Pathway

Pathway

At her desk at the aircraft manufacturer, the aeronautical engineer launches her computational fluid dynamics (CFD) analysis software. She’s putting the wing design she’s come up with to the test. After a few moments adjusting the program’s controls, she runs the simulation to calculate lift, drag and other parameters. Then she runs an animation that portrays in detail how air will flow over the wing.

To predict airflow, CFD software applies the mathematics of fluid dynamics, which calculates the path of individual molecules of air flowing over the wing. Then it aggregates these pathways, which are also called path lines, to predict the overall behavior of the fluid. This can help them design an airfoil, optimize a racecar design, tweak the shape of a wind-turbine blade for maximum efficiency, or perfect the shape of a turbine blade for a hydroelectric dam.

For some biomedical engineers, a pathway means the same thing. At Purdue University, for example, biomedical engineer Craig Goergen’s team analyzes fluid flow in the body to help determine how mechanical forces influence cardiovascular disease. The researchers are using CFD analysis to predict how blood will flow down two branching blood vessels. The program takes as input the geometry of the blood vessels, physical properties of the incoming blood, and resistance of the blood vessels downstream. It then calculates the blood’s velocity and pathways, which reveal pressure and shear stress on the blood vessel wall. These parameters in turn help predict how much a brain aneurysm will grow and when it could rupture.

For many physicians and biologists, pathways mean something quite different. The human genome includes about 25,000 genes, and inside our cells, those genes collectively produce 20,000 proteins. Genes are activated to produce their corresponding protein only in certain tissues and at certain times, enabling a liver cell to function very differently, for example, than a brain cell.

Proteins produced help carry out the vast majority of biological processes in the human body, including digestion, metabolism, respiration, and growth, and they do not work alone. Instead, proteins work by interacting with other proteins, with other types of cellular macromolecules, such as DNA, RNA or lipids, or with metabolites and other soluble molecules inside and outside the cell. These interactions occur in a particular sequence, and they produce a specific product or lead to a specific change in the cell. This sequence of interactions is a biological pathway.

Several types of biological pathways exist. Metabolic pathways refer to a series of enzyme-catalyzed chemical reactions in the cell. Metabolic pathways break down macronutrients in food such as carbohydrates, protein, and fats—into smaller molecules that cells can use as nutrients. Inside cells and tissues, they take nutrients and build up whatever proteins, carbohydrates, lipids, DNA and RNA the cell needs. Other metabolic pathways remove waste, supply energy to power the cell’s activities, or maintain cells and tissues in a healthy steady state that biologists call homeostasis.

In a genetic pathway, a group of genes works collectively to carry out a particular cellular function. For example, one gene may produce a regulatory protein that turns other genes on or off, while other genes produce enzymes or structural proteins. In a signal transduction pathway, a circulating molecule such as a hormone binds to a receptor, which sits either on the cell surface or inside the cell. This signals the cell to initiate biochemical changes. In this way, signals from outside a cell are relayed to the cell’s interior, and turn a biological process on or off, often by dialing the activity of a particular set of genes up or down.