Wednesday, 27 April 2011

Infectious Aromas

            If you learned anything from grade eight health class it should have been sweat stinks. Well, not the sweat really, but the bacteria that thrive on it. The truth is, all bacteria stink, or at least smell. The same way you and I produce odourous byproducts now and then, bacteria too take in food and expel smelly waste.

            Similar to you and your college roommates, not all bacteria smell the same. In fact, each species and strain has a signature bouquet. This is because of differences in the nutrients each bacteria takes up, and the subtle differences in how they each process that food.

            In the lab we sometimes use to our advantage the fact that some bacterial cultures smell like smelly feet, while others are more reminiscent of sun-bathed pumpkins. Just by smelling a culture flask or plate, I can tell whether my experiment is pristine or compromised by contamination. Although this helps tell me if I’ve wasted another week of my life, a group led by Ken Suslick of the University of Illinois is using the same principles to develop potentially lifesaving technology.

            In his research, Dr. Suslick has developed arrays of chemically-sensitive dyes to detect low levels of air-born chemicals. These dyes react with a range of compounds and change colour based on a variety of chemical characteristics. So where one chemical might cause a reaction that makes a dye turn blue, a different chemical might cause the same dye to turn pink. Dr. Suslick’s group has developed a printed grid of different dyes that react differently to each chemical. When exposed to a specific chemical, the grid becomes a colourful fingerprint of its reactivities.

            So how does this technology help in a medical setting? Like we established before, each bacteria has a different scent, and these scents are made up of chemical compounds. This means that each bacteria has a different coloured scent fingerprint detected by the dye matrix. By exposing the grid to a sample of the bacteria this test can be used to identify infectious organisms in a matter of hours, a process that could take days by traditional techniques. In fact, the accuracy of this method is so high that it can even be used to tell antibiotic resistant strains and garden-variety strains apart.

            Time matters when an unknown bacteria has set up shop in your body. This technology provides a colourful solution for a quick diagnosis.

Learn more in the the original research paper

Wednesday, 20 April 2011

Fixing the Nicks (and loops, and breaks...)

Our DNA is what defines us: as a species and as individuals. Maintaining DNA is something your body absolutely needs to do as a first step to keeping everything else in line. As many of us are aware, damaged DNA can lead to myriad health problems including all kinds of cancer. The structure and the sequence of DNA is also the life-code we pass on to our children. You can't give away holey hand-me-down genes.

            Unfortunately, our DNA is not kept under lock and key in a secure velvet box (as you might predict for so precious a molecule), but is accessed and processed constantly. This means a lot of wear and tear needing to be repaired. To manage the damage, your cells have enzymes for DNA repair. These proteins recognize damaged DNA and surgically remove specific corrupted segments to make way for replacement parts.

These enzymes (5’ structure-specific nucleases) belong to one family with a single structure, but somehow each recognizes a different type of DNA damage. Picture the DNA as a thick rope made by twisting two ropes together and then damaged by slicing or weakening one strand, cutting both together, cutting out a portion of one, or looping in an extra segment in one strand. Until now, no one knew how all of these forms could be recognized by a single basic enzyme structure with each individual enzyme only working on one type of damage.

This week in the journal Cell, a group of researches lead by Dr. Lorena Beese published results that explain the Swiss Army knife-like ability of this family of enzymes. They explain that the structure of the enzyme binds to a very sharp bend in the DNA that can only occur when it is damaged (picture the thick rope being harder to bend than its corrupted counterpart). Inside the active site of the enzyme, the two strands fray apart, making all the types of damage look very similar.

This explains why all these flavours of DNA damage are processed by the same type of enzyme, but how are the individual proteins able to distinguish between them? The same research group found that it is most likely lock and key-like recognition sites on the outside of the protein that are able (or unable) to bind the extra loops and strands that make the different damaged DNA structures unique. In this way, relatively minor alterations to the enzymes’ overall structure make them specific, allowing evolution to recycle the same tool for multiple purposes.

Nature hates to reinvent the wheel. Elegant evolutionary problem solving like this is what allows evolution to move forward while conserving energy. And let me tell you, our cells are hungry for energy, mmmmm...