gunsch is a Professor of Civil and Environmental Engineering and holds secondary appointments in the Nicholas School of the Environment and the Department of Biomedical Engineering. She joined the Duke Faculty in 2004 after obtaining her PhD from the University of Texas at Austin, her MS from Clemson University and her BS from Purdue University. Currently, she serves as the Director for PreMiEr, the National Science Foundation Engineering Research Center for Precision Microbiome Engineering which is a joint venture between Duke University, North Carolina A&T State University, North Carolina State University, the University of North Carolina – Chapel Hill and the University of North Carolina – Charlotte. She also serves as an Associate Director for the Duke Microbiome Center. Previous leadership roles include serving as Associate Dean for Research and Infrastructure for the Pratt School of Engineering (2021-2022), Associate Vice Provost for Faculty Advancement (2019-2021) and as the Director of IBIEM (Integrative Bioinformatics for Investigating and Engineering Microbiomes), a joint graduate training program between Duke and North Carolina A&T State University (2015-2021).
Dr. Gunsch’s research bridges environmental engineering and molecular biotechnology. Current research foci include investigating the ecological impacts of emerging contaminants on environmental microbiomes, developing microbiome engineering approaches for bioremediation, studying microbial evolution following exposure to anthropogenic contaminants and developing innovative water treatment technologies. Her work has been funded in excess of $36 million by the National Science Foundation, US Environmental Protection Agency, National Institute for Environmental Health and Safety as well as state funding agencies and private industry. Since becoming a faculty member, she has served as the primary mentor for 28 graduate students (8 MS and 20 PhD), 34 undergraduate students and 8 postdoctoral associates. She has been recognized for her research, teaching and service activities with several awards including the 2009 National Science Foundation Faculty Early Career Development Award, 2013 Langford Lectureship Award, 2016 Capers and Marion McDonald Award for Excellence in Mentoring and Advising and the 2016 American Society of Civil Engineers (ASCE) Walter L. Huber Civil Engineering Research Prize. Dr. Gunsch was also named ASCE Environmental & Water Resources Institute Fellow in 2022, Bass Fellow in 2016 and Fellow of the National Academy of Engineering for the United States Frontiers of Engineering in 2011 as well as the Indo-American Frontiers of Engineering in 2014.
She currently serves as Editor in Chief for Biodegradation. She is also a member of the Editorial Board for npj Clean Water and Industrial Biotechnology. She serves on the Association of Environmental Engineering and Science Professors (AEESP) Board of Directors and has previously held several leadership roles within the Environmental & Water Resources Institute (EWRI). Most recently, she served as the Environmental Council representative to the Technical Executive Committee to EWRI.
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