Exploring the Big Picture of Life's Smallest Mystery

The cramped lab, hidden in the very back of the third floor of Pearson
Hall, houses Miami’s cutting edge technology. Inside are some of Miami’s
greatest minds working with highly sensitive, state-of-the-art DNA
sequencing equipment they affectionately refer to as their “new toys.” In
fact, these “toys” have paved the way for the microbiology department to
become a competitive research facility. In turn the program has helped
attract new faculty members and improved teaching.

After receiving three grants totaling approximately $700,000 from the National Science Foundation, the Ohio Board of Regents and Miami’s Center for Bioinformatics and Functional Genomics (CBFG) has acquired the same equipment used in the facilities working to crack the code in human genome project.

Luis Actis is the director of the CBFG, a lab devoted to studying biological samples with the help of computers. He explained the new equipment is used to enhance studies conducted for the understanding of the how organisms evolve and change in different environmental conditions. Actis uses the facility for his research on sequencing the genomes of bacteria, and he hopes the equipment will help answer the “whats, whys and hows” of antibiotic resistance.

The largest new instrument performs tasks beyond the comprehension of most of the students and faculty at Miami. To Actis and a select few other faculty and students, the new toy is a 48-capillary ABI 3730 genetic analyzer that collects, stores and analyzes nucleotide sequences. To the rest of Miami, it is simply a machine that can make sense of 48 samples of DNA simultaneously. The ABI 3730 is an impressive addition considering that before, the lab’s most powerful sequencer could only process 16 samples at a time.

The sequencer that arrived to the lab in early September now sits next to a partner robot that prepares precise samples for the sequencer to use. Technically known as the Beckman-Coulter Biomek FX liquid handling system, this pipetting machine drastically cuts down the time and human error often associated with sample preparation helping lab workers conduct experiments with greater ease and producing more accurate results.

Bioinformatics coordinator Chris Wood oversees the use of the new equipment, which most of time consists of typing instructions into the computer and watching the robot and sequencer do most of the work.“Using a number of the machines in the lab, you can actually start to pinpoint which genes are active under certain conditions and it takes a lot less time then in the past,” said Wood. “An experiment that may have taken a couple of weeks or longer can now sometimes be done in a few days.”

The projects using the equipment focus on a number of scientific areas such as bacterial and viral genomics, microbial diversity, environmental genomics, evolutionary biology, functional genomics and protein biochemistry.

While the main purposes of the equipment are in the fields of microbiology, its use is not limited to faculty members in that department. Actis is only one of many who are finding the new equipment enhances their research results.

“We have people from the geology department, as well as the chemistry, biochemistry, zoology and botany departments who are using the DNA sequencer to help with projects they are doing,” Actis said. “We even have a faculty member from the anthropology department who wants to use it. Overall there are probably about 70 people on campus who are involved with our lab.”

With this acquisition for microbiology, department chair Anne Morris Hooke thinks it will make Miami a more attractive option for faculty candidates.“We have a number of people all working on important projects, but the new DNA sequencing equipment is the most exciting thing for our department right now,” said Hooke. “It has already helped bring in some of the faculty we hired this year.”

The faculty, however, are not alone in seeing the benefits this grant has provided. Students in many of the College of Arts and Science majors are working with the equipment. Actis, who teaches a microbial and molecular genetics laboratory in addition to other microbiology classes, explained that the new equipment makes the classroom experience much more practical.

“We used to just have to explain to students how these types of experiments worked,” Actis said. “ The older machines in the lab worked too slowly for the students to use, but now with the new equipment, we can bring them to the lab and, using the technology, they can actually see and do the experiment themselves.”

Senior microbiology major Emily Doerger has the new equipment to thank for making her stand out in the pool of graduate school applicants by putting her a step ahead of students from other colleges.

“The fact that I could write down that I know how to use these machines is huge,” said Doerger. “Not many students applying to grad school can say that; Miami has an amazing amount of equipment for an undergraduate institution.”

The new DNA sequencers have made Miami a training and teaching facility.“We worked hard to get the equipment here, now we want everyone to take advantage of it,” Wood said.

“The equipment is a little intimidating when you think about the information it is collecting, but it is actually relatively easy to use and is open to anyone,” Doerger said.

The CBFG is helping put the tiny pieces of life together by providing students and faculty the opportunity to stay on top of up-and-coming ideas and theories. From robotic arms to hollow, fiber optic tubing and computers to samples of DNA, the new pieces of equipment are giving Miami a glimpse into the big picture of life’s smallest mysteries.

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