5
Mellon (Andrew W.) Foundation
Principal Investigator: D. Barrington
Accomplishments & Outputs:
5
National Science Foundation
Principal Investigator: D. Barrington
Accomplishments & Outputs:
5
Hatch/MultiState
Principal Investigator: D. Barrington
Accomplishments & Outputs:
This project continues a program to implement web sharing of the extensive plant-information resources of the Pringle Herbarium in coordination with the development of the Unites States Virtual Herbarium, an approved multistate project involving 12 experiment stations and over 70 herbaria nationwide. The objectives of the project are to 1.) supervise the development of the Pringle Herbarium's digital images and data, 2.) provide our specimen data to the web through regional and taxon-specific national portals, 3.) participate in the U.S. Virtual Herbarium community's goal of integrating our specimen data with those of the other participating herbaria through appropriate portals, and 4.) continue to attract funding for including the remaining 190,000 specimens in on-line resources.
During FY 2014, using the resources in part provided by this multistate award, we won two grant proposals to the National Science Foundation to provide for digitization of our macrofungi collection (approximately 3000 specimens), and imaging and partial digitization of label data for all of our remaining vascular plant specimens not covered by other grants. Data are now being released through national internet portals. These include the following:
portal.neherbaria.org The portal for the Consortium of Northeast Herbaria. This is where the New England vascular plant specimen data are going.
bryophyteportal.org The link for accessing data from the 60 or so institutions that are supplying specimen data for bryophytes, including the Pringle.
lichenportal.org Ditto, for lichens
mycoportal.org ditto, for macrofungi
plants.jstor.org The JSTOR type plant specimen catalog.
http://lbcc1.acis.ufl.edu/ This is the volunteer site for the NSF grant that covers digitization of bryophytes and lichens.
https://www.idigbio.org
This is the central repository for all national natural history collection digitized data projects that are funded through NSF. Plus it has gobs of other information.
Progress was also made on currently funded projects arising out of the overall goal of the multistate project. These include the New England Vascular Plants (NEVP) NSF Thematic Collections Network project, for which phase one (the predigitization work) was completed with the help of an array of student trainees. The databasing for the Mellon Global Plants Initiative Grant was completed in FY 2014.
5
Hatch
Principal Investigator: D. Barrington
Accomplishments & Outputs:
5
National Institute of Food and Agriculture/Department of Agriculture
Principal Investigator: A. Wright
Accomplishments & Outputs:
Publications:
Ishaq, S.L. & A-D.G. Wright. 2014. Design and validation of four primers for next-generation sequencing to target the 18S rRNA gene of gastrointestinal ciliated protozoa. Appl. Environ. Microbiol. 80: 5515-5521. Impact Factor: 3.95.
Ishaq, S.L. & A-D.G. Wright. 2014. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microbial Ecology. 68: 185-195. Impact Factor: 3.28.
5a - Fungal and Plant Molecular Biology
5a
Hatch
Principal Investigator: J. Harris
Accomplishments & Outputs:
5a
Craighead (John E and Christina C) Foundation
Principal Investigator: J. Preston
Accomplishments & Outputs:
5a
National Science Foundation
Principal Investigator: J. Preston
Accomplishments & Outputs:
5a
Hatch
Principal Investigator: J. Preston
Accomplishments & Outputs:
5b - Microbiology and Cell Biology
Participation in the Global Plants Initiative by the University of Vermont's Pringle Herbarium
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Scanning of all of our known vascular plant type specimens, about 3400 specimens, was completed in FY 2013, using the high-resolution HerbScan device given to us by the project. 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 the ca. 400 significant and early Sellow specimens from Brazil and of our bryophyte and lichen type specimens to the project. All Sellow specimens were scanned by the end of the fiscal year as well as the bryophyte and lichen specimens. In FY 2014 we wrapped up this project with the scanning of additional significant collections from the Pringle Herbarium and shipped the data to the Mellon Foundation for publishing through the JSTOR Plants website, as required by the funding agency. Minor data processing remains to be done with a small amount of extended funding permitted by the agency.
CSBR: Natural History: Launching the University of Vermont Natural History Museum Step One: Securing the Collections
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The primary goal of our National Science Foundation Collections in support of Biological Research grant is to secure all of the newly inaugurated University of Vermont Natural History Museum's collections in secure cabinetry that makes pest control possible and damage from fire and flood less likely. As the collections are secured, we will systematically reorganize the major groups (orders, families) in the relevant current phylogenetic order. A secondary goal of this project is digitization of the collections. We propose to expand the currently funded and very active plant digitization program, as this activity will increase the efficiency of the collection transfer. In addition, we will expand digitization of the arthropod collection, photographing insects and labels in preparation for release through the Notes from Nature citizen science website.
In this report I detail the activities relating to the plant collections, as they fall under the jurisdiction of the College of Agriculture and Life Sciences, whereas the animal collections are administered by the College of Arts and Sciences. The funding for this grant was available July 1 of this year. Progress has been excellent. In respect to the cabinetry, we finalized the purchase order and placed the order with the chosen bidder, SteelFixtures, in August. The herbarium cabinets (for the plants) will be delivered the week of December 17. At the same time, the substantial activity relating to reorganization of the collection, under the direction of Dorothy Allard, is well underway, with the system fully implemented and approximately 10% of the collection reorganized. At the same time we have begun the digitization portion of the activity; two undergraduate students are engaged in this project and about on schedule.
In the coming year we will proceed with the reorganization and digitization. Also in the coming year the new cabinets for the plants will be placed on the 300 level in Torrey Hall. By the time of next annual report I expect the 300 level cabinets to have received their newly reorganized collections, leaving the much larger 400 level activity for the remaining two years of the grant funding.
Developing the US National Virtual Herbarium (from WDC12)
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Hatch Award: The Pringle Herbarium and the US National Virtual Herbarium
Genetic variation in relation to ecogeographic distribution in the fiddlehead fern (Matteuccia struthiopteris, Onocleaceae)
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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.
This year we have spent implementing the tools for sequencing DNA of the gene phosphoglucoisomerase (PGI), which we finished developing last year, to our first pilot populations of the fiddlehead fern. We identified two extremely diverse regions of the gene, intron 7 and intron 15, likely to harbor the variation needed to characterize genetic diversity at the population level. Especially interesting is our discovery of a region of tandem-repeated DNA (microsatellites) in intron 7. Using a microsatellite analysis approach, we hope to use these well-known hypervariable markers to characterize poplation level variation in our plants in the coming years. This year we also began a comparative analysis of non-synonymous substitutions (those that impact the PGI genotype) and other substitutions with the goal of testing for evidence of natural selection in our populations. Much of this work was done by our outstanding undergraduate researcher, Brendan Lyons.
Investigating the Rumen Bacteria of the North American Moose (Alces Alces) for the Potential for Improving Efficiency of Feed Digestion in Livestock
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Moose are wild ruminants that are able to subsist on highly fibrous plant matter, and very little is known about the microorganisms exist symbiotically in their digestive tract. Currently, bacteria from the rumen of Vermont moose are being cultivated and identified using DNA sequencing. Bacteria of interest, such as those capable of fiber degradation or those which produce beneficial by-products (i.e. lactic acid bacteria which are often used as pro-biotics) are being further investigated using culturing techniques and biochemical tests. A candidate bacterium (or bacteria) will be chosen, inoculated into the rumen of neonatal lambs, and allowed to colonize. Production indicators, such as weight gain and wool growth, as well as volatile fatty acid production and rumen pH, will be monitored to determine the effect of the inoculant. It is hypothesized that the bacteria from the moose will improve fiber degradation and production when inoculated into the sheep rumen. Previous studies have used various species of bacteria introduced into livestock with varying results, ranging from no effect, to several studies showing an increase in weight gain, milk production, meat quality, and immune health.
Ishaq, S.L., D. Reis, H. Lachance, & A-D.G. Wright. 2014. Descriptions of Streptococcus alcis sp. nov. and Streptococcus vermontensis sp. nov., and proposal of four new subspecies of Streptococcus gallolyticus isolated from the rumen of moose (Alces alces) in Vermont. Int. J. Syst. Evol. Microbiol. Impact Factor: 2.11. In Review
6 projects
Characterization of the role of the Medicago truncatula GIRAFFE gene in oxidative stress.
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 have found that the heme oxygenase is involved in involved in the aging of nitrogen-fixing root nodules. We have presented this work in scientific meetings.
Determining the Genetic Basis of Sympetaly in Petunia and Other Asterids
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The fusion of corolla tubes has evolved multiple times independently in flowering plants, possibly leading to increased pollinator specialization and net plant speciation. The aim of this project is to determine the role of candidate genes in the evolution of fused petals within the asterid core eudicots that comprise 25% of flowering plant diversity. To accomplish this aim, we are carrying out morphological, gene expression, and functional analyses on petunia that have fused petals, and carnation that lacks fused petals. We have developed two independent constructs to transcriptionally silence a single HANABA TARANU (PhHAN) gene and three NO APICAL MERISTEM (NAM)-like genes in petunia. All constructs were demonstrated to cause silencing in a gene-specific manner. HAN silencing results in premature plant death, whereas silencing of the NAM-like genes PhNAM, PhNH16, and PhNH15 results in a range of phenotypes that either increase fusion in sepals, stamens, and carpels, or reduce fusion in petals. Scanning electron microscopy suggests that loss of petal fusion in PhNAM- and PhNH16-silenced flowers is due to defective cell growth between the stamen attachment point and the lobes. Together, our data support the hypothesis that genes involved in petunia organ fusion work in a context- and zone-specific manner, perhaps explaining the high level of natural variation in corolla tube morphology. An MS student and postdoctoral researcher presented results of our work at the Botany 2014 meeting in Boise Idaho, the Evolution 2014 meeting in Raleigh North Carolina, and the Plant Biology Graduate Program Symposium at University of Massachusetts Amherst. In the next year we will continue to characterize the effect of candidate gene-silencing on petunia flower development, and will determine the spatio-temporal expression of these genes in both petunia and carnation.
Evolutionary Genetics of Vernalization Responsiveness in the Temperate Grass Subfamily Pooideae
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Grasses contain some of the worlds most important crops, several of which are locally adapted to cold temperate seasonal climates. We aim to determine the origins and genetic bases of chilling-induced grass flowering in the temperate subfamily Pooideae in order to understand how labile adaptation to seasonal cold is. By studying past response to climate change, we will be able to better predict the impact of future global change on plant performance, and identify genes that can be manipulated for better crop yield under novel local conditions. We have identified chilling-induced flowering in three distantly related species of "non-crown group" pooids, either suggesting that chilling response evolved at the base of Pooideae, or multiple times in both the non-crown group and the wheat/barley/oat-containing crown group. Preliminary expression data on the chilling response genes VERNALIZATION 1 (VRN1), VRN2, and VRN3 suggest that they are responding in a similar way to cold in both crown and non-crown pooids. However, there are exceptions, making the number of origins of chilling-induced flowering ambiguous. In the next year we will collect total messenger RNA from different time points across chilling experiments and carry out RNAseq to identify candidate genes involved in chilling response. Candidate genes will be compared across species in order to determine significant overlap suggestive of a single origin of chilling-response across Pooideae.
Evolution of a cold season adaptation in the temperate grass subfamily Pooideae
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Grasses contain some of the worlds most important crops, several of which are locally adapted to cold temperate seasonal climates. We aim to determine the origins and genetic bases of chilling-induced grass flowering in the temperate subfamily Pooideae in order to understand how labile adaptation to seasonal cold is. By studying past response to climate change, we will be able to better predict the impact of future global change on plant performance, and identify genes that can be manipulated for better crop yield under novel local conditions. We have identified chilling-induced flowering in three distantly related species of "non-crown group" pooids, either suggesting that chilling response evolved at the base of Pooideae, or multiple times in both the non-crown group and the wheat/barley/oat-containing crown group. Preliminary expression data on the chilling response genes VERNALIZATION 1 (VRN1), VRN2, and VRN3 suggest that they are responding in a similar way to cold in both crown and non-crown pooids. However, there are exceptions, making the number of origins of chilling-induced flowering ambiguous. Results of this work have been presented at the Botany 2014 meeting in Boise Idaho, the Northeast American Society of Plant Biology meeting in Rhode Island, and at a University of Arizona Plant Biology departmental seminar. In the next year we will collect total messenger RNA from different time points across chilling experiments and carry out RNAseq to identify candidate genes involved in chilling response. Candidate genes will be compared across species in order to determine significant overlap suggestive of a single origin of chilling-response across Pooideae.
4 projects