We are a group of people at Keene State College who want to learn and apply bioinformatics towards research and undergraduate education. We are faculty, staff and students from the School of Sciences and Social Sciences, primarily Biology and Computer Science. None of us have formal training in bioinformatics so we are learning from scratch. We do have a lot of help – we have a close working relationship with colleagues and mentors at the University of New Hampshire (more on that later). Most of the initial posts to this blog will be from Brian Moore and Loren Launen but our students Caitlin Smith, Raique Pereira, Katie Kiley and Sarah Sanders will be chiming in, as well as others, hopefully including our colleagues at UNH.
Our interest in bioinformatics began as a result of a current research project we host funded by the National Science Foundation through the New Hampshire EPSCoR New England Sustainability Consortium program (http://nhepscor.org/NEST). This project is lead by Loren Launen and is part of a larger Vibrio research project hosted at the University of New Hampshire in the groups of Stephen Jones and Cheryl Whistler. The project aims to genetically characterize the bacterium Vibrio vulnificus, a potential pathogen transmitted environmentally through exposure to marine water or ingestion of contaminated shellfish (mainly oysters). We are interested in understanding whether the V. vulnificus here in New Hampshire could pose a threat to human health. We are also interested in understanding the population structure and ecology of these local populations, and how they might be changing due to factors such as increasing water temperature. Recent research published from the Whistler group has demonstrated that a closely related pathogenic Vibrio species, Vibrio parahaemolyticus, is indeed increasing in numbers in the region due to the expansion of a pathogenic strain (ST36) derived from the Pacific Northwest (Xu et. al 2015, and references therein) and that these changes may be linked to environmental changes. These findings, and the seriousness of illness from V. vulnificus, motivate our work.
We are using a whole genome characterization approach. We receive isolates of V. vulnificus from UNH (they are collected and purified as part of the Vibrio monitoring program managed by S. Jones). We culture these isolates, extract genomic DNA and submit it for sequencing to the Hubbard Genome Center at UNH. The sequencing platform is an Illumina HiSeq 2500 which generates 250 bp paired end reads (short sequences). Then the data comes back to us (hosted on the UNH server) and we……apply bioinformatics. Which brings us to where we are now. What exactly does that mean and how will we do it? We knew initially we wanted to do two things. The first was to conduct multilocus sequence typing (MLST) analysis of specific house-keeping genes in our strains, using a program called srst2 (developed in the group of Katherine Holt and documented here). The second was to assemble and analyze our whole genomes. We had workshop-level experience with the second thanks to the group of Kelley Thomas from the Hubbard Genome Center, but little else in the way of knowledge. In the past four months, thanks to a lot of help from Feng Xu in the Whistler lab, and Jordan Ramsdell in the Thomas lab we have made what we think is a lot of progress in each area.
We are committed and excited rookies working with undergraduate students. We haven’t seen a lot of blogging from this perspective which is why we have started this – we want to share this experience because we don’t think we are alone in this. Many of the things we’ve learned might seem incredibly basic, but for us they were part of the process. Beginning this work when you have no formal training can be daunting, but also fun. We are getting a lot of help from incredibly generous people. We have also discovered that working as a team really helps us to solve problems. Going forward, much of this blog will focus on microbial genomics which is the major focus of our work right now. We anticipate expanding this into topics related to bringing bioinformatics into the classroom environment, and into different kinds of genomics projects. We are incredibly passionate about this work – in fact it’s become something of an obsession for some of us. We’re looking forward to sharing this!
(Some of) the Launen research group (left to right: Raique, Caitlin, Dr. Launen, and Brian). Missing (but coming in future posts): Sarah and Katie (Katherine), and pics of collaborators.
That’s it for now,
Loren & Brian