An award is made to Towson University to acquire the instrumentation that will allow the application of next-generation sequencing (NGS) technology to a large number of research programs involving graduate and undergraduate students. The research programs that will be supported are collaborative and range across biological sub-disciplines. Three research programs are described to exemplify the types of research programs that will be supported. Project one will use NGS for comparative analyses of RNA sequence data to uncover shared molecular-genetic mechanisms of wood evolution. In particular, the project seeks to explore evolutionary-developmental mechanisms responsible for multiple, parallel evolutionary origins of succulent woods, such as those found in the crop plants turnip and rutabaga. Project two will use NGS to develop evolutionary forecasting of pathogens. Evolutionary forecasting of pathogens calculates the probability of emergence or predominance of particular strains in association with certain diseases. The validity of the "high risk" designation for a strain will be experimentally explored in vivo by using a highly plastic veterinary pathogen (rather than a human pathogen) with an established experimental infection system in a proof-of-concept study. The parasitic bacterial species Mycoplasma synoviae relies on attachment to host cells to establish infection using a single allele of a multigene family, vlhA. Exploration of unexpressed copies of vlhA across strains by NGS is essential to the generation of predictive models of strain virulence. Evolutionary forecasts of M. synoviae strain virulence based on VlhA adhesins will then be validated in vivo. Project three will use NGS to develop and analyze microsatellite loci in house wrens. This will enable a test of the ?compatible alleles? hypothesis in the house wren by examining the prediction made by that hypothesis that extra-pair males that successfully father young will be less related genetically to females than are within-pair males. The use of next-generation sequencing technology will allow this prediction to be examined at a scale and depth not previously possible.
Broader Impacts The acquisition of instrumentation for next-generation sequencing will facilitate the following: 1) increased faculty-student production of peer-reviewed, published, and fundable research, 2) increased interdisciplinary research collaboration within and beyond the institution, 3) increased student research opportunities using cutting-edge technologies, 4) increased recruitment of high quality undergraduate and graduate students and faculty members, 5) increased opportunities for high-quality instruction on modern instrumentation in advanced lab courses, 6) increased training opportunities for minorities and high school teachers through established outreach programs. The ability to produce high sequence volumes at low cost enabled by the award will enhance the research done by the diverse Towson students and faculty, and the subsequent education of generations of students in K-12 education.
The award was used to purchase an Illumina MiSeq NextGeneration sequencing instrument to support the research of Towson University faculty and students, and the research of scientists and students at other institutions in the region. NextGeneration sequencing represents a huge leap forward in technology that has changed the way scientific research is done in many areas of the life sciences, and has made projects possible that were inconceivable just a few years ago. An illustration of this leap forward can be seen by considering the Human Genome Project. The Human Genome Project was carried out to determine the complete DNA sequence of single individual human genome. The project, using the previously available technology, required the work of thousands of scientists around the world working for nearly a decade to complete, at an estimated cost of $ 3 billion. Today, using NextGeneration technology, a single researcher could sequence a genome equivalent to a human genome in a week, at a material cost of approximately $1000. The instrument we have purchased, an Illumina MiSeq, is capable of sequencing 15 billion bases of DNA in a single run of less than two days. It has already been used to enable research by five principle investigators and their students at Towson University. The projects supported include: - An investigation of the effects of dietary selenium on the composition of the intestinal microbiome of mice that are being used as a model for colon tumor formation. - An investigation of the mechanisms that allow bacteria to evade phagocytosis. Mutant bacteria that have been selected for the ability to resist phagocytosis have been sequenced. A comparison of mutant genomes with those bacteria that have no resistance will provide insights into the mechanisms of resistance. - An investigation into the function of small proteins, defined as those containing 50 or fewer amino acids, in the bacterium Escherichia coli. A recently discovered small protein gene was deleted from the genome of a strain of E. coli, resulting in specific defects in growth and survival. This strain was further mutated, in some cases resulting in a restoration of normal growth and survival. These revertant mutants have been sequenced to determine what types of changes to the genome would allow suppression of the effects of deletion of the small protein gene. - An investigation into the evolutionary relationship of plant species through the sequencing of the chloroplast genomes of 23 different plants. - An investigation of the impact of urbanization on coyotes. NextGeneration sequencing of DNA isolated from coyote scat is allowing a comparison of diet and gut microbiome in two populations of coyotes, one in an urbanized environment and the other in a "natural" eastern woodland habitat. As can be seen above, the instrument has been used to enhance several, diverse research projects. In addition, the availability of this instrument on site has allowed our investigators and students to take control of sequencing projects and become familiar with the technical details of NextGeneration sequencing that would not be possible if sequencing was being done off-site. We see this last benefit as being particularly important in our role in training future scientists and in STEM workforce development.
