ODELAY! (One-Cell Doubling Evaluation of Living Arrays of Yeast)
Oct. 1, 2018 – It has never been easier to keep track of your health and wellness. Want to lose a little weight? Your cell phone will count the number of steps you take per day to help motivate you to stay active. Or you can use a “smart” watch or some other device; there are digital scales to help track your progress and measure the quality of air in your home. Want to count the number of calories you consume in a day? There's an app for that, and it can tell you how many calories were in that doughnut you just ate... and how many more steps you will need to take to avoid an unpleasant update on that weigh scale. Technology is so pervasive that it can be easy to take it for granted.
Measuring ‘things’ is a large part of being a scientist. That is why science and technology often go hand in hand. To make sure we are getting accurate, robust and precise measurements we want the latest technology that will help achieve that goal. What we measure is just as important as how we measure. For example, the standard method for measuring cell fitness has been to measure growth rates, or how fast cells divide. In organisms like the bacteria found in your mouth and gut, or – a personal favorite – brewer’s yeast, the ability to grow and divide is fast. Like on the order of 20 to 90 minutes. When placed into a liquid broth with lots of nutrients, these organisms multiply until the broth is milky with their progeny. A simple test measures the amount of light that transmits through the cloudy mixture to inform on how many cells are present. The more cells there are, the milkier the broth, and the greater the absorbance of light by the liquid. When tracked over time, the absorbance values can be plotted, and a growth rate determined.
In the Aitchison Lab, we can change what nutrients are available and measure the effect of these changes on growth. Or, we can make genetic alterations, and look at how those mutations alter growth. Of critical importance to human health, growth assays assist us in the development of new drugs. And of increasing relevance, growth assays can measure and detect antibiotic resistance.
While the technology to alter an organism’s genome is undergoing a revolution, the way that we measure cell growth hasn’t really changed in the past 80 years. Think about that, the methods for measuring growth are almost as old as the discovery of the first antibiotic drug, penicillin. In part, that is because the method is accurate, robust and precise at an affordable price... all good things for a scientist.
Yet the problem with these assays is that they look at the population and give you a single number. The resolution of these assays is too coarse-grained. So, if there is diversity in the population you won’t see it. The other challenge with these assays is that they do not track other characteristics of cell growth. When cells are in a new environment they sometimes have to switch gears and reconfigure themselves. So, what we are really interested in is measuring growth rates, and other parameters, in a quantitative and robust manner, from single cells.
Enter ODELAY! ...
ODELAY! is a tool and experimental workflow developed by scientists at the Center for Global Infectious Disease Research. The acronym stands for One-Cell Doubling Evaluation of Living Arrays of Yeast. (The method was first proposed by a fan of an album by Beck of the same name.) ODELAY! lets us measure many parameters of cell growth in very high resolution over time. It’s high throughput, high resolution microscopy. And it can measure single cells as they grow into colonies.
Existing methods do not track multiple characteristics of cell growth all at once, let alone measure this across an entire population of cells (or cell colonies). ODELAY! gives us a time-lapse of cell colony growth so that we can understand individual variations between cells. These variations exist even when the single cells have identical genomes. They can be small but understanding them is likely the key to understanding aspects of biology.
We play host to trillions of microbe guests. Some are hitchhikers, some are long-term residents, some are necessary for our health, and some, not so much. And there are many microbes that are usually harmless but would take advantage of us if they could.
A relevant example is in our ability to understand and respond to the phenonema of antibiotic resistance.
We currently face a crisis of our own making in the prevalence of drug resistant microbes. From overuse, to not finishing a prescription, there are many reasons for the emergence of drug resistant pathogens. Over time, drug treatments lose their effectiveness at controlling and halting infection. Our ability to measure single cells will be important to solving it. For instance, we know that when antibiotic resistance occurs, it doesn’t happen simultaneously in all cells of a bacterial infection. It rather begins in a few select bacteria that have acquired the ability to resist the drug. So, we need to look at the characteristics of these few bacteria that make them so different from the others.
Because ODELAY! measures single cells we can measure resistance and sensitivity directly. This allows us to track which cells in a population gain resistance in a controlled and reproducible manner. It also enables us to begin to understand what sorts of characteristics these cells have. It might be a genetic mutation or an epigenetic state that leads to resistance to a particular drug. By using ODELAY!, we can now track these characteristics on an individual cell level in real time instead of missing these features by measuring population averages.
ODELAY! is quickly becoming an essential tool in lab. One that will help us to defeat the challenge of antibiotic resistance. We hope you will stay tuned as we make new discoveries with this powerful research tool!
– Fred Mast, senior research scientist, Center for Global Infectious Disease Research