Less than 1% of all microorganisms observed in nature can be cultured in the laboratory, leaving researchers unable to study more than 99% of microorganisms in some environments - microorganisms that sometimes have unique abilities such as synthesis of compounds that could find use as new drugs or antibiotics. Metagenomics, the genomic reconstruction of unculturable microorganisms , is a powerful new tool for accessing the untapped resources of these organisms. In one approach, large fragments ofDMA from a sample containing unculturable microorganisms are extracted and cloned into a host such as E. coli to produce a metagenomics library. The library is then screened for utility of expressed compounds. Though new antibiotics and enzymes have been discovered with this method, successful production of compounds, such as antibiotics, synthesized by the original microorganism presents the difficult challenge of cloning fragments long enough to hold pathways encoded by gene clusters that are often over 100kb in length. Existing purification techniques tend to shear genomic DMAto fragments of 50kb or less. The discovery of a method to extract and purify high MW DMAfrom difficult samples such as soil will provide a breakthrough for metagenomics that may enable the discovery of many future drugs and antibiotics. We have recently demonstrated a non-linear electrophoretic method for DMA concentration that is capable of DMA manipulation and concentration without mechanical handling (such as centrifugation or pipetting). Extraction of DNA from bacterial lysate and 4,000 fold concentration factors have been demonstrated. This method is an excellent candidate for the next generation of methods for DNA extraction methods from complex samples such as soil or body fluids. We propose to develop an instrument to carry out this concentration method, validating its performance on extraction of high molecular weight DNA on soil samples for metagenomics studies aimed at discovery of new drugs and antibiotics. Licensing of this technology will be pursued to address other compelling applications including DNA extraction from body fluids for cancer biomarker and pathogen detection.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
3R01HG003640-03S1
Application #
7778514
Study Section
Special Emphasis Panel (ZRG1-BST-F (91))
Program Officer
Schloss, Jeffery
Project Start
2006-03-01
Project End
2009-08-31
Budget Start
2008-03-01
Budget End
2009-08-31
Support Year
3
Fiscal Year
2009
Total Cost
$112,913
Indirect Cost
Name
University of British Columbia
Department
Type
DUNS #
251949962
City
Vancouver
State
BC
Country
Canada
Zip Code
V6 1-Z3
Pel, Joel; Broemeling, David; Mai, Laura et al. (2009) Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules. Proc Natl Acad Sci U S A 106:14796-801
Broemeling, David J; Pel, Joel; Gunn, Dylan C et al. (2008) An instrument for automated purification of nucleic acids from contaminated forensic samples. JALA Charlottesv Va 13:40-48