Algorithm Offers Ability to Influence Systems Such as Living Cells

Featured In: Academia News

Thursday, May 12, 2024

Get daily Bioscience Technology industry top stories and headlines - Sign up now!

newsvine diigo google
slashdot
Share
Loading...

At first glance, a diagram of the complex network of genes that regulate cellular metabolism might seem hopelessly complex, and efforts to control such a system futile. However, an MIT researcher has come up with a new computational model that can analyze any type of complex network — biological, social or electronic — and reveal the critical points that can be used to control the entire system. Potential applications of this work, which appears as the cover story in the May 12 issue of Nature, include reprogramming adult cells and identifying new drug targets, says study author Jean-Jacques Slotine, an MIT professor of mechanical engineering and brain and cognitive sciences.

MIT and Northeastern University researchers devised a computer algorithm that can generate a controllability structure for any complex network. The red points are 'driver nodes,' which can control the rest of the nodes (green). (Source: Mauro Martino)

Slotine and his co-authors applied their model to dozens of real-life networks, including cell-phone networks, social networks, the networks that control gene expression in cells and the neuronal network of the C. elegans worm. For each, they calculated the percentage of points that need to be controlled in order to gain control of the entire system.

For sparse networks such as gene regulatory networks, they found the number is high, around 80 percent. For dense networks — such as neuronal networks — it’s more like 10 percent.

The paper, a collaboration with Albert-Laszlo Barabasi and Yang-Yu Liu of Northeastern University, builds on more than half a century of research in the field of control theory.

Control theory — the study of how to govern the behavior of dynamic systems — has guided the development of airplanes, robots, cars and electronics. The principles of control theory allow engineers to design feedback loops that monitor input and output of a system and adjust accordingly. One example is the cruise control system in a car.

However, while commonly used in engineering, control theory has been applied only intermittently to complex, self-assembling networks such as living cells or the Internet, Slotine says. Control research on large networks has been concerned mostly with questions of synchronization, he says.

In the past 10 years, researchers have learned a great deal about the organization of such networks, in particular their topology — the patterns of connections between different points, or nodes, in the network. Slotine and his colleagues applied traditional control theory to these recent advances, devising a new model for controlling complex, self-assembling networks.

“The area of control of networks is a very important one, and although much work has been done in this area, there are a number of open problems of outstanding practical significance,” says Adilson Motter, associate professor of physics at Northwestern University. The biggest contribution of the paper by Slotine and his colleagues is to identify the type of nodes that need to be targeted in order to control complex networks, says Motter, who was not involved with this research.

The researchers started by devising a new computer algorithm to determine how many nodes in a particular network need to be controlled in order to gain control of the entire network. (examples of nodes include members of a social network, or single neurons in the brain).

“The obvious answer is to put input to all of the nodes of the network, and you can, but that’s a silly answer,” Slotine says. “The question is how to find a much smaller set of nodes that allows you to do that.”

There are other algorithms that can answer this question, but most of them take far too long — years, even. The new algorithm quickly tells you both how many points need to be controlled, and where those points — known as “driver nodes” — are located.

Next, the researchers figured out what determines the number of driver nodes, which is unique to each network. They found that the number depends on a property called “degree distribution,” which describes the number of connections per node.

A higher average degree (meaning the points are densely connected) means fewer nodes are needed to control the entire network. Sparse networks, which have fewer connections, are more difficult to control, as are networks where the node degrees are highly variable.

In future work, Slotine and his collaborators plan to delve further into biological networks, such as those governing metabolism. Figuring out how bacterial metabolic networks are controlled could help biologists identify new targets for antibiotics by determining which points in the network are the most vulnerable.

Source: Massachusetts Institute of Technology

Join the Discussion
Rate Article: Average 0 out of 5
register or log in to comment on this article!

0 Comments

Add Comment

Text Only 2000 character limit

Page 1 of 1

Research Exchange

Bringing the Cell Image into Focus

Nov 2 2010

Improvements in transmission electron microscope (TEM) technology increase the power of this imaging tool for the study of cell biology.

Finding a Cure for Spinal Cord Injury with On-Demand LIMS

Oct 25 2010

The Miami Project to Cure Paralysis finds an on-demand laboratory information management system (LIMS) helps to accelerate discovery in its HCS projects.

Saving Cells: Image Processing for Improved Viability, Part II: Iterative Deconvolution

Oct 25 2010

3D light microscopy and deconvolution provide a means to investigate 3D structure, providing near-confocal quality images without the temporal requirements or potentially damaging phototoxicity associated with other 3D imaging technologies. This article is Part II in a series regarding viability, resolution improvement, and measurement in fluorescence imaging. Part I focused on spectral unmixing.

Saving Cells: Image Processing for Improved Viability

Sep 22 2010

This article is Part I of a two-part series regarding viability, resolution improvement, and measurement in fluorescence imaging. Part II will focus on deconvolution.

Evaluation of a New Nano-Type UV-Vis Spectrophotometer

Mar 3

Analysis of one- to four-microliter size samples for nucleic acids has become routine in many life science laboratories. However, until now, available instruments require considerable manipulation of the instrument and sample; some require manually recording the data. The user must typically lower and raise the arm manually, then wipe the sample manually from the target after each analysis. And fiberoptics used in some of these instruments are subject to deterioration.

Production of Recombinant Proteins and Monoclonal Antibodies in Hollow Fiber Bioreactors

Jan 25

While well-understood, robust and convenient, classical batch-style 2-D culture on non-porous supports or 3-D suspension culture in other devices are really not very biologically relevant models. Cell culture conditions can affect the quality of the antibody or protein produced.

Selecting Robots for Use in Drug Discovery and Testing

Dec 6 2010

Drug discovery and testing, with their need for speed, repeatability and verification, are ideally suited to benefit from robot automation. It is therefore not surprising that robots have been at the forefront of automation developments in both these areas.

HP Scalable Network Storage Systems for Life Sciences

Sep 13 2010

Life sciences research today is advancing exponentially, each step bringing us closer to the realization of truly personalized medicine–preventive care and treatments designed specifically for each individual. In the near future, PCPGM healthcare researchers expect to be able to use predictive genetic testing to create custom treatment plans for individuals and deliver dramatic improvements over today’s one-size-fits-all approach. But research capabilities are only part of the equation; current storage and operating capacities must also evolve to accommodate ever-expanding amounts of data before the goal of personalized medicine can be realized.

Using the Tecan Genesis Workstation to Automate a Cytometric Bead Array (CBA) Immunoassay

Mar 11 2010

The poster describe the process involved in automating a Cytometric Bead Array (CBA) immunoassay developed to measure relative concentrations of serum antibodies against Tetanus (TT), Sperm Whale Myoglobin (SWM) and Keyhole Limpet Hemocyanin (KLH) in KLH-immunized volunteers.

Ensuring Quality in Assays Performed with Automated Liquid Handlers

Feb 2 2010

The focus of this presentation is to highlight the need of ensuring quality in important assays performed with automated liquid handlers. Nearly all assays performed within a laboratory are volume-dependent. In turn, all concentrations of biological and chemical components in these assays, as well as the associated dilution protocols, are volume-dependent. Because analyte concentration is volume-dependent, an assay’s results might be falsely interpreted if liquid handler variability and inaccuracies are unknown or if the system(s) go unchecked for a long period.

Inkjet System for Protein Crystallography

Feb 1 2010

X-ray crystallography is used routinely by scientists to obtain the three dimensional structure of a biological molecule of interest.Such information can be used to determine how a pharmaceutical interacts with a protein target and what changes might improve functionality. However, the crystallization of macromolecules still remains a serious hindrance in structural determination despite impressive advances in screening methods and technologies.

Attention Deficit & Hyperactivity in a Drosophila Memory Mutant

Attention Deficit & Hyperactivity in a Drosophila Memory Mutant

Nov 9 2009

Action selection is modulated by external stimuli either directly or via memory retrieval. In a constantly changing environment, animals have evolved attention-like processes to effectively filter the incoming sensory stream. These attention-like processes, in turn, are modulated by memory. The neurobiological nature of how attention, action selection and memory are inter-connected is unknown. We describe here new phenotypes of the memory mutant radish in the fruit fly Drosophila.

Bone metabolic activity in hyperostosis cranialis interna measured with 18F-fluoride PET

3 hours ago

PURPOSE: (18)F-Fluoride PET/CT is a relatively undervalued diagnostic test to measure bone metabolism in bone diseases. Hyperostosis cranialis interna (HCI) is a (hereditary) bone disease characterised by endosteal hyperostosis and osteosclerosis of the skull...

Analyses of phenotypic and functional characteristics of CX3CR1-expressing natural killer cells

11 hours ago

Summary We previously demonstrated a correlation between the frequency of CX3CR1-expressing human natural killer (NK) cells and disease activity in multiple sclerosis and showed that CX3CR1(high) NK cells were more cytotoxic than their CX3CR1(neg/low)...

Identification and characterization of a bioactive lantibiotic produced by Staphylococcus warneri (82)

12 hours ago

Bacillus thuringiensis is widely used as agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 has high toxin to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of...

Identification and characterization of a bioactive lantibiotic produced by Staphylococcus warneri (81)

13 hours ago

Bacillus thuringiensis is widely used as agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 has high toxin to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of...

Prokariotic Cell Collection in Denmark

Nov 6 2009

I would like to know about a prokariotic cell collection in Denmark. Is there a cell bank in this country? I need a Lactobacillus strain for a fermentation assay and this information about the bank is very helpful for me.

Request for Entries

Oct 16 2009

Ask the Experts is your chance to get the answers to questions on applications, materials, methods, processes, and technologies. Email you question to bst_web@advantagemedia.com, and the editors of Bioscience Technology will find an appropriate expert to answer it. Watch this space in the future to see the questions your colleagues are posting.

STAY INFORMED: SUBSCRIBE TO

Magazine and E-mail Newsletters

Loading...
E-mail:   

MULTIMEDIA

Video:

Viewing SureFocus Slides

Jun 11 2010

A demonstration of SureFocus Microscope Slides in the review of AFB Smears. SureFocus Slides are a patent-pending breakthrough in tuberculosis detection, as their fluorescent staining circle remains visible during review, Fluorescence Microscopy.

Podcasts:

Allen Institute for Brain Research

Allen Institute for Brain Research

Oct 14 2009

Discussed in this interview are both the mouse brain project and the human cortex project with an emphasis on the importance of these projects to neuroscience research.

Top Stories and Headlines
EVERYDAY!

FREE Email Newsletter

Information: