Human disease often involves changes in the timing and level of gene expression, processes investigated by transcriptomics, the identification of each expressed gene and its transcriptional levels. Studies of the association of human variation with altered gene expression can lead to a deeper, mechanistic understanding of disease states and can suggest therapies. A promising route to discovery is the transcriptomic analysis of novel models of common human diseases in aquatic species for which few genomic resources presently exist. Breakthroughs in sequencing technologies have opened the door for transcriptomics in non-model organisms. As detailed at the Sept. 2010 workshop 'Realizing the Scientific Potential of Transcriptomics in Aquatic Models', several impediments currently hinder the successful use of these tools in aquatic model systems. The goal of this project is to overcome these barriers by developing the protocols and tools necessary for researchers to capitalize on recent advances in DNA sequencing technology to better perform transcriptome analyses on aquatic medical models. This project will develop optimal laboratory protocols, analytical theory and computational software for transcriptome analyses of aquatic models of human disease and will help researchers plan and analyze experimental results. Protocols and tools will be made available via the Galaxy web platform as easy-to-use interfaces for computational software and web-based tutorials. Because many researchers working with aquatic non-model organisms lack access to the latest sequencing facilities and computational expertise for the analysis of high throughput transcriptomics, mechanisms will be developed for aquatic model organism researchers to use the Univ. of Oregon High Throughput Sequencing Facility. Similarly, many researchers lack access to computer clusters sufficiently powerful to execute the computational demands of modern transcriptomics, so this project will increase the availability of computational pipelines running at the Univ. of Oregon. This project will therefore provide widely needed tools, raise barriers to progress, and improve methods and technologies for transcriptome analysis in aquatic medical models, thus advancing our understanding of the role of gene regulation in health and disease.

Public Health Relevance

Studies of gene expression in aquatic model organisms promise significant breakthroughs in our understanding of the genetic causes of human diseases that can significantly increase human health. This project will accelerate research on non-model aquatic organisms by developing best practices and tools, making resources and training available, providing resources for laboratories to generate and analyze new types of genetic data and by contributing to the training of computer scientists in bioinformatics.

National Institute of Health (NIH)
Office of The Director, National Institutes of Health (OD)
Resource-Related Research Projects (R24)
Project #
Application #
Study Section
Comparative Medicine Review Committee (RIRG)
Program Officer
Contreras, Miguel A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Oregon
Graduate Schools
United States
Zip Code
Schartl, Manfred; Walter, Ronald B (2016) Xiphophorus and Medaka Cancer Models. Adv Exp Med Biol 916:531-52
Shen, Yingjia; Chalopin, Domitille; Garcia, Tzintzuni et al. (2016) X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics 17:37
Pasquier, Jeremy; Cabau, Cédric; Nguyen, Thaovi et al. (2016) Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. BMC Genomics 17:368
Walter, Ronald B; Obara, Tomoko (2015) Workshop report: The medaka model for comparative assessment of human disease mechanisms. Comp Biochem Physiol C Toxicol Pharmacol 178:156-62
Boswell, William; Boswell, Mikki; Titus, James et al. (2015) Sex-specific molecular genetic response to UVB exposure in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol 178:76-85
Braasch, Ingo; Peterson, Samuel M; Desvignes, Thomas et al. (2015) A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. J Exp Zool B Mol Dev Evol 324:316-41
Desvignes, T; Batzel, P; Berezikov, E et al. (2015) miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 31:613-26
Walter, Ronald B; Walter, Dylan J; Boswell, William T et al. (2015) Exposure to fluorescent light triggers down regulation of genes involved with mitotic progression in Xiphophorus skin. Comp Biochem Physiol C Toxicol Pharmacol 178:93-103
Lu, Yuan; Bowswell, Mikki; Bowswell, William et al. (2015) Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure. Comp Biochem Physiol C Toxicol Pharmacol 178:86-92
Chang, Jordan; Lu, Yuan; Boswell, William T et al. (2015) Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol 178:104-15

Showing the most recent 10 out of 32 publications