Developing pineapple fruit has a small transcriptome dominated by metallothionein

In a first step toward understanding the molecular basis of pineapple fruit development, a sequencing project was initiated to survey a range of expressed sequences from green unripe and yellow ripe fruit tissue. A highly abundant metallothionein transcript was identified during library construction, and was estimated to account for up to 50% of all EST library clones. Library clones with metallothionein subtracted were sequenced, and 408 unripe green and 1140 ripe yellow edited EST clone sequences were retrieved. Clone redundancy was high, with the combined 1548 clone sequences clustering into just 634 contigs comprising 191 consensus sequences and 443 singletons. Half of the EST clone sequences clustered within 13.5% and 9.3% of contigs from green unripe and yellow ripe libraries, respectively, indicating that a small subset of genes dominate the majority of the transcriptome. Furthermore, sequence cluster analysis, northern analysis, and functional classification revealed major differences between genes expressed in the unripe green and ripe yellow fruit tissues. Abundant genes identified from the green fruit include a fruit bromelain and a bromelain inhibitor. Abundant genes identified in the yellow fruit library include a MADS box gene, and several genes normally associated with protein synthesis, including homologues of ribosomal L10 and the translation factors SUI1 and eIF5A. Both the green unripe and yellow ripe libraries contained high proportions of clones associated with oxidative stress responses and the detoxification of free radicals.

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did flat contain ail apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-rnRNA contamination during library construction, or alternatively represent nonspecific transcriptional noise. Here we Show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts Of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide Stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.

Construction and analysis of a metagenomic library from an enhanced biological phosphorus removal biomass

The enhanced biological phosphorus removal (EBPR) process is regularly used for the treatment of wastewater, but suffers from erratic performance. Successful EBPR relies on the growth of bacteria called polyphosphate-accumulating organisms (PAOs), which store phosphorus intracellularly as polyphosphate, thus removing it from wastewater. Metabolic models have been proposed which describe the measured chemical transformations, however genetic evidence is lacking to confirm these hypotheses. The aim of this research was to generate a metagenomic library from biomass enriched in PAOs as determined by phenotypic data and fluorescence in situ hybridisation (FISH) using probes specific for the only described PAO to date, Candidatus Accumulibacter phosphatis. DNA extraction methods were optimised and two fosmid libraries were constructed which contained 93 million base pairs of metagenomic data. Initial screening of the library for 16S rRNA genes revealed fosmids originating from a range of non-pure-cultured wastewater bacteria. The metagenomic libraries constructed will provide the ability to link phylogenetic and metabolic data for bacteria involved in nutrient removal from wastewater. Keywords DNA extraction; EBPR; metagenomic library; 16S rRNA gene.

Developing students' critical literacy: Exploring identity construction in young adult fiction

The authors use a critical literacy stance to engage students in a discussion of young adult literature from Australia and America. They offer a framework teachers can use to initiate discussions based on critical literacy in their own classrooms.

Muscularity, the habitus and the social construction of gender: Towards a gender-relevant physical education

This paper begins to develop the concept of gender-relevant physical education, combining the work of Pierre Bourdieu and his notion of the habitus and feminist philosopher Iris Marion Young's analysis of feminine motility. It draws on data generated from a study of young people's articulation of the relationships between muscularity, physicality and gender. The social construction of the body has been of central importance to the construction of femininities and masculinities, and has formed an enduring meta-theme through much of the research on physical education and gender. We build on the young people's insights to argue that Bourdieu's notions of the habitus and the exchange of physical capital provide a useful means of conceptualizing issues of embodiment and gender in school physical education and sport. We conclude by sketching an outline of gender-relevant physical education as a process of interrupting the habitus.

Social positioning and the construction of a youth sports club

This article uses the concept of social positioning to explore the construction of a youth sports club by young people, their parents and coaches. The year-long ethnography of Forest Athletics Club (FAC) identified two athlete positions of Samplers and Beginning Specializers. Four parents’ positions were identified, those of Non-Attenders, Spectators, Helpers and Committed Members. One coach position was the Committed Volunteer. Each of these positions was interdependent. Particular expectations, practices and values were attached to these positions. It is argued that the club operates according to multiple agendas and that FAC is a complex and dynamic social phenomenon that is practised differently by the three groups of key players.

The role of gender in the construction and evaluation of feedback effectiveness

This study investigated factors that influence managers’ conceptions and subordinates’ perceptions of effective feedback. A social rules perspective was used to operationalize male and female managers’ conceptions of effective negative feedback. In the first study, 68 male and female managers identified their optimal strategies for providing feedback to subordinates. Male and female managers endorsed different goals and tactics for giving negative feedback, particularly in terms of levels of participation and directness. In the second study, 116 male and female subordinates evaluated the comparative effectiveness and difficulty of these and other standard approaches to feedback. The female manager strategy was evaluated by both men and women as generally more task and relationship effective but not more difficult to enact.

Use of a probabilistic neural network to reduce costs of selecting construction rock

Rocks used as construction aggregate in temperate climates deteriorate to differing degrees because of repeated freezing and thawing. The magnitude of the deterioration depends on the rock's properties. Aggregate, including crushed carbonate rock, is required to have minimum geotechnical qualities before it can be used in asphalt and concrete. In order to reduce chances of premature and expensive repairs, extensive freeze-thaw tests are conducted on potential construction rocks. These tests typically involve 300 freeze-thaw cycles and can take four to five months to complete. Less time consuming tests that (1) predict durability as well as the extended freeze-thaw test or that (2) reduce the number of rocks subject to the extended test, could save considerable amounts of money. Here we use a probabilistic neural network to try and predict durability as determined by the freeze-thaw test using four rock properties measured on 843 limestone samples from the Kansas Department of Transportation. Modified freeze-thaw tests and less time consuming specific gravity (dry), specific gravity (saturated), and modified absorption tests were conducted on each sample. Durability factors of 95 or more as determined from the extensive freeze-thaw tests are viewed as acceptable—rocks with values below 95 are rejected. If only the modified freeze-thaw test is used to predict which rocks are acceptable, about 45% are misclassified. When 421 randomly selected samples and all four standardized and scaled variables were used to train aprobabilistic neural network, the rate of misclassification of 422 independent validation samples dropped to 28%. The network was trained so that each class (group) and each variable had its own coefficient (sigma). In an attempt to reduce errors further, an additional class was added to the training data to predict durability values greater than 84 and less than 98, resulting in only 11% of the samples misclassified. About 43% of the test data was classed by the neural net into the middle group—these rocks should be subject to full freeze-thaw tests. Thus, use of the probabilistic neural network would meanthat the extended test would only need be applied to 43% of the samples, and 11% of the rocks classed as acceptable would fail early.

Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia

We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large. numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, S'-end clusters identify regions that are potential promoters for 8637 known genes and S'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.

Coherent state construction of representations of osp(2|2) and primary fields of osp(2|2) conformal field theory

Representations of the superalgebra osp(2/2)(k)((1)) and current superalgebra. osp(2/2)k in the standard basis are investigated. All finite-dimensional typical and atypical representations of osp(2/2) are constructed by the vector coherent state method. Primary fields of the non-unitary conformal field theory associated with osp(2/2)(k)((1)) in the standard basis are obtained for arbitrary level k. (C) 2004 Elsevier B.V. All rights reserved.

Woodrow Wilson's ''Rhetorical restructuring'': The transformation of the American self and the construction of the German enemy

From a comprehensive study of the public addresses of Woodrow Wilson in the period following the outbreak of the war in Europe in August 1914 to the war's conclusion in June 1919, this essay examines Wilson's transformation of the long-held vision of America as merely a great example of liberty to its embodiment as the self-sacrificing champion of liberty. It will demonstrate how this transformation of the American "self" was inextricably connected to a changing image of the war and the construction of an enemy image of the German government.

The determinants of the vertical boundaries of the construction firm

In the last few years, transaction cost economics has become a popular theory within the construction research community. This approach has been singularly applied as a means to explain and predict phenomena concerning the construction firm, including its vertical boundaries. However, this is at a time when the chief proponents of transaction costs are urging researchers to take a pluralistic stance in relation to the theory of the firm. The aim of this paper is to develop a pluralistic approach to the vertical boundaries of the construction firm. In order to achieve this, an integrative framework is described, based on the development of the efficient boundaries problem and the capabilities approach to vertical integration. Specifically, this framework draws on the complementary strengths of transaction cost economics and the resource-based view. It is concluded that the potential relative merits of theoretical pluralism, in terms of the vertical boundaries of the construction firm, are sufficient grounds to motivate empirical testing of the predictions associated with the integrative framework of vertical integration presented