The Polytope Formalism: isomerism and associated unimolecular isomerisation

This thesis concerns the ontology of isomerism, this encompassing the conceptual frameworks and relationships that comprise the subject matter; the necessary formal definitions, nomenclature, and representations that have impacts reaching into unexpected areas such as drug registration and patent specifications; the requisite controlled and precise vocabulary that facilitates nuanced communication; and the digital/computational formalisms that underpin the chemistry software and database tools that empower chemists to perform much of their work. Using conceptual tools taken from Combinatorics, and Graph Theory, means are presented to provide a unified description of isomerism and associated unimolecular isomerisation spanning both constitutional isomerism and stereoisomerism called the Polytope Formalism. This includes unification of the varying approaches historically taken to describe and understand stereoisomerism in organic and inorganic compounds. Work for this Thesis began with the synthesis, isolation, and characterisation of compounds not adequately describable using existing IUPAC recommendations. Generalisation of the polytopal-rearrangements model of stereoisomerisation used for inorganic chemistry led to the prescriptions that could deal with the synthesised compounds, revealing an unrecognised fundamental form of isomerism called akamptisomerism. Following on, this Thesis describes how in attempting to place akamptisomerism within the context of existing stereoisomerism reveals significant systematic deficiencies in the IUPAC recommendations. These shortcomings have limited the conceptualisation of broad classes of compounds and hindered development of molecules for medicinal and technological applications. It is shown how the Polytope Formalism can be applied to the description of constitutional isomerism in a practical manner. Finally, a radically different medicinal chemistry design strategy with broad application, based upon the principles, is describe

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion

Recognition of an extended record of euglenoid cysts: Implications for the end-Triassic mass extinction

The enigmatic non-pollen palynomorph Chomotriletes, occurs consistently within sediments associated with the end-Triassic mass-extinction. Based on a detailed palynological survey and other published records from Europe, Chomotriletes is prevalent within the uppermost Rhaetian Contorta and Triletes Beds and its equivalents elsewhere. Chomotriletes is now a senior synonym for Permian Circulisporites, Meso- to Cenozoic Pseudoschizaea, and Quaternary to Recent Concentricystes. Its widespread occurrence has significance for our understanding of the end-Triassic mass-extinction, but its biological affinity and ecological preference have remained contentious for almost a century. We undertook a TEM examination of a Holocene and a Pliocene example of Concentricystes and found their structure to be a close match to the wall of Jurassic Pseudoschizaea from Italy that has been interpreted to belong to cysts of the Euglenophyceae. Together with a nascent understanding of a deep time record of the euglenoid, Moyeria, Chomotriletes helps document a terrestrial signature of the Euglenophyceae in the fossil record. An extensive literature survey indicates that Chomotriletes is associated with wetlands and riverine floodplain soils, and that it inhabited mainly temperate to tropical latitudes and continues to do so to the present day. Its presence in ancient marine sediments therefore indicates transport via weathering and erosion. The association with wetlands is in line with the ecological preferences of species of the Euglenophyceae. The presence of euglenoid cysts in association with the end-Triassic extinction fits a scenario in which enhanced rainfall followed by strong soil erosion resulted in the release and redeposition of Chomotriletes into shallow marine settings

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem

A horticultural study of Liriope and Ophiopogon: nomenclature, morphology, and culture

Liriopogons are evergreen perennials with a confusing taxonomy. New cultivars are being rapidly selected and named. The landscape industry uses them extensively and they are being planted in improper sites. Morphological studies were done at Louisiana State University in Baton Rouge, Louisiana to identify cultivars by comparing plants to botanical keys. Cultural studies were done at Burden Station in Baton Rouge, Louisiana by comparing cultivars in sun and 63% shade, and by greenhouse fertilization experiments, and pruning experiments. Plants were harvested, studied, dried and mounted in the Louisiana State University Herbarium as permanent record. Of the 19 cultivars of Liriope and Ophiopogon studied, there were two genera and eight species identified. These were studied for flower morphology on dissected flowers under microscope. Aztec grass, which had been labeled Ophiopogon jaburan was discovered to be Ophiopogon intermedius. Liriope muscari \u27Big Blue\u27 is L. muscari but some plantings in landscapes are L. exiliflora. The cultivar \u27Samantha\u27 has erroneously been classified L. muscari but cf. to L. exiliflora, according to the rhizomatous root system and spaces between flowers. \u27Evergreen Giant\u27 and Supergreen Giant were called cultivars of Liriope muscari and they are morphologically Liriope gigantea \u27Evergreen Giant\u27 and \u27Merton Jacobs\u27 Supergreen Giant™ respectively. A three-year study at Burden Center with 19 cultivars, sun and 63% shade treatment and six replications showed the top sun performing cultivar to be Liriope gigantea \u27Merton Jacobs\u27 Supergreen Giant™. The second was Liriope muscari \u27Big Blue.\u27 Liriope muscari \u27Monroe White\u27 and Ophiopogon japonicus \u27Silver Mist\u27 were the two low sun performers. The top shade performers were O. japonicus and O. japonicus \u27Nana.\u27 The low sun performers were Liriope muscari \u27Densiflora\u27 and Liriope gigantea \u27Evergreen Giant.\u27 Bib production benefited by 20% pruning in Ophiopogon intermedius but did not have significant effects on any other cultivar. Plant height, quality, N and P were the most influenced variables for all combinations of liquid fertilization + controlled release and liquid fertilizer alone over any of the controlled release rates of fertilization

Fossil fungi from early Tertiary deposits of southern England

A selective review of fungi in the fossil record is given, special consideration being given to the more dubious and perhaps extravagant claims for Precambrian occurrences of fossil fungi. The various taxonomic and nomenclatural methods that are used and have been proposed for both epiphyllous remains and dispersed fossil fungal spores are detailed and some alternative procedures are suggested. Especial emphasis is placed upon the necessity for population study techniques to establish taxonomic limits for variability within taxa for dispersed fossil fungal spores irrespective of which classification and nomenclatural system is followed. Two early Tertiary deposits, one Palaeocene (Newbury) and one Eocene (Hordle Cliff) have yielded extremely diverse fossil fungal floras, encompassing epiphyllous forms and dispersed spores. After a brief description of the geology of the two sites, the epiphyllous forms are studied in detail. Specimens attributable to the following form-taxa are reported for the first time from British Tertiary deposits: Callimothallus, Cribrites, Meliolinites, Trichothyrites, and Stomiopeltites and the creation of a new form-genus Actinopeltites is proposed. The modern affinities of these form-taxa in relation to taxonomic revisions of the living ascomycete families concerned is discussed.<p

Libri novi

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43287/1/11046_2005_Article_BF02053453.pd