2013 Annual Report Project Narratives

5

Mellon (Andrew W.) Foundation
Participation in the Global Plants Initiative by the University of Vermont's Pringle Herbarium .

Principal Investigator: D. Barrington

Accomplishments & Outputs:
The Pringle Herbarium is funded by the Mellon Foundation to provide images and data from its collection of type specimens to the research community at large over the worldwide web, referred to as a virtual herbarium. Previous work positioned herbarium staff to work effectively towards this goal; we have an informed protocol for virtual-herbarium work and shared our insights at meetings of the regional virtual herbarium groups to which we belong. The funded objective for the grant is the sharing of data from our collection of ca. 6500 vascular plant type specimens in a rapid and efficient manner. Type specimens are a high priority because they serve as the basis for definition of scientific names of plants. The goal is to have the large number of Latin American type collections in the Pringle Herbarium available to Latin American botanists and others unable to visit or afford postage for loans. Scanning of all of our known vascular plant type specimens (except for those too thick to be scanned), about 3400 specimens, was completed in FY 2013, using the high-resolution HerbScan device given to us by the project. Each image is about 200 MB in size. Because we had fewer vascular plant type specimens in the collection than we had originally estimated, we arranged with the Mellon Foundation to add the digitization of our special collection of Sellow specimens (roughly 400 in all) and of our bryophyte and lichen type specimens to the project. About half of the Sellow specimens were scanned by the end of the fiscal year along with a test run of a few bryophyte and lichen specimens. Databasing of specimen label data began by creating a small test batch that was entered into, and then exported from, our Specify 6.5 database, converted to XML (the required format), and sent to GPI for review along with the associated images; no errors were found and we were told we could continue with databasing. We are currently beginning the transition from scanning to databasing and have databased about 50 specimens so far.

Publications:
none

5

Hatch/Multistate
Developing the US National Virtual Herbarium (from WDC12) .

Principal Investigator: D. Barrington

Accomplishments & Outputs:
The goal of WERA 1015: The US National Virtual Herbarium (USVH) is to accelerate development of access to the specimen information in the nation's herbaria (dried plant research collections) by promoting collaboration among herbaria, existing and proposed regional networks, and providers of national resources. To achieve this goal, the steering committee has established the following objectives: Increase the number of US herbaria digitizing their collections and making their data available to GBIF. The ultimate goal is the provision of data and images from these collections as an integrated searchable database on the worldwide web. The local goal (at UVM) is the serving of data on Vermont plants, both native and introduced, to the general public. Access to these data, along with parallel data being served by the other herbaria participating in the multistate project WERA 1015, will provide the public as well as researchers access to an integrated database of plant distribution over time across the United States. In FY 2013, all of the herbarium's vascular plant type specimens were scanned, and a test batch of images and data were approved by GPI administrators. The databasing will be completed in FY 2014. In support of the databasing of specimen data, Allard also attended a workshop at Kansas University in August for advanced users of the Specify software. This NSF-funded software is what the Pringle Herbarium uses for databasing label data for specimens. Allard was invited to present a paper for the Consortium of Northeastern Herbaria (CNH) in the CollectionsWeb Stakeholders Workshop in May 2013, a workshop to bring together specimen data providers with the community of users of those data in an effort to facilitate communication between those groups and facilitate effective dissemination of data to benefit a broad community. This workshop was held at the Smithsonian Institution in Washington, D.C. In July, the University of Vermont hosted the annual meeting of the CNH. The meeting was organized by Allard with help from students and staff. It included a keynote address by Charles Davis (Harvard University Herbaria) on using specimen data to understand global change, presentations by consortium members, a field trip, a tour of the herbarium, and a georeferencing workshop; the workshop was conducted by Allard. Since the CNH has members from most herbaria in the northeastern US and southeastern Canada, the meeting provided a good opportunity to discuss advances in digitization with colleagues, particularly related to the NEVP grant. During FY 2013, approximately one third of the first phase of the NEVP digitization process was completed.

Publications:
none

5

Hatch
Genetic Diversity and Watershed in Vermont's fiddlehead fern (Matteuccia struthiopteris, Onocleaceae) .

Principal Investigator: D. Barrington

Accomplishments & Outputs:
The purpose of this project is to improve upon our previous survey of genetic variation in the fiddlehead fern, a non-timber forest product with potential sustainability threats. We are now working to identify DNA-sequence-based markers that will witness genetic variation in the fiddlehead fern, as proposed. Past analysis was based on Amplified Fragment Length Polymorphisms, a molecular approach that clearly has serious challenges. In the current year we have succeeded in expanding our sample of single-nucleotide-polymorphisms for the gene Phosphoglucoisomerase (PGIc), the target of our research. These regions now include two-thirds of the gene, thanks to the availability of a transcriptome for an allied plant. We have also expanded our sample to include a greater coverage of the variation in habitat preference encountered by the plants. Our current work is to strengthen the genetic data that document the distribution of genetic diversity in these plants. The knowledge of genetic diversity pattern will make it possible to make a conservation plan that provides for the maintenance of genetic diversity in the fiddlehead fern. The people of Vermont stand to benefit, as long-term sustainability of this non-timber forest product depends on substantial understanding of the resource. As the best known of the non-timber forest products, fiddleheads are an excellent model for developing policies on use of similar resources in Vermont.

Publications:
none

5a

National Science Foundation
Collaborative Research: Digitization TCN: Mobilizing New England Vascular Plant Specimen Data to Track Environmental Changes .

Principal Investigator: D. Barrington

Accomplishments & Outputs:
The New England Vascular Plants (NEVP) project will image and database all of the vascular plant specimens in the Pringle Herbarium from New England and provide the data over the internet. In FY 2013, we purchased a laptop and a label printer to conduct the project's first phase, which is called precapture. We developed and tested a work flow for this phase before beginning work. Using volunteers, paid staff and students, precapture involves working our way systematically through the collections, finding folders with specimens from New England, placing a label with basic taxonomic and geographic information and a QR code on each folder, and a barcode on each specimen sheet. The software for printing the labels was developed and provided by the PI for the project. Specimens are being repaired as needed, and annotation labels are being added to specimens that need updated names. Several botanists are helping with identification questions. The process has added benefit to the collection because of performing these tasks. In FY 2013, five students have worked on the project. One of the students is incorporating the work into a class for credit. Work progress is reported on a regular basis to the project PI through the NEVP web site. As of the end of September 2013 we had completed the precapture phase for 21,200 of our estimated 65,000 specimens. The folder labels will be used to provide data for our Specify database in the next phase, which is called primary digitization. In anticipation of beginning primary digitization, part of the necessary equipment has been purchased. In this phase, specimens will be imaged and more data will be entered from their labels. We are experimenting with the use of speech recognition software to speed the process. Phase two is likely to begin in mid- to late FY 14.

Publications:
none

5a

Hatch
Characterization of the role of the Medicago truncatula GIRAFFE gene in oxidative stress.

Principal Investigator: J. Harris

Accomplishments & Outputs:
The purpose of this project is to determine the role of the Medicago truncatula heme oxgenase enzyme in root growth and the development and functioning of symbiotic root nodules. We have found that this heme oxygenase enzyme regulates the root expression of certain enzymes involved in the generation or scavenging of reactive oxygen species, but does not significantly alter the effect of cadmium on root growth. We are currently testing whether the heme oxygenase is involved in involved in the aging of nitrogen-fixing root nodules. We have presented this work in scientific meetings.

Publications:
none

5a

Hatch
Fungal Biofilms and Development of New Anti-Fungal Drugs .

Principal Investigator: D. Johnson

Accomplishments & Outputs:
The goal of this project is to investigate the mechanisms by which the pathogenic yeast Candida albicans can form biofilms on abiotic surfaces, including map sap tubing. We have identified 21 small molecules that can block this biofilm formation on polystyrene microplates and are examining their role on tubing. Over the past year, we have successfully be able to induce biofilm formation on map sap tubing and contact lens and have shown that 3 small molecules can inhibit this process. We have also generated a quantitative assay to measure the amount of biofilms on these surfaces. We will be working on advancing the assay to different tubing and small molecules in the coming year, as well as examining the potential for incorporating the small molecules into the tubing using soaking methodology.

Publications:
NONE

5a

Hatch
Evolution of a cold season adaptation in the temperate grass subfamily Pooideae .

Principal Investigator: J. Preston

Accomplishments & Outputs:
The goal of this project is to determine the timing and number of origins of a flowering time adaptation - vernalization responsiveness - to temperate seasonal environments in the cereal grass-containing clade Pooideae. Vernalization is an extended period of cold that makes plants competent to respond to inductive flowering time signals, such as long days and warm temperatures. Thus, vernalization responsive plants use winter cold to prime them to get ready to flower under optimal conditions of the spring, leading to increased fitness. To date we have described the vernalization response of several pooid species with the specific aim of reconstructing when and where on the phylogenetic tree this trait evolved. We hypothesize that it will map to the base of the pooids, correlating with a geographic shift from the tropics to the temperate zone. We have also cloned and sequenced a number of candidate genes from different pooids that are known to be involved in vernalization response in wheat and barley (core pooids), and have determined their transcriptional response to cold. Our results so far support a single origin of vernalization in the pooids. These data were collected by a graduate student and facilitated training of an undergraduate in molecular biology techniques. The work has been presented at one national meeting (Plant Biology), in three seminars internationally, and has resulted in one peer-reviewed publication. Next year we will continue to characterize vernalization response and its genetic basis in a number of pooid species. We will compliment candidate gene expression analyses with whole transcriptome analyses for a few diverse species.

Publications:
Preston, J. C., and Sandve, S. R. (2013) Adaptations to seasonality and the winter freeze. Frontiers in Plant Evolution and Development. 4:167.

5c

Craighead (John E and Christina C) Foundation
Determining the Genetic Basis of Sympetaly in Petunia and Other Asterids .

Principal Investigator: J. Preston

Accomplishments & Outputs:
The goal of this project is to determine the genetic basis for evolution of fused petals in the asterid core eudicots. Fusion of petals into a tubular structure correlates with switches in pollinator preference, and thus is hypothesized be an important mechanism driving plant speciation. So far my lab has made significant progress in characterizing the expression and function of candidate petal fusion genes in asterid taxa, including petunia, lettuce, and carnation, to see if they correlate with the origin of petal fusion. We have silenced a number of genes in petunia, leading to plants that have free (rather than the normally fused) petals, and have found that some candidate fusion genes are expressed only on one side of the petals. These results have been presented at two national meetings (Evolution and Plant Biology), and we expect to have at least one publication of results in a peer-reviewed journal within the next year. In the coming year we will continue to collect evidence for the role of particular candidate genes in the evolution of petal fusion, focusing on the expression and function of CUC/NAM, HAN, and MAW genes in species with fused and unfused petals. This work will be carried out by a postdoc and a graduate student, and will facilitate training of an undergraduate student who will present their results at the UVM undergraduate research symposium.

Publications:
None so far.