Science Behind-the-Scenes: Do-It-Yourself OD Measurements with Dr. Chinna Devarapu and Vamsi Yallapgragada
Synthetic biologists have long had a fascination with hardware in biology; devices to simplify experiments and enhance repeatability are always in vogue. But one of the most basic experiments that a biologist can perform – namely, measuring the growth rate of an organism in a flask or tube – remains tedious and time-consuming.
Now, a team of engineers at Ireland’s University College Cork, the Cork Institute of Technology and Tyndall National Institute have developed ODX, an OD600 spectrophotometer adapted from low-cost fitness trackers. The hacked device costs less than $20 to build and enables cell growth measurements to be monitored in real-time through a smartphone application. ODX can be placed inside of bacterial incubators, even while flasks are shaking. The device will even send a notification when the OD reaches a target level.
I sat down with Dr. Chinna Devarapu (corresponding author) and Vamsi Yallapragada (joint first author, together with Uday Gowda) to learn more about ODX, discuss technical challenges, and highlight future plans for this work.
This interview on “ODX: A Fitness Tracker-Based Device for Continuous Bacterial Growth Monitoring”, published in Analytical Chemistry, has been edited for brevity.
Niko McCarty: Tell me about yourselves; what drew you to this project?
Vamsi Yallapragada: I’m a PhD student at University College Cork and a biologist by training. In our lab, we work on protein production and protein design projects, so a lot of my time is spent monitoring bacterial growth. Chinna, on the other hand, is a postdoctoral fellow at the Cork Institute of Technology and Uday, the co-first author, is a PhD student at the Cork Institute of Technology and Tyndall National Institute. We all came together to work on this problem.
Dr. Chinna Devarapu: Vamsi and I have a close relationship at work, and we frequently share our ideas. I often visit him in the laboratory, and almost always find him in front of the spectrophotometer measuring cell growth. My own interests lie in robotics and DIY hardware; microcontrollers, syringe pumps, that kind of thing. So obviously, our teaming up for this project seemed like a natural fit. When we finally decided to go all-in and pursue the ODX idea, partly out of a desire to alleviate some of Vamsi’s lab tasks, I decided to use components from a fitness tracker because they already have everything that you need; Bluetooth, integrated microcontrollers, sensors, and more. Fitness trackers are also very cheap and compact. But, most importantly, many fitness sensors have a heartrate sensor, which uses LEDs to measure your pulse. I immediately thought that we could use this to monitor bacterial growth.
Vamsi: The ODX device began more from frustration than invention or discovery. As a biologist, taking an OD reading every 20 minutes is a big pain. Every time we do growth curves, it felt like the whole day was wasted. Then, one day, Chinna said, “All right, why do you have to go and take a measurement every 20 minutes? Why can’t you monitor cells continuously?”. That’s when this project began. We approached Uday (co-first author) about the project, who is an engineer and is very skilled at electronics engineering and product design. The three of us teamed up and spent the next six or seven months building the device and optimizing it until our measurements were comparable to off-the-shelf spectrophotometers.
Niko: Could you walk me through the different components in the ODX?
Chinna: Well, the main component of the device is a fitness tracker, which already has many of the elements required, including the LED. One important thing that we realized is that, since optical density is measured at 600 nanometers, we need to find a LED that works in that range. Unfortunately, the LED in fitness sensors use a shorter wavelength. We also wanted to use an LED that maintains constant brightness even when it has low battery, for consistent OD measurements. For that, we added a constant voltage regulator and a constant current regulator. These three components are really the only things that go into an ODX device. The directions to assemble an ODX are also outlined in the paper.
Niko: Who is the target audience for this device? Why can’t labs just use plate readers to measure growth rates?
Vamsi: The maximum cell volume that can go into a plate reader is very small, at least compared to cells in a flask. Also, when you grow cells in a small volume, like a microplate, the fluid dynamics completely change. Cells grow very differently in a microplate compared to a flask. If you’re going for high-scale protein production, say, for NMR or X-ray crystallography, you need to grow cells in large volumes. This is really where our device shines – we can measure ODs continuously, without risking contamination, in a device that costs less than $30 to build.
Niko: Were there any major obstacles that arose during your efforts to get the ODX up-and-running?
Vamsi: Making the 3D-printed enclosure was probably the hardest part, but definitely not a major obstacle. We put a lot of time and thinking into the enclosure because it has to be compatible and hold all the components. It also needs to resist the shaking of the incubator.
Chinna: Another challenge that we ran into, at least when hacking the fitness tracker, was that we relied on an online community for help with our programming. None of us are particularly strong programmers, and it was especially difficult to find a programming library for the heart rate sensors; some libraries worked with the LED, but not with the Bluetooth, and vice versa. It also took quite a bit of time to get the smartphone application up-and-running. In the end, though, we are quite proud of the results. If we can do it, anybody can do it; this is very much a do-it-yourself device, and all of the instructions for building an ODX are available on our online GitHub page.
Niko: Do you have any plans for more DIY builds?
Chinna: We are working on a few devices similar to this one; some are based on fitness trackers, and others are being built from the ground up using microcontrollers. No matter what we do in the future, we want it to be available to everyone.
Niko: What comes next for both of you?
Vamsi: Well, we both like to integrate sciences and share the common goal of solving problems with simple technology, especially in biology. Since I like to tinker and work on lots of different projects, I currently plan to continue working on such projects that demand interdisciplinary skills..
Chinna: After publishing this project, we got a lot of requests from other people to build devices for them. I like that there is a flexibility here; we can both publish and create devices, or even sell devices, without operating as a startup. Or we can create a startup company for this device, or other devices in the future. Either way, I want to retain my freedom and continue working on DIY electronics in my free time, regardless of career path.
Niko: How do you envision that the ODX, and future devices, will help synthetic biologists in particular?
Vamsi: We hear this buzzword, synthetic biology, a lot these days. What I know about synthetic biology is that, at least partly, it aims to reduce costs and accelerate the pace of biological research by integrating various scientific disciplines. The ODX is a perfect example of this ambition, because monitoring bacterial growth is a primitive task, and an easy task. But it’s often overlooked by scientists because there are traditional methods to measure bacterial growth that are very effective. We built this device through the efforts of physicists, biologists, and engineers, and it’s already saving researchers a lot of time and energy.
Niko: If somebody wants to build an ODX device, where should they go for advice, how much will it cost, and how long will it take?
Chinna: An ODX can be built, from scratch, very quickly. We already did the troubleshooting, sorted out the programming libraries, built the application, and developed the 3D-printed enclosure. The best way to build an ODX is to read our paper, and especially the supplemental material. Buy a fitness tracker on Amazon or from an electronics store. The total cost should be between $15 and $30, and it should take less than five hours to build.
Vamsi Yallapragada is a PhD student at University College Cork, in Ireland. A biologist by training, he holds a Masters in biotechnology from the same institution. He previously invented and patented a DNA-based pen to prevent forgeries, called DYAGRAM. He is currently working on synthetic protein design in Dr. Mark Tangney’s lab.
Chinna Devarapu is a Marie Skłodowska-Curie Research Fellow at the Cork Institute of Technology. He completed his Ph.D. in physics at the University of Exeter, and was previously a research fellow in nanophotonics at the University of St. Andrews. He frequently writes about DIY electronics in his blog, scientistnobee.
Uday Gowda (co-first author) is a PhD student at Cork institute of technology and Tyndall national institute. He has a Masters in Photonics. Uday is currently working on studying laser dynamics for optical coherence tomography applications.
I think that this was a really cool blog. First off the information was displayed very well and I love the set up using dialog to portray the information. Not to mention the fact that biotechnology is a really cool and unique subject. I Hope you post more like this soon.