Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

Determining both the expression levels of mRNA and the regulation of its translation is important in understanding specialized cell functions. In this study, we describe both the expression profiles of cells within spatiotemporal domains of the Arabidopsis thaliana flower and the post-transcriptional regulation of these mRNAs, at nucleotide resolution. We express a tagged ribosomal protein under the promoters of three master regulators of flower development. By precipitating tagged polysomes, we isolated cell type specific mRNAs that are probably translating, and quantified those mRNAs through deep sequencing. Cell type comparisons identified known cell-specific transcripts and uncovered many new ones, from which we inferred cell type-specific hormone responses, promoter motifs and coexpressed cognate binding factor candidates, and splicing isoforms. By comparing translating mRNAs with steady-state overall transcripts, we found evidence for widespread post-transcriptional regulation at both the intron splicing and translational stages. Sequence analyses identified structural features associated with each step. Finally, we identified a new class of noncoding RNAs associated with polysomes. Findings from our profiling lead to new hypotheses in the understanding of flower development

Ontology-based semantic interpretation of cylindricity specification in the next-generation GPS

Cylindricity specification is one of the most important geometrical specifications in geometrical product development. This specification can be referenced from the rules and examples in tolerance standards and technical handbooks in practice. These rules and examples are described in the form of natural language, which may cause ambiguities since different designers may have different understandings on a rule or an example. To address the ambiguous problem, a categorical data model of cylindricity specification in the next-generation Geometrical Product Specifications (GPS) was proposed at the University of Huddersfield. The modeling language used in the categorical data model is category language. Even though category language can develop a syntactically correct data model, it is difficult to interpret the semantics of the cylindricity specification explicitly. This paper proposes an ontology-based approach to interpret the semantics of cylindricity specification on the basis of the categorical data model. A scheme for translating the category language to the OWL 2 Web Ontology Language (OWL 2) is presented in this approach. Through such a scheme, the categorical data model is translated into a semantically enriched model, i.e. an OWL 2 ontology for cylindricity specification. This ontology can interpret the semantics of cylindricity specification explicitly. As the benefits of such semantic interpretation, consistency checking, inference procedures and semantic queries can be performed on the OWL 2 ontology. The proposed approach could be easily extended to support the semantic interpretations of other kinds of geometrical specifications

Business success through process based application of simulation

Progressive design practices are increasingly cognisant of the potential of building energy simulation to assist the delivery of energy efficient, sustainable buildings. However, the success of any building performance assessment hinges on the capabilities of the tool; the collective competences of the team formed to apply it; and, crucially, the existence of an in-house framework within which simulation can be applied with confidence (McElroy and Clarke 1999). There is also a need for the professions to set up mechanisms that facilitate dialogue with vendors in order to influence tool capabilities. And on the related issues of building an in-house competency and a framework for application, the two core issues facing the professions are: i) a need for the development of in-house procedures for management of simulation; and ii) quality assurance of the related models and appraisal results

Stoichiometry and Change of the mRNA Closed-Loop Factors as Translating Ribosomes Transit from Initiation to Elongation

Protein synthesis is a highly efficient process and is under exacting control. Yet, the actual abundance of translation factors present in translating complexes and how these abundances change during the transit of a ribosome across an mRNA remains unknown. Using analytical ultracentrifugation with fluorescent detection we have determined the stoichiometry of the closed-loop translation factors for translating ribosomes. A variety of pools of translating polysomes and monosomes were identified, each containing different abundances of the closed-loop factors eIF4E, eIF4G, and PAB1 and that of the translational repressor, SBP1. We establish that closed-loop factors eIF4E/eIF4G dissociated both as ribosomes transited polyadenylated mRNA from initiation to elongation and as translation changed from the polysomal to monosomal state prior to cessation of translation. eIF4G was found to particularly dissociate from polyadenylated mRNA as polysomes moved to the monosomal state, suggesting an active role for translational repressors in this process. Consistent with this suggestion, translating complexes generally did not simultaneously contain eIF4E/eIF4G and SBP1, implying mutual exclusivity in such complexes. For substantially deadenylated mRNA, however, a second type of closed-loop structure was identified that contained just eIF4E and eIF4G. More than one eIF4G molecule per polysome appeared to be present in these complexes, supporting the importance of eIF4G interactions with the mRNA independent of PAB1. These latter closed-loop structures, which were particularly stable in polysomes, may be playing specific roles in both normal and disease states for specific mRNA that are deadenylated and/or lacking PAB1. These analyses establish a dynamic snapshot of molecular abundance changes during ribosomal transit across an mRNA in what are likely to be critical targets of regulation