http://hdl.handle.net/1957/1934 Tue, 21 May 2013 15:13:46 GMT 2013-05-21T15:13:46Z http://hdl.handle.net/1957/38585 Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR Van Auken, Kimberly; Fey, Petra; Berardini, Tanya Z.; Dodson, Robert; Cooper, Laurel; Li, Donghui; Chan, Juancarlos; Li, Yuling; Basu, Siddhartha; Muller, Hans-Michael; Chisholm, Rex; Huala, Eva; Sternberg, Paul W.; WormBase Consortium WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology. This is the publisher’s final pdf. The published article is copyrighted by Oxford University Press and can be found at: http://www.oxfordjournals.org/ Sat, 17 Nov 2012 00:00:00 GMT http://hdl.handle.net/1957/38585 2012-11-17T00:00:00Z http://hdl.handle.net/1957/38451 Ferric-Pyoverdine Recognition by Fpv Outer Membrane Proteins of Pseudomonas protegens Pf-5 Hartney, Sierra L.; Mazurier, Sylvie; Girard, Maeva K.; Mehnaz, Samina; Davis, Edward W. II; Gross, Harald; Lemanceau, Philippe; Loper, Joyce E. The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyochelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 also utilizes ferric complexes of some pyoverdines produced by other strains of Pseudomonas spp. as sources of iron. Previously, phylogenetic analysis of the 45 TonB-dependent outer membrane proteins in Pf-5 indicated that six are in a well-supported clade with ferric-pyoverdine receptors (Fpvs) from other Pseudomonas spp. We used a combination of phylogenetics, bioinformatics, mutagenesis, pyoverdine structural determinations, and cross-feeding bioassays to assign specific ferric-pyoverdine substrates to each of the six Fpvs of Pf-5. We identified at least one ferric-pyoverdine that was taken up by each of the six Fpvs of Pf-5. Functional redundancy of the Pf-5 Fpvs was also apparent, with some ferric-pyoverdines taken up by all mutants with a single Fpv deletion but not by a mutant having deletions in two of the Fpv-encoding genes. Finally, we demonstrated that phylogenetically related Fpvs take up ferric complexes of structurally related pyoverdines, thereby establishing structure-function relationships that can be employed in the future to predict the pyoverdine substrates of Fpvs in other Pseudomonas spp. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by American Society For Microbiology and can be found at:http://www.asm.org/. Fri, 01 Feb 2013 00:00:00 GMT http://hdl.handle.net/1957/38451 2013-02-01T00:00:00Z http://hdl.handle.net/1957/38288 Pararaucaria delfueyoi sp nov from the late jurassic canadon calcareo formation, chubut, argentina: Insights into the evolution of the cheirolepidiaceae Escapa, Ignacio H.; Cuneo, Nestor R.; Rothwell, Gar; Stockey, Ruth A. The discovery of 16 cylindrical conifer seed cones at the Estancia Vilan locality in the Late Jurassic Canadon Calcareo Formation of Chubut Province, Patagonia, Argentina, provides anatomically preserved specimens, allowing for the description of a second species of Pararaucaria (Cheirolepidiaceae). The new species, Pararaucaria delfueyoi, is similar in general features to the type species, Pararaucaria patagonica, but has a specifically diagnostic combination of characters that include cone size, seed number, features of histology, and seed size. Specimens are cylindrical with a narrow axis that bears helically arranged bract/scale complexes. The bract and scale diverge from the axis at 90 and separate from each other almost immediately. The ovuliferous scale extends toward the margin of the cone and then arches over to enclose two inverted nonwinged seeds within a pocket of tissue. Although the specimens are abraded such that the distal regions of the ovuliferous scales are not preserved, this combination of morphological and histological characters allows for the assignment of P. delfueyoi to the Cheirolepidiaceae with confidence. The co-occurrence of this cone with an undescribed species of Araucaria extends the geographic and stratigraphic ranges of this association, which previously has been known only from the Middle Jurassic of Santa Cruz Province of Patagonia. This extends the knowledge of anatomical variation among seed cones of Cheirolepidiaceae and improves our understanding of homology relationships for conifer seed cone structures. This is the publisher’s final pdf. The published article is copyrighted by The University of Chicago Press and can be found at: http://www.press.uchicago.edu/index.html. Fri, 01 Mar 2013 00:00:00 GMT http://hdl.handle.net/1957/38288 2013-03-01T00:00:00Z http://hdl.handle.net/1957/38301 A Perithecial Sordariomycete (Ascomycota, Diaporthales) from the Lower Cretaceous of Vancouver Island, British Columbia, Canada Bronson, Allison W.; Klymiuk, Ashley A.; Stockey, Ruth A.; Tomescu, Alexandru M. F. A perithecial ascomycete, Spataporthe taylori gen. et sp. nov., represented by >70 sporocarps is preserved by cellular permineralization in marine carbonate concretions dated at the Valanginian-Hauterivian boundary (Early Cretaceous) from Vancouver Island, British Columbia, Canada. The spheroid perithecia with lumina 330–470 µm wide and 220–320 µm high are densely distributed and entirely immersed in the tissues of a coniferous leaf. The perithecial wall consists of an outer layer of large pseudoparenchyma and an inner layer of thin filamentous nature. Perithecial necks are incompletely preserved due to taphonomic abrasion; they have a bell-shaped chamber at the base and a narrow channel, with longitudinally aligned hyphae above. The basal chamber of the neck is filled with a plug of pseudoparenchyma, which subsequently disintegrates to form a peripheral collar; periphyses are present on the basal chamber walls. A pseudoparenchymatous hymenium lines the bottom of perithecia. Asci are clavate, with thinly tapered bases, and small (30–47 µm long and 12–20 µm wide at tip), ornamented with minute papillae. They become detached from the hymenium to float freely in the perithecium. No unequivocal ascospores were found, although smaller units are present in some of the asci. The combination of immersed perithecia with complex wall structure and a well-defined hymenium, absence of paraphyses, and persistent, detachable inoperculate asci is consistent with order Diaporthales of class Sordariomycetes. The small clavate asci are comparable to those found in family Gnomoniaceae. Perithecioid ascomata are rare in the fossil record, and bona fide perithecia are known with certainty only from the Early Devonian Rhynie Chert and Cenozoic amber. Spataporthe taylori contributes a well-characterized Early Cretaceous occurrence, which is also the oldest to date, to the scarce fossil record of the Sordariomycetes and a second taxon to the fungal flora of the locality, which also includes a basidiomycete. As the oldest representative of the Diaporthales, Spataporthe provides a minimum age (136 Ma) for the order and a direct calibration point for studies of divergence times in the ascomycetes. This is the publisher’s final pdf. The published article is copyrighted by The University of Chicago Press and can be found at: http://www.press.uchicago.edu/index.html. Fri, 01 Mar 2013 00:00:00 GMT http://hdl.handle.net/1957/38301 2013-03-01T00:00:00Z