Penn Undergrads Make Biology More Accessible with Open-Source Plate Reader
By Lauren Salig
The annual International Genetically Engineered Machine (iGEM) competition challenges students to expand the field of synthetic biology to solve tangible problems. While most iGEM projects involve imbuing microorganisms with useful new traits and adding them to a global toolkit, Penn Engineering students took a unique approach to the iGEM challenge by creating an open-source blueprint for a mechanical instrument that could make biological research more accessible.
Penn Bioengineering undergraduate Andrew Clark and recent graduates Karol Szymula, now a research assistant in Penn’s Complex Systems Lab, and Michael Patterson, now the lab engineer for Penn Bioengineering’s Instructional Laboratories, contributed to the project that originated through the 2017 iGEM challenge. Graduate student Michael Magaraci, who started Penn’s iGEM program as an undergraduate, and Sevile Mannickarottu, director of Instructional Laboratories, also participated. Brian Chow, Assistant Professor in Bioengineering at Penn, who helped create the iGEM competition when he was an MIT graduate student, oversaw the project.
Their goal was to create instructions for a plate reader that would be affordable for laboratories or educators in the field to build for themselves. Their final invention could reduce the cost of acquiring a plate reader to a tenth of the price plate readers sell for now.
“Given how near-universally important they are to experimental bioengineering and biochemistry, I’m always surprised you do not find more in labs,” says Chow. “Plate readers may not be the most expensive equipment around, but they can still cost as much as a luxury car. Their cost is a real issue.”
The team published their design and instructions for building and operating the plate reader in the journal Biochemistry.
The project has since been featured in Chemical & Engineering News for its innovative approach to making plate readers easier to come by.
Chow told Alla Katsnelson of Chemical & Engineering News, “If you think about enabling technologies for any biology or bioengineering lab, a plate reader is top of the list, maybe after a fluorescence microscope.”
Plate readers are such a crucial part of biology labs because they are used for biological assays that indicate the amount or activity of a substance in a material. They do so by measuring light absorption and fluorescence signals. The processes enabled by plate readers allow biologists, biochemists, and bioengineers to learn critical information about the materials they work with.
The Penn Bioengineering students believed that if they could create a blueprint for an affordable plate reader, they could open the door to allow that technology into more classrooms and laboratories.
To create such a blueprint, they needed to figure out the design of three main plate reader parts: a spectrophotometer to detect light, a motor to move samples into the detector’s range, and software to automate the process and analyze the data.
They began addressing these three stages through the 2017 iGEM competition, but after the event ended, the team continued working to perfect their design.
Under Chow’s guidance, the students began testing out less expensive ways to create the three essential parts of a plate reader. After trying to create custom light detectors, the team determined that it was equally cost effective to buy a detector from an existing manufacturer that could still be custom-programmed through available software drivers.
However, the other two parts required significant innovation to arrive at the final product. To mimic more expensive motors that carefully control sample positioning, the team designed the plate reader’s frame out of pieces of T-slotted aluminum that fit together in a manner that Chow describes as “LEGO-like” and act as their own guiderails for motion. This frame, along with two simple motors, helps guide the sample’s movement through the reader.
“The motors only cost about $80 each, and, with the T-slotted aluminum frame, they gave us enough resolution to move the plate precisely. We weren’t able to replicate, but we found a pretty good alternative to what’s on the market,” says Szymula.
To address the software component of their device, the students used Python to write a program that could communicate with all of the electronic components and interpret the data collected by the plate reader.
Their final product includes design files for components and several dozens of pages of instructions on how to build and use the plate reader, all free to download from their Biochemistry paper or repositories like GitHub.
“I think one of the big benefits is that all of the components already exist on the market and work well. We took all of that and put it in one device,” says Szymula.
With the incredibly detailed specifications provided for the open-source hardware and software, laboratories could create their own plate reader or outsource the work to a machine shop for a relatively low cost. Chow’s team says that their plate reader costs less than $3,500 to construct, making it a viable option for researchers and educators with limited funds.
How well does the team’s plate reader stack up to commercial plate readers that cost ten times more? The open-source plate reader can detect substance concentrations as low as approximately 10 nanomolar as compared to the approximately 10 picomolar concentrations that commercial equipment can detect.
Although not as sensitive as the more expensive technology, Chow says that the open-source hardware is sufficient for common biological assay applications like ELISA.
The team’s invention won’t be replacing those expensive, top-notch plate readers in highly funded labs, but it might make the technology accessible. Providing classrooms and laboratories with access to an affordable plate reader could be a good way to train students and researchers to use this often exclusive technology that is so critically important to those in biology-related fields.
Szymula even imagines incorporating the construction of the plate reader into education:
“This was a project that I went into without having done anything like this before, but it turned out to be a nice accumulation of all the skills that I learned in my undergraduate bioengineering education,” says Szymula. “I think it would be really neat if engineering students, maybe juniors in a lab, had this as one of their projects: to put it together piece by piece and see how it uses the skills they’re learning.”
Beyond giving those in laboratories and classrooms an affordable plate reader option, the team’s blueprint is customizable. Researchers who construct their own plate reader have the option to modify the software or hardware for their specific needs.
“One of the beauties of DIY-Bio is that, because innovation is driven by true need, typically in cost reduction or customization, the technical solutions created inherently address a meaningful problem. We developed the open-source plate reader to empower others,” says Chow.