Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

International audienceABSTRACT: BACKGROUND: Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified. RESULTS: Here we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes, using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions. CONCLUSIONS: The experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate /hormone connections implicated by this time-series data is also evaluated

Absence of Kaposi\u27s Sarcoma-Associated Herpesvirus DNA in Bacillary Angiomatosis-Peliosis Lesions

Bartonella henselae and B. quintana induce an unusual vascular proliferative tissue response known as bacillary angiomatosis (BA) and bacillary peliosis (BP) in some human hosts. The mechanisms of Bartonella-associated vascular proliferation remain unclear. Although host factors probably play a role, microbial coinfection has not been ruled out. Because of the vascular proliferative characteristics noted in both Kaposi\u27s sarcoma (KS) and BA and occasional colocalization of KS and BA, the possibility was explored that KS-associated herpes virus (KSHV) might be associated with BA lesions. Tissues with BA and positive and negative control tissues were tested for the presence of KSHV DNA by a sensitive polymerase chain reaction assay. Only 1 of 10 BA tissues, a splenic biopsy, was positive in this assay; this tissue was from a patient with concomitant KS of the skin. Thus, KSHV is probably not involved in the vascular proliferative response seen in BA-BP

Educating consent? A conversation with Noam Chomsky on the university and business school education

In what follows, we present a conversation with Professor Noam Chomsky on the topic of whether the business school might be a site for progressive political change. The conversation covers a number of key issues related to pedagogy, corporate social responsibility and working conditions in the contemporary business school. We hope the conversion will contribute to the ongoing discussion about the role of the business school in neoliberal societies

Reflections on Modern Macroeconomics: Can We Travel Along a Safer Road?

In this paper we sketch some reflections on the pitfalls and inconsistencies of the research program - currently dominant among the profession - aimed at providing microfoundations to macroeconomics along a Walrasian perspective. We argue that such a methodological approach constitutes an unsatisfactory answer to a well-posed research question, and that alternative promising routes have been long mapped out but only recently explored. In particular, we discuss a recent agent-based, truly non-Walrasian macroeconomic model, and we use it to envisage new challenges for future research.Comment: Latex2e v1.6; 17 pages with 4 figures; for inclusion in the APFA5 Proceeding

Law, politics and the governance of English and Scottish joint-stock companies 1600-1850

This article examines the impact of law on corporate governance by means of a case study of joint-stock enterprise in England and Scotland before 1850. Based on a dataset of over 450 company constitutions together with qualitative information on governance practice, it finds little evidence to support the hypothesis that common-law regimes such as England were more supportive of economic growth than civil-law jurisdictions such as Scotland: indeed, levels of shareholder protection were slightly stronger in the civil-law zone. Other factors, such as local political institutions, played a bigger role in shaping organisational forms and business practice

Come back Marshall, all is forgiven? : Complexity, evolution, mathematics and Marshallian exceptionalism

Marshall was the great synthesiser of neoclassical economics. Yet with his qualified assumption of self-interest, his emphasis on variation in economic evolution and his cautious attitude to the use of mathematics, Marshall differs fundamentally from other leading neoclassical contemporaries. Metaphors inspire more specific analogies and ontological assumptions, and Marshall used the guiding metaphor of Spencerian evolution. But unfortunately, the further development of a Marshallian evolutionary approach was undermined in part by theoretical problems within Spencer's theory. Yet some things can be salvaged from the Marshallian evolutionary vision. They may even be placed in a more viable Darwinian framework.Peer reviewedFinal Accepted Versio

Public health research support through the European Structural Funds in Central and Eastern Europe and the Mediterranean

Background. Public health research provides evidence for practice across fields including health care, health promotion and health surveillance. Levels of public health research vary markedly across European Union (EU) countries, and are lowest in the EU’s new member states (in Central and Eastern Europe and the Mediterranean). However, these countries now receive most of the EU’s Structural Funds, some of which are allocated to research. Methods. STEPS, an EU-funded study, sought to assess support for public health research at national and European levels. To identify support through the Structural funds, STEPS drew information from country respondents and internet searches for all twelve EU new member states. Results. The EU allocates annually around €7 billion through the Structural Funds for member states’ own use on research. These funds can cover infrastructure, academic employment, and direct research grants. The programmes emphasise links to business. Support for health research includes major projects in biosciences, but direct support for public health research was found in only three countries – Cyprus, Latvia and Lithuania. Conclusions. Public health research is not prioritised in the EU’s Structural Funds programme in comparison with biomedicine. For the research dimension of the new European programme for Structural Funds 2014-2002, ministries of health should propose public health research to strengthen the evidence-base for European public health policy and practice