Navigation Links
Method of the future uses single-cell imaging to identify gene interactions
Date:2/8/2010

February 9, 2010 Cellular imaging offers a wealth of data about how cells respond to stimuli, but harnessing this technique to study biological systems is a daunting challenge. In a study published online in Genome Research (www.genome.org), researchers have developed a novel method of interpreting data from single-cell images to identify genetic interactions within biological networks, offering a glimpse into the future of high-throughput cell imaging analysis.

For years, scientists have been peering through a microscope at cells as they change appearance in response to different treatments, yet data collection is arduous, largely conducted qualitatively by eye. However, recent technological advances have led to the development of high-throughput image screening methods that can produce extensive datasets of hundreds of different morphological features.

With the ability to collect large imaging datasets, researchers from MIT and Harvard Medical School recognized an opportunity to explore the cellular networks that regulate cell morphology. "These images are an enormous source of data that is only beginning to be tapped," said MIT researcher Bonnie Berger, senior author of the work published today. "We realized we had enough data to go beyond classification and start to understand the mechanism behind the differences in shape."

To meet the challenge of interpreting cell image data, Berger and MIT graduate student Oaz Nir developed a novel computational model to identify genetic interactions using high-dimensional morphological data. Integrating prerequisite knowledge of a pathway, their model maps potential interactions within a network by looking for similar morphological features upon genetic perturbation.

The group demonstrated the method by analyzing the Rho-signaling network in fruit flies, a network that regulates cell adhesion and motility in eukaryotic organisms. In collaboration with Chris Bakal and Norbert Perrimon at Harvard Medical School, they "knocked-down" components of the Rho-signaling network using RNA interference and then imaged thousands of fly cells, gathering measurements of cell perimeter, nuclear area, and more than 150 other morphological features for each cell. The data was then passed through the computational framework to produce a set of high-confidence interactions, supported by confirmation of previously known interactions.

The group found that by making combinatorial knockdowns of Rho network components, their computational method was able to accurately infer Rho-signaling network interactions more precisely than when using only data from single knockdowns. Berger noted that this finding highlights the importance of combinatorial experiments for inferring complex networks, necessary to overcome natural redundancy in signaling pathways. As perturbation of the Rho pathway in humans has been implicated in cancer and other diseases, the authors believe that these predicted interactions will be excellent candidates for future study.

Berger expects that in combination with other sources of data, imaging as a new source of high-throughput data should appreciably increase the accuracy of known signaling networks. "This work provides a glimpse into the future," added Berger, "where looking under the microscope manually at cells one-by-one is replaced with automated high-throughput processing of many cellular images."


'/>"/>

Contact: Peggy Calicchia
calicchi@cshl.edu
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

Related biology news :

1. Safe water: simpler method for analyzing radium in water samples cuts testing time
2. Researchers develop simple method to create natural drug products
3. New method reveals substances on surfaces of any kind
4. Alternative methods proposed to detect pesticides and antibiotics in water and natural food
5. 454 Sequencing: Science paper describes a novel, highly efficient method of sequencing ancient DNA
6. Contraception: progress brings hope for new methods for men
7. From brains to behavior: Cold Spring Harbor Protocols features methods for neuroscience research
8. Cold Spring Harbor Protocols highlights a method that captures cell growth and activity
9. Team of scientists develops non-invasive method to track nerve-cell development in live human brain
10. New book presents methods to poke and prod individual molecules
11. Feinstein researchers develop new genetic method and identify novel genes for schizophrenia
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:1/22/2016)... DUBLIN , January 22, 2016 ... has announced the addition of the  ... to their offering. --> ... of the  "Global Behavioral Biometric Market ... --> Research and Markets ( http://www.researchandmarkets.com/research/4lmf2s/global_behavioral ...
(Date:1/20/2016)... Jan. 20, 2016 A market that just ... benefit from the explosion in genomics knowledge. Learn all ... Research. A range of dynamic trends are pushing market ... personalized medicine - pharmacogenomics - pathogen evolution - next ... markets - greater understanding of the role of genetic ...
(Date:1/18/2016)... , Jan. 18, 2016  Extenua Inc., ... that simplifies the use and access of ubiquitous ... go-to-market partnership with American Cyber.  ... extensive experience leading transformational C4ISR and Cyber initiatives ... integrating the latest proven technology solutions," said ...
Breaking Biology News(10 mins):
(Date:2/12/2016)... ... February 12, 2016 , ... The Pittcon 2016 Exposition, which ... will include 848 exhibitors (count as of February 9) of which 119 are ... used by the scientific community in industrial, academic, and government labs. The Exposition ...
(Date:2/12/2016)... FRANCISCO , February 12, 2016 ... Medicine Efforts by Enabling Scientific Understanding of Complex ... and Rare Diseases --> ... genomic diagnostics in South Asia and a leading provider ... would contribute $10 million to the GenomeAsia 100K ...
(Date:2/11/2016)... 2016  Vermillion, Inc. (NASDAQ: VRML ), a ... the formation of the Steering Committee for its Pelvic ... --> Pelvic masses can present physicians and healthcare ... pregnancy is ruled out, pelvic masses may include cancers ... benign ovarian tumors and gastrointestinal and urinary tract masses. ...
(Date:2/11/2016)... Feb. 11, 2016  Spectra BioPharma Selling Solutions (Spectra) ... provides biopharma companies the experience, expertise, operational delivery ... outsourced sales teams. Created in concert with industry ... the strategic and tactical needs of its clients ... through both personal and non-personal promotion. ...
Breaking Biology Technology: