SPECIMEN-BASED RESEARCH - BIOBANKS, TISSUE BANKS AND BIOLOGICAL REPOSITORIES

Improving Specimen Molecular Integrity and Data Aggregation, standardization and analyses in bio-repositories and biobanks

Although linked by data type, specimens and their associated data deposited in biological collections (bio-repositories, tissue banks, biobanks) exist within the confines of the context that generated them. To enhance the usability and value of biological collections, the next frontier is to give front-end users the capacity to generate inferences and predictions about biological processes in Earth and space-like environments by extracting, aggregating and modeling datasets from both the physical repositories and other relevant public data repositories (e.g., GenBank). The main goal of this project is to create the Datascape Analysis and Navigation Tool (DANTe), a tool to enable all users to access the integrated database, together with interactive modeling to infer the influence of environmental conditions on key biological processes. We will accomplish this by fulfilling the following objectives: 1) to automate the retrieval, aggregation/segmentation, and linkage of cross-dimensional data (i.e., text, OMICs, images, and other) from GeneLab and ground-based OMICs databases to generate real-time snapshots of current knowledge in the biology of systems and organisms; 2) to deploy machine learning modules to model, validate and test changes in biological processes influenced by the space environment; and 3) to make the browser-based DANTe available to the scientific community through a user-friendly interface coupled with extensible open-source analytical modules.

PUBLICATIONS

This project aims to develop better, cheaper and data-efficient protocols for biological collections for use in both medical and basic science research

Bioinformatics

Biomed

Forensic

Biotech

Corthals, A., Martin A, Warsi OM, Woller-Skar M, Lancaster W, Russel, A.L., Dávalos, L.M. (2015) From the Field to the Lab: Best Practices for Field Preservation of Bat Specimens for Molecular Analyses. PLoS ONE 10(3): e0118994

• Corthals, A., T. Koller, D. Martin, R. Rieger, E. I. Chen, L. M. Davalos. (2012) Detecting the Immune System Response of a 500 Year-Old Inca Mummy. PLoS ONE 7(7):e41244. doi:10.1371/journal.pone.0041244

• Dávalos, L. M., A. C. Bejarano, M. Hall, H. L. Correa, A. Corthals, O. J. Espejo. (2011) Forests and drugs: coca-driven deforestation in global biodiversity. Environmental Science and Technology, 45(4), 1219–1227

• Forshaw, R. and A. Corthals. (2011) Multidisciplinary Investigations of the Manchester Elliot Smith Skulls. Yearbook of Mummy Studies, 1, 57-62

• Savolainen V., G. Reeves, K. Davis, M P Powell & A Corthals eds. (2005) DNA banking for Biodiversity and conservation, Kew Publishing & IUCN

• Corthals, A. (2005) Now what? Pre and Post analysis preservation of ancient tissues and DNA. Proceedings of the Vth World Congress on Mummy studies. Journal of Biological Research, 80(1), 217-221

• Corthals, A. and R. Desalle. (2005) An Application of Tissue and DNA banking for Genomics and Conservation: The Ambrose Monell Cryo-Collection. Systematic Biology. 54(5):819–823

• Hanner, R., Corthals, A. and H.C. Dessauer. (2005) Salvage of genetically valuable tissues following a freezer failure. Molecular Phylogenetics and Evolution, Volume 34, Issue 2, February 2005, Pages 452-455

• Corthals, A., Breedlove, M. & Hanner, R. (2003) The online tissue specimen database of the Ambrose Monell Cryo Collection (AM-CC) at the American Museum of Natural History (AMNH). Biotech. Histochem. 78, 207

As Stakeholder/Biological Tool user:

• Hanner, R., A. Corthals, and R. DeSalle. (2009) Biodiversity, conservation, and genetic resources in modern museum and herbarium collections. In Conservation Genetics in the Age of Genomics. G. Amato, O. Ryder, H. Rosenbaum, and R. DeSalle (eds.). Columbia University Press, NY.

• Dávalos, L.M., and A. Corthals. (2008) A New Species of Lonchophylla Thomas (Chiroptera:Phyllostomidae) from the Foothills of the Cordillera Oriental and the Serranía del Perijá. American Museum Novitates, 3635: 1-16.

• Baldo, L., Prendini, L., Corthals, A. and Werren, J. (2007) Wolbachia are present in Southern African scorpions and cluster with supergroup F. Current Microbiology. 55 (5): 367-373

• Savolainen V., G. Reeves, K. Davis, M P Powell & A Corthals eds. (2005) DNA banking for Biodiversity and conservation, Kew Publishing & IUCN