Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Computational Tool Offers New Insight Into Key Biological Processes

06.03.2014

Researchers from North Carolina State University have developed a computational tool designed to guide future research on biochemical pathways by identifying which components in a biological system are related to specific biochemical processes, including those processes responsible for gene expression, cell signaling, stress response, and metabolism.

“Our goal was to identify modules, or functional units, which are critical to the performance of the biochemical pathways that govern a host of biological processes,” says Dr. Cranos Williams, an assistant professor of electrical and computer engineering at NC State and senior author of a paper describing the work.

“For example, a car has lots of modules – the parts that make it go, the parts that make it stop, the parts that let you steer, etc. If you understand those modules, you understand how the car works. But if you just have a list of parts, that’s not very helpful.

“And what we have right now for many biochemical pathways is essentially just a list of parts – metabolites, biochemical reactions and enzymes that facilitate those reactions – and, in some cases, how those parts change over time. What we need is a clear understanding of which parts work together. That’s where our new algorithm comes in.”

The researchers developed an algorithm that allows them to identify which parts – the metabolites, reactions and enzymes – are related to each other and can be grouped into functional modules. The algorithm also identifies whether an individual component plays a role in multiple modules. For example, an enzyme may play a primary role in critical stress response pathways and a secondary role in processes associated with programmed cell maintenance or death.

The algorithm also characterizes how the relationships between different modules and individual components may change over time and under different internal and external conditions.

The input for the algorithm comes from using well-established dynamic models to observe changes in concentrations of metabolites, reactions and enzymes under various conditions. The algorithm then processes that data to establish primary and secondary relationships between all of the constituent parts.

“When modifying biological processes, there are thousands of possible combinations of metabolites, reactions and enzymes for any given biochemical pathway,” Williams says. “Our work should help life scientists narrow down the list of key players in order to target their research efforts on functional groups that are most likely to improve our ability to understand and control important biological processes. This has applications in everything from biomedical research to agriculture to biofuels.”

The paper, “Hierarchical Modularization Of Biochemical Pathways Using Fuzzy-C Means Clustering,” is forthcoming from IEEE Transactions on Cybernetics. Lead author of the paper is Dr. Maria de Luis Balaguer, a former Ph.D. student at NC State.

-shipman-

Note to Editors: The study abstract follows.

“Hierarchical Modularization Of Biochemical Pathways Using Fuzzy-C Means Clustering”

Authors: Maria A. de Luis Balaguer and Cranos M. Williams, North Carolina State University

Published: forthcoming, IEEE Transactions on Cybernetics

DOI: 10.1109/TCYB.2013.2286679

Abstract: Biological systems that are representative of regulatory, metabolic, or signaling pathways can be highly complex. Mathematical models that describe such systems inherit this complexity. As a result, these models can often fail to provide a path toward the intuitive comprehension of these systems. More coarse information that allows a perceptive insight of the system is sometimes needed in combination with the model to understand control hierarchies or lower level functional relationships. In this paper, we present a method to identify relationships between components of dynamic models of biochemical pathways that reside in different functional groups. We find primary relationships and secondary relationships. The secondary relationships reveal connections that are present in the system, which current techniques that only identify primary relationships are unable to show. We also identify how relationships between components dynamically change over time. This results in a method that provides the hierarchy of the relationships among components, which can help us to understand the low level functional structure of the system and to elucidate potential hierarchical control. As a proof of concept, we apply the algorithm to the epidermal growth factor signal transduction pathway, and to the C3 photosynthesis pathway. We identify primary relationships among components that are in agreement with previous computational decomposition studies, and identify secondary relationships that uncover connections among components that current computational approaches were unable to reveal.

Matt Shipman | EurekAlert!

More articles from Life Sciences:

nachricht Ambush in a petri dish
24.11.2017 | Friedrich-Schiller-Universität Jena

nachricht Meadows beat out shrubs when it comes to storing carbon
23.11.2017 | Norwegian University of Science and Technology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: New proton record: Researchers measure magnetic moment with greatest possible precision

High-precision measurement of the g-factor eleven times more precise than before / Results indicate a strong similarity between protons and antiprotons

The magnetic moment of an individual proton is inconceivably small, but can still be quantified. The basis for undertaking this measurement was laid over ten...

Im Focus: Frictional Heat Powers Hydrothermal Activity on Enceladus

Computer simulation shows how the icy moon heats water in a porous rock core

Heat from the friction of rocks caused by tidal forces could be the “engine” for the hydrothermal activity on Saturn's moon Enceladus. This presupposes that...

Im Focus: Nanoparticles help with malaria diagnosis – new rapid test in development

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

IceCube experiment finds Earth can block high-energy particles from nuclear reactions

24.11.2017 | Physics and Astronomy

A 'half-hearted' solution to one-sided heart failure

24.11.2017 | Health and Medicine

Heidelberg Researchers Study Unique Underwater Stalactites

24.11.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>