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:12/2/2016)... , December 1, 2016 ... (Fingerprint, Voice), Future Technology (Iris Recognition System), Vehicle ... - Global Forecast to 2021", published by MarketsandMarkets, ... Million in 2016, and is projected to grow ... CAGR of 14.06%.      (Logo: http://photos.prnewswire.com/prnh/20160303/792302) ...
(Date:11/30/2016)... 30, 2016 Not many of us realize that we spend ? of ... we need to do it well. Inadequate sleep levels have been found to lead ... diabetes, and even cancer. Maybe now is the best time to rethink ... them to manage their sleep quality? Continue Reading ... ...
(Date:11/29/2016)... BioDirection, a privately held medical device company developing novel ... concussion and other traumatic brain injury (TBI), announced today ... the U.S. Food and Drug Administration (FDA) to review ... meeting company representatives reviewed plans for clinical development of ... a planned pilot trial. "We are ...
Breaking Biology News(10 mins):
(Date:12/8/2016)... -- The Board of Directors of the Pittsburgh Life ... only pure life sciences investment firm, today announced ... plan developed by the Nominating and Governance Committee over ... F. Jordan is selected to serve as President ... , who is elected to the position of Executive ...
(Date:12/8/2016)... 2016  OncoSec Medical Incorporated ("OncoSec") (NASDAQ: ... cancer immunotherapies, today announced financial results for the ... are delivering on our commitment to address an ... We are pleased with the early clinical response ... we are focused on advancing our lead program ...
(Date:12/8/2016)...  Biotheranostics today announced that new data will ... Cancer Index (BCI) in identifying which patients with ... for disease recurrence and might benefit from extended ... advancing the understanding of the value of BCI ... inform decisions related to patient treatment. These data ...
(Date:12/8/2016)... Washington, USA, and CARDIFF, UK (PRWEB) , ... ... ... circuits with very high precision light to control cells — optogenetics — is ... In the current state of the art, spatially patterned light projected via free-space ...
Breaking Biology Technology: