Silicate-based bioceramics for periodontal regeneration

Periodontal disease is characterized by the destruction of the tissues that attach the tooth to the alveolar bone. Various methods for regenerative periodontal therapy including the use of barrier membranes, bone replacement grafts, and growth factor delivery have been investigated; however, true regeneration of periodontal tissue is still a significant challenge to scientists and clinicians. The focus on periodontal tissue engineering has shifted from attempting to recreate tissue replacements/constructs to the development of biomaterials that incorporate and release regulatory signals to achieve in situ periodontal regeneration. The release of ions and molecular cues from biomaterials may help to unlock latent regenerative potential in the body by regulating cell proliferation and differentiation towards different lineages (e.g. osteoblasts and cementoblasts). Silicate-based bioactive materials, including bioactive silicate glasses and ceramics, have become the materials of choice for periodontal regeneration, due to their favourable osteoconductivity and bioactivity. This article will focus on the most recent advances in the in vitro and in vivo biological application of silicate-based ceramics, specifically as it relates to periodontal tissue engineering.

Design of a tangible data visualization

In this paper we describe the design of DNA Jewellery, which is a wearable tangible data representation of personal DNA profile data. An iterative design process was followed to develop a 3D form-language that could be mapped to standard DNA profile data, with the aim of retaining readability of data while also producing an aesthetically pleasing and unique result in the area of personalized design. The work explores design issues with the production of data tangibles, contributes to a growing body of research exploring tangible representations of data and highlights the importance of approaches that move between technology, art and design.

The past, present and future of carbon labelling for construction materials – a review

Global climate change is one of the most significant environmental issues that can harm human development. One central issue for the building and construction industry to address global climate change is the development of a credible and meaningful way to measure greenhouse gas (GHG) emissions. While Publicly Available Specification (PAS) 2050, the first international GHG standard, has been proven to be successful in standardizing the quantification process, its contribution to the management of carbon labels for construction materials is limited. With the recent publication of ISO 14067: Greenhouse gases – carbon footprint of products – requirements and guidelines for quantification and communication in May 2013, it is necessary for the building and construction industry to understand the past, present and future of the carbon labelling practices for construction materials. A systematic review shows that international GHG standards have been evolving in terms of providing additional guidance on communication and comparison, as well as less flexibility on the use of carbon labels. At the same time, carbon labelling schemes have been evolving on standardization and benchmarking. In addition, future actions are needed in the aspect of raising consumer awareness, providing benchmarking, ensuring standardization and developing simulation technologies in order for carbon labelling schemes for construction materials to provide credible, accurate and transparent information on GHG emissions.

How public owners communicate the sustainability requirements of green design-build projects

The design-build (DB) system is regarded as an effective means of delivering sustainable buildings. Specifying clear sustainability requirements to potential contractors is of great importance to project success. This research investigates the current state-of-the-practice for the definition of sustainability requirements within the public sectors of the U.S. construction market using a robust content analysis of 49 DB requests for proposals (RFPs). The results reveal that owners predominantly communicate their desired level of sustainability through the LEED certification system. The sustainability requirement has become an important dimension for the best-value evaluation of DB contractors with specific importance weightings of up to 25%. Additionally, owners of larger projects and who provide less design information in their RFPs generally allocate significantly higher importance weightings to sustainability requirements. The primary knowledge contribution of this study to the construction industry is the reveal of current trend in DB procurement for green projects. The findings also provide owners, architects, engineers, and constructors with an effective means of communicating sustainability objectives in solicitation documents.

Applying a validation framework to a working airport terminal model

Validation is an important issue in the development and application of Bayesian Belief Network (BBN) models, especially when the outcome of the model cannot be directly observed. Despite this, few frameworks for validating BBNs have been proposed and fewer have been applied to substantive real-world problems. In this paper we adopt the approach by Pitchforth and Mengersen (2013), which includes nine validation tests that each focus on the structure, discretisation, parameterisation and behaviour of the BBNs included in the case study. We describe the process and result of implementing a validation framework on a model of a real airport terminal system with particular reference to its effectiveness in producing a valid model that can be used and understood by operational decision makers. In applying the proposed validation framework we demonstrate the overall validity of the Inbound Passenger Facilitation Model as well as the effectiveness of the validity framework itself.

Actinidia DRM1 : an intrinsically disordered protein whose mRNA expression is inversely correlated with spring budbreak in Kiwifruit

Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein levels. It is predicted to be an intrinsically disordered protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia.

Analysis of expressed sequence tags from Actinidia : Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

Identification and characterization of flowering genes in kiwifruit : sequence conservation and role in kiwifruit flower development

Background Flower development in kiwifruit (Actinidia spp.) is initiated in the first growing season, when undifferentiated primordia are established in latent shoot buds. These primordia can differentiate into flowers in the second growing season, after the winter dormancy period and upon accumulation of adequate winter chilling. Kiwifruit is an important horticultural crop, yet little is known about the molecular regulation of flower development. Results To study kiwifruit flower development, nine MADS-box genes were identified and functionally characterized. Protein sequence alignment, phenotypes obtained upon overexpression in Arabidopsis and expression patterns suggest that the identified genes are required for floral meristem and floral organ specification. Their role during budbreak and flower development was studied. A spontaneous kiwifruit mutant was utilized to correlate the extended expression domains of these flowering genes with abnormal floral development. Conclusions This study provides a description of flower development in kiwifruit at the molecular level. It has identified markers for flower development, and candidates for manipulation of kiwifruit growth, phase change and time of flowering. The expression in normal and aberrant flowers provided a model for kiwifruit flower development.

Kiwifruit floral gene APETALA2 is alternatively spliced and accumulates in aberrant indeterminate flowers in the absence of miR172

In Arabidopsis, the identity of perianth and reproductive organs are specified by antagonistic action of two floral homeotic genes, APETALA2 (AP2) and AGAMOUS (AG). AP2 is also negatively regulated by an evolutionary conserved interaction with a microRNA, miR172, and has additional roles in general plant development. A kiwifruit gene with high levels of homology to AP2 and AP2-like genes from other plant species was identified. The transcript was abundant in the kiwifruit flower, particularly petal, suggesting a role in floral organ identity. Splice variants were identified, all containing both AP2 domains, including a variant that potentially produces a shorter transcript without the miRNA172 targeting site. Increased AP2 transcript accumulation was detected in the aberrant flowers of the mutant 'Pukekohe dwarf' with multiple perianth whorls and extended petaloid features. In contrast to normal kiwifruit flowers, the aberrant flowers failed to accumulate miR172 in the developing whorls, although accumulation was detected at the base of the flower. An additional role during dormancy in kiwifruit was proposed based on AP2 transcript accumulation in axillary buds before and after budbreak.

Protocol : A highly sensitive RT-PCR method for detection and quantification of microRNAs

MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding their roles in specific cells and tissues. However, gel-based assays currently used to detect miRNAs are very limited in terms of throughput, sensitivity and specificity. Here we provide protocols for detection and quantification of miRNAs by RT-PCR. We describe an end-point and real-time looped RT-PCR procedure and demonstrate detection of miRNAs from as little as 20 pg of plant tissue total RNA and from total RNA isolated from as little as 0.1 l of phloem sap. In addition, we have developed an alternative real-time PCR assay that can further improve specificity when detecting low abundant miRNAs. Using this assay, we have demonstrated that miRNAs are differentially expressed in the phloem sap and the surrounding vascular tissue. This method enables fast, sensitive and specific miRNA expression profiling and is suitable for facilitation of high-throughput detection and quantification of miRNA expression.

Interpretation of association rules with multi-tier granule mining

This study was a step forward to improve the performance for discovering useful knowledge – especially, association rules in this study – in databases. The thesis proposed an approach to use granules instead of patterns to represent knowledge implicitly contained in relational databases; and multi-tier structure to interpret association rules in terms of granules. Association mappings were proposed for the construction of multi-tier structure. With these tools, association rules can be quickly assessed and meaningless association rules can be justified according to the association mappings. The experimental results indicated that the proposed approach is promising.

The genome of the domesticated apple (Malus × domestica Borkh.)

We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

Conservation and divergence of four kiwifruit SVP-like MADS-box genes suggest distinct roles in kiwifruit bud dormancy and flowering

MADS-box genes similar to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been implicated in the regulation of flowering in annual species and bud dormancy in perennial species. Kiwifruit (Actinidia spp.) are woody perennial vines where bud dormancy and out-growth affect flower development. To determine the role of SVP-like genes in dormancy and flowering of kiwifruit, four MADS-box genes with homology to Arabidopsis SVP, designated SVP1, SVP2, SVP3, and SVP4, have been identified and analysed in kiwifruit and functionally characterized in Arabidopsis. Phylogenetic analysis indicate that these genes fall into different sub-clades within the SVP-like gene group, suggesting distinct functions. Expression was generally confined to vegetative tissues, and increased transcript accumulation in shoot buds over the winter period suggests a role for these genes in bud dormancy. Down-regulation before flower differentiation indicate possible roles as floral repressors. Over-expression and complementation studies in Arabidopsis resulted in a range of floral reversion phenotypes arising from interactions with Arabidopsis MADS-box proteins, but only SVP1 and SVP3 were able to complement the svp mutant. These results suggest that the kiwifruit SVP-like genes may have distinct roles during bud dormancy and flowering.

A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds

Budbreak in kiwifruit (Actinidia deliciosa) can be poor in locations that have warm winters with insufficient winter chilling. Kiwifruit vines are often treated with the dormancy-breaking chemical hydrogen cyanamide (HC) to increase and synchronize budbreak. This treatment also offers a tool to understand the processes involved in budbreak. A genomics approach is presented here to increase our understanding of budbreak in kiwifruit. Most genes identified following HC application appear to be associated with responses to stress, but a number of genes appear to be associated with the reactivation of growth. Three patterns of gene expression were identified: Profile 1, an HC-induced transient activation; Profile 2, an HC-induced transient activation followed by a growth-related activation; and Profile 3, HC- and growth-repressed. One group of genes that was rapidly up-regulated in response to HC was the glutathione S-transferase (GST) class of genes, which have been associated with stress and signalling. Previous budbreak studies, in three other species, also report up-regulated GST expression. Phylogenetic analysis of these GSTs showed that they clustered into two sub-clades, suggesting a strong correlation between their expression and budbreak across species.

Imaging of human lens lipids by desorption electrospray ionization mass spectrometry

The lipid composition of the human lens is distinct from most other tissues in that it is high in dihydrosphingomyelin and the most abundant glycerophospholipids in the lens are unusual 1-O-alkyl-ether linked phosphatidylethanolamines and phosphatidylserines. In this study, desorption electrospray ionization (DESI) mass spectrometry-imaging was used to determine the distribution of these lipids in the human lens along with other lipids including, ceramides, ceramide-1-phosphates, and lyso 1-O-alkyl ethers. To achieve this, 25 μm lens slices were mounted onto glass slides and analyzed using a linear ion-trap mass spectrometer equipped with a custom-built, 2-D automated DESI source. In contrast to other tissues that have been previously analyzed by DESI, the presence of a strong acid in the spray solvent was required to desorb lipids directly from lens tissue. Distinctive distributions were observed for [M + H]+ ions arising from each lipid class. Of particular interest were ionized 1-O-alkyl phosphatidylethanolamines and phosphatidylserines, PE (18:1e/18:1), and PS (18:1e/18:1), which were found in a thin ring in the outermost region of the lens. This distribution was confirmed by quantitative analysis of lenses that were sectioned into four distinct regions (outer, barrier, inner, and core), extracted and analyzed by electrospray ionization tandem mass spectrometry. DESI-imaging also revealed a complementary distribution for the structurally-related lyso 1-O-alkyl phosphatidylethanolamine, LPE (18:1e), which was localized closer to the centre of the lens. The data obtained in this study indicate that DESI-imaging is a powerful tool for determining the spatial distribution of human lens lipids. © 2010 American Society for Mass Spectrometry.