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Pokhilko A.,University of Edinburgh | Fernandez A.P.,University of Edinburgh | Edwards K.D.,University of Edinburgh | Edwards K.D.,Advanced Technologies Park | And 3 more authors.
Molecular Systems Biology | Year: 2012

Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene PSEUDO-RESPONSE REGULATOR 9 was repressed by an evening gene, previously identified with TIMING OF CAB EXPRESSION1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure. © 2012 EMBO and Macmillan Publishers Limited All rights reserved.

Cobano J.A.,University of Seville | Conde R.,University of Seville | Alejo D.,University of Seville | Ollero A.,Advanced Technologies Park
Proceedings - IEEE International Conference on Robotics and Automation | Year: 2011

This paper presents a collision-free path planning method for an aerial vehicle sharing airspace with other aerial vehicles. It is based on grid models and genetic algorithms to find safe trajectories. Monte-Carlo method is used to evaluate the best predicted trajectories considering different sources of uncertainty such as the wind, the inaccuracies in the vehicle model and limitations of on-board sensors and control system. © 2011 IEEE.

Eswaran S.,Advanced Technologies Park | Misra A.,Singapore Management University | Bergamaschi F.,IBM | La Porta T.,Pennsylvania State University
ACM Transactions on Sensor Networks | Year: 2012

This article develops a utility-based optimization framework for resource sharing by multiple competing missions in a mission-oriented wireless sensor network (WSN) environment. Prior work on network utility maximization (NUM) based optimization has focused on unicast flows with sender-based utilities in either wireline or wireless networks. In this work, we develop a generalized NUM model to consider three key new features observed in mission-centric WSN environments: i) the definition of the utility of an individual mission (receiver) as a joint function of data from multiple sensor sources; ii) the consumption of each sender's (sensor) data by multiple missions; and iii) the multicast-tree-based dissemination of each sensor's data flow, using link-layer broadcasts to exploit the "wireless broadcast advantage" in data forwarding. We show how a price-based, distributed protocol (WSN-NUM) can ensure optimal and proportionally fair rate allocation across multiple missions, without requiring any coordination among missions or sensors. We also discuss techniques to improve the speed of convergence of the protocol, which is essential in an environment as dynamic as the WSN. Further, we analyze the impact of various network and protocol parameters on the bandwidth utilization of the network, using a discrete-event simulation of a stationary wireless network. Finally, we corroborate our simulation-based performance results of the WSN-NUM protocol with an implementation of an 802.11b network. © 2012 ACM 1550-4859/2012/03-ART17 $10.00.

Massey E.D.,British American Tobacco | Hinchliffe S.,Advanced Technologies Park
Mutation Research - Genetic Toxicology and Environmental Mutagenesis | Year: 2010

Reference genotoxic compounds 2-aminoanthracene, diethylstilboesterol and vinblastine were tested in the in vitro micronucleus assay using Chinese hamster V79 derived cells in the laboratories of British American Tobacco in the UK. The work was conducted in support of the cytotoxicity measures recommended in the 2007 version of the OECD Test Guideline 487. The three compounds were positive in the assay in the presence and absence of the cytokinesis blocking agent cytochalasin B at concentrations that did not exceed the recommended cytotoxic limits determined by relative population doubling, relative increase in cell counts, relative cell counts and cytokinesis block proliferation index. Consequently, this work supports the hypothesis that relative population doubling, relative increase in cell counts and relative cell counts are appropriate measures of cytotoxicity for the non-cytokinesis blocked in vitro micronucleus assay. © 2009 Elsevier B.V.

Edwards K.D.,Advanced Technologies Park | Bombarely A.,Boyce Thompson Institute for Plant Research | Story G.W.,Advanced Technologies Park | Story G.W.,University of Cambridge | And 4 more authors.
BMC Genomics | Year: 2010

Background: Transcriptomics has resulted in the development of large data sets and tools for the progression of functional genomics and systems biology in many model organisms. Currently there is no commercially available microarray to allow such expression studies in Nicotiana tabacum (tobacco).Results: A custom designed Affymetrix tobacco expression microarray was generated from a set of over 40k unigenes and used to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas (TobEA). TobEA provides a snap shot of the transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. 772 of 2513 transcription factors previously identified in tobacco were mapped to the array, with 87% of them being expressed in at least one tissue in the atlas. Putative transcriptional networks were identified based on the co-expression of these transcription factors. Several interactions in a floral identity transcription factor network were consistent with previous results from other plant species. To broaden access and maximise the benefit of TobEA a set of tools were developed to provide researchers with expression information on their genes of interest via the Solanaceae Genomics Network (SGN) web site. The array has also been made available for public use via the Nottingham Arabidopsis Stock Centre microarray service.Conclusions: The generation of a tobacco expression microarray is an important development for research in this model plant. The data provided by TobEA represents a valuable resource for plant functional genomics and systems biology research and can be used to identify gene targets for both fundamental and applied scientific applications in tobacco. © 2010 Edwards et al; licensee BioMed Central Ltd.

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