Predicting the effects of changes on living systems

November 30, 2012 by Simon Mercer
Predicting the effects of changes on living systems

Can scientists predict what happens when they introduce a change into a living system—for example, if they change the structure of a gene or administer a drug? Just as changing one letter can completely change the meaning of a word, the change of a single letter of the genetic code (referred to as a single nucleotide polymorphism, or SNP) can subtly affect the meaning of a gene's instructions or alter them completely, making the effect of any change extremely hard to predict. Such changes are thought to be responsible for much of the variation between members of a single species—for example, in susceptibility to different diseases. The ability to successfully predict the effect of such changes would accelerate drug discovery and provide a deeper understanding of the processes of life.

In collaboration with Jasmin Fisher at Microsoft Research Cambridge, professor Yanay Ofran and his colleagues at Bar Ilan University have embarked on a program of scientific research that aims to resolve some of the questions underlying this overall goal, and some of their early results have now been published.

One of the researchers' first tasks was to determine whether it is possible to predict how a complex network of will change when a SNP (pronounced "snip") alters the function of one of the network's components. In an August 2012 paper entitled, "Static Network Structure Can Be Used to Model the Phenotypic Effects of Perturbations in " (available at Bioinformatics with paid subscription), the authors describe their success in analyzing static models of and correctly predicting the response to changes more than 80 percent of the time. This enables the functions of the network to be deduced, the foundation for building a more expressive .

Building static networks is a challenge in itself; before beginning this work, the researchers needed to understand which genes are active in a particular cell and what they do. In their latest publication entitled, "Assessing the Relationship between Conservation of Function and Conservation of Sequence Using Photosynthetic Proteins" (available at Bioinformatics with paid subscription), the Ofran lab has shown that, while sets of related genes with similar structure diverge in function more quickly than previously thought, selected smaller pieces of each gene may still be useful in predicting function.

There are many unresolved challenges along the way to the eventual goal of predicting the effect of a SNP—understanding which genes are switched on in which cells and how drugs interact with proteins are just two active areas of investigation—but once the goal is reached, an understanding of the functions of all genes and how changes affect biological systems could lead to the development of computational models to predict and cure many diseases.

Explore further: Mammalian cells with single chromosome set created

Related Stories

Mammalian cells with single chromosome set created

September 7, 2011

Researchers have created mammalian cells containing a single set of chromosomes for the first time in research funded by the Wellcome Trust and EMBO. The technique should allow scientists to better establish the relationships ...

As the worm turns, its secrets are revealed

April 28, 2011

An international team of scientists, led by researchers at the University of California, San Diego School of Medicine, have developed a new method for discerning the functions of previously uncharacterized genes and placing ...

Understanding why some people have propensity to disease

May 14, 2012

Aside from identical twins, no two individuals are completely identical genetically. Most differences between individuals are due to single nucleotide changes or polymorphisms (SNPs) – DNA sequence variations – ...

Road mapping could be key to curing TB

February 5, 2010

The complex chain of metabolic events in bacteria that lead to fatal diseases such as tuberculosis (TB) may be better understood using mathematical models, according to an article published in the February issue of Microbiology ...

Recommended for you

Microsoft aims at Apple with high-end PCs, 3D software

October 26, 2016

Microsoft launched a new consumer offensive Wednesday, unveiling a high-end computer that challenges the Apple iMac along with an updated Windows operating system that showcases three-dimensional content and "mixed reality."

Making it easier to collaborate on code

October 26, 2016

Git is an open-source system with a polarizing reputation among programmers. It's a powerful tool to help developers track changes to code, but many view it as prohibitively difficult to use.

Dutch unveil giant vacuum to clean outside air

October 25, 2016

Dutch inventors Tuesday unveiled what they called the world's first giant outside air vacuum cleaner—a large purifying system intended to filter out toxic tiny particles from the atmosphere surrounding the machine.

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

1 / 5 (1) Dec 01, 2012
"Can scientists predict what happens when they introduce a change into a living system—for example, if they change the structure of a gene or administer a drug?"

LOL... perhaps someone should have asked this before our food became 50%, 80%, 90% genetically modified. Oops. bon appetit. but that would have hurt profits so... shut up, eat your poison corn, and die quietly.

write this down and put it in a time capsule for a duration of your choosing, and see if doesn't come true: organ transplant lines for kidneys and livers are going to be growing exponentially. dwindling organ supply (from healthy humans) will fall further and further behind increasing organ demand (from people whose physiology is failing due to GMO's (or whatever reason makes you feel better))

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.