Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array

The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci).

Theoretical perspectives of enterprise architecture

The number of published Enterprise Architecture (EA) research has increased during the last few years. As a discipline, EA is still young and lacking theoretical foundation. Lately some research trying to ground EA to theory has been published, including linkage to systems theory. Enterprise Architecture can be defined as; (i) a formal description of the current and future state(s) of an organisation, and (ii) a managed change between these states to meet organisation’s stakeholders’ goals and to create value to the organisation. Based on this definition, this conceptual paper tries to shed light to theoretical underpinnings of EA from three theoretical perspectives; EA as a communication media, EA as an activity, and EA as an information technology system. Our conclusions are that; (i) EA can be categorised as a communication media and theoretically underpinned by ontology and semiotics, (ii) EA can be explained and theoretically underpinned by Activity Theory, and (iii) EA can be categorised as an information technology system and theoretically underpinned by General Systems Theory and Technology Acceptance Theory.

Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

A model intervenes: the many faces of moral hazard

This article builds on advances in social ontology to develop a new understanding of how mainstream economic modelling affects reality. We propose a new framework for analysing and describing how models intervene in the social sphere. This framework allows us to identify and articulate three key epistemic features of models as interventions: specificity, portability and formal precision. The second part of the article uses our framework to demonstrate how specificity, portability and formal precision explain the use of moral hazard models in a variety of different policy contexts, including worker compensation schemes, bank regulation and the euro-sovereign debt crisis.

An ontological approach to personalized medical knowledge recommendation

Knowledge recommendation has become a promising method in supporting the clinicians decisions and improving the quality of medical services in the constantly changing clinical environment. However, current medical knowledge management systems cannot understand users requirements accurately and realize personalized recommendation. Therefore this paper proposes an ontological approach based on semiotic principles to personalized medical knowledge recommendations. In particular, healthcare domain knowledge is conceptualized and an ontology-based user profile is built. Furthermore, the personalized recommendation mechanism is illustrated.

An ontological approach to personalized medical knowledge matching

Knowledge management has become a promising method in supporting the clinicians′ decisions and improving the quality of medical services in the constantly changing clinical environment. However, current medical knowledge management systems cannot understand users′ requirements accurately and realize personalized matching. Therefore this paper proposes an ontological approach based on semiotic principles to personalized medical knowledge matching. In particular, healthcare domain knowledge is conceptualized and an ontology-based user profile is built. Furthmore, the personalized matching mechanism and algorithm are illustrated.

Information analytics for healthcare service discovery

The concept of being ‘patient-centric’ is a challenge to many existing healthcare service provision practices. This paper focuses on the issue of referrals, where multiple stakeholders, i.e. general practitioners and patients, are encouraged to make a consensual decision based on patient needs. In this paper, we present an ontology-enabled healthcare service provision, which facilitates both patients and GPs in jointly deciding upon the referral decision. In the healthcare service provision model, we define three types of profile, which represents different stakeholders’ requirements. This model also comprises of a set of healthcare service discovery processes: articulating a service need, matching the need with the healthcare service offerings, and deciding on a best-fit service for acceptance. As a result, the healthcare service provision can carry out coherent analysis using personalised information and iterative processes that deal with requirements change over time.

Developing a knowledge management system using an ontological approach in global organisation

This paper introduces an ontology-based knowledge model for knowledge management. This model can facilitate knowledge discovery that provides users with insight for decision making. The users requiring the insight normally play different roles with different requirements in an organisation. To meet the requirements, insights are created by purposely aggregated transnational data. This involves a semantic data integration process. In this paper, we present a knowledge management system which is capable of representing knowledge requirements in a domain context and enabling the semantic data integration through ontology modeling. The knowledge domain context of United Bible Societies is used to illustrate the features of the knowledge management capabilities.

Calculating the application criticality and business risk from technology obsolescence

The problem of technology obsolescence in information intensive businesses (software and hardware no longer being supported and replaced by improved and different solutions) and a cost constrained market can severely increase costs and operational, and ultimately reputation risk. Although many businesses recognise technological obsolescence, the pervasive nature of technology often means they have little information to identify the risk and location of pending obsolescence and little money to apply to the solution. This paper presents a low cost structured method to identify obsolete software and the risk of their obsolescence where the structure of a business and its supporting IT resources can be captured, modelled, analysed and the risk to the business of technology obsolescence identified to enable remedial action using qualified obsolescence information. The technique is based on a structured modelling approach using enterprise architecture models and a heatmap algorithm to highlight high risk obsolescent elements. The method has been tested and applied in practice in three consulting studies carried out by Capgemini involving four UK police forces. However the generic technique could be applied to any industry based on plans to improve it using ontology framework methods. This paper contains details of enterprise architecture meta-models and related modelling.

Assessing the business risk of technology obsolescence through enterprise modelling

The problem of technology obsolescence in information intensive businesses (software and hardware no longer being supported and replaced by improved and different solutions) and a cost constrained market can severely increase costs and operational, and ultimately reputation risk. Although many businesses recognise technological obsolescence, the pervasive nature of technology often means they have little information to identify the risk and location of pending obsolescence and little money to apply to the solution. This paper presents a low cost structured method to identify obsolete software and the risk of their obsolescence where the structure of a business and its supporting IT resources can be captured, modelled, analysed and the risk to the business of technology obsolescence identified to enable remedial action using qualified obsolescence information. The technique is based on a structured modelling approach using enterprise architecture models and a heatmap algorithm to highlight high risk obsolescent elements. The method has been tested and applied in practice in two consulting studies carried out by Capgemini involving three UK police forces. However the generic technique could be applied to any industry based on plans to improve it using ontology framework methods. This paper contains details of enterprise architecture meta-models and related modelling.

The neoliberal way of war: a critical analysis of contemporary British security in policy and practice.

Dominant paradigms of causal explanation for why and how Western liberal-democracies go to war in the post-Cold War era remain versions of the 'liberal peace' or 'democratic peace' thesis. Yet such explanations have been shown to rest upon deeply problematic epistemological and methodological assumptions. Of equal importance, however, is the failure of these dominant paradigms to account for the 'neoliberal revolution' that has gripped Western liberal-democracies since the 1970s. The transition from liberalism to neoliberalism remains neglected in analyses of the contemporary Western security constellation. Arguing that neoliberalism can be understood simultaneously through the Marxian concept of ideology and the Foucauldian concept of governmentality – that is, as a complementary set of 'ways of seeing' and 'ways of being' – the thesis goes on to analyse British security in policy and practice, considering it as an instantiation of a wider neoliberal way of war. In so doing, the thesis draws upon, but also challenges and develops, established critical discourse analytic methods, incorporating within its purview not only the textual data that is usually considered by discourse analysts, but also material practices of security. This analysis finds that contemporary British security policy is predicated on a neoliberal social ontology, morphology and morality – an ideology or 'way of seeing' – focused on the notion of a globalised 'network-market', and is aimed at rendering circulations through this network-market amenable to neoliberal techniques of government. It is further argued that security practices shaped by this ideology imperfectly and unevenly achieve the realisation of neoliberal 'ways of being' – especially modes of governing self and other or the 'conduct of conduct' – and the re-articulation of subjectivities in line with neoliberal principles of individualism, risk, responsibility and flexibility. The policy and practice of contemporary British 'security' is thus recontextualised as a component of a broader 'neoliberal way of war'.

Relationships Among Murine CD11chigh Dendritic Cell Subsets as Revealed by Baseline Gene Expression Patterns

The functional relationships and properties of different subtypes of dendritic cells (DC) remain largely undefined. To better characterize these cells, we used global gene analysis to determine gene expression patterns among murine CD11c(high) DC subsets. CD4(+), CD8alpha(+), and CD8alpha(-) CD4(-) (double negative (DN)) DC were purified from spleens of normal C57/BL6 mice and analyzed using Affymetrix microarrays. The CD4(+) and CD8alpha(+) DC subsets showed distinct basal expression profiles differing by >200 individual genes. These included known DC subset markers as well as previously unrecognized, differentially expressed CD Ags such as CD1d, CD5, CD22, and CD72. Flow cytometric analysis confirmed differential expression in nine of nine cases, thereby validating the microarray analysis. Interestingly, the microarray expression profiles for DN cells strongly resembled those of CD4(+) DC, differing from them by <25 genes. This suggests that CD4(+) and DN DC are closely related phylogenetically, whereas CD8alpha(+) DC represent a more distant lineage, supporting the historical distinction between CD8alpha(+) and CD8alpha(-) DC. However, staining patterns revealed that in contrast to CD4(+) DC, the DN subset is heterogeneous and comprises at least two subpopulations. Gene Ontology and literature mining analyses of genes expressed differentially among DC subsets indicated strong associations with immune response parameters as well as cell differentiation and signaling. Such associations offer clues to possible unique functions of the CD11c(high) DC subsets that to date have been difficult to define as rigid distinctions.

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Coconut, Cocos nucifera L. is a major plantation crop, which ensures income for millions of people in the tropical region. Detailed molecular studies on zygotic embryo development would provide valuable clues for the identification of molecular markers to improve somatic embryogenesis. Since there is no ongoing genome project for this species, coconut expressed sequence tags (EST) would be an interesting technique to identify important coconut embryo specific genes as well as other functional genes in different biochemical pathways. The goal of this study was to analyse the ESTs by examining the transcriptome data of the different embryo tissue types together with one somatic tissue. Here, four cDNA libraries from immature embryo, mature embryo, microspore derived embryo and mature leaves were constructed. cDNA was sequenced by the Roche-454 GS-FLX system and assembled into 32621 putative unigenes and 155017 singletons. Of these unigenes, 18651 had significant sequence similarities to non-redundant protein database, from which 16153 were assigned to one or more gene ontology categories. Homologue genes, which are responsible for embryo development such as chitinase, beta-1,3-glucanase, ATP synthase CF0 subunit, thaumatin-like protein and metallothionein-like protein were identified among the embryo EST collection. Of the unigenes, 6694 were mapped into 139 KEGG pathways including carbohydrate metabolism, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism. This collection of 454-derived EST data generated from different tissue types provides a significant resource for genome wide studies and gene discovery of coconut, a non-model species.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.