A plant disease extension of the Infectious Disease Ontology

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism

A Phylogenetic Study of Arecaceae Based on Seedling Morphological and Anatomical Data

A morphological and anatomical survey was carried out of seedlings of 62 taxa of palms representing all major groups. The data were analyzed using cladistic parsimony analysis. Seedling data were analyzed independently and combined with adult morphological data. Outgroup selection was made within the family using the calamoids and Nypa fruticans; outside the family, the monocot family Dasypogonaceae were used. The analysis with the calamoids and Nypa fruticans as outgroups resolved some of the major groups. The combined analysis, using both seedling and adult data and Dasypogonaceae as the outgroup, provided better resolution. Most of the major groups were monophyletic although the coryphoids and arecoids appeared paraphyletic

Neochamberlainia, a new name for Chamberlainia Artabe, Zamuner & D. W. Stev. (Zamiaceae) non Chamberlainia Grout (Brachytheciaceae)

Artabe et al. (2005) described a new fossil cycad genus, Chamberlainia, from the Allen Formation (Late Cretaceous) of Baja de Santa Rosa, Río Negro Province, Argentina. Unfortunately, this name is preoccupied by a moss genus in the Brachytheciaceae, described by Grout (1928). Thus, Chamberlainia Artabe, Zamuner & D. W. Stev. is a later homonym (Art. 53.1, ICBN Vienna) and a new name is required.Facultad de Ciencias Naturales y Muse

The Plant Ontology: A common reference ontology for plants

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms

Cycads from the Triassic of Antarctica: Permineralized Cycad Leaves

Permineralized cycad petioles and/or rachides with associated pinnae are described from two Triassic localities in the Queen Alexandria Range, central Transantarctic Mountains, Antarctica. Petiole‐rachides display an inverted‐omega‐shaped arrangement of vascular bundles typical of most genera of extant Cycadales and exarch primary xylem that link them to the modern order. Pinnae associated with the Antarctic petiole‐rachides are thin, with regularly spaced vascular bundles. They are similar to those of extant Zamia and most other genera of extant Cycadales, whose pinnae lack midribs. Other Mesozoic fossil cycads (e.g., Charmorgia, Lyssoxylon, Lioxylon) have endarch petiole vascular bundles that in some cases were previously considered more similar to those of Bennettitales than those of Cycadales. We suggest, however, that the endarch xylem of these taxa is typical of Cycadales because in extant cycads, the protoxylem changes from endarch to exarch within the base of the petiole. Evolution of cycad leaf form is reviewed based on evidence from the fossil record

Neochamberlainia, a new name for Chamberlainia Artabe, Zamuner & D. W. Stev. (Zamiaceae) non Chamberlainia Grout (Brachytheciaceae)

Artabe et al. (2005) described a new fossil cycad genus, Chamberlainia, from the Allen Formation (Late Cretaceous) of Baja de Santa Rosa, Río Negro Province, Argentina. Unfortunately, this name is preoccupied by a moss genus in the Brachytheciaceae, described by Grout (1928). Thus, Chamberlainia Artabe, Zamuner & D. W. Stev. is a later homonym (Art. 53.1, ICBN Vienna) and a new name is required.Facultad de Ciencias Naturales y Muse

Neochamberlainia, a new name for Chamberlainia Artabe, Zamuner & D. W. Stev. (Zamiaceae) non Chamberlainia Grout (Brachytheciaceae)

Artabe et al. (2005) described a new fossil cycad genus, Chamberlainia, from the Allen Formation (Late Cretaceous) of Baja de Santa Rosa, Río Negro Province, Argentina. Unfortunately, this name is preoccupied by a moss genus in the Brachytheciaceae, described by Grout (1928). Thus, Chamberlainia Artabe, Zamuner & D. W. Stev. is a later homonym (Art. 53.1, ICBN Vienna) and a new name is required.Facultad de Ciencias Naturales y Muse

ESTimating plant phylogeny: lessons from partitioning

BACKGROUND: While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS: A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION: Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products

The Ursinus Weekly, March 12, 1962

Nobel Prize-winner here tonight: Dr. Linus Pauling to address special forum on Science and international relations • Book No more war! Dr. Pauling\u27s credo • Local high school pupils invited to PSEA panel • UC students attend I.C.G. convention • Student-faculty talent show to finish Campus Chest charity drive Friday • College\u27s concert band to perform next Thursday • Lauderdale braces for Spring influx • Civil liberty\u27s Cox visits U.C. campus • Campus Chest activities continue this week • Ursinus invites public to use College Library • St. Pat\u27s twist theme of frosh dance Saturday • Pre-med club to see films depicting Caesarian birth • Editorial: Just this once • Penna. folk festival planned for Harrisburg • Ursinus in the past • Curtain Club offers two plays; One-act shows given last Thursday • Women\u27s hairbreadth victories mark basketball play; Sansenbach stars • High scoring continues; Intramural finish nears • Mermaids win two in week\u27s action • Sports publicist evaluates season • Intramural corner • Cindermen seem strong as five lettermen return • Chief McClure hustles vagrant to county jail • Collegeville tops Phoenix YMCA basketball league • Collegeville firemen take part in Phila. exhibit • Faculty hoopsters triumph in benefit against girls • Graduate grantshttps://digitalcommons.ursinus.edu/weekly/1314/thumbnail.jp