High-throughput experimental methods are widely used today to identify genes and proteins involved in a particular process, but not all molecules in a pathway can be identified in this manner. To fill the gaps, a new computer program called ResponseNet follows the path of least resistance—like water flowing from sources to sinks in a terrain—to find the most efficient path through the maze of interacting molecules in a cell (the “interactome). The work was published in the March 2009 issue of Nature Genetics.

Despite their identical genomes, cells in the body develop distinct personalities—become neurons or liver cells, for instance—due to differences in gene expression. The mechanism that regulates this process has remained obscure, but a new study explains it using a simple thermodynamic model.

Patients with schizophrenia and other psychotic disorders are known to have adverse brain changes, such as reduced volume—but it’s unclear what comes first, the disease or the abnormality. Now, for the first time, researchers have shown that the brain is actually shrinking as psychosis unfolds. The results appear in the January 10 issue of Schizophrenia Research.

New computational model simulates how particles in the air get deposited in the lungs during breathing
Depending on their nature, microscopic particles suspended in air—called aerosols—can cause or treat disease when inhaled. A key factor in both cases is how the particles accumulate throughout the respiratory system. A new study uses fluid dynamics and an anatomically accurate human airway model to simulate this process, potentially paving the way for improved disease understanding and patient-specific drug delivery.

Researchers developing a new vaccine currently have no direct way of predicting its efficacy short of exposing patients to the disease. A new study that combines gene expression data with advanced computational analysis provides the first evidence that the vaccine-induced immune response can be predicted.

For patients suffering from nerve damage, neural regeneration is a faint hope. It rarely happens naturally, and attempts to coax new growth often fail. Researchers are trying to develop scaffolds to guide regenerating neurons in the body. But the best way to guide neural growth on these substrates remains unknown. So in vitro studies of neuronal behavior on these templates are a key first step. But such studies largely rely on trial and error rather than engineering principles.

The phi29 bacteriophage is an efficient infection machine—it fires its genome into a host bacterium, hijacks the host’s cellular equipment, and assembles an army of new viruses for its next mission. For the first time, scientists have produced sub-nanometer resolution pictures of the virus, revealing some striking new details—including an unexpectedly tight twist of DNA suggestive of how the virus springs into action. The results appear in the June issue of Structure.

In biology, many exciting events happen on the millisecond timescale—proteins fold, channels open and close, and enzymes act on their substrates. Atomic-level simulations of this duration are beyond the reach of current technology, but a new specialized computer called Anton—described in the July 2008 issue of Communications of the ACM—may change all this. Slated to be operational by the end of the year, the machine is projected to speed up molecular dynamics simulations 100-fold.

When we see dark clouds, we might grab an umbrella before heading outside.  We’ve long believed that showing such foresight requires a brain and complex information-processing capability. It turns out, though, that even microbes, which do not have brains or a nervous system, can learn to use cues from their surroundings to anticipate future events, according to a new research study based on both experimental and computational techniques.