As several members of the “Computational Analysis of Microbial Evolution: Building a Scaffold to Teach Next-Generation Sequencing in the Biology Department” research group joined together recently to take a closer look at a particular data set in question, proof of the foundation of the project — collaboration – was evident.
In an office at the George Mason University Sci-Tech campus in Manassas, Va., the discussion began with student Sarah Vanderplas, who graduated this year with a B.S. in Biology and concentrations in Biotech and Molecular Biology as well as Microbiology. Sarah chatted about how she and fellow student Jasmine Amirzadegan had edited source code to make an NGS device, the Oxford Nanopore, viable for classroom application. Sarah’s passion? Developing new computer programs that solve complex problems which, most of all, run efficiently.
Jasmine was the next to assess the data… A Ph.D. candidate studying Bioinformatics and Computational Biology, Jasmine has worked with Dr. Reid Schwebach (the Principle Investigator of the study who has since left the university) during 2016-2017 academic year. Jasmine was involved in the research during its post-data collection and computational processing phase. (Jasmine, Sarah, and a recent GMU alumni with a BS in Biology, Austin Warner, also created a curriculum for a 400 level independent research biology course: “Computational Microbiome Analysis.” Collectively, they helped students gain an understanding of proper computational analyses of the soil samples that had been previously collected by other students over a two-year period and to analyze bacteriophages within the soil in search for genomic markers.) Jasmine has also spent a substantial amount of her time at Mason sharing what she’s learned via class presentations, seminar lectures, teaching an undergraduate biology lab, and mentoring.
While Jasmine pulled up her chair to the computer churning out thousands of data points, Dr. Pat Gillevet (Co-PI on the project) was scanning the screen for the specific set in question. Gillevet, a professor in the Biology Department and also the Director of the Microbiome Analysis Center at the Sci-Tech campus, has a decades-long history in microbiology, biochemistry, molecular biology, bioinformatics, and molecular evolution. Gillevet honed his studies at, among others, the Center for Prokaryotic Genome Analysis, the Harvard Genome Laboratory, and the National Center for Human Genome Research at the National Institutes of Health.
The group was soon joined by lead PI Dr. Reid Schwebach, who has been steering this project since its inception. Schwebach’s extensive CV includes a wide array of degrees, ranging from a B.S. in Agriculture from the University of New Mexico, to a Ph.D. in Microbiology and Immunology from the Albert Einstein College of Medicine, to a M.A in International Educational Development with a concentration in School Leadership from Columbia University, with several more in between. While Schwebach has a vast amount of experience in phage ecology and microbiome coevolution, it becomes clear that his true calling is education and mentoring — skill sets developed while teaching science in a New York City public high school, are still on full view.
NGS: A Giant Leap Forward
Schwebach’s group then crosses the hallway to the state-of-the-art facility at the Microbiome Analysis Center where Gillevet and the students greet Technical Director Dr. Masoumeh Sikaroodi. Once in the lab, the team proudly gathers around the prized Next-Generation Sequencer (NGS). Gillevet recounts the extensive changes from the previous DNA sequencing processes as compared to the much more effective and affordable NGS. (Gillevet still keeps the former DNA sequencer from his days at NIH in his lab – part history lesson and part nostalgia.) Although the students do not share Gillevet’s personal experience with the former operations, although they do marvel at the capabilities and the staggering speed of NGS.
Schwebach and Gillevet agree that this avenue of Bioinformatics study provides authentic research opportunities for students. For these students, as well as dozens of others, this project has been a catalyst that inspired computational approaches in their course of study, coursework, and future research. Both Schwebach and Gillevet see Bioinformatics as a burgeoning career path in Virginia — particularly Northern Virginia.
The Extended Reach
However, while the science is still getting done, Schwebach’s project has morphed into a multi-faceted teaching and learning venture, with outcomes benefitting current students, future students, and faculty to include:
- Video curriculum modules developed by Jasmine, undergraduate Ro Abidalrahim, and University of Mary Washington graduate Stephanie Woods, including animations that explain critical aspects bioinformatics instruction, emphasizing Next-Generation Sequencing techniques;
- Development of ZOOM .mp4 tutorials to use QIIME software assisting with instruction and development of the NGS modules;
- Substantially-improved curriculum for career-relevant courses and degree concentrations in the Bioinformatics experience at Mason and at James Madison University thanks to exchange of expertise between Gillevet and Dr. Steve Cresawn at Madison;
- Planned collaboration with Dr. Aureliano Bombarely Gomez of Virginia Tech’s Biocomplexity Institute, using her phylogenesis data in support of the NGS teaching modules;
- Undergraduate students designing instructional resources for high school teachers to introduce bioinformatics curriculum in AP and IB high school biology courses and development of teacher workshops for high school teachers;
- Providing Governor’s School students with summer research experiences; (Schwebach is also the Coordinator of The Governor’s School @ Innovation Park) and lighting a pathway for future Governor’s school students to be regularly included in Bioinformatics programs;
- Plans to include the distance learning segments developed through this program into one of Schwebach’s pet projects “Rural and Diverse Student Scholars” — making available the online resources for high school students in rural Virginia to provide access to research opportunities as a gateway to pursue a degree in bioinformatics and computational biology.
The 4-VA grant also helped fund the phage ecology research course at Mason, which student Jennifer Jones took as an undergraduate and then helped teach after graduation. Due to her interest in bacteriophages and the soil microbiome, Jennifer decided to base her graduate thesis studies on the phage ecology research course. Jennifer works closely with both Gillevet and Schwebach using bioinformatics tools to develop novel primers to identify mycobacteriophage clusters. Her goal is to utilize these primers to assess the mycobacteriophage clusters within soil samples to determine dominant clusters. This allows for comparison of these clusters over time and to develop a better understanding of the coevolution between bacteria and bacteriophages. With the help of the 4-VA grant — the course, Phage Discovery, is now offered through the Biology Department as a semester-long course and is affiliated with the HHMI SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program) program. Lead instructor, Dr. Anne Scherer, has helped develop this curriculum as part of the 4-VA efforts.
Moving Ahead with Shared Resources, Research, and Virginia Jobs
Clearly, Schwebach relishes the chance to bring the research group – of all ages and interests – together to forward the project, but also, each other. “I believe strongly in the ‘one room schoolhouse’ approach to education,” explains Schwebach. “We all grow individually and as a group when we learn from each other’s interests, backgrounds, and methodologies.”
Moreover, Schwebach sees tremendous potential for his students and opportunities for job growth in the field. To take advantage of these possibilities, Jasmine and Sarah are currently compiling a list of relevant bioinformatics skills for an educational publication.
But most of all, Schwebach is particularly proud of the number of young women that have chosen this field of study, thanks to the continued outreach to attract students to this project and the field of Bioinformatics.
“I think about the tremendous effect this 4-VA grant has had on Virginia,” concludes Schwebach. “Look around this room – and just imagine what this one grant has provided for these students and so many others here at Mason. I would want our state leaders to understand the value and impact of this funding – it’s amazing.”