Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


New, automated tool successfully classifies and relates proteins in unprecedented way


Carnegie Mellon University research enables location proteomics

For the first time, researchers have automatically grouped fluorescently tagged proteins from high-resolution images of cells. This technical feat opens a new way to identify disease proteins and drug targets by helping to show which proteins cluster together inside a cell.

The approach, developed by Carnegie Mellon University, outperforms existing visual methods to localize proteins inside cells, says Professor Robert F. Murphy, whose report, "Data Mining in Genomics and Proteomics," appears in an upcoming special issue of the Journal of Biomedicine and Biotechnology. "Our approach really enables the new field of location proteomics, which describes and relates the location of proteins within cells," said Murphy, a professor of biological sciences, machine learning, and biomedical engineering. "This work should provide a more thorough understanding of cellular processes that underlie disease."

Using this approach to spot a protein cluster could help scientists identify a common protein structure that enables those proteins to gather in one part of the cell, according to Murphy. Getting this information is critical to foil a disease like cancer, where you might want to identify and disable part of a tumor cell’s machinery needed to process proteins for cancer growth. "Our tool represents a step forward because it is based on standardized features and not on features chosen by the human eye, which is unreliable. By automating the clustering of proteins inside cell images, we also can study thousands of images fast, objectively and without error," Murphy said.

Murphy’s tool has two key components. One is a set of subcellular location features (SLFs) that describe a protein’s location in a cell image. SLFs measure both simple and complex aspects of proteins, such as shape, texture, edge qualities and contrast against background features. Like fingerprints, a protein’s SLFs act as a unique set of identifiers. Using a set of established SLFs, Murphy then developed a computational strategy for automatically clustering, or grouping, proteins based on SLF similarities and differences. For his study, Murphy used images of randomly chosen, fluorescently labeled proteins. These proteins were produced inside living cells using a technology called CD tagging, which was developed by Jonathan Jarvik and Peter Berget, both associate professors of biological sciences at Carnegie Mellon. The computational analyses were carried out together with Xiang Chen, a graduate student in the Merck Computational Biology and Chemistry program.

Chen and Murphy found that the new tool outperformed existing methods of identifying overlapping proteins within cells, such as simple visual categorization of their locations. "Our tool outperformed clustering based on the terms developed by the Gene Ontology Consortium, the best previous way of describing protein location. We found that the Gene Ontology terms were too limited to describe the many complex location patterns we found. Of course, the other drawback of term-based approaches is that they have to be assigned manually by database curators, and this is often not consistent between different curators," said Murphy.

Murphy and his colleagues are currently amassing more protein image data using CD Tagging so that they can refine their approach further. They are also working on ways to "train" a general system that will work for different cell types.

Lauren Ward | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht Biologists unravel another mystery of what makes DNA go 'loopy'
16.03.2018 | Emory Health Sciences

nachricht Scientists map the portal to the cell's nucleus
16.03.2018 | Rockefeller University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Locomotion control with photopigments

Researchers from Göttingen University discover additional function of opsins

Animal photoreceptors capture light with photopigments. Researchers from the University of Göttingen have now discovered that these photopigments fulfill an...

Im Focus: Surveying the Arctic: Tracking down carbon particles

Researchers embark on aerial campaign over Northeast Greenland

On 15 March, the AWI research aeroplane Polar 5 will depart for Greenland. Concentrating on the furthest northeast region of the island, an international team...

Im Focus: Unique Insights into the Antarctic Ice Shelf System

Data collected on ocean-ice interactions in the little-researched regions of the far south

The world’s second-largest ice shelf was the destination for a Polarstern expedition that ended in Punta Arenas, Chile on 14th March 2018. Oceanographers from...

Im Focus: ILA 2018: Laser alternative to hexavalent chromium coating

At the 2018 ILA Berlin Air Show from April 25–29, the Fraunhofer Institute for Laser Technology ILT is showcasing extreme high-speed Laser Material Deposition (EHLA): A video documents how for metal components that are highly loaded, EHLA has already proved itself as an alternative to hard chrome plating, which is now allowed only under special conditions.

When the EU restricted the use of hexavalent chromium compounds to special applications requiring authorization, the move prompted a rethink in the surface...

Im Focus: Radar for navigation support from autonomous flying drones

At the ILA Berlin, hall 4, booth 202, Fraunhofer FHR will present two radar sensors for navigation support of drones. The sensors are valuable components in the implementation of autonomous flying drones: they function as obstacle detectors to prevent collisions. Radar sensors also operate reliably in restricted visibility, e.g. in foggy or dusty conditions. Due to their ability to measure distances with high precision, the radar sensors can also be used as altimeters when other sources of information such as barometers or GPS are not available or cannot operate optimally.

Drones play an increasingly important role in the area of logistics and services. Well-known logistic companies place great hope in these compact, aerial...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

International Tinnitus Conference of the Tinnitus Research Initiative in Regensburg

13.03.2018 | Event News

International Virtual Reality Conference “IEEE VR 2018” comes to Reutlingen, Germany

08.03.2018 | Event News

Latest News

Wandering greenhouse gas

16.03.2018 | Earth Sciences

'Frequency combs' ID chemicals within the mid-infrared spectral region

16.03.2018 | Physics and Astronomy

Biologists unravel another mystery of what makes DNA go 'loopy'

16.03.2018 | Life Sciences

Science & Research
Overview of more VideoLinks >>>