We propose to develop a biochip for parallel detection of thousands of microorganisms. It will serve as a genetic screen for the parallel detection, identification, and quantification of up to 10,000 unique microorganisms or gene targets and can be extended to include up to 30,000 targets in the near future. The need for such a comprehensive and broad-range screening tool has been recognized for years in many areas including diagnostics, air, water, food, animal, and plant safety, and bioprocess monitoring. However, its development was hampered by the ability to synthesize and test thousands of possible probes rapidly and economically. This problem is solved now because of the invention of a highly flexible and low-cost in-situ oligonucleotide biochip synthesis platform by the University of Michigan and Xeotron. It can produce biochips overnight without costing a fortune. It is highly flexible with respect to probe content which is software controlled. It uses traditional DNA synthesis chemistry modified to respond to light and thousands of microfluidic reactor array etched on silicon surface. ? ? This proposal combines the expertise in bioinformatics, phylogenetics, environmental engineering, and data interpretation for mixed microbial systems available at the Center for Microbial Ecology (CME) at Michigan State University (MSU) with the flexible biochip fabrication technology described above. Probes for the biochip will be designed and validated by researchers at CME, which is a world leader in developing new methodologies to track and identify microbes in complex microbial systems. Synthesis of the biochip will be carried out by UM and Xeotron. Xeotron currently has a $9M phase one venture capital and is fully geared to produce any chip developed on this platform. Ability to detect all microorganisms of interest in a given matrix together will significantly improve the management of health concerns related to microorganisms. ? ?

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Research Project (R01)
Project #
1R01RR018625-01
Application #
6676435
Study Section
Special Emphasis Panel (ZRG1-SSS-K (10))
Program Officer
Levy, Abraham
Project Start
2003-08-01
Project End
2006-07-31
Budget Start
2003-08-01
Budget End
2004-07-31
Support Year
1
Fiscal Year
2003
Total Cost
$436,151
Indirect Cost
Name
Michigan State University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
193247145
City
East Lansing
State
MI
Country
United States
Zip Code
48824
Srinivasan, Vidya; Stedtfeld, Robert D; Tourlousse, Dieter M et al. (2017) Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 139:15-21
Baushke, Samuel W; Stedtfeld, Robert D; Tourlousse, Dieter M et al. (2012) Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. J Microbiol Methods 90:29-35
Stedtfeld, Robert D; Tourlousse, Dieter M; Seyrig, Gregoire et al. (2012) Gene-Z: a device for point of care genetic testing using a smartphone. Lab Chip 12:1454-62
Stedtfeld, Robert D; Baushke, Samuel W; Tourlousse, Dieter M et al. (2008) Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl Environ Microbiol 74:3831-8
Miller, Sarah M; Tourlousse, Dieter M; Stedtfeld, Robert D et al. (2008) In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water. Appl Environ Microbiol 74:2200-9
Pozhitkov, Alex E; Rule, Rebecca A; Stedtfeld, Robert D et al. (2008) Concentration dependency of nonequilibrium thermal dissociation curves in complex target samples. J Microbiol Methods 74:82-8
Hua, Zhishan; Pal, Rohit; Srivannavit, Onnop et al. (2008) A light writable microfluidic ""flash memory"": optically addressed actuator array with latched operation for microfluidic applications. Lab Chip 8:488-91
Stedtfeld, Robert D; Baushke, Sam; Tourlousse, Dieter et al. (2007) Multiplex approach for screening genetic markers of microbial indicators. Water Environ Res 79:260-9
Tourlousse, Dieter M; Stedtfeld, Robert D; Baushke, Samuel W et al. (2007) Virulence factor activity relationships: challenges and development approaches. Water Environ Res 79:246-59
Pozhitkov, Alex E; Stedtfeld, Robert D; Hashsham, Syed A et al. (2007) Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Res 35:e70

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