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:2/3/2016)... DUBLIN , Feb. 3, 2016 /PRNewswire/ ... announced the addition of the "Emotion ... NLP, Machine Learning, and Others), Software Tools ... Application Areas, End Users,and Regions - Global ... offering. --> http://www.researchandmarkets.com/research/d8zjcd/emotion_detection ) ...
(Date:2/2/2016)... YORK , Feb. 2, 2016 Technology Enhancements ... presents an analysis of the digital and computed radiography ... Malaysia , and Indonesia ... trends and market size, as well as regional market ... country and discusses market penetration and market attractiveness, both ...
(Date:2/1/2016)... -- Today, the first day of American Heart Month, the ... first of its kind workplace health solution that leverages ... first application of Watson to ... Welltok will create a new offering that combines AHA,s ... on Welltok,s health optimization platform. The effort is intended ...
Breaking Biology News(10 mins):
(Date:2/4/2016)... -- - New FDA action date of July ... date of July 22, 2016   --> ... 2016   - Lifitegrast has the potential ... the treatment of signs and symptoms of dry eye disease in ... be the only product approved in the U.S. in the past decade indicated for the ...
(Date:2/4/2016)... ... February 04, 2016 , ... ... and triple quad LC-MS, host live demos and poster sessions, and present on ... exhibition. The conference takes place March 6 to 10 at the Georgia World ...
(Date:2/4/2016)... 2016 Beike Biotechnology, the Shenzhen ... a ceremony in late 2015 to mark their successful ... 2016. --> --> ... Personalized Cell Therapy" was hosted by the Shenzhen Cell ... subsidiaries of Beike Biotechnology Co., Ltd. ...
(Date:2/4/2016)... MENLO PARK, Calif. , Feb. 4, 2016 ... the "Company"), a biopharmaceutical company focused on the development and ... present at the 18 th Annual BIO CEO ... 10:00 a.m. EST in New York, NY ... CEO, will provide an update on the ongoing clinical trial ...
Breaking Biology Technology: