On-chip phenotypic screening and characterization of C. elegans enabled by microfluidics and image analysis methods

Cáceres Mendieta, Ivan de Carlos

Title:

On-chip phenotypic screening and characterization of C. elegans enabled by microfluidics and image analysis methods

dc.contributor.advisor	Lu, Hang
dc.contributor.author	Cáceres Mendieta, Ivan de Carlos
dc.contributor.committeeMember	Butera, Robert
dc.contributor.committeeMember	Streelman, Jeffrey T.
dc.contributor.committeeMember	Brand, Oliver
dc.contributor.committeeMember	Hu, Xiaoping
dc.contributor.department	Biomedical Engineering (Joint GT/Emory Department)
dc.date.accessioned	2015-01-12T20:28:02Z
dc.date.available	2015-01-13T06:30:04Z
dc.date.created	2013-12
dc.date.issued	2013-08-23
dc.date.submitted	December 2013
dc.date.updated	2015-01-12T20:28:02Z
dc.description.abstract	Since its introduction in 1960's, the model organism Caenorhabditis elegans has played a crucial role towards scientific discoveries because of its relatively simple anatomy, conserved biological mechanisms, and mapped genome. The organism also has a rapid generation time and produces a large number of isogenic progeny, making C. elegans an excellent system for conducting forward genetic screens. Conventional screening methods, however, are labor intensive and introduce potential experimental bias; typically, large-scale screens can take months to years. Thus, automated screening and characterization platforms can provide an opportunity to overcome this bottleneck. The objective of this thesis is to develop tools to perform rapid phenotypical characterization of C. elegans to enable automated genetic screening systems for neural development. To achieve this goal, I developed methods to increase throughput of worm handling using microfluidic devices and demonstrate software modules to phenotype unknown mutants using quantitative and morphological image analysis methods. Microfluidic devices are constructed from PDMS using established soft-lithography techniques. The emphasis on the simplification of existing designs greatly facilitates the adoption of our developed systems by other scientists. This thesis also includes image processing modules using various techniques to determine animal phenotypes. For example, we adapted standard thresholding methods to detect animal motor neurons, developed a modified granulometry algorithm to rapidly characterize large numbers of lipid droplets in 3D, and developed a probability model to determine neuronal process morphology. This work is significant because it increases current capabilities of screening small animals with morphological phenotypes by enhancing throughput and reducing human bias. Genes or gene functions that can be discovered using these methods can further elucidate mechanisms relevant to neural development, degeneration, maintenance, and function; these discoveries in turn can facilitate discoveries of potential therapeutic strategies for human neurological diseases.
dc.description.degree	Ph.D.
dc.embargo.terms	2014-12-01
dc.format.mimetype	application/pdf
dc.identifier.uri	http://hdl.handle.net/1853/52921
dc.language.iso	en_US
dc.publisher	Georgia Institute of Technology
dc.subject	Microfluidics
dc.subject	C. elegans
dc.subject	Image analysis
dc.subject	Automated
dc.subject	Genetic screening
dc.title	On-chip phenotypic screening and characterization of C. elegans enabled by microfluidics and image analysis methods
dc.type	Text
dc.type.genre	Dissertation
dspace.entity.type	Publication
local.contributor.advisor	Lu, Hang
local.contributor.corporatename	Wallace H. Coulter Department of Biomedical Engineering
local.contributor.corporatename	College of Engineering
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relation.isOrgUnitOfPublication	da59be3c-3d0a-41da-91b9-ebe2ecc83b66
relation.isOrgUnitOfPublication	7c022d60-21d5-497c-b552-95e489a06569
thesis.degree.level	Doctoral