Jetstream virtual accessibility powers bioinformatic research identifying novel antibiotic resistance mechanisms at Spelman College in Atlanta
Jetstream powers the lab of Maira Goytia at Spelman College, where she and undergraduate researchers analyze large sets of transcriptomic and genomic data, to explore the diversity of the Neisseria bacteria species.
Maira Goytia, assistant professor in the Department of Biology at Spelman College, an all-women historically black college/university (HBCU) in Atlanta, GA, researches the molecular mechanisms of antibiotic resistance in the sexually-transmitted bacterium N. gonorrhoea, and its relatives the commensal Neisseria species.
Since 2018, Goytia has led efforts to analyze large sets of transcriptomic and genomic data, to explore the diversity of the Neisseria species, which humans carry both orally and in the naso-pharynx, and impacts the dynamics of antibiotic resistance. “We still don’t know much about the diversity of antibiotic resistance mechanisms, mechanisms of genetic exchange, and evolutionary history of commensal Neisseria species,” said Goytia, whose interdisciplinary research combines wet lab microbiology with bioinformatics.
Goytia, whose research doubles as a training lab for undergraduate scientists, performs transcriptomics and genomics analyses requested the support of Jetstream and XSEDE computational resources, in collaboration with Crista Wadsworth, a professor of microbiology at the Rochester Institute of Technology. “These collaborations have been critical to helping my team of undergraduate research students move beyond the laboratory and into direct engagement with large genomics datasets,” said Goytia.
The students in my team at Spelman [an all-women HBCU] learned to be comfortable with large datasets, analyze them, and to find new avenues to further our research program,
Goytia’s lab investigates the differential genetic expression in bacteria grown in different conditions. For instance, in the presence of spermine, a polyamine, N. gonorrhoea displays lower susceptibility to antibiotics acting on the bacterial cell wall. This research branches off work published by Goytia in 2010 which demonstrated that spermine created a shield around the cell wall preventing antibiotics from reaching their target, the bacterial cell wall. “Overall, Jetstream allowed my undergraduate research students and me to find a critical complementary focus to our research and develop new projects,” said Goytia, who says over 20 young women scientists have worked alongside her, gaining experience in bioinformatics. “Jetstream and the scientists who helped us, triggered a new set of projects in my lab on comparative genomics of Neisseria species, transcriptomics of susceptible and resistant strains, and microbial community analysis in the human oral ecosystem,” she said.
Jetstream’s virtual interface provides Goytia’s undergraduate researchers with a resource which prepares them for opportunities of bioinformatic research even amidst the ongoing COVID-19 pandemic. “The students in my team at Spelman learned to be comfortable with large datasets, analyze them, and to find new avenues to further our research program,” said Goytia. “In the future, I hope to expand the bioinformatics research experience to a classroom setting, expanding the reach of computational biology to students of underrepresented groups in STEM,” she said.
David Y. Hancock, Principal Investigator of Jetstream at Indiana University’s Research Technologies, a center of the Pervasive Technology Institute, says Goytia’s work exemplifies the rapid adoption of the national science and engineering cloud environment. “Since 2014, Jetstream has become a critical, reliable resource among researchers and educators nationwide,” said Hancock. “The Jetstream team is proud to facilitate the next generation of scientists as they continue their training and research virtually, it is particularly rewarding to provide resources that allow a researcher and educator such as Dr. Goytia to adapt to COVID-19 related challenges,” he said.
About Jetstream Jetstream (Links to an external link.), led by the Indiana University Pervasive Technology Institute (PTI) (Links to an external link.), adds cloud-based, on-demand computing and data analysis resources to the national cyberinfrastructure. With a focus on ease of use and broad accessibility, Jetstream is designed for those who have not previously used high performance computing and software resources. The system is particularly geared toward twenty-first-century workforce development at small colleges and universities—especially historically black colleges and universities, minority-serving institutions, tribal colleges, and higher education institutions in EPSCoR states. Jetstream2, awarded in 2020, is a transformative update to the National Science Foundation’s science and engineering cloud infrastructure and will add an additional 8 petaFLOPS of virtual supercomputing power to simplify data analysis, boost discovery, and increase availability of AI resources.