WorldWideScience

Sample records for model organism arabidopsis

  1. Light, stress and herbivory : from photoprotection to trophic interactions using Arabidopsis thaliana as a model organism

    OpenAIRE

    Frenkel, Martin

    2008-01-01

    Photosynthesis is the most important process for nearly all life on earth. Photosynthetic organisms capture and transfer light energy from the sun into chemical energy which in turn provides a resource base for heterotrophic organisms. Natural light regimes are irregular and vary over magnitudes. At a certain light intensity, metabolic processes cannot keep up with the electron flow produced by the primary photoreactions, and thus reactive oxygen species (ROS) are produced. ROS are highly rea...

  2. Stem cell organization in Arabidopsis

    NARCIS (Netherlands)

    Wendrich, J.R.

    2016-01-01

    Growth of plant tissues and organs depends on continuous production of new cells, by niches of stem cells. Stem cells typically divide to give rise to one differentiating daughter and one non-differentiating daughter. This constant process of self-renewal ensures that the niches of stem cells or

  3. The development of Arabidopsis as a plant model

    NARCIS (Netherlands)

    Koornneef, M.; Meinke, D.W.

    2010-01-01

    Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology.

  4. Multiscale digital Arabidopsis predicts individual organ and whole-organism growth.

    Science.gov (United States)

    Chew, Yin Hoon; Wenden, Bénédicte; Flis, Anna; Mengin, Virginie; Taylor, Jasper; Davey, Christopher L; Tindal, Christopher; Thomas, Howard; Ougham, Helen J; de Reffye, Philippe; Stitt, Mark; Williams, Mathew; Muetzelfeldt, Robert; Halliday, Karen J; Millar, Andrew J

    2014-09-30

    Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes at multiple scales and link understanding from several research domains can help to tackle this problem. Such integrated models are more common in crop science and ecophysiology than in the research communities that elucidate molecular networks. Several laboratories have modeled particular aspects of growth in Arabidopsis thaliana, but it was unclear whether these existing models could productively be combined. We test this approach by constructing a multiscale model of Arabidopsis rosette growth. Four existing models were integrated with minimal parameter modification (leaf water content and one flowering parameter used measured data). The resulting framework model links genetic regulation and biochemical dynamics to events at the organ and whole-plant levels, helping to understand the combined effects of endogenous and environmental regulators on Arabidopsis growth. The framework model was validated and tested with metabolic, physiological, and biomass data from two laboratories, for five photoperiods, three accessions, and a transgenic line, highlighting the plasticity of plant growth strategies. The model was extended to include stochastic development. Model simulations gave insight into the developmental control of leaf production and provided a quantitative explanation for the pleiotropic developmental phenotype caused by overexpression of miR156, which was an open question. Modular, multiscale models, assembling knowledge from systems biology to ecophysiology, will help to understand and to engineer plant behavior from the genome to the field.

  5. Characterization of the ZAT1p zinc transporter from Arabidopsis thaliana in microbial model organisms and reconstituted proteoliposomes.

    Science.gov (United States)

    Bloss, Tanja; Clemens, Stephan; Nies, Dietrich H

    2002-03-01

    The ZAT1p zinc transporter from Arabidopsis thaliana (L.) Heynh. is a member of the cation diffusion facilitator (CDF) protein family. When heterologously expressed in Escherichia coli, ZAT1p bound zinc in a metal blot. Binding of zinc occurred mainly to the hydrophilic amino acid region from H182 to H232. A ZAT1p/ZAT1p*Delta(M1-I25) protein mixture was purified and reconstituted into proteoliposomes. Uptake of zinc into the proteoliposomes did not require a proton gradient across the liposomal membrane. ZAT1p did not transport cobalt, and transported cadmium at only 1% of the zinc transport rate. ZAT1p functioned as an uptake system for 65Zn2+ in two strains of the Gram-negative bacterium Ralstonia metallidurans, which were different in their content of zinc-efflux systems. The ZAT1 gene did not rescue increased zinc sensitivity of a Delta ZRC1single-mutant strain or of a Delta ZRC1 Delta COT1 double-mutant strain of Saccharomyces cerevisiae, but ZAT1 complemented this phenotype in a Delta SpZRC1 mutant strain of Schizosaccharomyces pombe.

  6. Hemoglobin is essential for normal growth of Arabidopsis organs

    DEFF Research Database (Denmark)

    Hebelstrup, Kim Henrik; Hunt, Peter; Dennis, Elizabeth

    2006-01-01

    In Arabidopsis thaliana, the class I hemoglobin AHb1 is transiently expressed in the hydathodes of leaves and in floral buds from young inflorescences. Nitric oxide (NO) accumulates to high levels in these organs when AHb1 is silenced, indicating an important role in metabolizing NO. AHb1-silenced...... lines are viable but show a mutant phenotype affecting the regions where AHb1 is expressed. Arabidopsis lines with an insertional knockout or overexpression of AHb2, a class II 3-on-3 hemoglobin, were generated. Seedlings overexpressing AHb2 show enhanced survival of hypoxic stress. The AHb2 knockout...... lines develop normally. However, when AHb2 knockout is combined with AHb1 silencing, seedlings die at an early vegetative stage suggesting that the two 3-on-3 hemoglobins, AHb1 and AHb2, together play an essential role for normal development of Arabidopsis seedlings. In conclusion, these results...

  7. The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning.

    Science.gov (United States)

    Plackett, Andrew R G; Powers, Stephen J; Phillips, Andy L; Wilson, Zoe A; Hedden, Peter; Thomas, Stephen G

    2018-06-01

    Linear modelling approaches detected significant gradients in organ growth and patterning across early flowers of the Arabidopsis inflorescence and uncovered evidence of new roles for gibberellin in floral development. Most flowering plants, including the genetic model Arabidopsis thaliana, produce multiple flowers in sequence from a reproductive shoot apex to form a flower spike (inflorescence). The development of individual flowers on an Arabidopsis inflorescence has typically been considered as highly stereotypical and uniform, but this assumption is contradicted by the existence of mutants with phenotypes visible in early flowers only. This phenomenon is demonstrated by mutants partially impaired in the biosynthesis of the phytohormone gibberellin (GA), in which floral organ growth is retarded in the first flowers to be produced but has recovered spontaneously by the 10th flower. We presently lack systematic data from multiple flowers across the Arabidopsis inflorescence to explain such changes. Using mutants of the GA 20-OXIDASE (GA20ox) GA biosynthesis gene family to manipulate endogenous GA levels, we investigated the dynamics of changing floral organ growth across the early Arabidopsis inflorescence (flowers 1-10). Modelling of floral organ lengths identified a significant, GA-independent gradient of increasing stamen length relative to the pistil in the wild-type inflorescence that was separable from other, GA-dependent effects. It was also found that the first flowers exhibited unstable organ patterning in contrast to later flowers and that this instability was prolonged by exogenous GA treatment. These findings indicate that the development of individual flowers is influenced by hitherto unknown factors acting across the inflorescence and also suggest novel functions for GA in floral patterning.

  8. Arabidopsis: an adequate model for dicot root systems?

    Directory of Open Access Journals (Sweden)

    Richard W Zobel

    2016-02-01

    Full Text Available The Arabidopsis root system is frequently considered to have only three classes of root: primary, lateral, and adventitious. Research with other plant species has suggested up to 8 different developmental/functional classes of root for a given plant root system. If Arabidopsis has only three classes of root, it may not be an adequate model for eudicot plant root systems. Recent research, however, can be interpreted to suggest that pre-flowering Arabidopsis does have at least five (5 of these classes of root. This then suggests that Arabidopsis root research can be considered an adequate model for eudicot plant root systems.

  9. Hemoglobin is essential for normal growth of Arabidopsis organs

    DEFF Research Database (Denmark)

    Hebelstrup, Kim Henrik; Hunt, Peter; Dennis, Elizabeth

    2006-01-01

    In Arabidopsis thaliana, the class I hemoglobin AHb1 is transiently expressed in the hydathodes of leaves and in floral buds from young inflorescences. Nitric oxide (NO) accumulates to high levels in these organs when AHb1 is silenced, indicating an important role in metabolizing NO. AHb1-silence...... suggests that 3-on-3 hemoglobins apart from a role in hypoxic stress play a general role under non-stressed conditions where they are essential for normal development by controlling the level of NO which tends to accumulate in floral buds and leaf hydathodes of plants......In Arabidopsis thaliana, the class I hemoglobin AHb1 is transiently expressed in the hydathodes of leaves and in floral buds from young inflorescences. Nitric oxide (NO) accumulates to high levels in these organs when AHb1 is silenced, indicating an important role in metabolizing NO. AHb1-silenced...... lines are viable but show a mutant phenotype affecting the regions where AHb1 is expressed. Arabidopsis lines with an insertional knockout or overexpression of AHb2, a class II 3-on-3 hemoglobin, were generated. Seedlings overexpressing AHb2 show enhanced survival of hypoxic stress. The AHb2 knockout...

  10. Arabidopsis and the Genetic Potential for the Phytoremediation of Toxic Elemental and Organic Pollutants

    OpenAIRE

    Cobbett, Christopher S.; Meagher, Richard B.

    2002-01-01

    In a process called phytoremediation, plants can be used to extract, detoxify, and/or sequester toxic pollutants from soil, water, and air. Phytoremediation may become an essential tool in cleaning the environment and reducing human and animal exposure to potential carcinogens and other toxins. Arabidopsis has provided useful information about the genetic, physiological, and biochemical mechanisms behind phytoremediation, and it is an excellent model genetic organism to test foreign gene expr...

  11. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Castleden Ian

    2010-11-01

    Full Text Available Abstract Background Arabidopsis thaliana is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (Oryza sativa. To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation. Results Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of cis-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis. Conclusions These results reveal significant divergence between Arabidopsis and rice, in terms of the

  12. Arabidopsis and the Genetic Potential for the Phytoremediation of Toxic Elemental and Organic Pollutants

    Science.gov (United States)

    Cobbett, Christopher S.; Meagher, Richard B.

    2002-01-01

    In a process called phytoremediation, plants can be used to extract, detoxify, and/or sequester toxic pollutants from soil, water, and air. Phytoremediation may become an essential tool in cleaning the environment and reducing human and animal exposure to potential carcinogens and other toxins. Arabidopsis has provided useful information about the genetic, physiological, and biochemical mechanisms behind phytoremediation, and it is an excellent model genetic organism to test foreign gene expression. This review focuses on Arabidopsis studies concerning: 1) the remediation of elemental pollutants; 2) the remediation of organic pollutants; and 3) the phytoremediation genome. Elemental pollutants include heavy metals and metalloids (e.g., mercury, lead, cadmium, arsenic) that are immutable. The general goal of phytoremediation is to extract, detoxify, and hyperaccumulate elemental pollutants in above-ground plant tissues for later harvest. A few dozen Arabidopsis genes and proteins that play direct roles in the remediation of elemental pollutants are discussed. Organic pollutants include toxic chemicals such as benzene, benzo(a)pyrene, polychlorinated biphenyls, trichloroethylene, trinitrotoluene, and dichlorodiphenyltrichloroethane. Phytoremediation of organic pollutants is focused on their complete mineralization to harmless products, however, less is known about the potential of plants to act on complex organic chemicals. A preliminary survey of the Arabidopsis genome suggests that as many as 700 genes encode proteins that have the capacity to act directly on environmental pollutants or could be modified to do so. The potential of the phytoremediation proteome to be used to reduce human exposure to toxic pollutants appears to be enormous and untapped. PMID:22303204

  13. Arabidopsis: an adequate model for dicot root systems

    Science.gov (United States)

    In the search for answers to pressing root developmental genetic issues, plant science has turned to a small genome dicot plant (Arabidopsis) to be used as a model to study and use to develop hypotheses for testing other species. Through out the published research only three classes of root are des...

  14. Gene Discovery and Functional Analyses in the Model Plant Arabidopsis

    DEFF Research Database (Denmark)

    Feng, Cai-ping; Mundy, J.

    2006-01-01

    The present mini-review describes newer methods and strategies, including transposon and T-DNA insertions, TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also discus...

  15. Continuous-time modeling of cell fate determination in Arabidopsis flowers

    Directory of Open Access Journals (Sweden)

    Angenent Gerco C

    2010-07-01

    Full Text Available Abstract Background The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored. Results We propose an ordinary differential equation (ODE model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant Arabidopsis thaliana. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known experimental expression data. The model is validated by simulation studies of known mutant plants. Conclusions The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in Arabidopsis, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.

  16. UFO: an Arabidopsis gene involved in both floral meristem and floral organ development.

    Science.gov (United States)

    Levin, J Z; Meyerowitz, E M

    1995-05-01

    We describe the role of the UNUSUAL FLORAL ORGANS (UFO) gene in Arabidopsis floral development based on a genetic and molecular characterization of the phenotypes of nine ufo alleles. UFO is required for the proper identity of the floral meristem and acts in three different aspects of the process that distinguishes flowers from shoots. UFO is involved in establishing the whorled pattern of floral organs, controlling the determinacy of the floral meristem, and activating the APETALA3 and PISTILLATA genes required for petal and stamen identity. In many respects, UFO acts in a manner similar to LEAFY, but the ufo mutant phenotype also suggests an additional role for UFO in defining boundaries within the floral primordia or controlling cell proliferation during floral organ growth. Finally, genetic interactions that prevent flower formation and lead to the generation of filamentous structures implicate UFO as a member of a new, large, and diverse class of genes in Arabidopsis necessary for flower formation.

  17. The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

    Directory of Open Access Journals (Sweden)

    Rangwala Sanjida H

    2010-03-01

    Full Text Available Abstract Background Sadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana. There is a wide degree of divergence among different elements, suggesting that these sequences are ancient in origin. Here we report the results of several lines of investigation into the genomic organization and evolutionary history of this element family. Results We present a classification scheme for Sadhu elements in A. thaliana, describing derivative elements related to the full-length elements we reported previously. We characterized Sadhu5 elements in a set of A. thaliana strains in order to trace the history of radiation in this subfamily. Sequences surrounding the target sites of different Sadhu insertions are consistent with mobilization by LINE retroelements. Finally, we identified Sadhu elements grouping into distinct subfamilies in two related species, Arabidopsis arenosa and Arabidopsis lyrata. Conclusions Our analyses suggest that the Sadhu retroelement family has undergone target primed reverse transcription-driven retrotransposition during the divergence of different A. thaliana strains. In addition, Sadhu elements can be found at moderate copy number in three distinct Arabidopsis species, indicating that the evolutionary history of these sequences can be traced back at least several millions of years.

  18. Gravity response mechanisms of lateral organs and the control of plant architecture in Arabidopsis

    Science.gov (United States)

    Mullen, J.; Hangarter, R.

    Most research on gravity responses in plants has focused on primary roots and shoots, which typically grow in a vertical orientation. However, the patterns of lateral organ formation and their growth orientation, which typically are not vertical, govern plant architecture. For example, in Arabidopsis, when lateral roots emerge from the primary root, they grow at a nearly horizontal orientation. As they elongate, the roots slowly curve until they eventually reach a vertical orientation. The regulation of this lateral root orientation is an important component affecting the overall root system architecture. We have found that this change in orientation is not simply due to the onset of gravitropic competence, as non-vertical lateral roots are capable of both positive and negative gravitropism. Thus, the horizontal growth of the new lateral roots is determined by what is called the gravitropic set-point angle (GSA). In Arabidopsis shoots, rosette leaves and inflorescence branches also display GSA-dependent developmental changes in their orientation. The developmental control of the GSA of lateral organs in Arabidopsis provides us with a useful system for investigating the components involved in regulating directionality of tropistic responses. We have identified several Arabidopsis mutants that have either altered lateral root orientations, altered orientation of lateral organs in the shoot, or both, but maintain normal primary organ orientation. The mgsa ({m}odified {g}ravitropic {s}et-point {a}ngle) mutants with both altered lateral root and shoot orientation show that there are common components in the regulation of growth orientation in the different organs. Rosette leaves and lateral roots also have in common a regulation of positioning by red light. Further molecular and physiological analyses of the GSA mutants will provide insight into the basis of GSA regulation and, thus, a better understanding of how gravity controls plant architecture. [This work was

  19. Kontrolle der Expression des UNUSUAL FLORAL ORGANS (UFO) Gens in Arabidopsis thaliana

    OpenAIRE

    Hobe, Martin

    2004-01-01

    Die vorliegende Arbeit befaßt sich mit der Kontrolle des Expressionsmusters des UNUSUAL FLORAL ORGANS (UFO) Gens von Arabidopsis thaliana. UFO wird im Sproß- und Blütenmeristemen aller Entwicklungsstadien der Pflanze exprimiert. In Blütenmeristemen agiert UFO als Kofaktor von LEAFY (LFY) bei der Aktivierung der Organidentitätsgene des zweiten und dritten Wirtels. UFO stellt also einen generellen Faktor der Musterbildung in Meristemen dar. Um regulatorische Gene, die die Expression von UFO bee...

  20. A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2013-12-01

    Full Text Available During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks. Enzymatic reactions are predicted by the sequence information. Pathways arise due to the participation of chemical compounds as substrates and products in these reactions. Although several of these comprehensive networks have been reconstructed for the genetic model plant Arabidopsis thaliana, the integration of experimental data is still challenging. Particularly the analysis of subcellular organization of plant cells limits the understanding of regulatory instances in these metabolic networks in vivo. In this study, we develop an approach for the functional integration of experimental high-throughput data into such large-scale networks. We present a subcellular metabolic network model comprising 524 metabolic intermediates and 548 metabolic interactions derived from a total of 2769 reactions. We demonstrate how to link the metabolite covariance matrix of different Arabidopsis thaliana accessions with the subcellular metabolic network model for the inverse calculation of the biochemical Jacobian, finally resulting in the calculation of a matrix which satisfies a Lyaponov equation involving a covariance matrix. In this way, differential strategies of metabolite compartmentation and involved reactions were identified in the accessions when exposed to low temperature.

  1. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis.

    Science.gov (United States)

    Mellor, Nathan; Péret, Benjamin; Porco, Silvana; Sairanen, Ilkka; Ljung, Karin; Bennett, Malcolm; King, John

    2015-02-07

    Emergence of new lateral roots from within the primary root in Arabidopsis has been shown to be regulated by the phytohormone auxin, via the expression of the auxin influx carrier LAX3, mediated by the ARF7/19 IAA14 signalling module (Swarup et al., 2008). A single cell model of the LAX3 and IAA14 auxin response was formulated and used to demonstrate that hysteresis and bistability may explain the experimentally observed 'all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. The model was tested further by using a parameter fitting algorithm to match model output with qRT-PCR mRNA expression data following exogenous auxin treatment. It was found that the model is able to show good agreement with the data, but only when the exogenous auxin signal is degraded over time, at a rate higher than that measured in the experimental medium, suggesting the triggering of an endogenous auxin homeostasis mechanism. Testing the model over a more physiologically relevant range of extracellular auxin shows bistability and hysteresis still occur when using the optimised parameters, providing the rate of LAX3 active auxin transport is sufficiently high relative to passive diffusion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Phosphatidic acid is a major phospholipid class in reproductive organs of Arabidopsis thaliana.

    Science.gov (United States)

    Yunus, Ian Sofian; Cazenave-Gassiot, Amaury; Liu, Yu-Chi; Lin, Ying-Chen; Wenk, Markus R; Nakamura, Yuki

    2015-01-01

    Phospholipids are the crucial components of biological membranes and signal transduction. Among different tissues, flower phospholipids are one of the least characterized features of plant lipidome. Here, we report that floral reproductive organs of Arabidopsis thaliana contain high levels of phosphatidic acid (PA), a known lipid second messenger. By using floral homeotic mutants enriched with specific floral organs, lipidomics study showed increased levels of PA species in ap3-3 mutant with enriched pistils. Accompanied gene expression study for 7 diacylglycerol kinases and 11 PA phosphatases revealed distinct floral organ specificity, suggesting an active phosphorylation/dephosphorylation between PA and diacylglycerol in flowers. Our results suggest that PA is a major phospholipid class in floral reproductive organs of A. thaliana.

  3. Genetics of the gravitropic set-point angle in lateral organs of Arabidopsis

    Science.gov (United States)

    Mullen, J.; Hangarter, R.

    Research on gravity responses in plants has mostly focused on primary roots and shoots, which typically orient to a vertical orientation. However, the distribution of lateral organs and their typically non-vertical growth orientation are critical for the determination of plant form. For example, in Arabidopsis, when lateral roots emerge from the primary root, they grow at a nearly horizontal orientation. As they elongate, the roots slowly curve until they eventually reach a vertical orientation. The regulation of this lateral root orientation is an important component affecting the overall root system architecture. We found that this change in orientation is not simply due to the onset of gravitropic competence, as non-vertical lateral roots are capable of both positive and negative gravitropism. Thus, the horizontal growth the new lateral roots is determined by what is called the gravitropic set-point angle (GSA). This developmental control of the GSA of lateral roots in Arabidopsis provides a useful system for investigating the components involved in regulating gravitropic responses. Using this system, we have identified several Arabidopsis mutants that have altered lateral root orientations but maintain normal primary root orientation. Two of these mutants also have altered orientation of their rosette leaves, indicating some common mechanisms in the positioning of root and shoot lateral organs. Rosette leaves and lateral roots also have in common a regulation of orientation by red light that may be due to red-light-dependent changes in the GSA. Further molecular and physiological analyses of the GSA mutants will provide insight into the basis of GSA regulation and, thus, a better understanding of how gravity controls plant architecture. [This work was supported by the National Aeronautics and Space Administration through grant no. NCC 2-1200.

  4. Effect of nickel on the organization of actin filaments in Arabidopsis thaliana primary root cells

    International Nuclear Information System (INIS)

    Goryunova, I.I.; Krasilenko, Yu.A.; Emets, A.I.; Blyum, Ya.B.

    2016-01-01

    The influence of one of the most toxic heavy metals - nickel (Ni 2+ ) - on the organization of actin filaments (microfilaments) of different types of Arabidopsis thaliana (L.) root cells is studied in living cells by the laser scanning microscopy. To visualize microfilaments, the A. thaliana line expressing chimeric gene gfp-fabd2 was used. Ni 2+ leads to a significant inhibition of the growth of the main root and disturbs its morphology, causing the swelling of epidermal cells and inducing a large number of abnormally long root hairs. For the first time, it has been shown that Ni 2+ disturbs the organization of actin filaments in cells, leading to morphological changes of a root as the main organ, being the first exposed to the intoxication by soil pollutants. It is found that the most sensitive to its action are actin filaments of epidermal cells of all growth zones of A. thaliana root

  5. SCF(SAP) controls organ size by targeting PPD proteins for degradation in Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Zhibiao; Li, Na; Jiang, Shan; Gonzalez, Nathalie; Huang, Xiahe; Wang, Yingchun; Inzé, Dirk; Li, Yunhai

    2016-04-06

    Control of organ size by cell proliferation and growth is a fundamental process, but the mechanisms that determine the final size of organs are largely elusive in plants. We have previously revealed that the ubiquitin receptor DA1 regulates organ size by repressing cell proliferation in Arabidopsis. Here we report that a mutant allele of STERILE APETALA (SAP) suppresses the da1-1 mutant phenotype. We show that SAP is an F-box protein that forms part of a SKP1/Cullin/F-box E3 ubiquitin ligase complex and controls organ size by promoting the proliferation of meristemoid cells. Genetic analyses suggest that SAP may act in the same pathway with PEAPOD1 and PEAPOD2, which are negative regulators of meristemoid proliferation, to control organ size, but does so independently of DA1. Further results reveal that SAP physically associates with PEAPOD1 and PEAPOD2, and targets them for degradation. These findings define a molecular mechanism by which SAP and PEAPOD control organ size.

  6. ASN1-encoded asparagine synthetase in floral organs contributes to nitrogen filling in Arabidopsis seeds.

    Science.gov (United States)

    Gaufichon, Laure; Marmagne, Anne; Belcram, Katia; Yoneyama, Tadakatsu; Sakakibara, Yukiko; Hase, Toshiharu; Grandjean, Olivier; Clément, Gilles; Citerne, Sylvie; Boutet-Mercey, Stéphanie; Masclaux-Daubresse, Céline; Chardon, Fabien; Soulay, Fabienne; Xu, Xiaole; Trassaert, Marion; Shakiebaei, Maryam; Najihi, Amina; Suzuki, Akira

    2017-08-01

    Despite a general view that asparagine synthetase generates asparagine as an amino acid for long-distance transport of nitrogen to sink organs, its role in nitrogen metabolic pathways in floral organs during seed nitrogen filling has remained undefined. We demonstrate that the onset of pollination in Arabidopsis induces selected genes for asparagine metabolism, namely ASN1 (At3g47340), GLN2 (At5g35630), GLU1 (At5g04140), AapAT2 (At5g19950), ASPGA1 (At5g08100) and ASPGB1 (At3g16150), particularly at the ovule stage (stage 0), accompanied by enhanced asparagine synthetase protein, asparagine and total amino acids. Immunolocalization confined asparagine synthetase to the vascular cells of the silique cell wall and septum, but also to the outer and inner seed integuments, demonstrating the post-phloem transport of asparagine in these cells to developing embryos. In the asn1 mutant, aberrant embryo cell divisions in upper suspensor cell layers from globular to heart stages assign a role for nitrogen in differentiating embryos within the ovary. Induction of asparagine metabolic genes by light/dark and nitrate supports fine shifts of nitrogen metabolic pathways. In transgenic Arabidopsis expressing promoter Ca MV 35S ::ASN1 fusion, marked metabolomics changes at stage 0, including a several-fold increase in free asparagine, are correlated to enhanced seed nitrogen. However, specific promoter Napin2S ::ASN1 expression during seed formation and a six-fold increase in asparagine toward the desiccation stage result in wild-type seed nitrogen, underlining that delayed accumulation of asparagine impairs the timing of its use by releasing amide and amino nitrogen. Transcript and metabolite profiles in floral organs match the carbon and nitrogen partitioning to generate energy via the tricarboxylic acid cycle, GABA shunt and phosphorylated serine synthetic pathway. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  7. Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.

    Science.gov (United States)

    Khan, Madiha; Ragni, Laura; Tabb, Paul; Salasini, Brenda C; Chatfield, Steven; Datla, Raju; Lock, John; Kuai, Xiahezi; Després, Charles; Proveniers, Marcel; Yongguo, Cao; Xiang, Daoquan; Morin, Halima; Rullière, Jean-Pierre; Citerne, Sylvie; Hepworth, Shelley R; Pautot, Véronique

    2015-11-01

    In the model plant Arabidopsis (Arabidopsis thaliana), endogenous and environmental signals acting on the shoot apical meristem cause acquisition of inflorescence meristem fate. This results in changed patterns of aerial development seen as the transition from making leaves to the production of flowers separated by elongated internodes. Two related BEL1-like homeobox genes, PENNYWISE (PNY) and POUND-FOOLISH (PNF), fulfill this transition. Loss of function of these genes impairs stem cell maintenance and blocks internode elongation and flowering. We show here that pny pnf apices misexpress lateral organ boundary genes BLADE-ON-PETIOLE1/2 (BOP1/2) and KNOTTED-LIKE FROM ARABIDOPSIS THALIANA6 (KNAT6) together with ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1). Inactivation of genes in this module fully rescues pny pnf defects. We further show that BOP1 directly activates ATH1, whereas activation of KNAT6 is indirect. The pny pnf restoration correlates with renewed accumulation of transcripts conferring floral meristem identity, including FD, SQUAMOSA PROMOTER-BINDING PROTEIN LIKE genes, LEAFY, and APETALA1. To gain insight into how this module blocks flowering, we analyzed the transcriptome of BOP1-overexpressing plants. Our data suggest a central role for the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-microRNA172 module in integrating stress signals conferred in part by promotion of jasmonic acid biosynthesis. These data reveal a potential mechanism by which repression of lateral organ boundary genes by PNY-PNF is essential for flowering. © 2015 American Society of Plant Biologists. All Rights Reserved.

  8. Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Bruno Huettel

    2008-10-01

    Full Text Available Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and

  9. Mediator subunit18 controls flowering time and floral organ identity in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Zhengui Zheng

    Full Text Available Mediator is a conserved multi-protein complex that plays an important role in regulating transcription by mediating interactions between transcriptional activator proteins and RNA polymerase II. Much evidence exists that Mediator plays a constitutive role in the transcription of all genes transcribed by RNA polymerase II. However, evidence is mounting that specific Mediator subunits may control the developmental regulation of specific subsets of RNA polymerase II-dependent genes. Although the Mediator complex has been extensively studied in yeast and mammals, only a few reports on Mediator function in flowering time control of plants, little is known about Mediator function in floral organ identity. Here we show that in Arabidopsis thaliana, MEDIATOR SUBUNIT 18 (MED18 affects flowering time and floral organ formation through FLOWERING LOCUS C (FLC and AGAMOUS (AG. A MED18 loss-of-function mutant showed a remarkable syndrome of later flowering and altered floral organ number. We show that FLC and AG mRNA levels and AG expression patterns are altered in the mutant. Our results support parallels between the regulation of FLC and AG and demonstrate a developmental role for Mediator in plants.

  10. Arabidopsis thaliana resistance to insects, mediated by an earthworm-produced organic soil amendment.

    Science.gov (United States)

    Cardoza, Yasmin J

    2011-02-01

    Vermicompost is an organic soil amendment produced by earthworm digestion of organic waste. Studies show that plants grown in soil amended with vermicompost grow faster, are more productive and are less susceptible to a number of arthropod pests. In light of these studies, the present study was designed to determine the type of insect resistance (antixenosis or antibiosis) present in plants grown in vermicompost-amended potting soil. Additionally, the potential role of microarthropods, entomopathogenic organisms and non-pathogenic microbial flora found in vermicompost on insect resistance induction was investigated. Findings show that vermicompost from two different sources (Raleigh, North Carolina, and Portland, Oregon) were both effective in causing Arabidopsis plants to be resistant to the generalist herbivore Helicoverpa zea (Boddie). However, while the Raleigh (Ral) vermicompost plant resistance was expressed as both non-preference (antixenosis) and milder (lower weight and slower development) toxic effect (antibiosis) resistance, Oregon (OSC) vermicompost plant resistance was expressed as acute antibiosis, resulting in lower weights and higher mortality rates. Vermicompost causes plants to have non-preference (antixenosis) and toxic (antibiosis) effects on insects. This resistance affects insect development and survival on plants grown in vermicompost-amended soil. Microarthropods and entomopathogens do not appear to have a role in the resistance, but it is likely that resistance is due to interactions between the microbial communities in vermicompost with plant roots, as is evident from vermicompost sterilization assays conducted in this study. Copyright © 2010 Society of Chemical Industry.

  11. Structure and organ specificity of an anionic peroxidase from Arabidopsis thaliana cell suspension culture

    DEFF Research Database (Denmark)

    Ostergaard, L; Abelskov, A K; Mattsson, O

    1996-01-01

    The predominant peroxidase (pI 3.5) (E.C. 1.11.1.7) of an Arabidopsis thaliana cell suspension culture was purified and partially sequenced. Oligonucleotides were designed and a specific probe was obtained. A cDNA clone was isolated from an Arabidopsis cell suspension cDNA library and completely ...

  12. Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis

    NARCIS (Netherlands)

    Khan, Madiha; Ragni, Laura; Tabb, Paul; Salasini, Brenda C; Chatfield, Steven; Datla, Raju; Lock, John; Kuai, Xiahezi; Després, Charles; Proveniers, Marcel; Yongguo, Cao; Xiang, Daoquan; Morin, Halima; Rullière, Jean-Pierre; Citerne, Sylvie; Hepworth, Shelley R; Pautot, Véronique

    2015-01-01

    In the model plant Arabidopsis (Arabidopsis thaliana), endogenous and environmental signals acting on the shoot apical meristem cause acquisition of inflorescence meristem fate. This results in changed patterns of aerial development seen as the transition from making leaves to the production of

  13. Using Higher-Order Dynamic Bayesian Networks to Model Periodic Data from the Circadian Clock of Arabidopsis Thaliana

    Science.gov (United States)

    Daly, Rónán; Edwards, Kieron D.; O'Neill, John S.; Aitken, Stuart; Millar, Andrew J.; Girolami, Mark

    Modelling gene regulatory networks in organisms is an important task that has recently become possible due to large scale assays using technologies such as microarrays. In this paper, the circadian clock of Arabidopsis thaliana is modelled by fitting dynamic Bayesian networks to luminescence data gathered from experiments. This work differs from previous modelling attempts by using higher-order dynamic Bayesian networks to explicitly model the time lag between the various genes being expressed. In order to achieve this goal, new techniques in preprocessing the data and in evaluating a learned model are proposed. It is shown that it is possible, to some extent, to model these time delays using a higher-order dynamic Bayesian network.

  14. Suberized transport barriers in Arabidopsis, barley and rice roots: From the model plant to crop species.

    Science.gov (United States)

    Kreszies, Tino; Schreiber, Lukas; Ranathunge, Kosala

    2018-02-07

    Water is the most important prerequisite for life and plays a major role during uptake and transport of nutrients. Roots are the plant organs that take up the major part of water, from the surrounding soil. Water uptake is related to the root system architecture, root growth, age and species dependent complex developmental changes in the anatomical structures. The latter is mainly attributed to the deposition of suberized barriers in certain layers of cell walls, such as endo- and exodermis. With respect to water permeability, changes in the suberization of roots are most relevant. Water transport or hydraulic conductivity of roots (Lp r ) can be described by the composite transport model and is known to be very variable between plant species and growth conditions and root developmental states. In this review, we summarize how anatomical structures and apoplastic barriers of roots can diversely affect water transport, comparing the model plant Arabidopsis with crop plants, such as barley and rice. Results comparing the suberin amounts and water transport properties indicate that the common assumption that suberin amount negatively correlates with water and solute transport through roots may not always be true. The composition, microstructure and localization of suberin may also have a great impact on the formation of efficient barriers to water and solutes. Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.

  15. Inhibition of phospholipase C disrupts cytoskeletal organization and gravitropic growth in Arabidopsis roots.

    Science.gov (United States)

    Andreeva, Zornitza; Barton, Deborah; Armour, William J; Li, Min Y; Liao, Li-Fen; McKellar, Heather L; Pethybridge, Kylie A; Marc, Jan

    2010-10-01

    The phospholipase protein superfamily plays an important role in hormonal signalling and cellular responses to environmental stimuli. There is also growing evidence for interactions between phospholipases and the cytoskeleton. In this report we used a pharmacological approach to investigate whether inhibiting a member of the phospholipase superfamily, phospholipase C (PLC), affects microtubules and actin microfilaments as well as root growth and morphology of Arabidopsis thaliana seedlings. Inhibiting PLC activity using the aminosteroid U73122 significantly inhibited root elongation and disrupted root morphology in a concentration-dependent manner, with the response being saturated at 5 μM, whereas the inactive analogue U73343 was ineffective. The primary root appeared to lose growth directionality accompanied by root waving and formation of curls. Immunolabelling of roots exposed to increasingly higher U73122 concentrations revealed that the normal transverse arrays of cortical microtubules in the elongation zone became progressively more disorganized or depolymerized, with the disorganization appearing within 1 h of incubation. Likewise, actin microfilament arrays also were disrupted. Inhibiting PLC using an alternative inhibitor, neomycin, caused similar disruptions to both cytoskeletal organization and root morphology. In seedlings gravistimulated by rotating the culture plates by 90°, both U73122 and neomycin disrupted the normal gravitropic growth of roots and etiolated hypocotyls. The effects of PLC inhibitors are therefore consistent with the notion that, as with phospholipases A and D, PLC likewise interacts with the cytoskeleton, alters growth morphology, and is involved in gravitropism.

  16. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in Arabidopsis.

    Science.gov (United States)

    Kim, Soo Youn; Xu, Zheng-Yi; Song, Kyungyoung; Kim, Dae Heon; Kang, Hyangju; Reichardt, Ilka; Sohn, Eun Ju; Friml, Jirí; Juergens, Gerd; Hwang, Inhwan

    2013-08-01

    Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4-(4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.

  17. The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology

    Science.gov (United States)

    It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (P...

  18. Modulation of modeled microgravity on radiation-induced bystander effects in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ting [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Sun, Qiao [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Xu, Wei; Li, Fanghua [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Li, Huasheng; Lu, Jinying [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Wu, Lijun; Wu, Yuejin [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Liu, Min [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Bian, Po [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China)

    2015-03-15

    Highlights: • The effects of microgravity on the radiation-induced bystander effects (RIBE) were definitely demonstrated. • The effects of microgravity on RIBE might be divergent for different biological events. • The microgravity mainly modified the generation or transport of bystander signals at early stage. - Abstract: Both space radiation and microgravity have been demonstrated to have inevitable impact on living organisms during space flights and should be considered as important factors for estimating the potential health risk for astronauts. Therefore, the question whether radiation effects could be modulated by microgravity is an important aspect in such risk evaluation. Space particles at low dose and fluence rate, directly affect only a fraction of cells in the whole organism, which implement radiation-induced bystander effects (RIBE) in cellular response to space radiation exposure. The fact that all of the RIBE experiments are carried out in a normal gravity condition bring forward the need for evidence regarding the effect of microgravity on RIBE. In the present study, a two-dimensional rotation clinostat was adopted to demonstrate RIBE in microgravity conditions, in which the RIBE was assayed using an experimental system of root-localized irradiation of Arabidopsis thaliana (A. thaliana) plants. The results showed that the modeled microgravity inhibited significantly the RIBE-mediated up-regulation of expression of the AtRAD54 and AtRAD51 genes, generation of reactive oxygen species (ROS) and transcriptional activation of multicopy P35S:GUS, but made no difference to the induction of homologous recombination by RIBE, showing divergent responses of RIBE to the microgravity conditions. The time course of interaction between the modeled microgravity and RIBE was further investigated, and the results showed that the microgravity mainly modulated the processes of the generation or translocation of the bystander signal(s) in roots.

  19. The Arabidopsis thaliana-Alternaria brassicicola pathosystem: A model interaction for investigating seed transmission of necrotrophic fungi

    Directory of Open Access Journals (Sweden)

    Pochon Stephanie

    2012-05-01

    Full Text Available Abstract Background Seed transmission constitutes a major component of the parasitic cycle for several fungal pathogens. However, very little is known concerning fungal or plant genetic factors that impact seed transmission and mechanisms underlying this key biological trait have yet to be clarified. Such lack of available data could be probably explained by the absence of suitable model pathosystem to study plant-fungus interactions during the plant reproductive phase. Results Here we report on setting up a new pathosystem that could facilitate the study of fungal seed transmission. Reproductive organs of Arabidopsis thaliana were inoculated with Alternaria brassicicola conidia. Parameters (floral vs fruit route, seed collection date, plant and silique developmental stages that could influence the seed transmission efficiency were tested to define optimal seed infection conditions. Microscopic observations revealed that the fungus penetrates siliques through cellular junctions, replum and stomata, and into seed coats either directly or through cracks. The ability of the osmosensitive fungal mutant nik1Δ3 to transmit to A. thaliana seeds was analyzed. A significant decrease in seed transmission rate was observed compared to the wild-type parental strain, confirming that a functional osmoregulation pathway is required for efficient seed transmission of the fungus. Similarly, to test the role of flavonoids in seed coat protection against pathogens, a transparent testa Arabidopsis mutant (tt4-1 not producing any flavonoid was used as host plant. Unexpectedly, tt4-1 seeds were infected to a significantly lower extent than wild-type seeds, possibly due to over-accumulation of other antimicrobial metabolites. Conclusions The Arabidopsis thaliana-Alternaria brassicicola pathosystem, that have been widely used to study plant-pathogen interactions during the vegetative phase, also proved to constitute a suitable model pathosystem for detailed analysis

  20. Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model.

    Science.gov (United States)

    Reiser, Leonore; Berardini, Tanya Z; Li, Donghui; Muller, Robert; Strait, Emily M; Li, Qian; Mezheritsky, Yarik; Vetushko, Andrey; Huala, Eva

    2016-01-01

    Databases and data repositories provide essential functions for the research community by integrating, curating, archiving and otherwise packaging data to facilitate discovery and reuse. Despite their importance, funding for maintenance of these resources is increasingly hard to obtain. Fueled by a desire to find long term, sustainable solutions to database funding, staff from the Arabidopsis Information Resource (TAIR), founded the nonprofit organization, Phoenix Bioinformatics, using TAIR as a test case for user-based funding. Subscription-based funding has been proposed as an alternative to grant funding but its application has been very limited within the nonprofit sector. Our testing of this model indicates that it is a viable option, at least for some databases, and that it is possible to strike a balance that maximizes access while still incentivizing subscriptions. One year after transitioning to subscription support, TAIR is self-sustaining and Phoenix is poised to expand and support additional resources that wish to incorporate user-based funding strategies. Database URL: www.arabidopsis.org. © The Author(s) 2016. Published by Oxford University Press.

  1. Arabidopsis thaliana: A model host plant to study plant-pathogen interaction using rice false smut isolates of Ustilaginoidea virens

    Directory of Open Access Journals (Sweden)

    Mebeaselassie eAndargie

    2016-02-01

    Full Text Available Rice false smut fungus which is a biotrophic fungal pathogen causes an important rice disease and bring a severe damage where rice is cultivated. We established a new fungal-plant pathosystem where Ustilaginoidea virens was able to interact compatibly with the model plant Arabidopsis thaliana. Disease symptoms were apparent on the leaves of the plants after 6 days of post inoculation in the form of chlorosis. Cytological studies showed that U. virens caused a heavy infestation inside the cells of the chlorotic tissues. Development and colonization of aerial mycelia in association with floral organ, particularly on anther and stigma of the flowers after 3 weeks of post inoculation was evident which finally caused infection on the developing seeds and pod tissues. The fungus adopts a uniquely biotrophic infection strategy in roots and spreads without causing a loss of host cell viability. We have also demonstrated that U. virens isolates infect Arabidopsis and the plant subsequently activates different defense response mechanisms which are witnessed by the expression of pathogenesis-related genes, PR-1, PR-2, PR-5, PDF1.1 and PDF1.2. The established A. thaliana–U. virens pathosystem will now permit various follow-up molecular genetics and gene expression experiments to be performed to identify the defense signals and responses that restrict fungal hyphae colonization in planta and also provide initial evidence for tissue-adapted fungal infection strategies.

  2. Effect of modeled microgravity on radiation-induced adaptive response of root growth in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Deng, Chenguang; Wang, Ting; Wu, Jingjing; Xu, Wei; Li, Huasheng; Liu, Min

    2017-01-01

    Highlights: • The radio-adaptive response (RAR) of A. thaliana root growth is modulated in microgravity. • The DNA damage repairs in RAR are regulated by microgravity. • The phytohormone auxin plays a regulatory role in the modulation of microgravity on RAR of root growth. - Abstract: Space particles have an inevitable impact on organisms during space missions; radio-adaptive response (RAR) is a critical radiation effect due to both low-dose background and sudden high-dose radiation exposure during solar storms. Although it is relevant to consider RAR within the context of microgravity, another major space environmental factor, there is no existing evidence as to its effects on RAR. In the present study, we established an experimental method for detecting the effects of gamma-irradiation on the primary root growth of Arabidopsis thaliana, in which RAR of root growth was significantly induced by several dose combinations. Microgravity was simulated using a two-dimensional rotation clinostat. It was shown that RAR of root growth was significantly inhibited under the modeled microgravity condition, and was absent in pgm-1 plants that had impaired gravity sensing in root tips. These results suggest that RAR could be modulated in microgravity. Time course analysis showed that microgravity affected either the development of radio-resistance induced by priming irradiation, or the responses of plants to challenging irradiation. After treatment with the modeled microgravity, attenuation in priming irradiation-induced expressions of DNA repair genes (AtKu70 and AtRAD54), and reduced DNA repair efficiency in response to challenging irradiation were observed. In plant roots, the polar transportation of the phytohormone auxin is regulated by gravity, and treatment with an exogenous auxin (indole-3-acetic acid) prevented the induction of RAR of root growth, suggesting that auxin might play a regulatory role in the interaction between microgravity and RAR of root growth.

  3. Effect of modeled microgravity on radiation-induced adaptive response of root growth in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Chenguang [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences (China); Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province (China); Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Wang, Ting [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences (China); Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province (China); Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031 (China); Wu, Jingjing [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences (China); Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province (China); Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Xu, Wei [Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences (China); Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province (China); Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031 (China); Li, Huasheng; Liu, Min [China Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); and others

    2017-02-15

    Highlights: • The radio-adaptive response (RAR) of A. thaliana root growth is modulated in microgravity. • The DNA damage repairs in RAR are regulated by microgravity. • The phytohormone auxin plays a regulatory role in the modulation of microgravity on RAR of root growth. - Abstract: Space particles have an inevitable impact on organisms during space missions; radio-adaptive response (RAR) is a critical radiation effect due to both low-dose background and sudden high-dose radiation exposure during solar storms. Although it is relevant to consider RAR within the context of microgravity, another major space environmental factor, there is no existing evidence as to its effects on RAR. In the present study, we established an experimental method for detecting the effects of gamma-irradiation on the primary root growth of Arabidopsis thaliana, in which RAR of root growth was significantly induced by several dose combinations. Microgravity was simulated using a two-dimensional rotation clinostat. It was shown that RAR of root growth was significantly inhibited under the modeled microgravity condition, and was absent in pgm-1 plants that had impaired gravity sensing in root tips. These results suggest that RAR could be modulated in microgravity. Time course analysis showed that microgravity affected either the development of radio-resistance induced by priming irradiation, or the responses of plants to challenging irradiation. After treatment with the modeled microgravity, attenuation in priming irradiation-induced expressions of DNA repair genes (AtKu70 and AtRAD54), and reduced DNA repair efficiency in response to challenging irradiation were observed. In plant roots, the polar transportation of the phytohormone auxin is regulated by gravity, and treatment with an exogenous auxin (indole-3-acetic acid) prevented the induction of RAR of root growth, suggesting that auxin might play a regulatory role in the interaction between microgravity and RAR of root growth.

  4. Accumulation and phytotoxicity of perfluorooctanoic acid in the model plant species Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Yang, Xinping; Ye, Chengchen; Liu, Yu; Zhao, Fang-Jie

    2015-01-01

    Perfluorooctanoic acid (PFOA) is widely used in the manufacture of many industrial and household products. To assess the potential environmental risk of PFOA, its accumulation, translocation and phytotoxic effects were investigated using the model plant species Arabidopsis thaliana. Exposure to 18 μM PFOA-F in agar plates did not affect plant growth, but 181–1811 μM PFOA-F inhibited root and shoot growth. PFOA was more phytotoxic on shoot growth than NaF at the equivalent F concentration, with the latter having 3.9–7.6 times higher EC50 for shoot biomass than PFOA. PFOA was efficiently translocated from roots to shoots, where it existed as intact PFOA molecules without transformation evidenced by the 19 F NMR spectra. PFOA caused a significant increase in the concentration of H 2 O 2 and malondialdehyde (MDA) in shoots, indicating that oxidative stress is a likely cause of PFOA phytotoxicity. - Highlights: • PFOA is more phytotoxic on shoot growth than NaF at the equivalent F concentration. • PFOA is readily taken up and translocated from roots to shoots. • PFOA exists as intact molecules without transformation in Arabidopsis shoots. • PFOA causes oxidative stress in Arabidopsis shoots. - Perfluorooctanoic acid causes oxidative stress and is more phytotoxic on shoot growth than inorganic fluoride at the equivalent F concentration.

  5. The ASK1 gene regulates development and interacts with the UFO gene to control floral organ identity in Arabidopsis.

    Science.gov (United States)

    Zhao, D; Yang, M; Solava, J; Ma, H

    1999-09-01

    Normal flower development likely requires both specific and general regulators. We have isolated an Arabidopsis mutant ask1-1 (for -Arabidopsis skp1-like1-1), which exhibits defects in both vegetative and reproductive development. In the ask1-1mutant, rosette leaf growth is reduced, resulting in smaller than normal rosette leaves, and internodes in the floral stem are shorter than normal. Examination of cell sizes in these organs indicates that cell expansion is normal in the mutant, but cell number is reduced. In the mutant, the numbers of petals and stamens are reduced, and many flowers have one or more petals with a reduced size. In addition, all mutant flowers have short stamen filaments. Furthermore, petal/stamen chimeric organs are found in many flowers. These results indicate that the ASK1 gene affects the size of vegetative and floral organs. The ask1 floral phenotype resembles somewhat that of the Arabidopsis ufo mutants in that both genes affect whorls 2 and 3. We therefore tested for possible interactions between ASK1 and UFO by analyzing the phenotypes of ufo-2 ask1-1 double mutant plants. In these plants, vegetative development is similar to that of the ask1-1 single mutant, whereas the floral defects are more severe than those in either single mutant. Interior to the first whorl, the double mutant flowers have more sepals or sepal-like organs than are found in ufo-2, and less petals than ask1-1. Our results suggest that ASK1 interacts with UFO to control floral organ identity in whorls 2 and 3. This is very intriguing because ASK1 is very similar in sequence to the yeast SKP1 protein and UFO contains an F-box, a motif known to interact with SKP1 in yeast. Although the precise mechanism of ASK1 and UFO action is unknown, our results support the hypothesis that these two proteins physically interact in vivo. Copyright 1999 Wiley-Liss, Inc.

  6. Structure and biochemical function of a prototypical Arabidopsis U-box domain

    DEFF Research Database (Denmark)

    Andersen, Pernille; Kragelund, Birthe B; Olsen, Addie N

    2004-01-01

    U-box proteins, as well as other proteins involved in regulated protein degradation, are apparently over-represented in Arabidopsis compared with other model eukaryotes. The Arabidopsis protein AtPUB14 contains a typical U-box domain followed by an Armadillo repeat region, a domain organization t...

  7. Arabidopsis thaliana: A model host plant to study plant-pathogen interaction using Chilean field isolates of Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    JUAN GONZÁLEZ

    2006-01-01

    Full Text Available One of the fungal pathogens that causes more agriculture damage is Botrytis cinerea. Botrytis is a constant threat to crops because the fungus infects a wide range of host species, both native and cultivated. Furthermore, Botrytis persists on plant debris in and on the soil. Some of the most serious diseases caused by Botrytis include gray mold on vegetables and fruits, such as grapes and strawberries. Botrytis also causes secondary soft rot of fruits and vegetables during storage, transit and at the market. In many plant-pathogen interactions, resistance often is associated with the deposition of callose, accumulation of autofluorescent compounds, the synthesis and accumulation of salicylic acid as well as pathogenesis-related proteins. Arabidopsis thaliana has been used as a plant model to study plant-pathogen interaction. The genome of Arabidopsis has been completely sequenced and this plant serves as a good genetic and molecular model. In this study, we demonstrate that Chilean field isolates infect Arabidopsis thaliana and that Arabidopsis subsequently activates several defense response mechanisms associated with a hypersensitive response. Furthermore, we propose that Arabidopsis may be used as a model host species to analyze the diversity associated with infectivity among populations of Botrytis cinerea field isolates

  8. Systemic resistance induced by volatile organic compounds emitted by plant growth-promoting fungi in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Hushna Ara Naznin

    Full Text Available Volatile organic compounds (VOC were extracted and identified from plant growth-promoting fungi (PGPF, Phoma sp., Cladosporium sp. and Ampelomyces sp., using gas chromatography-mass spectrometry (GC-MS. Among the three VOC extracted, two VOC blends (emitted from Ampelomyces sp. and Cladosporium sp. significantly reduced disease severity in Arabidopsis plants against Pseudomonas syringae pv. tomato DC3000 (Pst. Subsequently, m-cresol and methyl benzoate (MeBA were identified as major active volatile compounds from Ampelomyces sp. and Cladosporium sp., respectively, and found to elicit induced systemic resistance (ISR against the pathogen. Molecular signaling for disease suppression by the VOC were investigated by treating different mutants and transgenic Arabidopsis plants impaired in salicylic acid (SA or Jasmonic acid (JA/ethylene (ET signaling pathways with m-cresol and MeBA followed by challenge inoculation with Pst. Results show that the level of protection was significantly lower when JA/ET-impaired mutants were treated with MeBA, and in SA-, and JA/ET-disrupted mutants after m-cresol treatment, indicating the involvement of these signal transduction pathways in the ISR primed by the volatiles. Analysis of defense-related genes by real-time qRT-PCR showed that both the SA-and JA-signaling pathways combine in the m-cresol signaling of ISR, whereas MeBA is mainly involved in the JA-signaling pathway with partial recruitment of SA-signals. The ET-signaling pathway was not employed in ISR by the volatiles. Therefore, this study identified two novel volatile components capable of eliciting ISR that may be promising candidates in biological control strategy to protect plants from diseases.

  9. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.

    Science.gov (United States)

    Zaag, Rim; Tamby, Jean Philippe; Guichard, Cécile; Tariq, Zakia; Rigaill, Guillem; Delannoy, Etienne; Renou, Jean-Pierre; Balzergue, Sandrine; Mary-Huard, Tristan; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Brunaud, Véronique

    2015-01-01

    CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein-protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

    DEFF Research Database (Denmark)

    Ma, Ligeng; Chen, Chen; Liu, Xigang

    2005-01-01

    Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional...... with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression...... patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice...

  11. Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

    Directory of Open Access Journals (Sweden)

    Ingkasuwan Papapit

    2012-08-01

    Full Text Available Abstract Background Starch serves as a temporal storage of carbohydrates in plant leaves during day/night cycles. To study transcriptional regulatory modules of this dynamic metabolic process, we conducted gene regulation network analysis based on small-sample inference of graphical Gaussian model (GGM. Results Time-series significant analysis was applied for Arabidopsis leaf transcriptome data to obtain a set of genes that are highly regulated under a diurnal cycle. A total of 1,480 diurnally regulated genes included 21 starch metabolic enzymes, 6 clock-associated genes, and 106 transcription factors (TF. A starch-clock-TF gene regulation network comprising 117 nodes and 266 edges was constructed by GGM from these 133 significant genes that are potentially related to the diurnal control of starch metabolism. From this network, we found that β-amylase 3 (b-amy3: At4g17090, which participates in starch degradation in chloroplast, is the most frequently connected gene (a hub gene. The robustness of gene-to-gene regulatory network was further analyzed by TF binding site prediction and by evaluating global co-expression of TFs and target starch metabolic enzymes. As a result, two TFs, indeterminate domain 5 (AtIDD5: At2g02070 and constans-like (COL: At2g21320, were identified as positive regulators of starch synthase 4 (SS4: At4g18240. The inference model of AtIDD5-dependent positive regulation of SS4 gene expression was experimentally supported by decreased SS4 mRNA accumulation in Atidd5 mutant plants during the light period of both short and long day conditions. COL was also shown to positively control SS4 mRNA accumulation. Furthermore, the knockout of AtIDD5 and COL led to deformation of chloroplast and its contained starch granules. This deformity also affected the number of starch granules per chloroplast, which increased significantly in both knockout mutant lines. Conclusions In this study, we utilized a systematic approach of microarray

  12. Network modeling reveals prevalent negative regulatory relationships between signaling sectors in Arabidopsis immune signaling.

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    Masanao Sato

    Full Text Available Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways. Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network. The plant immune signaling network, which controls inducible responses to pathogen attack, is such a complex network. We studied the Arabidopsis immune signaling network upon challenge with a strain of the bacterial pathogen Pseudomonas syringae expressing the effector protein AvrRpt2 (Pto DC3000 AvrRpt2. This bacterial strain feeds multiple inputs into the signaling network, allowing many parts of the network to be activated at once. mRNA profiles for 571 immune response genes of 22 Arabidopsis immunity mutants and wild type were collected 6 hours after inoculation with Pto DC3000 AvrRpt2. The mRNA profiles were analyzed as detailed descriptions of changes in the network state resulting from the genetic perturbations. Regulatory relationships among the genes corresponding to the mutations were inferred by recursively applying a non-linear dimensionality reduction procedure to the mRNA profile data. The resulting static network model accurately predicted 23 of 25 regulatory relationships reported in the literature, suggesting that predictions of novel regulatory relationships are also accurate. The network model revealed two striking features: (i the components of the network are highly interconnected; and (ii negative regulatory relationships are common between signaling sectors. Complex regulatory relationships, including a novel negative regulatory relationship between the early microbe-associated molecular pattern-triggered signaling sectors and the salicylic acid sector, were further validated. We propose that prevalent negative regulatory relationships among the signaling sectors make the plant immune signaling network a "sector

  13. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.

    Science.gov (United States)

    García-Gómez, Mónica L; Azpeitia, Eugenio; Álvarez-Buylla, Elena R

    2017-04-01

    The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell type. Our results

  14. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Mónica L García-Gómez

    2017-04-01

    Full Text Available The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell

  15. TONNEAU2/FASS Regulates the Geometry of Microtubule Nucleation and Cortical Array Organization in Interphase Arabidopsis Cells[C][W

    Science.gov (United States)

    Kirik, Angela; Ehrhardt, David W.; Kirik, Viktor

    2012-01-01

    Organization of microtubules into ordered arrays involves spatial and temporal regulation of microtubule nucleation. Here, we show that acentrosomal microtubule nucleation in plant cells involves a previously unknown regulatory step that determines the geometry of microtubule nucleation. Dynamic imaging of interphase cortical microtubules revealed that the ratio of branching to in-bundle microtubule nucleation on cortical microtubules is regulated by the Arabidopsis thaliana B′′ subunit of protein phosphatase 2A, which is encoded by the TONNEAU2/FASS (TON2) gene. The probability of nucleation from γ-tubulin complexes localized at the cell cortex was not affected by a loss of TON2 function, suggesting a specific role of TON2 in regulating the nucleation geometry. Both loss of TON2 function and ectopic targeting of TON2 to the plasma membrane resulted in defects in cell shape, suggesting the importance of TON2-mediated regulation of the microtubule cytoskeleton in cell morphogenesis. Loss of TON2 function also resulted in an inability for cortical arrays to reorient in response to light stimulus, suggesting an essential role for TON2 and microtubule branching nucleation in reorganization of microtubule arrays. Our data establish TON2 as a regulator of interphase microtubule nucleation and provide experimental evidence for a novel regulatory step in the process of microtubule-dependent nucleation. PMID:22395485

  16. Adaptor Protein Complex 2–Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis[W

    Science.gov (United States)

    Kim, Soo Youn; Xu, Zheng-Yi; Song, Kyungyoung; Kim, Dae Heon; Kang, Hyangju; Reichardt, Ilka; Sohn, Eun Ju; Friml, Jiří; Juergens, Gerd; Hwang, Inhwan

    2013-01-01

    Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4-(4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2–dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs. PMID:23975898

  17. Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana.

    Science.gov (United States)

    Araya, Takao; Kubo, Takuya; von Wirén, Nicolaus; Takahashi, Hideki

    2016-03-01

    Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with: (i) inhibition of primary root growth under nitrogen limitation or on ammonium; (ii) rapid progression of lateral root emergence in response to ammonium; and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies. © 2015 Institute of Botany, Chinese Academy of Sciences.

  18. A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network.

    Directory of Open Access Journals (Sweden)

    Felipe Leal Valentim

    Full Text Available Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1 mutation has a larger impact on APETALA1 (AP1, which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1 by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

  19. Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling

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    María Francisca eAguayo

    2015-02-01

    Full Text Available Polyols are enzymatically-produced plant compounds which can act as compatible solutes during periods of abiotic stress. NAD+-dependent SORBITOL DEHYDROGENASE (SDH, E.C. 1.1.1.14 from Arabidopsis thaliana L. (AtSDH is capable of oxidizing several polyols including sorbitol, ribitol and xylitol. In the present study, enzymatic assays using recombinant AtSDH demonstrated a higher specificity constant for xylitol compared to sorbitol and ribitol, all of which are C2 (S and C4 (R polyols. Enzyme activity was reduced by preincubation with ethylenediaminetetraacetic acid (EDTA, indicating a requirement for zinc ions. In humans, it has been proposed that sorbitol becomes part of a pentahedric coordination sphere of the catalytic zinc during the reaction mechanism. In order to determine the validity of this pentahedric coordination model in a plant SDH, homology modeling and Molecular Dynamics simulations of AtSDH ternary complexes with the three polyols were performed using crystal structures of human and Bemisia argentifolii (Genn. (Hemiptera: Aleyrodidae SDHs as scaffolds. The results indicate that the differences in interaction with structural water molecules correlate very well with the observed enzymatic parameters, validate the proposed pentahedric coordination of the catalytic zinc ion in a plant SDH, and provide an explanation for why AtSDH shows a preference for polyols with a chirality of C2 (S and C4 (R.

  20. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in arabidopsis

    NARCIS (Netherlands)

    Simonini, Sara; Deb, Joyita; Moubayidin, Laila; Stephenson, Pauline; Valluru, Manoj; Freire-Rios, Alejandra; Sorefan, Karim; Weijers, Dolf; Friml, Jiří; Østergaard, Lars

    2016-01-01

    Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through

  1. Cyclin-like F-box protein plays a role in growth and development of the three model species Medicago truncatula, Lotus japonicus, and Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Boycheva I

    2015-08-01

    Full Text Available Irina Boycheva,1 Valya Vassileva,2 Miglena Revalska,1 Grigor Zehirov,2 Anelia Iantcheva1 1Department of Functional Genetics Legumes, 2AgroBioInstitute, Department of Plant Stress Molecular Biology, Institute of Plant Physiology and Genetics, Sofia, Bulgaria Abstract: In eukaryotes, F-box proteins are one of the main components of the SCF complex that belongs to the family of ubiquitin E3 ligases, which catalyze protein ubiquitination and maintain the balance between protein synthesis and degradation. In the present study, we clarified the role and function of the gene encoding cyclin-like F-box protein from Medicago truncatula using transgenic plants of the model species M. truncatula, Lotus japonicas, and Arabidopsis thaliana generated by Agrobacterium-mediated transformation. Morphological and transcriptional analyses combined with flow cytometry and histochemistry demonstrated the participation of this protein in many aspects of plant growth and development, including processes of indirect somatic embryogenesis and symbiotic nodulation. The cyclin-like F-box gene showed expression in all plant organs and tissues comprised of actively dividing cells. The observed variations in root and hypocotyl growth, leaf and silique development, ploidy levels, and leaf parameters in the obtained transgenic lines demonstrated the effects of this gene on organ development. Furthermore, knockdown of cyclin-like F-box led to accumulation of higher levels of the G2/M transition-specific gene cyclin B1:1 (CYCB1:1, suggesting its possible role in cell cycle control. Together, the collected data suggest a similar role of the cyclin-like F-box protein in the three model species, providing evidence for the functional conservation of the studied gene. Keywords: cyclin-like F-box, model legumes, Arabidopsis thaliana, plant growth, plant development, cell cycle

  2. Virtual Organizations: Trends and Models

    Science.gov (United States)

    Nami, Mohammad Reza; Malekpour, Abbaas

    The Use of ICT in business has changed views about traditional business. With VO, organizations with out physical, geographical, or structural constraint can collaborate with together in order to fulfill customer requests in a networked environment. This idea improves resource utilization, reduces development process and costs, and saves time. Virtual Organization (VO) is always a form of partnership and managing partners and handling partnerships are crucial. Virtual organizations are defined as a temporary collection of enterprises that cooperate and share resources, knowledge, and competencies to better respond to business opportunities. This paper presents an overview of virtual organizations and main issues in collaboration such as security and management. It also presents a number of different model approaches according to their purpose and applications.

  3. Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

    Directory of Open Access Journals (Sweden)

    Alvarez-Buylla Elena R

    2010-10-01

    Full Text Available Abstract Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. Results We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. Conclusions These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not

  4. Model-Based Analysis of Arabidopsis Leaf Epidermal Cells Reveals Distinct Division and Expansion Patterns for Pavement and Guard Cells1[W][OA

    Science.gov (United States)

    Asl, Leila Kheibarshekan; Dhondt, Stijn; Boudolf, Véronique; Beemster, Gerrit T.S.; Beeckman, Tom; Inzé, Dirk; Govaerts, Willy; De Veylder, Lieven

    2011-01-01

    To efficiently capture sunlight for photosynthesis, leaves typically develop into a flat and thin structure. This development is driven by cell division and expansion, but the individual contribution of these processes is currently unknown, mainly because of the experimental difficulties to disentangle them in a developing organ, due to their tight interconnection. To circumvent this problem, we built a mathematic model that describes the possible division patterns and expansion rates for individual epidermal cells. This model was used to fit experimental data on cell numbers and sizes obtained over time intervals of 1 d throughout the development of the first leaf pair of Arabidopsis (Arabidopsis thaliana). The parameters were obtained by a derivative-free optimization method that minimizes the differences between the predicted and experimentally observed cell size distributions. The model allowed us to calculate probabilities for a cell to divide into guard or pavement cells, the maximum size at which it can divide, and its average cell division and expansion rates at each point during the leaf developmental process. Surprisingly, average cell cycle duration remained constant throughout leaf development, whereas no evidence for a maximum cell size threshold for cell division of pavement cells was found. Furthermore, the model predicted that neighboring cells of different sizes within the epidermis expand at distinctly different relative rates, which could be verified by direct observations. We conclude that cell division seems to occur independently from the status of cell expansion, whereas the cell cycle might act as a timer rather than as a size-regulated machinery. PMID:21693673

  5. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Science.gov (United States)

    Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

    2008-01-01

    Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

  6. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Directory of Open Access Journals (Sweden)

    Arce-Johnson Patricio

    2008-07-01

    Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

  7. The role of COBRA-LIKE 2 function, as part of the complex network of interacting pathways regulating Arabidopsis seed mucilage polysaccharide matrix organization.

    Science.gov (United States)

    Ben-Tov, Daniela; Idan-Molakandov, Anat; Hugger, Anat; Ben-Shlush, Ilan; Günl, Markus; Yang, Bo; Usadel, Björn; Harpaz-Saad, Smadar

    2018-05-01

    The production of hydrophilic mucilage along the course of seed coat epidermal cell differentiation is a common adaptation in angiosperms. Previous studies have identified COBRA-LIKE 2 (COBL2), a member of the COBRA-LIKE gene family, as a novel component required for crystalline cellulose deposition in seed coat epidermal cells. In recent years, Arabidopsis seed coat epidermal cells (SCEs), also called mucilage secretory cells, have emerged as a powerful model system for the study of plant cell wall components biosynthesis, secretion, assembly and de muro modification. Despite accumulating data, the molecular mechanism of COBL function remains largely unknown. In the current research, we utilized genetic interactions to study the role of COBL2 as part of the protein network required for seed mucilage production. Using correlative phenotyping of structural and biochemical characteristics, unique features of the cobl2 extruded mucilage are revealed, including: 'unraveled' ray morphology, loss of primary cell wall 'pyramidal' organization, reduced Ruthenium red staining intensity of the adherent mucilage layer, and increased levels of the monosaccharides arabinose and galactose. Examination of the cobl2cesa5 double mutant provides insight into the interface between COBL function and cellulose deposition. Additionally, genetic interactions between cobl2 and fei1fei2 as well as between each of these mutants to mucilage-modified 2 (mum2) suggest that COBL2 functions independently of the FEI-SOS pathway. Altogether, the presented data place COBL2 within the complex protein network required for cell wall deposition in the context of seed mucilage and introduce new methodology expending the seed mucilage phenotyping toolbox. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

  8. CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation.

    Science.gov (United States)

    Miki, Daisuke; Zhang, Wenxin; Zeng, Wenjie; Feng, Zhengyan; Zhu, Jian-Kang

    2018-05-17

    Homologous recombination-based gene targeting is a powerful tool for precise genome modification and has been widely used in organisms ranging from yeast to higher organisms such as Drosophila and mouse. However, gene targeting in higher plants, including the most widely used model plant Arabidopsis thaliana, remains challenging. Here we report a sequential transformation method for gene targeting in Arabidopsis. We find that parental lines expressing the bacterial endonuclease Cas9 from the egg cell- and early embryo-specific DD45 gene promoter can improve the frequency of single-guide RNA-targeted gene knock-ins and sequence replacements via homologous recombination at several endogenous sites in the Arabidopsis genome. These heritable gene targeting can be identified by regular PCR. Our approach enables routine and fine manipulation of the Arabidopsis genome.

  9. An overview of the gene regulatory network controlling trichome development in the model plant, Arabidopsis

    Directory of Open Access Journals (Sweden)

    Sitakanta ePattanaik

    2014-06-01

    Full Text Available Trichomes are specialized epidermal cells located on aerial parts of plants and are associated with a wide array of biological processes. Trichomes protect plants from adverse conditions including UV light and herbivore attack and are also an important source of a number of phytochemicals. The simple unicellular trichomes of Arabidopsis serve as an excellent model to study molecular mechanism of cell differentiation and pattern formation in plants. The emerging picture suggests that the developmental process is controlled by a transcriptional network involving three major groups of transcription factors: the R2R3 MYB, basic helix-loop-helix (bHLH and WD40 repeat (WDR protein. These regulatory proteins form a trimeric activator complex that positively regulates trichome development. The single repeat R3 MYBs act as negative regulators of trichome development. They compete with the R2R3 MYBs to bind the bHLH factor and form a repressor complex. In addition to activator-repressor mechanism, a depletion mechanism may operate in parallel during trichome development. In this mechanism, the bHLH factor traps the WDR protein which results in depletion of WDR protein in neighboring cells. Consequently, the cells with high levels of bHLH and WDR proteins are developed into trichomes. A group of C2H2 zinc finger TFs has also been implicated in trichome development. Phytohormones, including gibberellins and jasmonic acid, play significant roles in this developmental process. Recently, microRNAs have been shown to be involved in trichome development. Furthermore, it has been demonstrated that the activities of the key regulatory proteins involved in trichome development are controlled by the 26S/ubiquitin proteasome system (UPS, highlighting the complexity of the regulatory network controlling this developmental process. To complement several excellent recent relevant reviews, this review focuses on the transcriptional network and hormonal interplay

  10. Effect of modeled microgravity on UV-C-induced interplant communication of Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Ting; Xu, Wei; Li, Huasheng; Deng, Chenguang; Zhao, Hui; Wu, Yuejin; Liu, Min; Wu, Lijun; Lu, Jinying; Bian, Po

    2017-12-01

    Controlled ecological life support systems (CELSS) will be an important feature of long-duration space missions of which higher plants are one of the indispensable components. Because of its pivotal role in enabling plants to cope with environmental stress, interplant communication might have important implications for the ecological stability of such CELSS. However, the manifestations of interplant communication in microgravity conditions have yet to be fully elucidated. To address this, a well-established Arabidopsis thaliana co-culture experimental system, in which UV-C-induced airborne interplant communication is evaluated by the alleviation of transcriptional gene silencing (TGS) in bystander plants, was placed in microgravity modeled by a two-dimensional rotating clinostat. Compared with plants under normal gravity, TGS alleviation in bystander plants was inhibited in microgravity. Moreover, TGS alleviation was also prevented when plants of the pgm-1 line, which are impaired in gravity sensing, were used in either the UV-C-irradiated or bystander group. In addition to the specific TGS-loci, interplant communication-shaped genome-wide DNA methylation in bystander plants was altered under microgravity conditions. These results indicate that interplant communications might be modified in microgravity. Time course analysis showed that microgravity interfered with both the production of communicative signals in UV-C-irradiated plants and the induction of epigenetic responses in bystander plants. This was further confirmed by the experimental finding that microgravity also prevented the response of bystander plants to exogenous methyl jasmonate (JA) and methyl salicylate (SA), two well-known airborne signaling molecules, and down-regulated JA and SA biosynthesis in UV-C-irradiated plants. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Model of organ dose combination

    International Nuclear Information System (INIS)

    Valley, J.-F.; Lerch, P.

    1977-01-01

    The ICRP recommendations are based on the limitation of the dose to each organ. In the application and for a unique source the critical organ concept allows to limit the calculation and represents the irradiation status of an individuum. When several sources of radiation are involved the derivation of the dose contribution of each source to each organ is necessary. In order to represent the irradiation status a new parameter is to be defined. Propositions have been made by some authors, in particular by Jacobi introducing at this level biological parameters like the incidence rate of detriment and its severity. The new concept is certainly richer than a simple dose notion. However, in the actual situation of knowledge about radiation effects an intermediate parameter, using only physical concepts and the maximum permissible doses to the organs, seems more appropriate. The model, which is a generalization of the critical organ concept and shall be extended in the future to take the biological effects into account, will be presented [fr

  12. Transgenic Arabidopsis Gene Expression System

    Science.gov (United States)

    Ferl, Robert; Paul, Anna-Lisa

    2009-01-01

    The Transgenic Arabidopsis Gene Expression System (TAGES) investigation is one in a pair of investigations that use the Advanced Biological Research System (ABRS) facility. TAGES uses Arabidopsis thaliana, thale cress, with sensor promoter-reporter gene constructs that render the plants as biomonitors (an organism used to determine the quality of the surrounding environment) of their environment using real-time nondestructive Green Fluorescent Protein (GFP) imagery and traditional postflight analyses.

  13. The studies on the toxicity mechanism of environmentally hazardous natural (IAA) and synthetic (NAA) auxin--The experiments on model Arabidopsis thaliana and rat liver plasma membranes.

    Science.gov (United States)

    Hąc-Wydro, Katarzyna; Flasiński, Michał

    2015-06-01

    This paper concerns the studies towards membrane-damage effect of two auxins: indole-3-acetic acid - IAA and 1-naphthaleneacetic acid - NAA on plant (Arabidopsis thaliana) and animal (rat liver) model membranes. The foregoing auxins are plant growth regulators widely used in agriculture to control the quality of the crop. However, their accumulation in the environment makes them hazardous for the living organisms. The aim of our investigations was to compare the effect of natural (IAA) vs. synthetic (NAA) auxin on the organization of plant and animal model membranes and find a possible correlation between membrane-disturbing effect of these compounds and their toxicity. The collected data evidenced that auxins cause destabilization of membranes, decrease their condensation and weakens interactions of molecules. The alterations in the morphology of model systems were also noticed. The foregoing effects of auxins are concentration-dependent and additionally NAA was found to act on animal vs. plant membranes more selectively than IAA. Interestingly, both IAA and NAA induce the strongest disordering in model lipid system at the concentration, which is frequently reported as toxic to animal and plants. Based on the above findings it was proposed that membrane-damage effect induced by IAA and NAA may be important from the point of view of the mechanism of toxicity of these compounds and cannot be ignored in further investigations in this area. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Expression pattern of the AHP gene family from Arabidopsis thaliana and organ specific alternative splicing in the AHP5 gene

    Czech Academy of Sciences Publication Activity Database

    Hradilová, Jana; Brzobohatý, Břetislav

    2007-01-01

    Roč. 51, č. 2 (2007), s. 257-267 ISSN 0006-3134 Grant - others:GA MŠk(CZ) LN00A081; GA AV ČR(CZ) IAA600040612 Program:LN; IA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : Arabidopsis two component systems * gene expression analysis * real time RT-PCR Subject RIV: BO - Biophysics Impact factor: 1.259, year: 2007

  15. FYVE zinc-finger proteins in the plant model Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Jensen, R B; La Cour, T; Albrethsen, J

    2001-01-01

    Classic FYVE zinc-finger domains recognize the phosphoinositide signal PtdIns3P and share the basic (R/K)(1)(R/K)HHCR(6) (single-letter amino acid codes) consensus sequence. This domain is present in predicted PtdIns3P 5-kinases and lipases from Arabidopsis thaliana. Other Arabidopsis proteins......) of the basic motif. Dot-blot and liposome-binding assays were used in vitro to examine the phospholipid-binding ability of isolated PRAF domains. Whereas the PH domain preferentially bound PtdIns(4,5)P(2), the variant FYVE domain showed a weaker charge-dependent binding of phosphoinositides. In contrast....... A biochemical function for PRAF was indicated by its ability to catalyse guanine nucleotide exchange on some of the small GTPases of the Rab family, permitting a discussion of the biological roles of plant FYVE proteins and their regulation by phosphoinositides....

  16. Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

    Directory of Open Access Journals (Sweden)

    Ina Koch

    2017-06-01

    Full Text Available Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem.Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs.Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the

  17. Metabolism of ibuprofen in higher plants: A model Arabidopsis thaliana cell suspension culture system

    Czech Academy of Sciences Publication Activity Database

    Maršík, Petr; Šíša, Miroslav; Lacina, O.; Moťková, Kateřina; Langhansová, Lenka; Rezek, Jan; Vaněk, Tomáš

    2017-01-01

    Roč. 220, JAN (2017), s. 383-392 ISSN 0269-7491 R&D Projects: GA ČR(CZ) GA14-22593S Grant - others:European Regional Development Fund(XE) CZ.2.16/3.1.00/24014 Institutional support: RVO:61389030 Keywords : Arabidopsis thaliana * Ibuprofen * Metabolism * Plant cells * Sequestration Subject RIV: CE - Biochemistry OBOR OECD: Plant sciences, botany Impact factor: 5.099, year: 2016

  18. Spermine modulates the expression of two probable polyamine transporter genes and determines growth responses to cadaverine in Arabidopsis.

    Science.gov (United States)

    Sagor, G H M; Berberich, Thomas; Kojima, Seiji; Niitsu, Masaru; Kusano, Tomonobu

    2016-06-01

    Two genes, LAT1 and OCT1 , are likely to be involved in polyamine transport in Arabidopsis. Endogenous spermine levels modulate their expression and determine the sensitivity to cadaverine. Arabidopsis spermine (Spm) synthase (SPMS) gene-deficient mutant was previously shown to be rather resistant to the diamine cadaverine (Cad). Furthermore, a mutant deficient in polyamine oxidase 4 gene, accumulating about twofold more of Spm than wild type plants, showed increased sensitivity to Cad. It suggests that endogenous Spm content determines growth responses to Cad in Arabidopsis thaliana. Here, we showed that Arabidopsis seedlings pretreated with Spm absorbs more Cad and has shorter root growth, and that the transgenic Arabidopsis plants overexpressing the SPMS gene are hypersensitive to Cad, further supporting the above idea. The transgenic Arabidopsis overexpressing L-Amino acid Transporter 1 (LAT1) absorbed more Cad and showed increased Cad sensitivity, suggesting that LAT1 functions as a Cad importer. Recently, other research group reported that Organic Cation Transporter 1 (OCT1) is a causal gene which determines the Cad sensitivity of various Arabidopsis accessions. Furthermore, their results suggested that OCT1 is involved in Cad efflux. Thus we monitored the expression of OCT1 and LAT1 during the above experiments. Based on the results, we proposed a model in which the level of Spm content modulates the expression of OCT1 and LAT1, and determines Cad sensitivity of Arabidopsis.

  19. An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof

    Science.gov (United States)

    Costa, Michael A.; Collins, R. Eric; Anterola, Aldwin M.; Cochrane, Fiona C.; Davin, Laurence B.; Lewis, Norman G.

    2003-01-01

    The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member

  20. A genetic screen for modifiers of UFO meristem activity identifies three novel FUSED FLORAL ORGANS genes required for early flower development in Arabidopsis.

    Science.gov (United States)

    Levin, J Z; Fletcher, J C; Chen, X; Meyerowitz, E M

    1998-06-01

    In a screen to identify novel genes required for early Arabidopsis flower development, we isolated four independent mutations that enhance the Ufo phenotype toward the production of filamentous structures in place of flowers. The mutants fall into three complementation groups, which we have termed FUSED FLORAL ORGANS (FFO) loci. ffo mutants have specific defects in floral organ separation and/or positioning; thus, the FFO genes identify components of a boundary formation mechanism(s) acting between developing floral organ primordia. FFO1 and FFO3 have specific functions in cauline leaf/stem separation and in first- and third-whorl floral organ separation, with FFO3 likely acting to establish and FFO1 to maintain floral organ boundaries. FFO2 acts at early floral stages to regulate floral organ number and positioning and to control organ separation within and between whorls. Plants doubly mutant for two ffo alleles display additive phenotypes, indicating that the FFO genes may act in separate pathways. Plants doubly mutant for an ffo gene and for ufo, lfy, or clv3 reveal that the FFO genes play roles related to those of UFO and LFY in floral meristem initiation and that FFO2 and FFO3 may act to control cell proliferation late in inflorescence development.

  1. Arabidopsis thaliana sucrose phosphate synthase (sps) genes are expressed differentially in organs and tissues, and their transcription is regulated by osmotic stress.

    Science.gov (United States)

    Solís-Guzmán, María Gloria; Argüello-Astorga, Gerardo; López-Bucio, José; Ruiz-Herrera, León Francisco; López-Meza, Joel Edmundo; Sánchez-Calderón, Lenin; Carreón-Abud, Yazmín; Martínez-Trujillo, Miguel

    2017-11-01

    Sucrose is synthesized from UDP-Glc and Fru-6-phosphate via the activity of sucrose-phosphate synthase (SPS) enzymes, which produce Suc-6-phosphate. Suc-6-phosphate is rapidly dephosphorylated by phosphatases to produce Suc and inorganic phosphate. Arabidopsis has four sps genes encoding SPS enzymes. Of these enzymes, AtSPS1F and AtSPS2F have been grouped with other dicotyledonous SPS enzymes, while AtSPS3F and AtSPS4F are included in groups with both dicotyledonous and monocotyledonous SPS enzymes. In this work, we generated Arabidopsis thaliana transformants containing the promoter region of each sps gene fused to gfp::uidA reporter genes. A detailed characterization of expression conferred by the sps promoters in organs and tissues was performed. We observed expression of AtSPS1F, AtSPS2F and AtSPS3F in the columella roots of the plants that support sucrose synthesis. Hence, these findings support the idea that sucrose synthesis occurs in the columella cells, and suggests that sucrose has a role in this tissue. In addition, the expression of AtSPS4F was identified in embryos and suggests its participation in this developmental stage. Quantitative transcriptional analysis of A. thaliana plants grown in media with different osmotic potential showed that AtSPS2F and AtSPS4F respond to osmotic stress. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. The genome of Arabidopsis thaliana.

    OpenAIRE

    Goodman, H M; Ecker, J R; Dean, C

    1995-01-01

    Arabidopsis thaliana is a small flowering plant that is a member of the family cruciferae. It has many characteristics--diploid genetics, rapid growth cycle, relatively low repetitive DNA content, and small genome size--that recommend it as the model for a plant genome project. The current status of the genetic and physical maps, as well as efforts to sequence the genome, are presented. Examples are given of genes isolated by using map-based cloning. The importance of the Arabidopsis project ...

  3. Identification and Expression Profiling of Radiation-sensitive Genes Using Plant Model System, Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Kim, Dong-Sub; Kang, Si-Yong; Lee, Geung-Joo; Kim, Jin-Baek

    2008-06-01

    The purpose of this study is to characterize genes specifically expressed in response to ionizing energy (gamma-rays) of acute irradiation and elucidate signalling mechanisms via functional analysis of isolated genes in Arabidopsis thaliana. Recent improvements in DNA microarray technologies and bioinformatics have made it possible to look for common features of ionizing radiation-responsive genes and their regulatory regions. It has produced massive quantities of gene expression and other functional genomics data, and its application will increase in plant genomics. In this study, we used oligonucleotide microarrays to detect the Arabidopsis genes expressed differentially by a gamma-irradiation during the vegetative (VT, 21 DAG) and reproductive (RT, 28 DAG) stages. Wild-type (Ler) Arabidopsis was irradiated with gamma-rays with 100 and 800 Gy doses. Among the 21,500 genes represented in the Agilent chip, approximately 13,500 ( ∼ 61.4 %) responsive genes to ν -irradiation were expressed with signal intensity greater than 192 when compared to the combined control (non-irradiated vegetative and reproductive pool). Expression patterns of several radiation inducible genes were confirmed by RT-PCR and Northern blotting. Our microarray results may contribute to an overall understanding of the type and quantities of genes that are expressed by an acute gamma-irradiation. In addition, to investigate the oxidative damage caused by irradiation, RT-PCR analysis for the expression of antioxidant isoenzyme genes, and a Transmission Electron Microscope (TEM) observation for visualizing the H 2 O 2 scavenging activity in leaves were applied

  4. Identification and Expression Profiling of Radiation-sensitive Genes Using Plant Model System, Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong-Sub; Kang, Si-Yong; Lee, Geung-Joo; Kim, Jin-Baek

    2008-06-15

    The purpose of this study is to characterize genes specifically expressed in response to ionizing energy (gamma-rays) of acute irradiation and elucidate signalling mechanisms via functional analysis of isolated genes in Arabidopsis thaliana. Recent improvements in DNA microarray technologies and bioinformatics have made it possible to look for common features of ionizing radiation-responsive genes and their regulatory regions. It has produced massive quantities of gene expression and other functional genomics data, and its application will increase in plant genomics. In this study, we used oligonucleotide microarrays to detect the Arabidopsis genes expressed differentially by a gamma-irradiation during the vegetative (VT, 21 DAG) and reproductive (RT, 28 DAG) stages. Wild-type (Ler) Arabidopsis was irradiated with gamma-rays with 100 and 800 Gy doses. Among the 21,500 genes represented in the Agilent chip, approximately 13,500 ({sup {approx}}61.4 %) responsive genes to {nu} -irradiation were expressed with signal intensity greater than 192 when compared to the combined control (non-irradiated vegetative and reproductive pool). Expression patterns of several radiation inducible genes were confirmed by RT-PCR and Northern blotting. Our microarray results may contribute to an overall understanding of the type and quantities of genes that are expressed by an acute gamma-irradiation. In addition, to investigate the oxidative damage caused by irradiation, RT-PCR analysis for the expression of antioxidant isoenzyme genes, and a Transmission Electron Microscope (TEM) observation for visualizing the H{sub 2}O{sub 2} scavenging activity in leaves were applied.

  5. The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Gutiérrez Rodrigo A

    2008-09-01

    Full Text Available Abstract Background Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix™ ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants. Results We used bioinformatics methods to analyze publicly available data obtained using the ATH1 chip from Affymetrix. A total of 1887 ATH1 hybridizations were normalized and filtered to eliminate low-quality hybridizations. We classified and compared control and treatment hybridizations and determined differential gene expression. The largest differences in gene expression were observed when comparing samples obtained from different organs. On average, ten-fold more genes were differentially expressed between organs as compared to any other experimental variable. We defined "gene responsiveness" as the number of comparisons in which a gene changed its expression significantly. We defined genes with the highest and lowest responsiveness levels as hypervariable and housekeeping genes, respectively. Remarkably, housekeeping genes were best distinguished from hypervariable genes by differences in methylation status in their transcribed regions. Moreover, methylation in the transcribed region was inversely correlated (R2 = 0.8 with gene responsiveness on a genome-wide scale. We provide an example of this negative relationship using genes encoding TCA cycle enzymes, by contrasting their regulatory responsiveness to nitrate and methylation status in their transcribed regions. Conclusion Our results indicate that the Arabidopsis transcriptome is largely established during development and is comparatively stable when faced with external perturbations. We suggest a novel functional role for DNA methylation in the transcribed region as a key determinant

  6. The Organization Pattern of Root Border-Like Cells of Arabidopsis Is Dependent on Cell Wall Homogalacturonan12[C][W

    Science.gov (United States)

    Durand, Caroline; Vicré-Gibouin, Maïté; Follet-Gueye, Marie Laure; Duponchel, Ludovic; Moreau, Myriam; Lerouge, Patrice; Driouich, Azeddine

    2009-01-01

    Border-like cells are released by Arabidopsis (Arabidopsis thaliana) root tips as organized layers of several cells that remain attached to each other rather than completely detached from each other, as is usually observed in border cells of many species. Unlike border cells, cell attachment between border-like cells is maintained after their release into the external environment. To investigate the role of cell wall polysaccharides in the attachment and organization of border-like cells, we have examined their release in several well-characterized mutants defective in the biosynthesis of xyloglucan, cellulose, or pectin. Our data show that among all mutants examined, only quasimodo mutants (qua1-1 and qua2-1), which have been characterized as producing less homogalacturonan, had an altered border-like cell phenotype as compared with the wild type. Border-like cells in both lines were released as isolated cells separated from each other, with the phenotype being much more pronounced in qua1-1 than in qua2-1. Further analysis of border-like cells in the qua1-1 mutant using immunocytochemistry and a set of anti-cell wall polysaccharide antibodies showed that the loss of the wild-type phenotype was accompanied by (1) a reduction in homogalacturonan-JIM5 epitope in the cell wall of border-like cells, confirmed by Fourier transform infrared microspectrometry, and (2) the secretion of an abundant mucilage that is enriched in xylogalacturonan and arabinogalactan-protein epitopes, in which the cells are trapped in the vicinity of the root tip. PMID:19448034

  7. Evaluation of Arabidopsis thaliana as a model host for Xylella fastidiosa.

    Science.gov (United States)

    Rogers, Elizabeth E

    2012-06-01

    The bacterium Xylella fastidiosa causes a number of plant diseases of significant economic impact. To date, progress determining mechanisms of host-plant susceptibility, tolerance, or resistance has been slow, due in large part to the long generation time and limited available genetic resources for grape, almond, and other known hosts of X. fastidiosa. To overcome many of these limitations, Arabidopsis thaliana has been evaluated as a host for X. fastidiosa. A pin-prick inoculation method has been developed to infect Arabidopsis with X. fastidiosa. Following infection, X. fastidiosa multiplies and can be detected by microscopy, polymerase chain reaction, and isolation. The ecotypes Van-0, LL-0, and Tsu-1 all allow more growth of strain X. fastidiosa Temecula than the reference ecotype Col-0. Affymetrix ATH1 microarray analysis of inoculated vs. noninoculated Tsu-1 reveals gene expression changes that differ greatly from changes seen after infection with apoplast-colonizing bacteria such as Psuedomonas syringae pvs. tomato or syringae. Many genes responsive to oxidative stress are differentially regulated, while classic pathogenesis-related genes are not induced by X. fastidiosa infection.

  8. Database Description - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Database Description General information of database Database n... BioResource Center Hiroshi Masuya Database classification Plant databases - Arabidopsis thaliana Organism T...axonomy Name: Arabidopsis thaliana Taxonomy ID: 3702 Database description The Arabidopsis thaliana phenome i...heir effective application. We developed the new Arabidopsis Phenome Database integrating two novel database...seful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing

  9. using stereochemistry models in teaching organic compounds

    African Journals Online (AJOL)

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    The purpose of the study was to find out the effect of stereochemistry models on students' ... consistent with the names given to organic compounds. Some of ... Considering class level, what is the performance of the students in naming organic.

  10. Tree-Structured Digital Organisms Model

    Science.gov (United States)

    Suzuki, Teruhiko; Nobesawa, Shiho; Tahara, Ikuo

    Tierra and Avida are well-known models of digital organisms. They describe a life process as a sequence of computation codes. A linear sequence model may not be the only way to describe a digital organism, though it is very simple for a computer-based model. Thus we propose a new digital organism model based on a tree structure, which is rather similar to the generic programming. With our model, a life process is a combination of various functions, as if life in the real world is. This implies that our model can easily describe the hierarchical structure of life, and it can simulate evolutionary computation through mutual interaction of functions. We verified our model by simulations that our model can be regarded as a digital organism model according to its definitions. Our model even succeeded in creating species such as viruses and parasites.

  11. Phytoremediation of the organic Xenobiotic simazine by p450-1a2 transgenic Arabidopsis thaliana plants.

    Science.gov (United States)

    Azab, Ehab; Hegazy, Ahmad K; El-Sharnouby, Mohamed E; Abd Elsalam, Hassan E

    2016-01-01

    The potential use of human P450-transgenic plants for phytoremediation of pesticide contaminated soils was tested in laboratory and greenhouse experiments. The transgenic P450 CYP1A2 gene Arabidopsis thaliana plants metabolize number of herbicides, insecticides and industrial chemicals. The P450 isozymes CYP1A2 expressed in A. thaliana were examined regarding the herbicide simazine (SIM). Transgenic A. thaliana plants expressing CYP1A2 gene showed significant resistance to SIM supplemented either in plant growth medium or sprayed on foliar parts. The results showed that SIM produces harmful effect on both rosette diameter and primary root length of the wild type (WT) plants. In transgenic A. thaliana lines, the rosette diameter and primary root length were not affected by SIM concentrations used in this experiment. The results indicate that CYP1A2 can be used as a selectable marker for plant transformation, allowing efficient selection of transgenic lines in growth medium and/or in soil-grown plants. The transgenic A. thaliana plants exhibited a healthy growth using doses of up to 250 μmol SIM treatments, while the non-transgenic A. thaliana plants were severely damaged with doses above 50 μmol SIM treatments. The transgenic A. thaliana plants can be used as phytoremediator of environmental SIM contaminants.

  12. Modelling organic particles in the atmosphere

    International Nuclear Information System (INIS)

    Couvidat, Florian

    2012-01-01

    Organic aerosol formation in the atmosphere is investigated via the development of a new model named H 2 O (Hydrophilic/Hydrophobic Organics). First, a parameterization is developed to take into account secondary organic aerosol formation from isoprene oxidation. It takes into account the effect of nitrogen oxides on organic aerosol formation and the hydrophilic properties of the aerosols. This parameterization is then implemented in H 2 O along with some other developments and the results of the model are compared to organic carbon measurements over Europe. Model performance is greatly improved by taking into account emissions of primary semi-volatile compounds, which can form secondary organic aerosols after oxidation or can condense when temperature decreases. If those emissions are not taken into account, a significant underestimation of organic aerosol concentrations occurs in winter. The formation of organic aerosols over an urban area was also studied by simulating organic aerosols concentration over the Paris area during the summer campaign of Megapoli (July 2009). H 2 O gives satisfactory results over the Paris area, although a peak of organic aerosol concentrations from traffic, which does not appear in the measurements, appears in the model simulation during rush hours. It could be due to an underestimation of the volatility of organic aerosols. It is also possible that primary and secondary organic compounds do not mix well together and that primary semi volatile compounds do not condense on an organic aerosol that is mostly secondary and highly oxidized. Finally, the impact of aqueous-phase chemistry was studied. The mechanism for the formation of secondary organic aerosol includes in-cloud oxidation of glyoxal, methylglyoxal, methacrolein and methylvinylketone, formation of methyltetrols in the aqueous phase of particles and cloud droplets, and the in-cloud aging of organic aerosols. The impact of wet deposition is also studied to better estimate the

  13. Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein.

    Directory of Open Access Journals (Sweden)

    Yuno Lee

    Full Text Available 2-Cys peroxiredoxins (Prxs play important roles in the protection of chloroplast proteins from oxidative damage. Arabidopsis NADPH-dependent thioredoxin reductase isotype C (AtNTRC was identified as efficient electron donor for chloroplastic 2-Cys Prx-A. There are three isotypes (A, B, and C of thioredoxin reductase (TrxR in Arabidopsis. AtNTRA contains only TrxR domain, but AtNTRC consists of N-terminal TrxR and C-terminal thioredoxin (Trx domains. AtNTRC has various oligomer structures, and Trx domain is important for chaperone activity. Our previous experimental study has reported that the hybrid protein (AtNTRA-(Trx-D, which was a fusion of AtNTRA and Trx domain from AtNTRC, has formed variety of structures and shown strong chaperone activity. But, electron transfer mechanism was not detected at all. To find out the reason of this problem with structural basis, we performed two different molecular dynamics (MD simulations on AtNTRC and AtNTRA-(Trx-D proteins with same cofactors such as NADPH and flavin adenine dinucleotide (FAD for 50 ns. Structural difference has found from superimposition of two structures that were taken relatively close to average structure. The main reason that AtNTRA-(Trx-D cannot transfer the electron from TrxR domain to Trx domain is due to the difference of key catalytic residues in active site. The long distance between TrxR C153 and disulfide bond of Trx C387-C390 has been observed in AtNTRA-(Trx-D because of following reasons: i unstable and unfavorable interaction of the linker region, ii shifted Trx domain, and iii different or weak interface interaction of Trx domains. This study is one of the good examples for understanding the relationship between structure formation and reaction activity in hybrid protein. In addition, this study would be helpful for further study on the mechanism of electron transfer reaction in NADPH-dependent thioredoxin reductase proteins.

  14. Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa

    Czech Academy of Sciences Publication Activity Database

    Kolář, Filip; Fuxová, G.; Záveská, E.; Nagano, A. J.; Hyklová, L.; Lučanová, Magdalena; Kudoh, H.; Marhold, K.

    2016-01-01

    Roč. 25, č. 16 (2016), s. 3929-3949 ISSN 0962-1083 Institutional support: RVO:67985939 Keywords : approximate Bayesian computatuion * niche differentiation * phytogeography * Arabidopsis Subject RIV: EF - Botanics Impact factor: 6.086, year: 2016

  15. The Arabidopsis halophytic relative Thellungiella halophila tolerates nitrogen-limiting conditions by maintaining growth, nitrogen uptake, and assimilation.

    Science.gov (United States)

    Kant, Surya; Bi, Yong-Mei; Weretilnyk, Elizabeth; Barak, Simon; Rothstein, Steven J

    2008-07-01

    A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low (15)NO(3)(-) supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.

  16. Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis.

    Science.gov (United States)

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Muhammad Aaqil; Waqas, Muhammad; Kang, Sang-Mo; Yun, Byung-Wook; Lee, In-Jung

    2017-08-08

    We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.

  17. Structural insight into the binding interactions of modeled structure of Arabidopsis thaliana urease with urea: an in silico study.

    Science.gov (United States)

    Yata, Vinod Kumar; Thapa, Arun; Mattaparthi, Venkata Satish Kumar

    2015-01-01

    Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of A. thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modeled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modeled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398, and Thr679 residues of A. thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori, and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modeled A. thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426, and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole, this study expounds the salient structural features as well the binding interactions of the modeled structure of A. thaliana urease.

  18. Organic production in a dynamic CGE model

    DEFF Research Database (Denmark)

    Jacobsen, Lars Bo

    2004-01-01

    for conventional production into land for organic production, a period of two years must pass before the land being transformed can be used for organic production. During that time, the land is counted as land of the organic industry, but it can only produce the conventional product. To handle this rule, we make......Concerns about the impact of modern agriculture on the environment have in recent years led to an interest in supporting the development of organic farming. In addition to environmental benefits, the aim is to encourage the provision of other “multifunctional” properties of organic farming...... such as rural amenities and rural development that are spillover benefit additional to the supply of food. In this paper we further develop an existing dynamic general equilibrium model of the Danish economy to specifically incorporate organic farming. In the model and input-output data each primary...

  19. A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

    Science.gov (United States)

    Gopalan, Suresh; Ausubel, Frederick M

    2008-01-01

    An unintended consequence of global industrialization and associated societal rearrangements is new interactions of microbes and potential hosts (especially mammals and plants), providing an opportunity for the rapid emergence of host-microbe adaptation and eventual establishment of new microbe-related diseases. We describe a new model system comprising the model plant Arabidopsis thaliana and several microbes, each representing different modes of interaction, to study such "maladaptations". The model microbes include human and agricultural pathogens and microbes that are commonly considered innocuous. The system has a large knowledge base corresponding to each component organism and is amenable to high-throughput automation assisted perturbation screens for identifying components that modulate host-pathogen interactions. This would aid in the study of emergence and progression of host-microbe maladaptations in a controlled environment.

  20. Patterning and lifetime of plasma membrane-localized cellulose synthase is dependent on actin organization in Arabidopsis interphase cells

    NARCIS (Netherlands)

    Sampathkumar, A.; Gutierrez, R.; McFarlane, H.E.; Bringmann, M.; Lindeboom, J.J.; Emons, A.M.C.; Samuels, L.; Ketelaar, T.; Ehrhardt, D.W.; Persson, S.

    2013-01-01

    The actin and microtubule cytoskeletons regulate cell shape across phyla, from bacteria to metazoans. In organisms with cell walls, the wall acts as a primary constraint of shape, and generation of specific cell shape depends on cytoskeletal organization for wall deposition and/or cell expansion. In

  1. Cardiac Electromechanical Models: From Cell to Organ

    Directory of Open Access Journals (Sweden)

    Natalia A Trayanova

    2011-08-01

    Full Text Available The heart is a multiphysics and multiscale system that has driven the development of the most sophisticated mathematical models at the frontiers of computation physiology and medicine. This review focuses on electromechanical (EM models of the heart from the molecular level of myofilaments to anatomical models of the organ. Because of the coupling in terms of function and emergent behaviors at each level of biological hierarchy, separation of behaviors at a given scale is difficult. Here, a separation is drawn at the cell level so that the first half addresses subcellular/single cell models and the second half addresses organ models. At the subcelluar level, myofilament models represent actin-myosin interaction and Ca-based activation. Myofilament models and their refinements represent an overview of the development in the field. The discussion of specific models emphasizes the roles of cooperative mechanisms and sarcomere length dependence of contraction force, considered the cellular basis of the Frank-Starling law. A model of electrophysiology and Ca handling can be coupled to a myofilament model to produce an EM cell model, and representative examples are summarized to provide an overview of the progression of field. The second half of the review covers organ-level models that require solution of the electrical component as a reaction-diffusion system and the mechanical component, in which active tension generated by the myocytes produces deformation of the organ as described by the equations of continuum mechanics. As outlined in the review, different organ-level models have chosen to use different ionic and myofilament models depending on the specific application; this choice has been largely dictated by compromises between model complexity and computational tractability. The review also addresses application areas of EM models such as cardiac resynchronization therapy and the role of mechano-electric coupling in arrhythmias and

  2. Project-matrix models of marketing organization

    Directory of Open Access Journals (Sweden)

    Gutić Dragutin

    2009-01-01

    Full Text Available Unlike theory and practice of corporation organization, in marketing organization numerous forms and contents at its disposal are not reached until this day. It can be well estimated that marketing organization today in most of our companies and in almost all its parts, noticeably gets behind corporation organization. Marketing managers have always been occupied by basic, narrow marketing activities as: sales growth, market analysis, market growth and market share, marketing research, introduction of new products, modification of products, promotion, distribution etc. They rarely found it necessary to focus a bit more to different aspects of marketing management, for example: marketing planning and marketing control, marketing organization and leading. This paper deals with aspects of project - matrix marketing organization management. Two-dimensional and more-dimensional models are presented. Among two-dimensional, these models are analyzed: Market management/products management model; Products management/management of product lifecycle phases on market model; Customers management/marketing functions management model; Demand management/marketing functions management model; Market positions management/marketing functions management model. .

  3. Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.

    Science.gov (United States)

    Wittenberg, Alexander H J; van der Lee, Theo; Cayla, Cyril; Kilian, Andrzej; Visser, Richard G F; Schouten, Henk J

    2005-08-01

    Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F(2) population obtained from a Col x Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.

  4. The Zebrafish Model Organism Database (ZFIN)

    Data.gov (United States)

    U.S. Department of Health & Human Services — ZFIN serves as the zebrafish model organism database. It aims to: a) be the community database resource for the laboratory use of zebrafish, b) develop and support...

  5. Complex Systems and Self-organization Modelling

    CERN Document Server

    Bertelle, Cyrille; Kadri-Dahmani, Hakima

    2009-01-01

    The concern of this book is the use of emergent computing and self-organization modelling within various applications of complex systems. The authors focus their attention both on the innovative concepts and implementations in order to model self-organizations, but also on the relevant applicative domains in which they can be used efficiently. This book is the outcome of a workshop meeting within ESM 2006 (Eurosis), held in Toulouse, France in October 2006.

  6. Characterization of Plant Growth under Single-Wavelength Laser Light Using the Model Plant Arabidopsis Thaliana

    KAUST Repository

    Ooi, Amanda

    2016-12-01

    Indoor horticulture offers a promising solution for sustainable food production and is becoming increasingly widespread. However, it incurs high energy and cost due to the use of artificial lighting such as high-pressure sodium lamps, fluorescent light or increasingly, the light-emitting diodes (LEDs). The energy efficiency and light quality of currently available lighting is suboptimal, therefore less than ideal for sustainable and cost-effective large-scale plant production. Here, we demonstrate the use of high-powered single-wavelength lasers for indoor horticulture. Lasers are highly energy-efficient and can be remotely guided to the site of plant growth, thus reducing on-site heat accumulation. Besides, laser beams can be tailored to match the absorption profiles of different plants. We have developed a prototype laser growth chamber and demonstrate that laser-grown plants can complete a full growth cycle from seed to seed with phenotypes resembling those of plants grown under LEDs. Importantly, the plants have lower expression of proteins diagnostic for light and radiation stress. The phenotypical, biochemical and proteomic data show that the singlewavelength laser light is suitable for plant growth and therefore, potentially able to unlock the advantages of this next generation lighting technology for highly energy-efficient horticulture. Furthermore, stomatal movement partly determines the plant productivity and stress management. Abscisic acid (ABA) induces stomatal closure by promoting net K+-efflux from guard cells through outwardrectifying K+ (K+ out) channels to regulate plant water homeostasis. Here, we show that the Arabidopsis thaliana guard cell outward-rectifying K+ (ATGORK) channel is a direct target for ABA in the regulation of stomatal aperture and hence gas exchange and transpiration. Addition of (±)-ABA, but not the biologically inactive (−)-isomer, increases K+ out channel activity in Vicia faba guard cell protoplast. A similar ABA

  7. Growing Arabidopsis in vitro: cell suspensions, in vitro culture, and regeneration.

    Science.gov (United States)

    Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar

    2014-01-01

    An understanding of basic methods in Arabidopsis tissue culture is beneficial for any laboratory working on this model plant. Tissue culture refers to the aseptic growth of cells, organs, or plants in a controlled environment, in which physical, nutrient, and hormonal conditions can all be easily manipulated and monitored. The methodology facilitates the production of a large number of plants that are genetically identical over a relatively short growth period. Techniques, including callus production, cell suspension cultures, and plant regeneration, are all indispensable tools for the study of cellular biochemical and molecular processes. Plant regeneration is a key technology for successful stable plant transformation, while cell suspension cultures can be exploited for metabolite profiling and mining. In this chapter we report methods for the successful and highly efficient in vitro regeneration of plants and production of stable cell suspension lines from leaf explants of both Arabidopsis thaliana and Arabidopsis halleri.

  8. Modeling self-organization of novel organic materials

    Science.gov (United States)

    Sayar, Mehmet

    In this thesis, the structural organization of oligomeric multi-block molecules is analyzed by computational analysis of coarse-grained models. These molecules form nanostructures with different dimensionalities, and the nanostructured nature of these materials leads to novel structural properties at different length scales. Previously, a number of oligomeric triblock rodcoil molecules have been shown to self-organize into mushroom shaped noncentrosymmetric nanostructures. Interestingly, thin films of these molecules contain polar domains and a finite macroscopic polarization. However, the fully polarized state is not the equilibrium state. In the first chapter, by solving a model with dipolar and Ising-like short range interactions, we show that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a ≈ 6 nm), leading to a reduction in the repulsive dipolar interactions that oppose polar order within layers. This enables the formation of a striped pattern with polar domains of alternating directions. The energies of the possible structures at zero temperature are computed exactly and results of Monte Carlo simulations are provided at non-zero temperatures. In the second chapter, the macroscopic polarization of such nanostructured films is analyzed in the presence of a short range surface interaction. The surface interaction leads to a periodic domain structure where the balance between the up and down domains is broken, and therefore films of finite thickness have a net macroscopic polarization. The polarization per unit volume is a function of film thickness and strength of the surface interaction. Finally, in chapter three, self-organization of organic molecules into a network of one dimensional objects is analyzed. Multi-block organic dendron rodcoil molecules were found to self-organize into supramolecular nanoribbons (threads) and

  9. A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family.

    Science.gov (United States)

    Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L; Salt, Jennifer N; Goring, Daphne R

    2004-01-01

    The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis.

  10. A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family1[w

    Science.gov (United States)

    Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L.; Salt, Jennifer N.; Goring, Daphne R.

    2004-01-01

    The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis. PMID:14657406

  11. The conceptual model of organization social responsibility

    OpenAIRE

    LUO, Lan; WEI, Jingfu

    2014-01-01

    With the developing of the research of CSR, people more and more deeply noticethat the corporate should take responsibility. Whether other organizations besides corporatesshould not take responsibilities beyond their field? This paper puts forward theconcept of organization social responsibility on the basis of the concept of corporate socialresponsibility and other theories. And the conceptual models are built based on theconception, introducing the OSR from three angles: the types of organi...

  12. Putting "Organizations" into an Organization Theory Course: A Hybrid CAO Model for Teaching Organization Theory

    Science.gov (United States)

    Hannah, David R.; Venkatachary, Ranga

    2010-01-01

    In this article, the authors present a retrospective analysis of an instructor's multiyear redesign of a course on organization theory into what is called a hybrid Classroom-as-Organization model. It is suggested that this new course design served to apprentice students to function in quasi-real organizational structures. The authors further argue…

  13. Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses

    Directory of Open Access Journals (Sweden)

    Brenner Wolfram G

    2012-07-01

    Full Text Available Abstract Background The plant hormone cytokinin regulates growth and development of roots and shoots in opposite ways. In shoots it is a positive growth regulator whereas it inhibits growth in roots. It may be assumed that organ-specific regulation of gene expression is involved in these differential activities, but little is known about it. To get more insight into the transcriptional events triggered by cytokinin in roots and shoots, we studied genome-wide gene expression in cytokinin-treated and cytokinin-deficient roots and shoots. Results It was found by principal component analysis of the transcriptomic data that the immediate-early response to a cytokinin stimulus differs from the later response, and that the transcriptome of cytokinin-deficient plants is different from both the early and the late cytokinin induction response. A higher cytokinin status in the roots activated the expression of numerous genes normally expressed predominantly in the shoot, while a lower cytokinin status in the shoot reduced the expression of genes normally more active in the shoot to a more root-like level. This shift predominantly affected nuclear genes encoding plastid proteins. An organ-specific regulation was assigned to a number of genes previously known to react to a cytokinin signal, including root-specificity for the cytokinin hydroxylase gene CYP735A2 and shoot specificity for the cell cycle regulator gene CDKA;1. Numerous cytokinin-regulated genes were newly discovered or confirmed, including the meristem regulator genes SHEPHERD and CLAVATA1, auxin-related genes (IAA7, IAA13, AXR1, PIN2, PID, several genes involved in brassinosteroid (CYP710A1, CYP710A2, DIM/DWF and flavonol (MYB12, CHS, FLS1 synthesis, various transporter genes (e.g. HKT1, numerous members of the AP2/ERF transcription factor gene family, genes involved in light signalling (PhyA, COP1, SPA1, and more than 80 ribosomal genes. However, contrasting with the fundamental difference of

  14. Arabidopsis peroxisome proteomics

    Directory of Open Access Journals (Sweden)

    John D. Bussell

    2013-04-01

    Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

  15. Phylogeny-dominant classification of J-proteins in Arabidopsis thaliana and Brassica oleracea.

    Science.gov (United States)

    Zhang, Bin; Qiu, Han-Lin; Qu, Dong-Hai; Ruan, Ying; Chen, Dong-Hong

    2018-04-05

    Hsp40s or DnaJ/J-proteins are evolutionarily conserved in all organisms as co-chaperones of molecular chaperone HSP70s that mainly participate in maintaining cellular protein homeostasis, such as protein folding, assembly, stabilization, and translocation under normal conditions as well as refolding and degradation under environmental stresses. It has been reported that Arabidopsis J-proteins are classified into four classes (types A-D) according to domain organization, but their phylogenetic relationships are unknown. Here, we identified 129 J-proteins in the world-wide popular vegetable Brassica oleracea, a close relative of the model plant Arabidopsis, and also revised the information of Arabidopsis J-proteins based on the latest online bioresources. According to phylogenetic analysis with domain organization and gene structure as references, the J-proteins from Arabidopsis and B. oleracea were classified into 15 main clades (I-XV) separated by a number of undefined small branches with remote relationship. Based on the number of members, they respectively belong to multigene clades, oligo-gene clades, and mono-gene clades. The J-protein genes from different clades may function together or separately to constitute a complicated regulatory network. This study provides a constructive viewpoint for J-protein classification and an informative platform for further functional dissection and resistant genes discovery related to genetic improvement of crop plants.

  16. The Arabidopsis Halophytic Relative Thellungiella halophila Tolerates Nitrogen-Limiting Conditions by Maintaining Growth, Nitrogen Uptake, and Assimilation1[W][OA

    Science.gov (United States)

    Kant, Surya; Bi, Yong-Mei; Weretilnyk, Elizabeth; Barak, Simon; Rothstein, Steven J.

    2008-01-01

    A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low 15NO3− supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance. PMID:18467466

  17. Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

    Science.gov (United States)

    Pittman, Jon K; Hirschi, Kendal D

    2016-12-01

    The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

  18. Safety Cultural Competency Modeling in Nuclear Organizations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sa Kil; Oh, Yeon Ju; Luo, Meiling; Lee, Yong Hee [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    The nuclear safety cultural competency model should be supplemented through a bottom-up approach such as behavioral event interview. The developed model, however, is meaningful for determining what should be dealt for enhancing safety cultural competency of nuclear organizations. The more details of the developing process, results, and applications will be introduced later. Organizational culture include safety culture in terms of its organizational characteristics.

  19. A STRATEGIC MANAGEMENT MODEL FOR SERVICE ORGANIZATIONS

    OpenAIRE

    Andreea ZAMFIR

    2013-01-01

    This paper provides a knowledge-based strategic management of services model, with a view to emphasise an approach to gaining competitive advantage through knowledge, people and networking. The long-term evolution of the service organization is associated with the way in which the strategic management is practised.

  20. Expanding on Successful Concepts, Models, and Organization

    Science.gov (United States)

    If the goal of the AEP framework was to replace existing exposure models or databases for organizing exposure data with a concept, we would share Dr. von Göetz concerns. Instead, the outcome we promote is broader use of an organizational framework for exposure science. The f...

  1. Biochemical and structural properties of cyanases from Arabidopsis thaliana and Oryza sativa.

    Directory of Open Access Journals (Sweden)

    Dan Qian

    Full Text Available Cyanate is toxic to all organisms. Cyanase converts cyanate to CO₂ and NH₃ in a bicarbonate-dependent reaction. The biophysical functions and biochemical characteristics of plant cyanases are poorly studied, although it has been investigated in a variety of proteobacteria, cyanobacteria and fungi. In this study, we characterised plant cyanases from Arabidopsis thaliana and Oryza sativa (AtCYN and OsCYN. Prokaryotic-expressed AtCYN and OsCYN both showed cyanase activity in vitro. Temperature had a similar influence on the activity of both cyanases, but pH had a differential impact on AtCYN and OsCYN activity. Homology modelling provided models of monomers of AtCYN and OsCYN, and a coimmunoprecipitation assay and gel filtration indicated that AtCYN and OsCYN formed homodecamers. The analysis of single-residue mutants of AtCYN indicated that the conserved catalytic residues also contributed to the stability of the homodecamer. KCNO treatment inhibited Arabidopsis germination and early seedling growth. Plants containing AtCYN or OsCYN exhibited resistance to KCNO stress, which demonstrated that one role of cyanases in plants is detoxification. Transcription level of AtCYN was higher in the flower than in other organs of Arabidopsis. AtCYN transcription was not significantly affected by KCNO treatment in Arabidopsis, but was induced by salt stress. This research broadens our knowledge on plant detoxification of cyanate via cyanase.

  2. Emergent organization in a model market

    Science.gov (United States)

    Yadav, Avinash Chand; Manchanda, Kaustubh; Ramaswamy, Ramakrishna

    2017-09-01

    We study the collective behaviour of interacting agents in a simple model of market economics that was originally introduced by Nørrelykke and Bak. A general theoretical framework for interacting traders on an arbitrary network is presented, with the interaction consisting of buying (namely consumption) and selling (namely production) of commodities. Extremal dynamics is introduced by having the agent with least profit in the market readjust prices, causing the market to self-organize. In addition to examining this model market on regular lattices in two-dimensions, we also study the cases of random complex networks both with and without community structures. Fluctuations in an activity signal exhibit properties that are characteristic of avalanches observed in models of self-organized criticality, and these can be described by power-law distributions when the system is in the critical state.

  3. A comprehensive dataset of genes with a loss-of-function mutant phenotype in Arabidopsis.

    Science.gov (United States)

    Lloyd, Johnny; Meinke, David

    2012-03-01

    Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.

  4. Integrated modelling of two xenobiotic organic compounds

    DEFF Research Database (Denmark)

    Lindblom, Erik Ulfson; Gernaey, K.V.; Henze, Mogens

    2006-01-01

    This paper presents a dynamic mathematical model that describes the fate and transport of two selected xenobiotic organic compounds (XOCs) in a simplified representation. of an integrated urban wastewater system. A simulation study, where the xenobiotics bisphenol A and pyrene are used as reference...... compounds, is carried out. Sorption and specific biological degradation processes are integrated with standardised water process models to model the fate of both compounds. Simulated mass flows of the two compounds during one dry weather day and one wet weather day are compared for realistic influent flow...... rate and concentration profiles. The wet weather day induces resuspension of stored sediments, which increases the pollutant load on the downstream system. The potential of the model to elucidate important phenomena related to origin and fate of the model compounds is demonstrated....

  5. Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes

    Science.gov (United States)

    Nallu, Sumitha; Wang, Lin; Botanga, Christopher J.; Gomez, S. Karen; Costa, Liliana M.; Harrison, Maria J.; Samac, Deborah A.; Glazebrook, Jane; Katagiri, Fumiaki; Gutierrez-Marcos, Jose F.; VandenBosch, Kathryn A.

    2013-01-01

    Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species. PMID:23527067

  6. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

    Directory of Open Access Journals (Sweden)

    Mesfin Tesfaye

    Full Text Available Plant genomes contain several hundred defensin-like (DEFL genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.

  7. Structure-function relationship of a plant NCS1 member - Homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis

    KAUST Repository

    Witz, Sandra

    2014-03-12

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. 2014 Witz et al.

  8. Modelling the behaviour of organic degradation products

    International Nuclear Information System (INIS)

    Cross, J.E.; Ewart, F.T.; Greenfield, B.F.

    1989-03-01

    Results are presented from recent studies at Harwell which show that the degradation products which are formed when certain organic waste materials are exposed to the alkaline conditions typical of a cementitious environment, can enhance the solubility of plutonium, even at pH values as high as 12, by significant factors. Characterisation of the degradation products has been undertaken but the solubility enhancement does not appear to be related to the concentration of any of the major organic species that have been identified in the solutions. While it has not been possible to identify by analysis the organic ligand responsible for the increased solubility of plutonium, the behaviour of D-Saccharic acid does approach the behaviour of the degradation products. The PHREEQE code has been used to simulate the solubility of plutonium in the presence of D-Saccharic acid and other model degradation products, in order to explain the solubility enhancement. The extrapolation of the experimental conditions to the repository is the major objective, but in this work the ability of a model to predict the behaviour of plutonium over a range of experimental conditions has been tested. (author)

  9. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana.

    Science.gov (United States)

    Zhu, Liucun; Zhang, Yu-Hang; Su, Fangchu; Chen, Lei; Huang, Tao; Cai, Yu-Dong

    2016-01-01

    Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.

  10. Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection

    Science.gov (United States)

    Pseudomonas syringae is a Gram-negative bacterial pathogen that causes disease on more than 100 different plant species, including the model plant Arabidopsis thaliana. Dissection of the Arabidopsis thaliana-Pseudomonas syringae pathosystem has identified many factors that contribute to successful ...

  11. Reference: 749 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available former mutant had decreased electron transport rates, a lower DeltapH gradient across the grana membranes, r...the PSII particles of these plants were organized in unusual two-dimensional arrays in the grana membranes. ...d the electron transport rate in grana membranes of Arabidopsis. 4 1012-28 18381925 2008 Apr The Plant cell

  12. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  13. Arabidopsis protocols

    National Research Council Canada - National Science Library

    Martínez-Zapater, José M; Salinas, Julio

    1998-01-01

    ... the interest of geneticists and molecular biologists, not only from the plant field, but from other research fields needing a novel model system. In recent years, high expectations for Plant Biotechnology in the next century, together with the need for basic information in every area of plant biology, have served to mobilize resources and orient much new...

  14. Virtuous organization: A structural equation modeling approach

    Directory of Open Access Journals (Sweden)

    Majid Zamahani

    2013-02-01

    Full Text Available For years, the idea of virtue was unfavorable among researchers and virtues were traditionally considered as culture-specific, relativistic and they were supposed to be associated with social conservatism, religious or moral dogmatism, and scientific irrelevance. Virtue and virtuousness have been recently considered seriously among organizational researchers. The proposed study of this paper examines the relationships between leadership, organizational culture, human resource, structure and processes, care for community and virtuous organization. Structural equation modeling is employed to investigate the effects of each variable on other components. The data used in this study consists of questionnaire responses from employees in Payam e Noor University in Yazd province. A total of 250 questionnaires were sent out and a total of 211 valid responses were received. Our results have revealed that all the five variables have positive and significant impacts on virtuous organization. Among the five variables, organizational culture has the most direct impact (0.80 and human resource has the most total impact (0.844 on virtuous organization.

  15. Simulation of organ patterning on the floral meristem using a polar auxin transport model.

    Directory of Open Access Journals (Sweden)

    Simon van Mourik

    Full Text Available An intriguing phenomenon in plant development is the timing and positioning of lateral organ initiation, which is a fundamental aspect of plant architecture. Although important progress has been made in elucidating the role of auxin transport in the vegetative shoot to explain the phyllotaxis of leaf formation in a spiral fashion, a model study of the role of auxin transport in whorled organ patterning in the expanding floral meristem is not available yet. We present an initial simulation approach to study the mechanisms that are expected to play an important role. Starting point is a confocal imaging study of Arabidopsis floral meristems at consecutive time points during flower development. These images reveal auxin accumulation patterns at the positions of the organs, which strongly suggests that the role of auxin in the floral meristem is similar to the role it plays in the shoot apical meristem. This is the basis for a simulation study of auxin transport through a growing floral meristem, which may answer the question whether auxin transport can in itself be responsible for the typical whorled floral pattern. We combined a cellular growth model for the meristem with a polar auxin transport model. The model predicts that sepals are initiated by auxin maxima arising early during meristem outgrowth. These form a pre-pattern relative to which a series of smaller auxin maxima are positioned, which partially overlap with the anlagen of petals, stamens, and carpels. We adjusted the model parameters corresponding to properties of floral mutants and found that the model predictions agree with the observed mutant patterns. The predicted timing of the primordia outgrowth and the timing and positioning of the sepal primordia show remarkable similarities with a developing flower in nature.

  16. The glossyhead1 allele of acc1 reveals a principal role for multidomain acetyl-coenzyme a carboxylase in the biosynthesis of cuticular waxes by Arabidopsis

    KAUST Repository

    Lu, Shiyou; Zhao, Huayan; Parsons, Eugene P.; Xu, Changcheng; Kosma, Dylan K.; Xu, Xiaojing; Chao, Daiyin; Lohrey, Gregory T.; Bangarusamy, Dhinoth Kumar; Wang, Guangchao; Bressan, Ray Anthony; Jenks, Matthew A.

    2011-01-01

    A novel mutant of Arabidopsis (Arabidopsis thaliana), having highly glossy inflorescence stems, postgenital fusion in floral organs, and reduced fertility, was isolated from an ethyl methanesulfonate-mutagenized population and designated glossyhead1

  17. An Organization's Extended (Soft) Competencies Model

    Science.gov (United States)

    Rosas, João; Macedo, Patrícia; Camarinha-Matos, Luis M.

    One of the steps usually undertaken in partnerships formation is the assessment of organizations’ competencies. Typically considered competencies of a functional or technical nature, which provide specific outcomes can be considered as hard competencies. Yet, the very act of collaboration has its specific requirements, for which the involved organizations must be apt to exercise other type of competencies that affect their own performance and the partnership success. These competencies are more of a behavioral nature, and can be named as soft-competencies. This research aims at addressing the effects of the soft competencies on the performance of the hard ones. An extended competencies model is thus proposed, allowing the construction of adjusted competencies profiles, in which the competency levels are adjusted dynamically according to the requirements of collaboration opportunities.

  18. Modeling photocurrent transients in organic solar cells

    International Nuclear Information System (INIS)

    Hwang, I; Greenham, N C

    2008-01-01

    We investigate the transient photocurrents of organic photovoltaic devices in response to a sharp turn-on of illumination, by numerical modeling of the drift-diffusion equations. We show that the photocurrent turn-on dynamics are determined not only by the transport dynamics of free charges, but also by the time required for the population of geminate charge pairs to reach its steady-state value. The dissociation probability of a geminate charge pair is found to be a key parameter in determining the device performance, not only by controlling the efficiency at low intensities, but also in determining the fate of charge pairs formed by bimolecular recombination at high intensities. Bimolecular recombination is shown to reduce the turn-on time at high intensities, since the typical distance traveled by a charge pair is reduced.

  19. Computational modeling of Metal-Organic Frameworks

    Science.gov (United States)

    Sung, Jeffrey Chuen-Fai

    In this work, the metal-organic frameworks MIL-53(Cr), DMOF-2,3-NH 2Cl, DMOF-2,5-NH2Cl, and HKUST-1 were modeled using molecular mechanics and electronic structure. The effect of electronic polarization on the adsorption of water in MIL-53(Cr) was studied using molecular dynamics simulations of water-loaded MIL-53 systems with both polarizable and non-polarizable force fields. Molecular dynamics simulations of the full systems and DFT calculations on representative framework clusters were utilized to study the difference in nitrogen adsorption between DMOF-2,3-NH2Cl and DMOF-2,5-NH 2Cl. Finally, the control of proton conduction in HKUST-1 by complexation of molecules to the Cu open metal site was investigated using the MS-EVB methodology.

  20. Bioavailability of nanoparticulate hematite to Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Marusenko, Yevgeniy; Shipp, Jessie; Hamilton, George A.; Morgan, Jennifer L.L.; Keebaugh, Michael; Hill, Hansina; Dutta, Arnab; Zhuo, Xiaoding; Upadhyay, Nabin; Hutchings, James; Herckes, Pierre; Anbar, Ariel D.; Shock, Everett; Hartnett, Hilairy E.

    2013-01-01

    The environmental effects and bioavailability of nanoparticulate iron (Fe) to plants are currently unknown. Here, plant bioavailability of synthesized hematite Fe nanoparticles was evaluated using Arabidopsis thaliana (A. thaliana) as a model. Over 56-days of growing wild-type A. thaliana, the nanoparticle-Fe and no-Fe treatments had lower plant biomass, lower chlorophyll concentrations, and lower internal Fe concentrations than the Fe-treatment. Results for the no-Fe and nanoparticle-Fe treatments were consistently similar throughout the experiment. These results suggest that nanoparticles (mean diameter 40.9 nm, range 22.3–67.0 nm) were not taken up and therefore not bioavailable to A. thaliana. Over 14-days growing wild-type and transgenic (Type I/II proton pump overexpression) A. thaliana, the Type I plant grew more than the wild-type in the nanoparticle-Fe treatment, suggesting Type I plants cope better with Fe limitation; however, the nanoparticle-Fe and no-Fe treatments had similar growth for all plant types. -- Highlights: ► Iron nanoparticles were synthesized and assessed for bioavailability to Arabidopsis. ► Arabidopsis grew better in the presence of EDTA-bound iron than nanoparticulate iron. ► Arabidopsis grew the same in the presence of nanoparticulate iron compared to no iron. -- Synthesized iron nanoparticles were not bioavailable to Arabidopsis thaliana in agar nutrient media

  1. Analysis of MADS-Box Gene Family Reveals Conservation in Floral Organ ABCDE Model of Moso Bamboo (Phyllostachys edulis

    Directory of Open Access Journals (Sweden)

    Zhanchao Cheng

    2017-05-01

    Full Text Available Mini chromosome maintenance 1, agamous, deficiens, and serum response factor (MADS-box genes are transcription factors which play fundamental roles in flower development and regulation of floral organ identity. However, till date, identification and functions of MADS-box genes remain largely unclear in Phyllostachys edulis. In view of this, we performed a whole-genome survey and identified 34 MADS-box genes in P. edulis, and based on phylogeny, they were classified as MIKCC, MIKC∗, Mα, and Mβ. The detailed analysis about gene structure and motifs, phylogenetic classification, comparison of gene divergence and duplication are provided. Interestingly, expression patterns for most genes were found similar to those of Arabidopsis and rice, indicating that the well-established ABCDE model can be applied to P. edulis. Moreover, we overexpressed PheMADS15, an AP1-like gene, in Arabidopsis, and found that the transgenic plants have early flowering phenotype, suggesting that PheMADS15 might be a regulator of flowering transition in P. edulis. Taken together, this study provides not only insightful comprehension but also useful information for understanding the functions of MADS-box genes in P. edulis.

  2. A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis1[W][OA

    Science.gov (United States)

    Lloyd, Johnny; Meinke, David

    2012-01-01

    Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms. PMID:22247268

  3. Impact of ubiquitous inhibitors on the GUS gene reporter system: evidence from the model plants Arabidopsis, tobacco and rice and correction methods for quantitative assays of transgenic and endogenous GUS

    Directory of Open Access Journals (Sweden)

    Gerola Paolo D

    2009-12-01

    Full Text Available Abstract Background The β-glucuronidase (GUS gene reporter system is one of the most effective and employed techniques in the study of gene regulation in plant molecular biology. Improving protocols for GUS assays have rendered the original method described by Jefferson amenable to various requirements and conditions, but the serious limitation caused by inhibitors of the enzyme activity in plant tissues has thus far been underestimated. Results We report that inhibitors of GUS activity are ubiquitous in organ tissues of Arabidopsis, tobacco and rice, and significantly bias quantitative assessment of GUS activity in plant transformation experiments. Combined with previous literature reports on non-model species, our findings suggest that inhibitors may be common components of plant cells, with variable affinity towards the E. coli enzyme. The reduced inhibitory capacity towards the plant endogenous GUS discredits the hypothesis of a regulatory role of these compounds in plant cells, and their effect on the bacterial enzyme is better interpreted as a side effect due to their interaction with GUS during the assay. This is likely to have a bearing also on histochemical analyses, leading to inaccurate evaluations of GUS expression. Conclusions In order to achieve reliable results, inhibitor activity should be routinely tested during quantitative GUS assays. Two separate methods to correct the measured activity of the transgenic and endogenous GUS are presented.

  4. Model for Railway Infrastructure Management Organization

    Directory of Open Access Journals (Sweden)

    Gordan Stojić

    2012-03-01

    Full Text Available The provision of appropriate quality rail services has an important role in terms of railway infrastructure: quality of infrastructure maintenance, regulation of railway traffic, line capacity, speed, safety, train station organization, the allowable lines load and other infrastructure parameters.The analysis of experiences in transforming the railway systems points to the conclusion that there is no unique solution in terms of choice for institutional rail infrastructure management modes, although more than nineteen years have passed from the beginning of the implementation of the Directive 91/440/EEC. Depending on the approach to the process of restructuring the national railway company, adopted regulations and caution in its implementation, the existence or absence of a clearly defined transport strategy, the willingness to liberalize the transport market, there are several different ways for institutional management of railway infrastructure.A hybrid model for selection of modes of institutional rail infrastructure management was developed based on the theory of artificial intelligence, theory of fuzzy sets and theory of multicriteria optimization.KEY WORDSmanagement, railway infrastructure, organizational structure, hybrid model

  5. Project-matrix models of marketing organization

    OpenAIRE

    Gutić Dragutin; Rudelj Siniša

    2009-01-01

    Unlike theory and practice of corporation organization, in marketing organization numerous forms and contents at its disposal are not reached until this day. It can be well estimated that marketing organization today in most of our companies and in almost all its parts, noticeably gets behind corporation organization. Marketing managers have always been occupied by basic, narrow marketing activities as: sales growth, market analysis, market growth and market share, marketing research, introdu...

  6. Functional evidence for the critical amino-terminal conserved domain and key amino acids of Arabidopsis 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE.

    Science.gov (United States)

    Hsieh, Wei-Yu; Sung, Tzu-Ying; Wang, Hsin-Tzu; Hsieh, Ming-Hsiun

    2014-09-01

    The plant 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (HDR) catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which are common precursors for the synthesis of plastid isoprenoids. The Arabidopsis (Arabidopsis thaliana) genomic HDR transgene-induced gene-silencing lines are albino, variegated, or pale green, confirming that HDR is essential for plants. We used Escherichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabidopsis HDR. The predicted model reveals that cysteine (Cys)-122, Cys-213, and Cys-350 are involved in iron-sulfur cluster formation and that histidine (His)-152, His-241, glutamate (Glu)-242, Glu-243, threonine (Thr)-244, Thr-312, serine-379, and asparagine-381 are related to substrate binding or catalysis. Glu-242 and Thr-244 are conserved only in cyanobacteria, green algae, and land plants, whereas the other key amino acids are absolutely conserved from bacteria to plants. We used site-directed mutagenesis and complementation assay to confirm that these amino acids, except His-152 and His-241, were critical for Arabidopsis HDR function. Furthermore, the Arabidopsis HDR contains an extra amino-terminal domain following the transit peptide that is highly conserved from cyanobacteria, and green algae to land plants but not existing in the other bacteria. We demonstrated that the amino-terminal conserved domain was essential for Arabidopsis and cyanobacterial HDR function. Further analysis of conserved amino acids in the amino-terminal conserved domain revealed that the tyrosine-72 residue was critical for Arabidopsis HDR. These results suggest that the structure and reaction mechanism of HDR evolution have become specific for oxygen-evolving photosynthesis organisms and that HDR probably evolved independently in cyanobacteria versus other prokaryotes. © 2014

  7. The Time Is Right to Focus on Model Organism Metabolomes

    Directory of Open Access Journals (Sweden)

    Arthur S. Edison

    2016-02-01

    Full Text Available Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.

  8. Proteomics of Arabidopsis seed germination and priming

    NARCIS (Netherlands)

    Gallardo, K.; Job, C.; Groot, S.P.C.; Puype, M.; Demol, H.; Vandekerckhove, J.; Job, D.

    2003-01-01

    To better understand seed germination, a complex developmental process, we developed a proteome analysis of the model plant Arabidopsis for which complete genome sequence is now available. Among about 1,300 total seed proteins resolved in two-dimensional gels, changes in the abundance (up- and

  9. System identification of the Arabidopsis plant circadian system

    Science.gov (United States)

    Foo, Mathias; Somers, David E.; Kim, Pan-Jun

    2015-02-01

    The circadian system generates an endogenous oscillatory rhythm that governs the daily activities of organisms in nature. It offers adaptive advantages to organisms through a coordination of their biological functions with the optimal time of day. In this paper, a model of the circadian system in the plant Arabidopsis (species thaliana) is built by using system identification techniques. Prior knowledge about the physical interactions of the genes and the proteins in the plant circadian system is incorporated in the model building exercise. The model is built by using primarily experimentally-verified direct interactions between the genes and the proteins with the available data on mRNA and protein abundances from the circadian system. Our analysis reveals a great performance of the model in predicting the dynamics of the plant circadian system through the effect of diverse internal and external perturbations (gene knockouts and day-length changes). Furthermore, we found that the circadian oscillatory rhythm is robust and does not vary much with the biochemical parameters except those of a light-sensitive protein P and a transcription factor TOC1. In other words, the circadian rhythmic profile is largely a consequence of the network's architecture rather than its particular parameters. Our work suggests that the current experimental knowledge of the gene-to-protein interactions in the plant Arabidopsis, without considering any additional hypothetical interactions, seems to suffice for system-level modeling of the circadian system of this plant and to present an exemplary platform for the control of network dynamics in complex living organisms.

  10. Models of care and organization of services.

    Science.gov (United States)

    Markova, Alina; Xiong, Michael; Lester, Jenna; Burnside, Nancy J

    2012-01-01

    This article examines the overall organization of services and delivery of health care in the United States. Health maintenance organization, fee-for-service, preferred provider organizations, and the Veterans Health Administration are discussed, with a focus on structure, outcomes, and areas for improvement. An overview of wait times, malpractice, telemedicine, and the growing population of physician extenders in dermatology is also provided. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Organization model and formalized description of nuclear enterprise information system

    International Nuclear Information System (INIS)

    Yuan Feng; Song Yafeng; Li Xudong

    2012-01-01

    Organization model is one of the most important models of Nuclear Enterprise Information System (NEIS). Scientific and reasonable organization model is the prerequisite that NEIS has robustness and extendibility, and is also the foundation of the integration of heterogeneous system. Firstly, the paper describes the conceptual model of the NEIS on ontology chart, which provides a consistent semantic framework of organization. Then it discusses the relations between the concepts in detail. Finally, it gives the formalized description of the organization model of NEIS based on six-tuple array. (authors)

  12. 3D Bioprinting of Tissue/Organ Models.

    Science.gov (United States)

    Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

    2016-04-04

    In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Kinome profiling of Arabidopsis using arrays of kinase consensus substrates

    Directory of Open Access Journals (Sweden)

    Pieterse Corné MJ

    2007-02-01

    Full Text Available Abstract Background Kinome profiling aims at the parallel analysis of kinase activities in a cell. Novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. The arrays described in this paper were already used to determine kinase activities in mammalian systems, but since substrates from many organisms are present we decided to test these arrays for the determination of kinase activities in the model plant species Arabidopsis thaliana. Results Kinome profiling using Arabidopsis cell extracts resulted in the labelling of many consensus peptides by kinases from the plant, indicating the usefulness of this kinome profiling tool for plants. Method development showed that fresh and frozen plant material could be used to make cell lysates containing active kinases. Dilution of the plant extract increased the signal to noise ratio and non-radioactive ATP enhances full development of spot intensities. Upon infection of Arabidopsis with an avirulent strain of the bacterial pathogen Pseudomonas syringae pv. tomato, we could detect differential kinase activities by measuring phosphorylation of consensus peptides. Conclusion We show that kinome profiling on arrays with consensus substrates can be used to monitor kinase activities in plants. In a case study we show that upon infection with avirulent P. syringae differential kinase activities can be found. The PepChip can for example be used to purify (unknown kinases that play a role in P. syringae infection. This paper shows that kinome profiling using arrays of consensus peptides is a valuable new tool to study signal-transduction in plants. It complements the available methods for genomics and proteomics research.

  14. Zinc tolerance and accumulation in stable cell suspension cultures and in vitro regenerated plants of the emerging model plant Arabidopsis halleri (Brassicaceae).

    Science.gov (United States)

    Vera-Estrella, Rosario; Miranda-Vergara, Maria Cristina; Barkla, Bronwyn J

    2009-03-01

    Arabidopsis halleri is increasingly employed as a model plant for studying heavy metal hyperaccumulation. With the aim of providing valuable tools for studies on cellular physiology and molecular biology of metal tolerance and transport, this study reports the development of successful and highly efficient methods for the in vitro regeneration of A. halleri plants and production of stable cell suspension lines. Plants were regenerated from leaf explants of A. halleri via a three-step procedure: callus induction, somatic embryogenesis and shoot development. Efficiency of callus proliferation and regeneration depended on the initial callus induction media and was optimal in the presence of 1 mg L(-1) 2,4-dichlorophenoxyacetic acid, and 0.05 mg L(-1) benzylaminopurine. Subsequent shoot and root regeneration from callus initiated under these conditions reached levels of 100% efficiency. High friability of the callus supported the development of cell suspension cultures with minimal cellular aggregates. Characterization of regenerated plants and cell cultures determined that they maintained not only the zinc tolerance and requirement of the whole plant but also the ability to accumulate zinc; with plants accumulating up to 50.0 micromoles zinc g(-1) FW, and cell suspension cultures 30.9 micromoles zinc g(-1) DW. Together this work will provide the experimental basis for furthering our knowledge of A. halleri as a model heavy metal hyperaccumulating plant.

  15. Authentication in Virtual Organizations: A Reputation Based PKI Interconnection Model

    Science.gov (United States)

    Wazan, Ahmad Samer; Laborde, Romain; Barrere, Francois; Benzekri, Abdelmalek

    Authentication mechanism constitutes a central part of the virtual organization work. The PKI technology is used to provide the authentication in each organization involved in the virtual organization. Different trust models are proposed to interconnect the different PKIs in order to propagate the trust between them. While the existing trust models contain many drawbacks, we propose a new trust model based on the reputation of PKIs.

  16. Mining the plant-herbivore interface with a leafmining Drosophila of Arabidopsis

    Science.gov (United States)

    Whiteman, Noah K.; Groen, Simon C.; Chevasco, Daniela; Bear, Ashley; Beckwith, Noor; Gregory, T. Ryan; Denoux, Carine; Mammarella, Nicole; Ausubel, Frederick M.; Pierce, Naomi E.

    2010-01-01

    Experimental infections of Arabidopsis thaliana (Arabidopsis) with genomically characterized plant pathogens such as Pseudomonas syringae have facilitated dissection of canonical eukaryotic defense pathways and parasite virulence factors. Plants are also attacked by herbivorous insects, and the development of an ecologically relevant genetic model herbivore that feeds on Arabidopsis will enable the parallel dissection of host defense and reciprocal resistance pathways such as those involved in xenobiotic metabolism. An ideal candidate is Scaptomyza flava, a drosophilid fly whose leafmining larvae are true herbivores that can be found in nature feeding on Arabidopsis and other crucifers. Here we describe the eukaryotic life cycle of S. flava on Arabidopsis, and use multiple approaches to characterize the response of Arabidopsis to S. flava attack. Oviposition choice tests and growth performance assays on different Arabidopsis ecotypes, defense-related mutants, and hormone and chitin-treated plants revealed significant differences in host preference and variation in larval performance across Arabidopsis accessions. The jasmonate (JA) and glucosinolate pathways in Arabidopsis are important in mediating quantitative resistance against S. flava, and priming with JA or chitin resulted in increased resistance. Expression of xenobiotic detoxification genes was reduced in S. flava larvae reared on Arabidopsis JA signaling mutants, and increased in plants pre-treated with chitin. These results and future research directions are discussed in the context of developing a genetic model system to analyze insect/plant interactions. PMID:21073583

  17. Reference: 584 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ing in Arabidopsis thaliana shoot and root stem cell organizers. 7137 811-4 17429400 2007 Apr Nature Hashimo...nda K et al. 2007 Apr. Nature 446(7137):811-4. Throughout the lifespan of a plant, which in some cases can l... 584 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u17429400i Sarkar Ana

  18. Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species

    International Nuclear Information System (INIS)

    Chia, D.W.; Yoder, T.J.; Reiter, W.D.; Gibson, S.I.

    2000-01-01

    Photoassimilates are used by plants for production of energy, as carbon skeletons and in transport of fixed carbon between different plant organs. Many studies have been devoted to characterizing the factors that. regulate photoassimilate concentrations in different plant species. Most studies examining photoassimilate concentrations in C(sub 3) plants have focused on analyzing starch and soluble sugars. However, work presented here demonstrates that a number of C(sub 3) plants, including the popular model organism Arabidopsis thaliana (L.) Heynh., and agriculturally important plants, such as soybean[Glycine ma (L.) Merr.], contain significant quantities of furnaric acid. In fact, furnaric acid can accumulate to levels of several mg per g fresh weight in A-abidopsis leaves, often exceeding starch and soluble sugar levels. Furnaric acid is a component of the tricarboxylic acid cycle and, like starch and soluble sugars, can be metabolized to yield energy and carbon skeletons for production of other compounds. Fumaric acid concentrations increase with plant age and light intensity in Arabidopsis leaves. Arabidopsis phloem exudates contain significant quantities of fumaric acid, raising the possibility that fumaric acid may function in carbon transport

  19. Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species

    Energy Technology Data Exchange (ETDEWEB)

    Chia, D.W.; Yoder, T.J.; Reiter, W.D.; Gibson, S.I.

    2000-10-01

    Photoassimilates are used by plants for production of energy, as carbon skeletons and in transport of fixed carbon between different plant organs. Many studies have been devoted to characterizing the factors that. regulate photoassimilate concentrations in different plant species. Most studies examining photoassimilate concentrations in C{sub 3} plants have focused on analyzing starch and soluble sugars. However, work presented here demonstrates that a number of C{sub 3} plants, including the popular model organism Arabidopsis thaliana (L.) Heynh., and agriculturally important plants, such as soybean [Glycine ma (L.) Merr.], contain significant quantities of furnaric acid. In fact, furnaric acid can accumulate to levels of several mg per g fresh weight in A-abidopsis leaves, often exceeding starch and soluble sugar levels. Furnaric acid is a component of the tricarboxylic acid cycle and, like starch and soluble sugars, can be metabolized to yield energy and carbon skeletons for production of other compounds. Fumaric acid concentrations increase with plant age and light intensity in Arabidopsis leaves. Arabidopsis phloem exudates contain significant quantities of fumaric acid, raising the possibility that fumaric acid may function in carbon transport.

  20. MODELING OF MANAGEMENT PROCESSES IN AN ORGANIZATION

    Directory of Open Access Journals (Sweden)

    Stefan Iovan

    2016-05-01

    Full Text Available When driving any major change within an organization, strategy and execution are intrinsic to a project’s success. Nevertheless, closing the gap between strategy and execution remains a challenge for many organizations [1]. Companies tend to focus more on execution than strategy for quick results, instead of taking the time needed to understand the parts that make up the whole, so the right execution plan can be put in place to deliver the best outcomes. A large part of this understands that business operations don’t fit neatly within the traditional organizational hierarchy. Business processes are often messy, collaborative efforts that cross teams, departments and systems, making them difficult to manage within a hierarchical structure [2]. Business process management (BPM fills this gap by redefining an organization according to its end-to-end processes, so opportunities for improvement can be identified and processes streamlined for growth, revenue and transformation. This white paper provides guidelines on what to consider when using business process applications to solve your BPM initiatives, and the unique capabilities software systems provides that can help ensure both your project’s success and the success of your organization as a whole. majority of medium and small businesses, big companies and even some guvermental organizations [2].

  1. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...

  2. Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria

    NARCIS (Netherlands)

    Wintermans, Paul C A; Bakker, Peter A H M; Pieterse, Corné M J

    The plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417r stimulates lateral root formation and increases shoot growth in Arabidopsis thaliana (Arabidopsis). These plant growth-stimulating effects are partly caused by volatile organic compounds (VOCs) produced by the bacterium.

  3. Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria

    NARCIS (Netherlands)

    Wintermans, P.C.A.; Bakker, P.A.H.M.; Pieterse, C.M.J.

    2016-01-01

    The plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417r stimulates lateral root formation and increases shoot growth in Arabidopsis thaliana (Arabidopsis). These plant growth-stimulating effects are partly caused by volatile organic compounds (VOCs) produced by the bacterium.

  4. Self-Organizing Map Models of Language Acquisition

    Directory of Open Access Journals (Sweden)

    Ping eLi

    2013-11-01

    Full Text Available Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic PDP architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development.

  5. Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

    Science.gov (United States)

    Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

    2017-02-01

    Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  6. Intracellular localization of Arabidopsis sulfurtransferases.

    Science.gov (United States)

    Bauer, Michael; Dietrich, Christof; Nowak, Katharina; Sierralta, Walter D; Papenbrock, Jutta

    2004-06-01

    Sulfurtransferases (Str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. In all organisms analyzed to date, small gene families encoding Str proteins have been identified. The gene products were localized to different compartments of the cells. Our interest concerns the localization of Str proteins encoded in the nuclear genome of Arabidopsis. Computer-based prediction methods revealed localization in different compartments of the cell for six putative AtStrs. Several methods were used to determine the localization of the AtStr proteins experimentally. For AtStr1, a mitochondrial localization was demonstrated by immunodetection in the proteome of isolated mitochondria resolved by one- and two-dimensional gel electrophoresis and subsequent blotting. The respective mature AtStr1 protein was identified by mass spectrometry sequencing. The same result was obtained by transient expression of fusion constructs with the green fluorescent protein in Arabidopsis protoplasts, whereas AtStr2 was exclusively localized to the cytoplasm by this method. Three members of the single-domain AtStr were localized in the chloroplasts as demonstrated by transient expression of green fluorescent protein fusions in protoplasts and stomata, whereas the single-domain AtStr18 was shown to be cytoplasmic. The remarkable subcellular distribution of AtStr15 was additionally analyzed by transmission electron immunomicroscopy using a monospecific antibody against green fluorescent protein, indicating an attachment to the thylakoid membrane. The knowledge of the intracellular localization of the members of this multiprotein family will help elucidate their specific functions in the organism.

  7. The initiative on Model Organism Proteomes (iMOP) Session

    DEFF Research Database (Denmark)

    Schrimpf, Sabine P; Mering, Christian von; Bendixen, Emøke

    2012-01-01

    iMOP – the Initiative on Model Organism Proteomes – was accepted as a new HUPO initiative at the Ninth HUPO meeting in Sydney in 2010. A goal of iMOP is to integrate research groups working on a great diversity of species into a model organism community. At the Tenth HUPO meeting in Geneva...

  8. Modeling the Explicit Chemistry of Anthropogenic and Biogenic Organic Aerosols

    Energy Technology Data Exchange (ETDEWEB)

    Madronich, Sasha [Univ. Corporation for Atmospheric Research, Boulder, CO (United States)

    2015-12-09

    The atmospheric burden of Secondary Organic Aerosols (SOA) remains one of the most important yet uncertain aspects of the radiative forcing of climate. This grant focused on improving our quantitative understanding of SOA formation and evolution, by developing, applying, and improving a highly detailed model of atmospheric organic chemistry, the Generation of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) model. Eleven (11) publications have resulted from this grant.

  9. Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Mara Sangiovanni

    2013-12-01

    Full Text Available Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the Arabidopsis genome is characterized by an inherently complex organization, since it has undergone ancient whole genome duplications, followed by gene reduction, diploidization events and extended rearrangements, which relocated and split up the retained portions. These events, together with probable chromosome reductions, dramatically increased the genome complexity, limiting its role as a reference. The identification of paralogs and single copy genes within a highly duplicated genome is a prerequisite to understand its organization and evolution and to improve its exploitation in comparative genomics. This is still controversial, even in the widely studied Arabidopsis genome. This is also due to the lack of a reference bioinformatics pipeline that could exhaustively identify paralogs and singleton genes. We describe here a complete computational strategy to detect both duplicated and single copy genes in a genome, discussing all the methodological issues that may strongly affect the results, their quality and their reliability. This approach was used to analyze the organization of Arabidopsis nuclear protein coding genes, and besides classifying computationally defined paralogs into networks and single copy genes into different classes, it unraveled further intriguing aspects concerning the genome annotation and the gene relationships in this reference plant species. Since our results may be useful for comparative genomics and genome functional analyses, we organized a dedicated web interface to make them accessible to the scientific community.

  10. Saccharomyces cerevisiae as a model organism: a comparative study.

    Directory of Open Access Journals (Sweden)

    Hiren Karathia

    Full Text Available BACKGROUND: Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. CONCLUSIONS/SIGNIFICANCE: The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

  11. Induction and characterization of Arabidopsis mutants by Ion beam

    International Nuclear Information System (INIS)

    Yoon, Y. H.; Choi, J. D.; Park, J. Y.; Lee, J. R.; Sohn, H. S.

    2008-03-01

    This study was conducted to search the proper conditions and times for irradiating proton beam to seeds generally used for induction of mutant. Arabidopsis as model plants has good characters that is a short generation time, producing a lot of seeds, sequenced genome, developed maker. This points were the best materials for plant breeding for this study. The data of inducing mutants of Arabidopsis is used to be applicate to crops have more longer generation that is the final goals of this study. The goals of this project were to inducing and characterizing arabidopsis mutants by the proton ion beam and γ-ray. As well as, the purpose of this study was securing more than 10 lines of arabidopsis mutants in this project and also to know the changed DNA structure of the mutants using the basic data for applying to the more study

  12. Induction and characterization of Arabidopsis mutants by Ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Y. H.; Choi, J. D.; Park, J. Y.; Lee, J. R.; Sohn, H. S. [Gyeongbuk Institute for Bio Industry, Andong (Korea, Republic of)

    2008-03-15

    This study was conducted to search the proper conditions and times for irradiating proton beam to seeds generally used for induction of mutant. Arabidopsis as model plants has good characters that is a short generation time, producing a lot of seeds, sequenced genome, developed maker. This points were the best materials for plant breeding for this study. The data of inducing mutants of Arabidopsis is used to be applicate to crops have more longer generation that is the final goals of this study. The goals of this project were to inducing and characterizing arabidopsis mutants by the proton ion beam and {gamma}-ray. As well as, the purpose of this study was securing more than 10 lines of arabidopsis mutants in this project and also to know the changed DNA structure of the mutants using the basic data for applying to the more study

  13. The System Dynamics Model for Development of Organic Agriculture

    Science.gov (United States)

    Rozman, Črtomir; Škraba, Andrej; Kljajić, Miroljub; Pažek, Karmen; Bavec, Martina; Bavec, Franci

    2008-10-01

    Organic agriculture is the highest environmentally valuable agricultural system, and has strategic importance at national level that goes beyond the interests of agricultural sector. In this paper we address development of organic farming simulation model based on a system dynamics methodology (SD). The system incorporates relevant variables, which affect the development of the organic farming. The group decision support system (GDSS) was used in order to identify most relevant variables for construction of causal loop diagram and further model development. The model seeks answers to strategic questions related to the level of organically utilized area, levels of production and crop selection in a long term dynamic context and will be used for simulation of different policy scenarios for organic farming and their impact on economic and environmental parameters of organic production at an aggregate level.

  14. A linear solvation energy relationship model of organic chemical partitioning to dissolved organic carbon.

    Science.gov (United States)

    Kipka, Undine; Di Toro, Dominic M

    2011-09-01

    Predicting the association of contaminants with both particulate and dissolved organic matter is critical in determining the fate and bioavailability of chemicals in environmental risk assessment. To date, the association of a contaminant to particulate organic matter is considered in many multimedia transport models, but the effect of dissolved organic matter is typically ignored due to a lack of either reliable models or experimental data. The partition coefficient to dissolved organic carbon (K(DOC)) may be used to estimate the fraction of a contaminant that is associated with dissolved organic matter. Models relating K(DOC) to the octanol-water partition coefficient (K(OW)) have not been successful for many types of dissolved organic carbon in the environment. Instead, linear solvation energy relationships are proposed to model the association of chemicals with dissolved organic matter. However, more chemically diverse K(DOC) data are needed to produce a more robust model. For humic acid dissolved organic carbon, the linear solvation energy relationship predicts log K(DOC) with a root mean square error of 0.43. Copyright © 2011 SETAC.

  15. Modeling the influence of organic acids on soil weathering

    Science.gov (United States)

    Lawrence, Corey R.; Harden, Jennifer W.; Maher, Kate

    2014-01-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  16. Daphnia as an Emerging Epigenetic Model Organism

    Directory of Open Access Journals (Sweden)

    Kami D. M. Harris

    2012-01-01

    Full Text Available Daphnia offer a variety of benefits for the study of epigenetics. Daphnia’s parthenogenetic life cycle allows the study of epigenetic effects in the absence of confounding genetic differences. Sex determination and sexual reproduction are epigenetically determined as are several other well-studied alternate phenotypes that arise in response to environmental stressors. Additionally, there is a large body of ecological literature available, recently complemented by the genome sequence of one species and transgenic technology. DNA methylation has been shown to be altered in response to toxicants and heavy metals, although investigation of other epigenetic mechanisms is only beginning. More thorough studies on DNA methylation as well as investigation of histone modifications and RNAi in sex determination and predator-induced defenses using this ecologically and evolutionarily important organism will contribute to our understanding of epigenetics.

  17. Initiation of Setaria as a model plant

    Directory of Open Access Journals (Sweden)

    Xianmin DIAO,James SCHNABLE,Jeffrey L. BENNETZEN,Jiayang LI

    2014-02-01

    Full Text Available Model organisms such as Arabidopsis (Arabidopsis thaliana and rice (Oryza sativa have proven essential for efficient scientific discovery and development of new methods. With the diversity of plant lineages, some important processes such as C4 photosynthesis are not found in either Arabidopsis or rice, so new model species are needed. Due to their small diploid genomes, short life cycles, self-pollination, small adult statures and prolific seed production, domesticated foxtail millet (Setaria italica and its wild ancestor, green foxtail (S. viridis, have recently been proposed as novel model species for functional genomics of the Panicoideae, especially for study of C4 photosynthesis. This review outlines the development of these species as model organisms, and discusses current challenges and future potential of a Setaria model.

  18. Nematodes: Model Organisms in High School Biology

    Science.gov (United States)

    Bliss, TJ; Anderson, Margery; Dillman, Adler; Yourick, Debra; Jett, Marti; Adams, Byron J.; Russell, RevaBeth

    2007-01-01

    In a collaborative effort between university researchers and high school science teachers, an inquiry-based laboratory module was designed using two species of insecticidal nematodes to help students apply scientific inquiry and elements of thoughtful experimental design. The learning experience and model are described in this article. (Contains 4…

  19. Ahp2 (Hop2) function in Arabidopsis thaliana (Ler) is required for stabilization of close alignment and synaptonemal complex formation except for the two short arms that contain nucleolus organizer regions.

    Science.gov (United States)

    Stronghill, P; Pathan, N; Ha, H; Supijono, E; Hasenkampf, C

    2010-08-01

    A cytological comparative analysis of male meiocytes was performed for Arabidopsis wild type and the ahp2 (hop2) mutant with emphasis on ahp2's largely uncharacterized prophase I. Leptotene progression appeared normal in ahp2 meiocytes; chromosomes exhibited regular axis formation and assumed a typical polarized nuclear organization. In contrast, 4',6'-diamidino-2-phenylindole-stained ahp2 pachytene chromosome spreads demonstrated a severe reduction in stabilized pairing. However, transmission electron microscopy (TEM) analysis of sections from meiocytes revealed that ahp2 chromosome axes underwent significant amounts of close alignment (44% of total axis). This apparent paradox strongly suggests that the Ahp2 protein is involved in the stabilization of homologous chromosome close alignment. Fluorescent in situ hybridization in combination with Zyp1 immunostaining revealed that ahp2 mutants undergo homologous synapsis of the nucleolus-organizer-region-bearing short arms of chromosomes 2 and 4, despite the otherwise "nucleus-wide" lack of stabilized pairing. The duration of ahp2 zygotene was significantly prolonged and is most likely due to difficulties in chromosome alignment stabilization and subsequent synaptonemal complex formation. Ahp2 and Mnd1 proteins have previously been shown, "in vitro," to form a heterodimer. Here we show, "in situ," that the Ahp2 and Mnd1 proteins are synchronous in their appearance and disappearance from meiotic chromosomes. Both the Ahp2 and Mnd1 proteins localize along the chromosomal axis. However, localization of the Ahp2 protein was entirely foci-based whereas Mnd1 protein exhibited an immunostaining pattern with some foci along the axis and a diffuse staining for the rest of the chromosome.

  20. Self-organized quantum rings : Physical characterization and theoretical modeling

    NARCIS (Netherlands)

    Fomin, V.M.; Gladilin, V.N.; Devreese, J.T.; Koenraad, P.M.; Fomin, V.M.

    2014-01-01

    An adequate modeling of the self-organized quantum rings is possible only on the basis of the modern characterization of those nanostructures.We discuss an atomic-scale analysis of the indium distribution of self-organized InGaAs quantum rings (QRs). The analysis of the shape, size and composition

  1. Resilient organizations: matrix model and service line management.

    Science.gov (United States)

    Westphal, Judith A

    2005-09-01

    Resilient organizations modify structures to meet the demands of the marketplace. The author describes a structure that enables multihospital organizations to innovate and rapidly adapt to changes. Service line management within a matrix model is an evolving organizational structure for complex systems in which nurses are pivotal members.

  2. (Tropical) soil organic matter modelling: problems and prospects

    NARCIS (Netherlands)

    Keulen, van H.

    2001-01-01

    Soil organic matter plays an important role in many physical, chemical and biological processes. However, the quantitative relations between the mineral and organic components of the soil and the relations with the vegetation are poorly understood. In such situations, the use of models is an

  3. Investigating ecological speciation in non-model organisms

    DEFF Research Database (Denmark)

    Foote, Andrew David

    2012-01-01

    Background: Studies of ecological speciation tend to focus on a few model biological systems. In contrast, few studies on non-model organisms have been able to infer ecological speciation as the underlying mechanism of evolutionary divergence. Questions: What are the pitfalls in studying ecological...... speciation in non-model organisms that lead to this bias? What alternative approaches might redress the balance? Organism: Genetically differentiated types of the killer whale (Orcinus orca) exhibiting differences in prey preference, habitat use, morphology, and behaviour. Methods: Review of the literature...... on killer whale evolutionary ecology in search of any difficulty in demonstrating causal links between variation in phenotype, ecology, and reproductive isolation in this non-model organism. Results: At present, we do not have enough evidence to conclude that adaptive phenotype traits linked to ecological...

  4. Modelling the self-organization and collapse of complex networks

    Indian Academy of Sciences (India)

    Modelling the self-organization and collapse of complex networks. Sanjay Jain Department of Physics and Astrophysics, University of Delhi Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore Santa Fe Institute, Santa Fe, New Mexico.

  5. Self-organizing map models of language acquisition

    Science.gov (United States)

    Li, Ping; Zhao, Xiaowei

    2013-01-01

    Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic parallel distributed processing architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper, we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development. We suggest future directions in which these models can be extended, to better connect with behavioral and neural data, and to make clear predictions in testing relevant psycholinguistic theories. PMID:24312061

  6. Labour Quality Model for Organic Farming Food Chains

    OpenAIRE

    Gassner, B.; Freyer, B.; Leitner, H.

    2008-01-01

    The debate on labour quality in science is controversial as well as in the organic agriculture community. Therefore, we reviewed literature on different labour quality models and definitions, and had key informant interviews on labour quality issues with stakeholders in a regional oriented organic agriculture bread food chain. We developed a labour quality model with nine quality categories and discussed linkages to labour satisfaction, ethical values and IFOAM principles.

  7. Xanthusbase: adapting wikipedia principles to a model organism database

    OpenAIRE

    Arshinoff, Bradley I.; Suen, Garret; Just, Eric M.; Merchant, Sohel M.; Kibbe, Warren A.; Chisholm, Rex L.; Welch, Roy D.

    2006-01-01

    xanthusBase () is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leve...

  8. Knowledge Loss: A Defensive Model In Nuclear Research Organization Memory

    International Nuclear Information System (INIS)

    Mohamad Safuan Bin Sulaiman; Muhd Noor Muhd Yunus

    2013-01-01

    Knowledge is an essential part of research based organization. It should be properly managed to ensure that any pitfalls of knowledge retention due to knowledge loss of both tacit and explicit is mitigated. Audit of the knowledge entities exist in the organization is important to identify the size of critical knowledge. It is very much related to how much know-what, know-how and know-why experts exist in the organization. This study conceptually proposed a defensive model for Nuclear Malaysia's organization memory and application of Knowledge Loss Risk Assessment (KLRA) as an important tool for critical knowledge identification. (author)

  9. NEW MODEL FOR QUANTIFICATION OF ICT DEPENDABLE ORGANIZATIONS RESILIENCE

    Directory of Open Access Journals (Sweden)

    Zora Arsovski

    2011-03-01

    Full Text Available Business environment today demands high reliable organizations in every segment to be competitive on the global market. Beside that, ICT sector is becoming irreplaceable in many fields of business, from the communication to the complex systems for process control and production. To fulfill those requirements and to develop further, many organizations worldwide are implementing business paradigm called - organizations resilience. Although resilience is well known term in many science fields, it is not well studied due to its complex nature. This paper is dealing with developing the new model for assessment and quantification of ICT dependable organizations resilience.

  10. A model to accumulate fractionated dose in a deforming organ

    International Nuclear Information System (INIS)

    Yan Di; Jaffray, D.A.; Wong, J.W.

    1999-01-01

    Purpose: Measurements of internal organ motion have demonstrated that daily organ deformation exists throughout the course of radiation treatment. However, a method of constructing the resultant dose delivered to the organ volume remains a difficult challenge. In this study, a model to quantify internal organ motion and a method to construct a cumulative dose in a deforming organ are introduced. Methods and Materials: A biomechanical model of an elastic body is used to quantify patient organ motion in the process of radiation therapy. Intertreatment displacements of volume elements in an organ of interest is calculated by applying an finite element method with boundary conditions, obtained from multiple daily computed tomography (CT) measurements. Therefore, by incorporating also the measurements of daily setup error, daily dose delivered to a deforming organ can be accumulated by tracking the position of volume elements in the organ. Furthermore, distribution of patient-specific organ motion is also predicted during the early phase of treatment delivery using the daily measurements, and the cumulative dose distribution in the organ can then be estimated. This dose distribution will be updated whenever a new measurement becomes available, and used to reoptimize the ongoing treatment. Results: An integrated process to accumulate dosage in a daily deforming organ was implemented. In this process, intertreatment organ motion and setup error were systematically quantified, and incorporated in the calculation of the cumulative dose. An example of the rectal wall motion in a prostate treatment was applied to test the model. The displacements of volume elements in the rectal wall, as well as the resultant doses, were calculated. Conclusion: This study is intended to provide a systematic framework to incorporate daily patient-specific organ motion and setup error in the reconstruction of the cumulative dose distribution in an organ of interest. The realistic dose

  11. Charge carrier relaxation model in disordered organic semiconductors

    International Nuclear Information System (INIS)

    Lu, Nianduan; Li, Ling; Sun, Pengxiao; Liu, Ming

    2013-01-01

    The relaxation phenomena of charge carrier in disordered organic semiconductors have been demonstrated and investigated theoretically. An analytical model describing the charge carrier relaxation is proposed based on the pure hopping transport theory. The relation between the material disorder, electric field and temperature and the relaxation phenomena has been discussed in detail, respectively. The calculated results reveal that the increase of electric field and temperature can promote the relaxation effect in disordered organic semiconductors, while the increase of material disorder will weaken the relaxation. The proposed model can explain well the stretched-exponential law by adopting the appropriate parameters. The calculation shows a good agreement with the experimental data for organic semiconductors

  12. The scale of population structure in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Alexander Platt

    2010-02-01

    Full Text Available The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

  13. Modelling the fate of organic micropollutants in stormwater ponds

    DEFF Research Database (Denmark)

    Vezzaro, Luca; Eriksson, Eva; Ledin, Anna

    2011-01-01

    ). The four simulated organic stormwater MP (iodopropynyl butylcarbamate — IPBC, benzene, glyphosate and pyrene) were selected according to their different urban sources and environmental fate. This ensures that the results can be extended to other relevant stormwater pollutants. All three models use......Urban water managers need to estimate the potential removal of organic micropollutants (MP) in stormwater treatment systems to support MP pollution control strategies. This study documents how the potential removal of organic MP in stormwater treatment systems can be quantified by using multimedia...... models. The fate of four different MP in a stormwater retention pond was simulated by applying two steady-state multimedia fate models (EPI Suite and SimpleBox) commonly applied in chemical risk assessment and a dynamic multimedia fate model (Stormwater Treatment Unit Model for Micro Pollutants — STUMP...

  14. Gene expression in response to cryoprotectant and liquid nitrogen exposure in Arabidopsis shoot tips

    Science.gov (United States)

    Arabidopsis thaliana is an ideal model system to study plant cryopreservation at the molecular level. We have developed reliable cryopreservation methods for Arabidopsis shoot tips using Plant Vitrification Solution 2 and Plant Vitrification Solution 3 (PVS3) cryoprotectants. We have made use of th...

  15. Genes encoding calmodulin-binding proteins in the Arabidopsis genome

    Science.gov (United States)

    Reddy, Vaka S.; Ali, Gul S.; Reddy, Anireddy S N.

    2002-01-01

    Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

  16. Modelling the fate of oxidisable organic contaminants in groundwater

    DEFF Research Database (Denmark)

    Barry, D.A.; Prommer, H.; Miller, C.T.

    2002-01-01

    modelling framework is illustrated by pertinent examples, showing the degradation of dissolved organics by microbial activity limited by the availability of nutrients or electron acceptors (i.e., changing redox states), as well as concomitant secondary reactions. Two field-scale modelling examples......Subsurface contamination by organic chemicals is a pervasive environmental problem, susceptible to remediation by natural or enhanced attenuation approaches or more highly engineered methods such as pump-and-treat, amongst others. Such remediation approaches, along with risk assessment...... are discussed, the Vejen landfill (Denmark) and an example where metal contamination is remediated by redox changes wrought by injection of a dissolved organic compound. A summary is provided of current and likely future challenges to modelling of oxidisable organics in the subsurface. (C) 2002 Elsevier Science...

  17. Drosophila melanogaster as a model organism to study nanotoxicity.

    Science.gov (United States)

    Ong, Cynthia; Yung, Lin-Yue Lanry; Cai, Yu; Bay, Boon-Huat; Baeg, Gyeong-Hun

    2015-05-01

    Drosophila melanogaster has been used as an in vivo model organism for the study of genetics and development since 100 years ago. Recently, the fruit fly Drosophila was also developed as an in vivo model organism for toxicology studies, in particular, the field of nanotoxicity. The incorporation of nanomaterials into consumer and biomedical products is a cause for concern as nanomaterials are often associated with toxicity in many in vitro studies. In vivo animal studies of the toxicity of nanomaterials with rodents and other mammals are, however, limited due to high operational cost and ethical objections. Hence, Drosophila, a genetically tractable organism with distinct developmental stages and short life cycle, serves as an ideal organism to study nanomaterial-mediated toxicity. This review discusses the basic biology of Drosophila, the toxicity of nanomaterials, as well as how the Drosophila model can be used to study the toxicity of various types of nanomaterials.

  18. Proton-transfer-reaction mass spectrometry as a new tool for real time analysis of root-secreted volatile organic compounds in arabidopsis

    NARCIS (Netherlands)

    Steeghs, M.M.L.; Bais, H.P.; de Gouw, J.; Goldan, P.; Kuster, W.; Northway, M.; Fall, R.; Vivanco, J.M.

    2004-01-01

    Plant roots release about 5% to 20% of all photosynthetically-fixed carbon, and as a result create a carbon-rich environment for numerous rhizosphere organisms, including plant pathogens and symbiotic microbes. Although some characterization of root exudates has been achieved, especially of

  19. PS II model based analysis of transient fluorescence yield measured on whole leaves of Arabidopsis thaliana after excitation with light flashes of different energies.

    Science.gov (United States)

    Belyaeva, N E; Schmitt, F-J; Paschenko, V Z; Riznichenko, G Yu; Rubin, A B; Renger, G

    2011-02-01

    Our recently presented PS II model (Belyaeva et al., 2008) was improved in order to permit a consistent simulation of Single Flash Induced Transient Fluorescence Yield (SFITFY) traces that were earlier measured by Steffen et al. (2005) on whole leaves of Arabidopsis (A.) thaliana at four different energies of the actinic flash. As the essential modification, the shape of the actinic flash was explicitly taken into account assuming that an exponentially decaying rate simulates the time dependent excitation of PS II by the 10 ns actinic flash. The maximum amplitude of this excitation exceeds that of the measuring light by 9 orders of magnitude. A very good fit of the SFITFY data was achieved in the time domain from 100 ns to 10s for all actinic flash energies (the maximum energy of 7.5 × 10¹⁶ photons/(cm²flash) is set to 100%, the relative energies of weaker actinic flashes were of ∼8%, 4%, ∼1%). Our model allows the calculation and visualization of the transient PS II redox state populations ranging from the dark adapted state, via excitation energy and electron transfer steps induced by pulse excitation, followed by final relaxation into the stationary state eventually attained under the measuring light. It turned out that the rate constants of electron transfer steps are invariant to intensity of the actinic laser flash. In marked contrast, an increase of the actinic flash energy by more than two orders of magnitude from 5.4×10¹⁴ photons/(cm²flash) to 7.5×10¹⁶ photons/(cm²flash), leads to an increase of the extent of fluorescence quenching due to carotenoid triplet (³Car) formation by a factor of 14 and of the recombination reaction between reduced primary pheophytin (Phe(-)) and P680(+) by a factor of 3 while the heat dissipation in the antenna complex remains virtually constant. The modified PS II model offers new opportunities to compare electron transfer and dissipative parameters for different species (e.g. for the green algae and the

  20. Mutant mice: experimental organisms as materialised models in biomedicine.

    Science.gov (United States)

    Huber, Lara; Keuck, Lara K

    2013-09-01

    Animal models have received particular attention as key examples of material models. In this paper, we argue that the specificities of establishing animal models-acknowledging their status as living beings and as epistemological tools-necessitate a more complex account of animal models as materialised models. This becomes particularly evident in animal-based models of diseases that only occur in humans: in these cases, the representational relation between animal model and human patient needs to be generated and validated. The first part of this paper presents an account of how disease-specific animal models are established by drawing on the example of transgenic mice models for Alzheimer's disease. We will introduce an account of validation that involves a three-fold process including (1) from human being to experimental organism; (2) from experimental organism to animal model; and (3) from animal model to human patient. This process draws upon clinical relevance as much as scientific practices and results in disease-specific, yet incomplete, animal models. The second part of this paper argues that the incompleteness of models can be described in terms of multi-level abstractions. We qualify this notion by pointing to different experimental techniques and targets of modelling, which give rise to a plurality of models for a specific disease. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Spatial arrangement of organic compounds on a model mineral surface: implications for soil organic matter stabilization.

    Science.gov (United States)

    Petridis, Loukas; Ambaye, Haile; Jagadamma, Sindhu; Kilbey, S Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie A

    2014-01-01

    The complexity of the mineral-organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise.

  2. A Framework for Formal Modeling and Analysis of Organizations

    NARCIS (Netherlands)

    Jonker, C.M.; Sharpanskykh, O.; Treur, J.; P., Yolum

    2007-01-01

    A new, formal, role-based, framework for modeling and analyzing both real world and artificial organizations is introduced. It exploits static and dynamic properties of the organizational model and includes the (frequently ignored) environment. The transition is described from a generic framework of

  3. Healing models for organizations: description, measurement, and outcomes.

    Science.gov (United States)

    Malloch, K

    2000-01-01

    Healthcare leaders are continually searching for ways to improve their ability to provide optimal healthcare services, be financially viable, and retain quality caregivers, often feeling like such goals are impossible to achieve in today's intensely competitive environment. Many healthcare leaders intuitively recognize the need for more humanistic models and the probable connection with positive patient outcomes and financial success but are hesitant to make significant changes in their organizations because of the lack of model descriptions or documented recognition of the clinical and financial advantages of humanistic models. This article describes a study that was developed in response to the increasing work in humanistic or healing environment models and the need for validation of the advantages of such models. The healthy organization model, a framework for healthcare organizations that incorporates humanistic healing values within the traditional structure, is presented as a result of the study. This model addresses the importance of optimal clinical services, financial performance, and staff satisfaction. The five research-based organizational components that form the framework are described, and key indicators of organizational effectiveness over a five-year period are presented. The resulting empirical data are strongly supportive of the healing model and reflect positive outcomes for the organization.

  4. An Arabidopsis callose synthase

    DEFF Research Database (Denmark)

    Ostergaard, Lars; Petersen, Morten; Mattsson, Ole

    2002-01-01

    in the Arabidopsis mpk4 mutant which exhibits systemic acquired resistance (SAR), elevated beta-1,3-glucan synthase activity, and increased callose levels. In addition, AtGsl5 is a likely target of salicylic acid (SA)-dependent SAR, since AtGsl5 mRNA accumulation is induced by SA in wild-type plants, while...... expression of the nahG salicylate hydroxylase reduces AtGsl5 mRNA levels in the mpk4 mutant. These results indicate that AtGsl5 is likely involved in callose synthesis in flowering tissues and in the mpk4 mutant....

  5. A self-organized criticality model for plasma transport

    International Nuclear Information System (INIS)

    Carreras, B.A.; Newman, D.; Lynch, V.E.

    1996-01-01

    Many models of natural phenomena manifest the basic hypothesis of self-organized criticality (SOC). The SOC concept brings together the self-similarity on space and time scales that is common to many of these phenomena. The application of the SOC modelling concept to the plasma dynamics near marginal stability opens new possibilities of understanding issues such as Bohm scaling, profile consistency, broad band fluctuation spectra with universal characteristics and fast time scales. A model realization of self-organized criticality for plasma transport in a magnetic confinement device is presented. The model is based on subcritical resistive pressure-gradient-driven turbulence. Three-dimensional nonlinear calculations based on this model show the existence of transport under subcritical conditions. This model that includes fluctuation dynamics leads to results very similar to the running sandpile paradigm

  6. An Ising model for metal-organic frameworks

    Science.gov (United States)

    Höft, Nicolas; Horbach, Jürgen; Martín-Mayor, Victor; Seoane, Beatriz

    2017-08-01

    We present a three-dimensional Ising model where lines of equal spins are frozen such that they form an ordered framework structure. The frame spins impose an external field on the rest of the spins (active spins). We demonstrate that this "porous Ising model" can be seen as a minimal model for condensation transitions of gas molecules in metal-organic frameworks. Using Monte Carlo simulation techniques, we compare the phase behavior of a porous Ising model with that of a particle-based model for the condensation of methane (CH4) in the isoreticular metal-organic framework IRMOF-16. For both models, we find a line of first-order phase transitions that end in a critical point. We show that the critical behavior in both cases belongs to the 3D Ising universality class, in contrast to other phase transitions in confinement such as capillary condensation.

  7. Regional Persistent Organic Pollutants' Environmental Impact Assessment and Control Model

    Directory of Open Access Journals (Sweden)

    Jurgis Staniskis

    2008-10-01

    Full Text Available The sources of formation, environmental distribution and fate of persistent organic pollutants (POPs are increasingly seen as topics to be addressed and solved at the global scale. Therefore, there are already two international agreements concerning persistent organic pollutants: the Protocol of 1998 to the 1979 Convention on the Long-Range Transboundary Air Pollution on Persistent Organic Pollutants (Aarhus Protocol; and the Stockholm Convention on Persistent Organic Pollutants. For the assessment of environmental pollution of POPs, for the risk assessment, for the evaluation of new pollutants as potential candidates to be included in the POPs list of the Stokholmo or/and Aarhus Protocol, a set of different models are developed or under development. Multimedia models help describe and understand environmental processes leading to global contamination through POPs and actual risk to the environment and human health. However, there is a lack of the tools based on a systematic and integrated approach to POPs management difficulties in the region.

  8. Modelization of tritium transfer into the organic compartments of algae

    International Nuclear Information System (INIS)

    Bonotto, S.; Gerber, G.B.; Arapis, G.; Kirchmann, R.

    1982-01-01

    Uptake of tritium oxide and its conversion into organic tritium was studied in four different types of algae with widely varying size and growth characteristics (Acetabularia acetabulum, Boergesenia forbesii, two strains of Chlamydomonas and Dunaliella bioculata). Water in the cell and the vacuales equilibrates rapidly with external tritium water. Tritium is actively incorporated into organically bound form as the organisms grow. During the stationary phase, incorporation of tritium is slow. There exists a discrimination against the incorporation of tritium into organically bound form. A model has been elaborated taking in account these different factors. It appears that transfer of organic tritium by algae growing near the sites of release would be significant only for actively growing algae. Algae growing slowly may, however, be useful as cumulative indicators of discontinuous tritium release. (author)

  9. MODELLING CONSUMERS' DEMAND FOR ORGANIC FOOD PRODUCTS: THE SWEDISH EXPERIENCE

    Directory of Open Access Journals (Sweden)

    Manuchehr Irandoust

    2016-07-01

    Full Text Available This paper attempts to examine a few factors characterizing consumer preferences and behavior towards organic food products in the south of Sweden using a proportional odds model which captures the natural ordering of dependent variables and any inherent nonlinearities. The findings show that consumer's choice for organic food depends on perceived benefits of organic food (environment, health, and quality and consumer's perception and attitudes towards labelling system, message framing, and local origin. In addition, high willingness to pay and income level will increase the probability to buy organic food, while the cultural differences and socio-demographic characteristics have no effect on consumer behaviour and attitudes towards organic food products. Policy implications are offered.

  10. Modeling cadmium in the feed chain and cattle organs

    OpenAIRE

    Fels-Klerx, van der, H.J.; Romkens, P.F.A.M.; Franz, E.; Raamsdonk, van, L.W.D.

    2011-01-01

    The objectives of this study were to estimate cadmium contamination levels in different scenarios related to soil characteristics and assumptions regarding cadmium accumulation in the animal tissues, using quantitative supply chain modeling. The model takes into account soil cadmium levels, soil pH, soil-to-plant transfer, animal consumption patterns, and transfer into animal organs (liver and kidneys). The model was applied to cattle up to the age of six years which were fed roughage (maize ...

  11. Lotka-Volterra competition models for sessile organisms.

    Science.gov (United States)

    Spencer, Matthew; Tanner, Jason E

    2008-04-01

    Markov models are widely used to describe the dynamics of communities of sessile organisms, because they are easily fitted to field data and provide a rich set of analytical tools. In typical ecological applications, at any point in time, each point in space is in one of a finite set of states (e.g., species, empty space). The models aim to describe the probabilities of transitions between states. In most Markov models for communities, these transition probabilities are assumed to be independent of state abundances. This assumption is often suspected to be false and is rarely justified explicitly. Here, we start with simple assumptions about the interactions among sessile organisms and derive a model in which transition probabilities depend on the abundance of destination states. This model is formulated in continuous time and is equivalent to a Lotka-Volterra competition model. We fit this model and a variety of alternatives in which transition probabilities do not depend on state abundances to a long-term coral reef data set. The Lotka-Volterra model describes the data much better than all models we consider other than a saturated model (a model with a separate parameter for each transition at each time interval, which by definition fits the data perfectly). Our approach provides a basis for further development of stochastic models of sessile communities, and many of the methods we use are relevant to other types of community. We discuss possible extensions to spatially explicit models.

  12. Modeling Temperature Dependent Singlet Exciton Dynamics in Multilayered Organic Nanofibers

    DEFF Research Database (Denmark)

    de Sousa, Leonardo Evaristo; de Oliveira Neto, Pedro Henrique; Kjelstrup-Hansen, Jakob

    2018-01-01

    Organic nanofibers have shown potential for application in optoelectronic devices because of the tunability of their optical properties. These properties are influenced by the electronic structure of the molecules that compose the nanofibers, but also by the behavior of the excitons generated...... dynamics in multilayered organic nanofibers. By simulating absorption and emission spectra, the possible Förster transitions are identified. Then, a Kinetic Monte Carlo (KMC) model is employed in combination with a genetic algorithm to theoretically reproduce time resolved photoluminescence measurements...

  13. Regulatory Proteolysis in Arabidopsis-Pathogen Interactions.

    Science.gov (United States)

    Pogány, Miklós; Dankó, Tamás; Kámán-Tóth, Evelin; Schwarczinger, Ildikó; Bozsó, Zoltán

    2015-09-24

    Approximately two and a half percent of protein coding genes in Arabidopsis encode enzymes with known or putative proteolytic activity. Proteases possess not only common housekeeping functions by recycling nonfunctional proteins. By irreversibly cleaving other proteins, they regulate crucial developmental processes and control responses to environmental changes. Regulatory proteolysis is also indispensable in interactions between plants and their microbial pathogens. Proteolytic cleavage is simultaneously used both by plant cells, to recognize and inactivate invading pathogens, and by microbes, to overcome the immune system of the plant and successfully colonize host cells. In this review, we present available results on the group of proteases in the model plant Arabidopsis thaliana whose functions in microbial pathogenesis were confirmed. Pathogen-derived proteolytic factors are also discussed when they are involved in the cleavage of host metabolites. Considering the wealth of review papers available in the field of the ubiquitin-26S proteasome system results on the ubiquitin cascade are not presented. Arabidopsis and its pathogens are conferred with abundant sets of proteases. This review compiles a list of those that are apparently involved in an interaction between the plant and its pathogens, also presenting their molecular partners when available.

  14. Photorepair mutants of Arabidopsis

    International Nuclear Information System (INIS)

    Jiang, C.Z.; Yee, J.; Mitchell, D.L.; Britt, A.B.

    1997-01-01

    UV radiation induces two major DNA damage products, the cyclobutane pyrimidine dimer (CPD) and, at a lower frequency, the pyrimidine (6-4) pyrimidinone dimer (6-4 product). Although Escherichia coli and Saccharomyces cerevisiae produce a CPD-specific photolyase that eliminates only this class of dimer, Arabidopsis thaliana, Drosophila melanogaster, Crotalus atrox, and Xenopus laevis have recently been shown to photoreactivate both CPDs and 6-4 products. We describe the isolation and characterization of two new classes of mutants of Arabidopsis, termed uvr2 and uvr3, that are defective in the photoreactivation of CPDs and 6-4 products, respectively. We demonstrate that the CPD photolyase mutation is genetically linked to a DNA sequence encoding a type II (metazoan) CPD photolyase. In addition, we are able to generate plants in which only CPDs or 6-4 products are photoreactivated in the nuclear genome by exposing these mutants to UV light and then allowing them to repair one or the other class of dimers. This provides us with a unique opportunity to study the biological consequences of each of these two major UV-induced photoproducts in an intact living system

  15. Arabidopsis thickvein mutation affects vein thickness and organ vascularization, and resides in a provascular cell-specific spermine synthase involved in vein definition and in polar auxin transport.

    Science.gov (United States)

    Clay, Nicole K; Nelson, Timothy

    2005-06-01

    Polar auxin transport has been implicated in the induction of vascular tissue and in the definition of vein positions. Leaves treated with chemical inhibitors of polar auxin transport exhibited vascular phenotypes that include increased vein thickness and vascularization. We describe a recessive mutant, thickvein (tkv), which develops thicker veins in leaves and in inflorescence stems. The increased vein thickness is attributable to an increased number of vascular cells. Mutant plants have smaller leaves and shorter inflorescence stems, and this reduction in organ size and height is accompanied by an increase in organ vascularization, which appears to be attributable to an increase in the recruitment of cells into veins. Furthermore, although floral development is normal, auxin transport in the inflorescence stem is significantly reduced in the mutant, suggesting that the defect in auxin transport is responsible for the vascular phenotypes. In the primary root, the veins appear morphologically normal, but root growth in the tkv mutant is hypersensitive to exogenous cytokinin. The tkv mutation was found to reside in the ACL5 gene, which encodes a spermine synthase and whose expression is specific to provascular cells. We propose that ACL5/TKV is involved in vein definition (defining the boundaries between veins and nonvein regions) and in polar auxin transport, and that polyamines are involved in this process.

  16. Electrochemical model of the polyaniline based organic memristive device

    International Nuclear Information System (INIS)

    Demin, V. A.; Erokhin, V. V.; Kashkarov, P. K.; Kovalchuk, M. V.

    2014-01-01

    The electrochemical organic memristive device with polyaniline active layer is a stand-alone device designed and realized for reproduction of some synapse properties in the innovative electronic circuits, including the neuromorphic networks capable for learning. In this work, a new theoretical model of the polyaniline memristive is presented. The developed model of organic memristive functioning was based on the detailed consideration of possible electrochemical processes occuring in the active zone of this device. Results of the calculation have demonstrated not only the qualitative explanation of the characteristics observed in the experiment but also the quantitative similarities of the resultant current values. It is shown how the memristive could behave at zero potential difference relative to the reference electrode. This improved model can establish a basis for the design and prediction of properties of more complicated circuits and systems (including stochastic ones) based on the organic memristive devices

  17. A model-independent view of the mature organization

    Energy Technology Data Exchange (ETDEWEB)

    Hanna, M.; Langston, D.

    1996-12-31

    Over the last 10 years, industry has been dealing with the issues of process and organizational maturity. This focus on process is driven by the success that manufacturing organizations have had implementing the management principles of W. Edwards Deming and Joseph M. Juran. The organizational-maturity focus is driven by organizations striving to be ISO 9000 compliant or to achieve a specific level on one of the maturity models. Unfortunately, each of the models takes a specific view into what is a very broad arena. That is to say, each model addresses only a specific subset of the characteristics of maturity. This paper attempts to extend beyond these specific views to answer the general question, What is a mature organization and its relationship to Quantitative management and statistical process control?

  18. Molecular analysis of the replication program in unicellular model organisms.

    Science.gov (United States)

    Raghuraman, M K; Brewer, Bonita J

    2010-01-01

    Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program of replication in particular. But what exactly is a temporal program of replication, and how might it arise? In this article, we explore this question, drawing again on the wealth of experimental information in unicellular model organisms.

  19. Self-organized Criticality Model for Ocean Internal Waves

    International Nuclear Information System (INIS)

    Wang Gang; Hou Yijun; Lin Min; Qiao Fangli

    2009-01-01

    In this paper, we present a simple spring-block model for ocean internal waves based on the self-organized criticality (SOC). The oscillations of the water blocks in the model display power-law behavior with an exponent of -2 in the frequency domain, which is similar to the current and sea water temperature spectra in the actual ocean and the universal Garrett and Munk deep ocean internal wave model [Geophysical Fluid Dynamics 2 (1972) 225; J. Geophys. Res. 80 (1975) 291]. The influence of the ratio of the driving force to the spring coefficient to SOC behaviors in the model is also discussed. (general)

  20. Device model investigation of bilayer organic light emitting diodes

    International Nuclear Information System (INIS)

    Crone, B. K.; Davids, P. S.; Campbell, I. H.; Smith, D. L.

    2000-01-01

    Organic materials that have desirable luminescence properties, such as a favorable emission spectrum and high luminescence efficiency, are not necessarily suitable for single layer organic light-emitting diodes (LEDs) because the material may have unequal carrier mobilities or contact limited injection properties. As a result, single layer LEDs made from such organic materials are inefficient. In this article, we present device model calculations of single layer and bilayer organic LED characteristics that demonstrate the improvements in device performance that can occur in bilayer devices. We first consider an organic material where the mobilities of the electrons and holes are significantly different. The role of the bilayer structure in this case is to move the recombination away from the electrode that injects the low mobility carrier. We then consider an organic material with equal electron and hole mobilities but where it is not possible to make a good contact for one carrier type, say electrons. The role of a bilayer structure in this case is to prevent the holes from traversing the device without recombining. In both cases, single layer device limitations can be overcome by employing a two organic layer structure. The results are discussed using the calculated spatial variation of the carrier densities, electric field, and recombination rate density in the structures. (c) 2000 American Institute of Physics

  1. Green Algae as Model Organisms for Biological Fluid Dynamics

    Science.gov (United States)

    Goldstein, Raymond E.

    2015-01-01

    In the past decade, the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimeters), their geometric regularity, the ease with which they can be cultured, and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

  2. There Is No Simple Model of the Plasma Membrane Organization

    Science.gov (United States)

    Bernardino de la Serna, Jorge; Schütz, Gerhard J.; Eggeling, Christian; Cebecauer, Marek

    2016-01-01

    Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure. PMID:27747212

  3. Efficient Plastid Transformation in Arabidopsis.

    Science.gov (United States)

    Yu, Qiguo; Lutz, Kerry Ann; Maliga, Pal

    2017-09-01

    Plastid transformation is routine in tobacco ( Nicotiana tabacum ) but 100-fold less frequent in Arabidopsis ( Arabidopsis thaliana ), preventing its use in plastid biology. A recent study revealed that null mutations in ACC2 , encoding a plastid-targeted acetyl-coenzyme A carboxylase, cause hypersensitivity to spectinomycin. We hypothesized that plastid transformation efficiency should increase in the acc2 background, because when ACC2 is absent, fatty acid biosynthesis becomes dependent on translation of the plastid-encoded ACC β-carboxylase subunit. We bombarded ACC2 -defective Arabidopsis leaves with a vector carrying a selectable spectinomycin resistance ( aadA ) gene and gfp , encoding the green fluorescence protein GFP. Spectinomycin-resistant clones were identified as green cell clusters on a spectinomycin medium. Plastid transformation was confirmed by GFP accumulation from the second open reading frame of a polycistronic messenger RNA, which would not be translated in the cytoplasm. We obtained one to two plastid transformation events per bombarded sample in spectinomycin-hypersensitive Slavice and Columbia acc2 knockout backgrounds, an approximately 100-fold enhanced plastid transformation frequency. Slavice and Columbia are accessions in which plant regeneration is uncharacterized or difficult to obtain. A practical system for Arabidopsis plastid transformation will be obtained by creating an ACC2 null background in a regenerable Arabidopsis accession. The recognition that the duplicated ACCase in Arabidopsis is an impediment to plastid transformation provides a rational template to implement plastid transformation in related recalcitrant crops. © 2017 American Society of Plant Biologists. All Rights Reserved.

  4. An Ontology for Modeling Complex Inter-relational Organizations

    Science.gov (United States)

    Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

    This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

  5. Zebrabase: An intuitive tracking solution for aquatic model organisms

    OpenAIRE

    Oltova, Jana; Bartunek, Petr; Machonova, Olga; Svoboda, Ondrej; Skuta, Ctibor; Jindrich, Jindrich

    2018-01-01

    Small fish species, like zebrafish or medaka, are constantly gaining popularity in basic research and disease modeling as a useful alternative to rodent model organisms. However, the tracking options for fish within a facility are rather limited. Here, we present an aquatic species tracking database, Zebrabase, developed in our zebrafish research and breeding facility that represents a practical and scalable solution and an intuitive platform for scientists, fish managers and caretakers, in b...

  6. Identifying the transition to the maturation zone in three ecotypes of Arabidopsis thaliana roots.

    Science.gov (United States)

    Cajero Sánchez, Wendy; García-Ponce, Berenice; Sánchez, María de la Paz; Álvarez-Buylla, Elena R; Garay-Arroyo, Adriana

    2018-01-01

    The Arabidopsis thaliana (hereafter Arabidopsis) root has become a useful model for studying how organ morphogenesis emerge from the coordination and balance of cell proliferation and differentiation, as both processes may be observed and quantified in the root at different stages of development. Hence, being able to objectively identify and delimit the different stages of root development has been very important. Up to now, three different zones along the longitudinal axis of the primary root of Arabidopsis, have been identified: the root apical meristematic zone (RAM) with two domains [the proliferative (PD) and the transition domain (TD)], the elongation zone (EZ) and the maturation zone (MZ). We previously reported a method to quantify the length of the cells of the meristematic and the elongation zone, as well as the boundaries or transitions between the root domains along the growing part of the Arabidopsis root. In this study, we provide a more accurate criterion to identify the MZ. Traditionally, the transition between the EZ to the MZ has been established by the emergence of the first root-hair bulge in the epidermis, because this emergence coincides with cell maturation in this cell type. But we have found here that after the emergence of the first root-hair bulge some cells continue to elongate and we have confirmed this in three different Arabidopsis ecotypes. We established the limit between the EZ and the MZ by looking for the closest cortical cell with a longer length than the average cell length of 10 cells after the cortical cell closest to the epidermal cell with the first root-hair bulge in these three ecotypes. In Col-0 and Ws this cell is four cells above the one with the root hair bulge and, in the Ler ecotype, this cell is five cells above. To unambiguously identifying the site at which cells stop elongating and attain their final length and fate at the MZ, we propose to calculate the length of completely elongated cortical cells counting 10

  7. A model of virtual organization for corporate visibility and ...

    African Journals Online (AJOL)

    This paper considers the existing numerous research in business, Information and Communication Technology (ICT), examines a theoretical framework for value creation in a virtual world. Following a proposed model, a new strategic paradigm is created for corporate value; and virtual organization (VO) apply the use of ...

  8. Modeling of the transient mobility in disordered organic semiconductors

    NARCIS (Netherlands)

    Germs, W.C.; Van der Holst, J.M.M.; Van Mensfoort, S.L.M.; Bobbert, P.A.; Coehoorn, R.

    2011-01-01

    In non-steady-state experiments, the electrical response of devicesbased on disordered organic semiconductors often shows a large transient contribution due to relaxation of the out-of-equilibrium charge-carrier distribution. We have developed a model describing this process, based only on the

  9. An Integrated Model for Effective Knowledge Management in Chinese Organizations

    Science.gov (United States)

    An, Xiaomi; Deng, Hepu; Wang, Yiwen; Chao, Lemen

    2013-01-01

    Purpose: The purpose of this paper is to provide organizations in the Chinese cultural context with a conceptual model for an integrated adoption of existing knowledge management (KM) methods and to improve the effectiveness of their KM activities. Design/methodology/approaches: A comparative analysis is conducted between China and the western…

  10. Waste Reduction Model (WARM) Resources for Small Businesses and Organizations

    Science.gov (United States)

    This page provides a brief overview of how EPA’s Waste Reduction Model (WARM) can be used by small businesses and organizations. The page includes a brief summary of uses of WARM for the audience and links to other resources.

  11. SOMPROF: A vertically explicit soil organic matter model

    NARCIS (Netherlands)

    Braakhekke, M.C.; Beer, M.; Hoosbeek, M.R.; Kruijt, B.; Kabat, P.

    2011-01-01

    Most current soil organic matter (SOM) models represent the soil as a bulk without specification of the vertical distribution of SOM in the soil profile. However, the vertical SOM profile may be of great importance for soil carbon cycling, both on short (hours to years) time scale, due to

  12. Modeling growth of specific spoilage organisms in tilapia ...

    African Journals Online (AJOL)

    Tilapia is an important aquatic fish, but severe spoilage of tilapia is most likely related to the global aquaculture. The spoilage is mostly caused by specific spoilage organisms (SSO). Therefore, it is very important to use microbial models to predict the growth of SSO in tilapia. This study firstly verified Pseudomonas and Vibrio ...

  13. There Is No Simple Model of the Plasma Membrane Organization

    Czech Academy of Sciences Publication Activity Database

    de la serna, J. B.; Schütz, G.; Eggeling, Ch.; Cebecauer, Marek

    2016-01-01

    Roč. 4, SEP 2016 (2016), 106 ISSN 2296-634X R&D Projects: GA ČR GA15-06989S Institutional support: RVO:61388955 Keywords : plasma membrane * membrane organization models * heterogeneous distribution Subject RIV: CF - Physical ; Theoretical Chemistry

  14. Lamination of organic solar cells and organic light emitting devices: Models and experiments

    International Nuclear Information System (INIS)

    Oyewole, O. K.; Yu, D.; Du, J.; Asare, J.; Fashina, A.; Anye, V. C.; Zebaze Kana, M. G.; Soboyejo, W. O.

    2015-01-01

    In this paper, a combined experimental, computational, and analytical approach is used to provide new insights into the lamination of organic solar cells and light emitting devices at macro- and micro-scales. First, the effects of applied lamination force (on contact between the laminated layers) are studied. The crack driving forces associated with the interfacial cracks (at the bi-material interfaces) are estimated along with the critical interfacial crack driving forces associated with the separation of thin films, after layer transfer. The conditions for successful lamination are predicted using a combination of experiments and computational models. Guidelines are developed for the lamination of low-cost organic electronic structures

  15. Sustainable Organic Farming For Environmental Health A Social Development Model

    Directory of Open Access Journals (Sweden)

    Ijun Rijwan Susanto

    2015-05-01

    Full Text Available ABSTRACT In this study the researcher attempted 1 to understand the basic features of organic farming in The Paguyuban Pasundans Cianjur 2 to describe and understand how the stakeholders were are able to internalize the challenges of organic farming on their lived experiences in the community 3 to describe and understand how the stakeholders were are able to internalize and applied the values of benefits of organic farming in support of environmental health on their lived experiences in the community 4 The purpose was to describe and understand how the stakeholders who are able to articulate their ideas regarding the model of sustainable organic farming 5 The Policy Recommendation for Organic Farming. The researcher employed triangulation thorough finding that provides breadth and depth to an investigation offering researchers a more accurate picture of the phenomenon. In the implementation of triangulation researchers conducted several interviews to get saturation. After completion of the interview results are written compiled and shown to the participants to check every statement by every participant. In addition researchers also checked the relevant documents and direct observation in the field The participants of this study were the stakeholders namely 1 The leader of Paguyuban Pasundans Organic Farmer Cianjur PPOFC 2 Members of Paguyuban Pasundans Organic FarmersCianjur 3 Leader of NGO 4 Government officials of agriculture 5 Business of organic food 6 and Consumer of organic food. Generally the findings of the study revealed the following 1 PPOFC began to see the reality as the impact of modern agriculture showed in fertility problems due to contaminated soil by residues of agricultural chemicals such as chemical fertilizers and chemical pesticides. So he wants to restore the soil fertility through environmentally friendly of farming practices 2 the challenges of organic farming on their lived experiences in the community farmers did not

  16. On the influence of the exposure model on organ doses

    International Nuclear Information System (INIS)

    Drexler, G.; Eckerl, H.

    1988-01-01

    Based on the design characteristics of the MIRD-V phantom, two sex-specific adult phantoms, ADAM and EVA were introduced especially for the calculation of organ doses resulting from external irradiation. Although the body characteristics of all the phantoms are in good agreement with those of the reference man and woman, they have some disadvantages related to the location and shape of organs and the form of the whole body. To overcome these disadvantages related to the location and shape of organs and form of the whole body. To overcome these disadvantages related to the location and shape of organs and the form of the whole body. To overcome these disadvantages and to obtain more realistic phantoms, a technique based on computer tomographic data (voxel-phantom) was developed. This technique allows any physical phantom or real body to be converted into computer files. The improvements are of special importance with regard to the skeleton, because a better modeling of the bone surfaces and separation of hard bone and bone marrow can be achieved. For photon irradiation, the sensitivity of the model on organ doses or the effective dose equivalent is important for operational radiation protection

  17. Modeling of secondary organic aerosol yields from laboratory chamber data

    Directory of Open Access Journals (Sweden)

    M. N. Chan

    2009-08-01

    Full Text Available Laboratory chamber data serve as the basis for constraining models of secondary organic aerosol (SOA formation. Current models fall into three categories: empirical two-product (Odum, product-specific, and volatility basis set. The product-specific and volatility basis set models are applied here to represent laboratory data on the ozonolysis of α-pinene under dry, dark, and low-NOx conditions in the presence of ammonium sulfate seed aerosol. Using five major identified products, the model is fit to the chamber data. From the optimal fitting, SOA oxygen-to-carbon (O/C and hydrogen-to-carbon (H/C ratios are modeled. The discrepancy between measured H/C ratios and those based on the oxidation products used in the model fitting suggests the potential importance of particle-phase reactions. Data fitting is also carried out using the volatility basis set, wherein oxidation products are parsed into volatility bins. The product-specific model is most likely hindered by lack of explicit inclusion of particle-phase accretion compounds. While prospects for identification of the majority of SOA products for major volatile organic compounds (VOCs classes remain promising, for the near future empirical product or volatility basis set models remain the approaches of choice.

  18. Reference: 783 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available xpression of the Arabidopsis 10-kilodalton acyl-coenzyme A-binding protein ACBP6 en...phospholipid metabolism in Arabidopsis, including the possibility of ACBP6 in the cytosolic trafficking of phosphatidylcholine. Overe

  19. Reference: 774 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available an essential gene, the disruption of which causes embryonic lethality. Plants carrying a hypomorphic smg7 mu...e progression from anaphase to telophase in the second meiotic division in Arabidopsis. Arabidopsis SMG7 is

  20. Accounting for microbial habitats in modeling soil organic matter dynamics

    Science.gov (United States)

    Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

    2017-04-01

    The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

  1. Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

    Science.gov (United States)

    Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

    2016-10-13

    In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various

  2. [Biomechanical modeling of pelvic organ mobility: towards personalized medicine].

    Science.gov (United States)

    Cosson, Michel; Rubod, Chrystèle; Vallet, Alexandra; Witz, Jean-François; Brieu, Mathias

    2011-11-01

    Female pelvic mobility is crucial for urinary, bowel and sexual function and for vaginal delivery. This mobility is ensured by a complex organ suspension system composed of ligaments, fascia and muscles. Impaired pelvic mobility affects one in three women of all ages and can be incapacitating. Surgical management has a high failure rate, largely owing to poor knowledge of the organ support system, including the barely discernible ligamentous system. We propose a 3D digital model of the pelvic cavity based on MRI images and quantitative tools, designed to locate the pelvic ligaments. We thus obtain a coherent anatomical and functional model which can be used to analyze pelvic pathophysiology. This work represents a first step towards creating a tool for localizing and characterizing the source of pelvic imbalance. We examine possible future applications of this model, in terms of personalized therapy and prevention.

  3. Modeling Secondary Organic Aerosol Formation From Emissions of Combustion Sources

    Science.gov (United States)

    Jathar, Shantanu Hemant

    Atmospheric aerosols exert a large influence on the Earth's climate and cause adverse public health effects, reduced visibility and material degradation. Secondary organic aerosol (SOA), defined as the aerosol mass arising from the oxidation products of gas-phase organic species, accounts for a significant fraction of the submicron atmospheric aerosol mass. Yet, there are large uncertainties surrounding the sources, atmospheric evolution and properties of SOA. This thesis combines laboratory experiments, extensive data analysis and global modeling to investigate the contribution of semi-volatile and intermediate volatility organic compounds (SVOC and IVOC) from combustion sources to SOA formation. The goals are to quantify the contribution of these emissions to ambient PM and to evaluate and improve models to simulate its formation. To create a database for model development and evaluation, a series of smog chamber experiments were conducted on evaporated fuel, which served as surrogates for real-world combustion emissions. Diesel formed the most SOA followed by conventional jet fuel / jet fuel derived from natural gas, gasoline and jet fuel derived from coal. The variability in SOA formation from actual combustion emissions can be partially explained by the composition of the fuel. Several models were developed and tested along with existing models using SOA data from smog chamber experiments conducted using evaporated fuel (this work, gasoline, fischertropschs, jet fuel, diesels) and published data on dilute combustion emissions (aircraft, on- and off-road gasoline, on- and off-road diesel, wood burning, biomass burning). For all of the SOA data, existing models under-predicted SOA formation if SVOC/IVOC were not included. For the evaporated fuel experiments, when SVOC/IVOC were included predictions using the existing SOA model were brought to within a factor of two of measurements with minor adjustments to model parameterizations. Further, a volatility

  4. Predicting long-term organic carbon dynamics in organically amended soils using the CQESTR model

    Energy Technology Data Exchange (ETDEWEB)

    Plaza, Cesar; Polo, Alfredo [Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Inst. de Ciencias Agrarias; Gollany, Hero T. [Columbia Plateau Conservation Research Center, Pendleton, OR (United States). USDA-ARS; Baldoni, Guido; Ciavatta, Claudio [Bologna Univ. (Italy). Dept. of Agroenvironmental Sciences and Technologies

    2012-04-15

    Purpose: The CQESTR model is a process-based C model recently developed to simulate soil organic matter (SOM) dynamics and uses readily available or easily measurable input parameters. The current version of CQESTR (v. 2.0) has been validated successfully with a number of datasets from agricultural sites in North America but still needs to be tested in other geographic areas and soil types under diverse organic management systems. Materials and methods: We evaluated the predictive performance of CQESTR to simulate long-term (34 years) soil organic C (SOC) changes in a SOM-depleted European soil either unamended or amended with solid manure, liquid manure, or crop residue. Results and discussion: Measured SOC levels declined over the study period in the unamended soil, remained constant in the soil amended with crop residues, and tended to increase in the soils amended with manure, especially with solid manure. Linear regression analysis of measured SOC contents and CQESTR predictions resulted in a correlation coefficient of 0.626 (P < 0.001) and a slope and an intercept not significantly different from 1 and 0, respectively (95% confidence level). The mean squared deviation and root mean square error were relatively small. Simulated values fell within the 95% confidence interval of the measured SOC, and predicted errors were mainly associated with data scattering. Conclusions: The CQESTR model was shown to predict, with a reasonable degree of accuracy, the organic C dynamics in the soils examined. The CQESTR performance, however, could be improved by adding an additional parameter to differentiate between pre-decomposed organic amendments with varying degrees of stability. (orig.)

  5. Growth rate distribution in the forming lateral root of arabidopsis.

    Science.gov (United States)

    Szymanowska-Pułka, Joanna; Lipowczan, Marcin

    2014-10-01

    Microscopic observations of lateral roots (LRs) in Arabidopsis thaliana reveal that the cross-sectional shape of the organ changes from its basal to its apical region. The founder cells for LRs are elongated along the parent root axis, and thus from the site of initiation the base of LRs resemble an ellipse. The circumference of the apical part of LRs is usually a circle. The objective of this study was to analyse the characteristics of changes in the growth field of LRs possessing various shapes in their basal regions. The LRs of the wild type (Col-0) and two transgenic arabidopsis lines were analysed. On the basis of measurements of the long and short diameters (DL and DS, respectively) of the ellipse-like figure representing the bases of particular LRs, their asymmetry ratios (DL/DS) were determined. Possible differences between accessions were analysed by applying statistical methods. No significant differences between accessions were detected. Comparisons were therefore made of the maximal, minimal and mean value of the ratio of all the LRs analysed. Taking into consideration the lack of circular symmetry of the basal part, rates of growth were determined at selected points on the surface of LRs by the application of the growth tensor method, a mathematical tool previously applied only to describe organs with rotational symmetry. Maps showing the distribution of growth rates were developed for surfaces of LRs of various asymmetry ratios. The maps of growth rates on the surfaces of LRs having various shapes of the basal part show differences in both the geometry and the manner of growth, thus indicating that the manner of growth of the LR primordium is correlated to its shape. This is the first report of a description of growth of an asymmetric plant organ using the growth tensor method. The mathematical modelling adopted in the study provides new insights into plant organ formation and shape. © The Author 2014. Published by Oxford University Press on

  6. Organized versus self-organized criticality in the abelian sandpile model

    OpenAIRE

    Fey-den Boer, AC Anne; Redig, FHJ Frank

    2005-01-01

    We define stabilizability of an infinite volume height configuration and of a probability measure on height configurations. We show that for high enough densities, a probability measure cannot be stabilized. We also show that in some sense the thermodynamic limit of the uniform measures on the recurrent configurations of the abelian sandpile model (ASM) is a maximal element of the set of stabilizable measures. In that sense the self-organized critical behavior of the ASM can be understood in ...

  7. IT Business Value Model for Information Intensive Organizations

    Directory of Open Access Journals (Sweden)

    Antonio Carlos Gastaud Maçada

    2012-01-01

    Full Text Available Many studies have highlighted the capacity Information Technology (IT has for generating value for organizations. Investments in IT made by organizations have increased each year. Therefore, the purpose of the present study is to analyze the IT Business Value for Information Intensive Organizations (IIO - e.g. banks, insurance companies and securities brokers. The research method consisted of a survey that used and combined the models from Weill and Broadbent (1998 and Gregor, Martin, Fernandez, Stern and Vitale (2006. Data was gathered using an adapted instrument containing 5 dimensions (Strategic, Informational, Transactional, Transformational and Infra-structure with 27 items. The instrument was refined by employing statistical techniques such as Exploratory and Confirmatory Factorial Analysis through Structural Equations (first and second order Model Measurement. The final model is composed of four factors related to IT Business Value: Strategic, Informational, Transactional and Transformational, arranged in 15 items. The dimension Infra-structure was excluded during the model refinement process because it was discovered during interviews that managers were unable to perceive it as a distinct dimension of IT Business Value.

  8. Scalability of Sustainable Business Models in Hybrid Organizations

    Directory of Open Access Journals (Sweden)

    Adam Jabłoński

    2016-02-01

    Full Text Available The dynamics of change in modern business create new mechanisms for company management to determine their pursuit and the achievement of their high performance. This performance maintained over a long period of time becomes a source of ensuring business continuity by companies. An ontological being enabling the adoption of such assumptions is such a business model that has the ability to generate results in every possible market situation and, moreover, it has the features of permanent adaptability. A feature that describes the adaptability of the business model is its scalability. Being a factor ensuring more work and more efficient work with an increasing number of components, scalability can be applied to the concept of business models as the company’s ability to maintain similar or higher performance through it. Ensuring the company’s performance in the long term helps to build the so-called sustainable business model that often balances the objectives of stakeholders and shareholders, and that is created by the implemented principles of value-based management and corporate social responsibility. This perception of business paves the way for building hybrid organizations that integrate business activities with pro-social ones. The combination of an approach typical of hybrid organizations in designing and implementing sustainable business models pursuant to the scalability criterion seems interesting from the cognitive point of view. Today, hybrid organizations are great spaces for building effective and efficient mechanisms for dialogue between business and society. This requires the appropriate business model. The purpose of the paper is to present the conceptualization and operationalization of scalability of sustainable business models that determine the performance of a hybrid organization in the network environment. The paper presents the original concept of applying scalability in sustainable business models with detailed

  9. A taxonomy of nursing care organization models in hospitals.

    Science.gov (United States)

    Dubois, Carl-Ardy; D'Amour, Danielle; Tchouaket, Eric; Rivard, Michèle; Clarke, Sean; Blais, Régis

    2012-08-28

    Over the last decades, converging forces in hospital care, including cost-containment policies, rising healthcare demands and nursing shortages, have driven the search for new operational models of nursing care delivery that maximize the use of available nursing resources while ensuring safe, high-quality care. Little is known, however, about the distinctive features of these emergent nursing care models. This article contributes to filling this gap by presenting a theoretically and empirically grounded taxonomy of nursing care organization models in the context of acute care units in Quebec and comparing their distinctive features. This study was based on a survey of 22 medical units in 11 acute care facilities in Quebec. Data collection methods included questionnaire, interviews, focus groups and administrative data census. The analytical procedures consisted of first generating unit profiles based on qualitative and quantitative data collected at the unit level, then applying hierarchical cluster analysis to the units' profile data. The study identified four models of nursing care organization: two professional models that draw mainly on registered nurses as professionals to deliver nursing services and reflect stronger support to nurses' professional practice, and two functional models that draw more significantly on licensed practical nurses (LPNs) and assistive staff (orderlies) to deliver nursing services and are characterized by registered nurses' perceptions that the practice environment is less supportive of their professional work. This study showed that medical units in acute care hospitals exhibit diverse staff mixes, patterns of skill use, work environment design, and support for innovation. The four models reflect not only distinct approaches to dealing with the numerous constraints in the nursing care environment, but also different degrees of approximations to an "ideal" nursing professional practice model described by some leaders in the

  10. A taxonomy of nursing care organization models in hospitals

    Science.gov (United States)

    2012-01-01

    Background Over the last decades, converging forces in hospital care, including cost-containment policies, rising healthcare demands and nursing shortages, have driven the search for new operational models of nursing care delivery that maximize the use of available nursing resources while ensuring safe, high-quality care. Little is known, however, about the distinctive features of these emergent nursing care models. This article contributes to filling this gap by presenting a theoretically and empirically grounded taxonomy of nursing care organization models in the context of acute care units in Quebec and comparing their distinctive features. Methods This study was based on a survey of 22 medical units in 11 acute care facilities in Quebec. Data collection methods included questionnaire, interviews, focus groups and administrative data census. The analytical procedures consisted of first generating unit profiles based on qualitative and quantitative data collected at the unit level, then applying hierarchical cluster analysis to the units’ profile data. Results The study identified four models of nursing care organization: two professional models that draw mainly on registered nurses as professionals to deliver nursing services and reflect stronger support to nurses’ professional practice, and two functional models that draw more significantly on licensed practical nurses (LPNs) and assistive staff (orderlies) to deliver nursing services and are characterized by registered nurses’ perceptions that the practice environment is less supportive of their professional work. Conclusions This study showed that medical units in acute care hospitals exhibit diverse staff mixes, patterns of skill use, work environment design, and support for innovation. The four models reflect not only distinct approaches to dealing with the numerous constraints in the nursing care environment, but also different degrees of approximations to an “ideal” nursing professional practice

  11. In silico identification of known osmotic stress responsive genes from Arabidopsis in soybean and Medicago

    Directory of Open Access Journals (Sweden)

    Nina M. Soares-Cavalcanti

    2012-01-01

    Full Text Available Plants experience various environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. The present research aimed to evaluate a set of genes involved in osmotic response, comparing soybean and medicago with the well-described Arabidopsis thaliana model plant. Based on 103 Arabidopsis proteins from 27 categories of osmotic stress response, comparative analyses against Genosoja and Medicago truncatula databases allowed the identification of 1,088 soybean and 1,210 Medicago sequences. The analysis showed a high number of sequences and high diversity, comprising genes from all categories in both organisms. Genes with unknown function were among the most representative, followed by transcription factors, ion transport proteins, water channel, plant defense, protein degradation, cellular structure, organization & biogenesis and senescence. An analysis of sequences with unknown function allowed the annotation of 174 soybean and 217 Medicago sequences, most of them concerning transcription factors. However, for about 30% of the sequences no function could be attributed using in silico procedures. The establishment of a gene set involved in osmotic stress responses in soybean and barrel medic will help to better understand the survival mechanisms for this type of stress condition in legumes.

  12. Proteomic analysis of Arabidopsis seed germination and priming

    NARCIS (Netherlands)

    Gallardo, K.; Job, C.; Groot, S.P.C.; Puype, M.; Demol, H.; Vandekerckhove, J.; Job, D.

    2001-01-01

    To better understand seed germination, a complex developmental process, we developed a proteome analysis of the model plant Arabidopsis for which complete genome sequence is now available. Among about 1,300 total seed proteins resolved in two-dimensional gels, changes in the abundance (up- and

  13. Gene expression in arabidopsis shoot tips after liquid nitrogen exposure

    Science.gov (United States)

    Arabidopsis thaliana shoot tips can be successfully cryopreserved using either Plant Vitrification Solution 2 (PVS2) or Plant Vitrification Solution 3 (PVS3) as the cryoprotectant. We used this model system to identify suites of genes that were either upregulated or downregulated as shoot tips recov...

  14. Sugar signalling during germination and early seedling establishment in Arabidopsis

    NARCIS (Netherlands)

    Dekkers, S.J.W.

    2006-01-01

    Sugars have pronounced effects on many plant processes like gene expression, germination and early seedling development. Several screens for sugar insensitive mutants were performed to identify genes involved in sugar response pathways using the model plant Arabidopsis. These include sun, gin and

  15. Mathematical Models Light Up Plant Signaling

    NARCIS (Netherlands)

    Chew, Y.H.; Smith, R.W.; Jones, H.J.; Seaton, D.D.; Grima, R.; Halliday, K.J.

    2014-01-01

    Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis

  16. Signals of speciation within Arabidopsis thaliana in comparison with its relatives

    NARCIS (Netherlands)

    Alcazar, R.; Pecinka, A.; Aarts, M.G.M.; Fransz, P.F.; Koornneef, M.

    2012-01-01

    The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to

  17. Molecular analysis of the replication program in unicellular model organisms

    OpenAIRE

    Raghuraman, M. K.; Brewer, Bonita J.

    2010-01-01

    Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program o...

  18. Understanding rare disease pathogenesis: a grand challenge for model organisms.

    Science.gov (United States)

    Hieter, Philip; Boycott, Kym M

    2014-10-01

    In this commentary, Philip Hieter and Kym Boycott discuss the importance of model organisms for understanding pathogenesis of rare human genetic diseases, and highlight the work of Brooks et al., "Dysfunction of 60S ribosomal protein L10 (RPL10) disrupts neurodevelopment and causes X-linked microcephaly in humans," published in this issue of GENETICS. Copyright © 2014 by the Genetics Society of America.

  19. Quasi-dynamic model for an organic Rankine cycle

    International Nuclear Information System (INIS)

    Bamgbopa, Musbaudeen O.; Uzgoren, Eray

    2013-01-01

    Highlights: • Study presents a simplified transient modeling approach for an ORC under variable heat input. • The ORC model is presented as a synthesis of its models of its sub-components. • The model is compared to benchmark numerical simulations and experimental data at different stages. - Abstract: When considering solar based thermal energy input to an organic Rankine cycle (ORC), intermittent nature of the heat input does not only adversely affect the power output but also it may prevent ORC to operate under steady state conditions. In order to identify reliability and efficiency of such systems, this paper presents a simplified transient modeling approach for an ORC operating under variable heat input. The approach considers that response of the system to heat input variations is mainly dictated by the evaporator. Consequently, overall system is assembled using dynamic models for the heat exchangers (evaporator and condenser) and static models of the pump and the expander. In addition, pressure drop within heat exchangers is neglected. The model is compared to benchmark numerical and experimental data showing that the underlying assumptions are reasonable for cases where thermal input varies in time. Furthermore, the model is studied on another configuration and mass flow rates of both the working fluid and hot water and hot water’s inlet temperature to the ORC unit are shown to have direct influence on the system’s response

  20. Sordaria macrospora, a model organism to study fungal cellular development.

    Science.gov (United States)

    Engh, Ines; Nowrousian, Minou; Kück, Ulrich

    2010-12-01

    During the development of multicellular eukaryotes, the processes of cellular growth and organogenesis are tightly coordinated. Since the 1940s, filamentous fungi have served as genetic model organisms to decipher basic mechanisms underlying eukaryotic cell differentiation. Here, we focus on Sordaria macrospora, a homothallic ascomycete and important model organism for developmental biology. During its sexual life cycle, S. macrospora forms three-dimensional fruiting bodies, a complex process involving the formation of different cell types. S. macrospora can be used for genetic, biochemical and cellular experimental approaches since diverse tools, including fluorescence microscopy, a marker recycling system and gene libraries, are available. Moreover, the genome of S. macrospora has been sequenced and allows functional genomics analyses. Over the past years, our group has generated and analysed a number of developmental mutants which has greatly enhanced our fundamental understanding about fungal morphogenesis. In addition, our recent research activities have established a link between developmental proteins and conserved signalling cascades, ultimately leading to a regulatory network controlling differentiation processes in a eukaryotic model organism. This review summarizes the results of our recent findings, thus advancing current knowledge of the general principles and paradigms underpinning eukaryotic cell differentiation and development. Copyright © 2010 Elsevier GmbH. All rights reserved.

  1. Aging, neurogenesis, and caloric restriction in different model organisms.

    Science.gov (United States)

    Arslan-Ergul, Ayca; Ozdemir, A Tugrul; Adams, Michelle M

    2013-08-01

    Brain aging is a multifactorial process that is occurring across multiple cognitive domains. A significant complaint that occurs in the elderly is a decrement in learning and memory ability. Both rodents and zebrafish exhibit a similar problem with memory during aging. The neurobiological changes that underlie this cognitive decline are complex and undoubtedly influenced by many factors. Alterations in the birth of new neurons and neuron turnover may contribute to age-related cognitive problems. Caloric restriction is the only non-genetic intervention that reliably increases life span and healthspan across multiple organisms although the molecular mechanisms are not well-understood. Recently the zebrafish has become a popular model organism for understanding the neurobiological consequences but to date very little work has been performed. Similarly, few studies have examined the effects of dietary restriction in zebrafish. Here we review the literature related to memory decline, neurogenesis, and caloric restriction across model organisms and suggest that zebrafish has the potential to be an important animal model for understanding the complex interactions between age, neurobiological changes in the brain, and dietary regimens or their mimetics as interventions.

  2. Turbulence and Self-Organization Modeling Astrophysical Objects

    CERN Document Server

    Marov, Mikhail Ya

    2013-01-01

    This book focuses on the development of continuum models of natural turbulent media. It provides a theoretical approach to the solutions of different problems related to the formation, structure and evolution of astrophysical and geophysical objects. A stochastic modeling approach is used in the mathematical treatment of these problems, which reflects self-organization processes in open dissipative systems. The authors also consider examples of ordering for various objects in space throughout their evolutionary processes. This volume is aimed at graduate students and researchers in the fields of mechanics, astrophysics, geophysics, planetary and space science.

  3. Conceptual hierarchical modeling to describe wetland plant community organization

    Science.gov (United States)

    Little, A.M.; Guntenspergen, G.R.; Allen, T.F.H.

    2010-01-01

    Using multivariate analysis, we created a hierarchical modeling process that describes how differently-scaled environmental factors interact to affect wetland-scale plant community organization in a system of small, isolated wetlands on Mount Desert Island, Maine. We followed the procedure: 1) delineate wetland groups using cluster analysis, 2) identify differently scaled environmental gradients using non-metric multidimensional scaling, 3) order gradient hierarchical levels according to spatiotem-poral scale of fluctuation, and 4) assemble hierarchical model using group relationships with ordination axes and post-hoc tests of environmental differences. Using this process, we determined 1) large wetland size and poor surface water chemistry led to the development of shrub fen wetland vegetation, 2) Sphagnum and water chemistry differences affected fen vs. marsh / sedge meadows status within small wetlands, and 3) small-scale hydrologic differences explained transitions between forested vs. non-forested and marsh vs. sedge meadow vegetation. This hierarchical modeling process can help explain how upper level contextual processes constrain biotic community response to lower-level environmental changes. It creates models with more nuanced spatiotemporal complexity than classification and regression tree procedures. Using this process, wetland scientists will be able to generate more generalizable theories of plant community organization, and useful management models. ?? Society of Wetland Scientists 2009.

  4. Silkworm: A Promising Model Organism in Life Science.

    Science.gov (United States)

    Meng, Xu; Zhu, Feifei; Chen, Keping

    2017-09-01

    As an important economic insect, silkworm Bombyx mori (L.) (Lepidoptera: Bombycidae) has numerous advantages in life science, such as low breeding cost, large progeny size, short generation time, and clear genetic background. Additionally, there are rich genetic resources associated with silkworms. The completion of the silkworm genome has further accelerated it to be a modern model organism in life science. Genomic studies showed that some silkworm genes are highly homologous to certain genes related to human hereditary disease and, therefore, are a candidate model for studying human disease. In this article, we provided a review of silkworm as an important model in various research areas, including human disease, screening of antimicrobial agents, environmental safety monitoring, and antitumor studies. In addition, the application potentiality of silkworm model in life sciences was discussed. © The Author 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  5. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...... (HRP C). HRP C is 54% identical to ATP N in sequence. When the structures of four class III plant peroxidases are superimposed, the regions with structural differences are non-randomly distributed; all are located in one half of the molecule. The architecture of the haem pocket of ATP N is very similar...... to that of HRP C, in agreement with the low small-molecule substrate specificity of all class III peroxidases. The structure of ATP N suggests that the pH dependence of the substrate turnover will differ from that of HRP C owing to differences in polarity of the residues in the substrate-access channel. Since...

  6. An Instructional Development Model for Global Organizations: The GOaL Model.

    Science.gov (United States)

    Hara, Noriko; Schwen, Thomas M.

    1999-01-01

    Presents an instructional development model, GOaL (Global Organization Localization), for use by global organizations. Topics include gaps in language, culture, and needs; decentralized processes; collaborative efforts; predetermined content; multiple perspectives; needs negotiation; learning within context; just-in-time training; and bilingual…

  7. Dryout modeling in support of the organic tank safety project

    International Nuclear Information System (INIS)

    Simmons, C.S.

    1998-08-01

    This work was performed for the Organic Tank Safety Project to evaluate the moisture condition of the waste surface organic-nitrate bearing tanks that are classified as being conditionally safe because sufficient water is present. This report describes the predictive modeling procedure used to predict the moisture content of waste in the future, after it has been subjected to dryout caused by water vapor loss through passive ventilation. This report describes a simplified procedure for modeling the drying out of tank waste. Dryout occurs as moisture evaporates from the waste into the headspace and then exits the tank through ventilation. The water vapor concentration within the waste of the headspace is determined by the vapor-liquid equilibrium, which depends on the waste's moisture content and temperature. This equilibrium has been measured experimentally for a variety of waste samples and is described by a curve called the water vapor partial pressure isotherm. This curve describes the lowering of the partial pressure of water vapor in equilibrium with the waste relative to pure water due to the waste's chemical composition and hygroscopic nature. Saltcake and sludge are described by two distinct calculations that emphasize the particular physical behavior or each. A simple, steady-state model is devised for each type to obtain the approximate drying behavior. The report shows the application of the model to Tanks AX-102, C-104, and U-105

  8. Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

    Science.gov (United States)

    Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

    2012-12-01

    Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

  9. MIANN models in medicinal, physical and organic chemistry.

    Science.gov (United States)

    González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

  10. OBJECT ORIENTED MODELLING, A MODELLING METHOD OF AN ECONOMIC ORGANIZATION ACTIVITY

    Directory of Open Access Journals (Sweden)

    TĂNĂSESCU ANA

    2014-05-01

    Full Text Available Now, most economic organizations use different information systems types in order to facilitate their activity. There are different methodologies, methods and techniques that can be used to design information systems. In this paper, I propose to present the advantages of using the object oriented modelling at the information system design of an economic organization. Thus, I have modelled the activity of a photo studio, using Visual Paradigm for UML as a modelling tool. For this purpose, I have identified the use cases for the analyzed system and I have presented the use case diagram. I have, also, realized the system static and dynamic modelling, through the most known UML diagrams.

  11. Identification of Polyadenylation Sites within Arabidopsis Thaliana

    KAUST Repository

    Kalkatawi, Manal

    2011-09-01

    Machine Learning (ML) is a field of artificial intelligence focused on the design and implementation of algorithms that enable creation of models for clustering, classification, prediction, ranking and similar inference tasks based on information contained in data. Many ML algorithms have been successfully utilized in a variety of applications. The problem addressed in this thesis is from the field of bioinformatics and deals with the recognition of polyadenylation (poly(A)) sites in the genomic sequence of the plant Arabidopsis thaliana. During the RNA processing, a tail consisting of a number of consecutive adenine (A) nucleotides is added to the terminal nucleotide of the 3’- untranslated region (3’UTR) of the primary RNA. The process in which these A nucleotides are added is called polyadenylation. The location in the genomic DNA sequence that corresponds to the start of terminal A nucleotides (i.e. to the end of 3’UTR) is known as a poly(A) site. Recognition of the poly(A) sites in DNA sequence is important for better gene annotation and understanding of gene regulation. In this study, we built an artificial neural network (ANN) for the recognition of poly(A) sites in the Arabidopsis thaliana genome. Our study demonstrates that this model achieves improved accuracy compared to the existing predictive models for this purpose. The key factor contributing to the enhanced predictive performance of our ANN model is a distinguishing set of features used in creation of the model. These features include a number of physico-chemical characteristics of relevance, such as dinucleotide thermodynamic characteristics, electron-ion interaction potential, etc., but also many of the statistical properties of the DNA sequences from the region surrounding poly(A) site, such as nucleotide and polynucleotide properties, common motifs, etc. Our ANN model was compared in performance with several other ML models, as well as with the PAC tool that is specifically developed for

  12. Organization And Financing Models Of Health Service In Selected Countries

    Directory of Open Access Journals (Sweden)

    Branimir Marković

    2009-07-01

    Full Text Available The introductory part of the work gives a short theoretical presentation regarding possible financing models of health services in the world. In the applicative part of the work we shall present the basic practical models of financing health services in the countries that are the leaders of classic methods of health services financing, e. g. the USA, Great Britain, Germany and Croatia. Working out the applicative part of the work we gave the greatest significance to analysis of some macroeconomic indicators in health services (tendency of total health consumption in relation to GDP, average consumption per insured person etc., to structure analysis of health insurance and just to the scheme of health service organization and financing. We presume that each model of health service financing contains certain limitations that can cause problem (weak organization, increase of expenses etc.. This is the reason why we, in the applicative part of the work, paid a special attention to analysis of financial difficulties in the health sector and pointed to the needs and possibilities of solving them through possible reform measures. The end part of the work aims to point out to advantages and disadvantages of individual financing sources through the comparison method (budgetary – taxes or social health insurance – contributions.

  13. A neural model of figure-ground organization.

    Science.gov (United States)

    Craft, Edward; Schütze, Hartmut; Niebur, Ernst; von der Heydt, Rüdiger

    2007-06-01

    Psychophysical studies suggest that figure-ground organization is a largely autonomous process that guides--and thus precedes--allocation of attention and object recognition. The discovery of border-ownership representation in single neurons of early visual cortex has confirmed this view. Recent theoretical studies have demonstrated that border-ownership assignment can be modeled as a process of self-organization by lateral interactions within V2 cortex. However, the mechanism proposed relies on propagation of signals through horizontal fibers, which would result in increasing delays of the border-ownership signal with increasing size of the visual stimulus, in contradiction with experimental findings. It also remains unclear how the resulting border-ownership representation would interact with attention mechanisms to guide further processing. Here we present a model of border-ownership coding based on dedicated neural circuits for contour grouping that produce border-ownership assignment and also provide handles for mechanisms of selective attention. The results are consistent with neurophysiological and psychophysical findings. The model makes predictions about the hypothetical grouping circuits and the role of feedback between cortical areas.

  14. Molecular simulation of a model of dissolved organic matter.

    Science.gov (United States)

    Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S; Schulten, Hans-Rolf

    2005-08-01

    A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na+ or Ca2+ were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal-humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na+, Ca2+ was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca2+. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

  15. Modeling nanostructure-enhanced light trapping in organic solar cells

    DEFF Research Database (Denmark)

    Adam, Jost

    A promising approach for improving the power conversion efficiencies of organic solar cells (OSCs) is by incorporating nanostructures in their thin film architecture to improve the light absorption in the device’s active polymer layers. Here, we present a modelling framework for the prediction...... of optical and plasmonic field enhancement by nanostructures in (or close to) the active layers and electrodes in OSCs. We incorporate finite-difference time-domain (FDTD) calculations alongside semi- analytical approaches, as the rigorous coupled-wave analysis (RCWA) and mode-coupling theory. Our simulation...

  16. Exploiting natural variation in Arabidopsis

    NARCIS (Netherlands)

    Molenaar, J.A.; Keurentjes, J.J.B.; Sanchez-Serrano, J.J.; Salinas, J.

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of

  17. Antithrombin III in animal models of sepsis and organ failure.

    Science.gov (United States)

    Dickneite, G

    1998-01-01

    Antithrombin III (AT III) is the physiological inhibitor of thrombin and other serine proteases of the clotting cascade. In the development of sepsis, septic shock and organ failure, the plasma levels of AT III decrease considerably, suggesting the concept of a substitution therapy with the inhibitor. A decrease of AT III plasma levels might also be associated with other pathological disorders like trauma, burns, pancreatitis or preclampsia. Activation of coagulation and consumption of AT III is the consequence of a generalized inflammation called SIRS (systemic inflammatory response syndrome). The clotting cascade is also frequently activated after organ transplantation, especially if organs are grafted between different species (xenotransplantation). During the past years AT III has been investigated in numerous corresponding disease models in different animal species which will be reviewed here. The bulk of evidence suggests, that AT III substitution reduces morbidity and mortality in the diseased animals. While gaining more experience with AT III, the concept of substitution therapy to maximal baseline plasma levels (100%) appears to become insufficient. Evidence from clinical and preclinical studies now suggests to adjust the AT III plasma levels to about 200%, i.e., doubling the normal value. During the last few years several authors proposed that AT III might not only be an anti-thrombotic agent, but to have in addition an anti-inflammatory effect.

  18. A Multiagent Modeling Environment for Simulating Work Practice in Organizations

    Science.gov (United States)

    Sierhuis, Maarten; Clancey, William J.; vanHoof, Ron

    2004-01-01

    In this paper we position Brahms as a tool for simulating organizational processes. Brahms is a modeling and simulation environment for analyzing human work practice, and for using such models to develop intelligent software agents to support the work practice in organizations. Brahms is the result of more than ten years of research at the Institute for Research on Learning (IRL), NYNEX Science & Technology (the former R&D institute of the Baby Bell telephone company in New York, now Verizon), and for the last six years at NASA Ames Research Center, in the Work Systems Design and Evaluation group, part of the Computational Sciences Division (Code IC). Brahms has been used on more than ten modeling and simulation research projects, and recently has been used as a distributed multiagent development environment for developing work practice support tools for human in-situ science exploration on planetary surfaces, in particular a human mission to Mars. Brahms was originally conceived of as a business process modeling and simulation tool that incorporates the social systems of work, by illuminating how formal process flow descriptions relate to people s actual located activities in the workplace. Our research started in the early nineties as a reaction to experiences with work process modeling and simulation . Although an effective tool for convincing management of the potential cost-savings of the newly designed work processes, the modeling and simulation environment was only able to describe work as a normative workflow. However, the social systems, uncovered in work practices studied by the design team played a significant role in how work actually got done-actual lived work. Multi- tasking, informal assistance and circumstantial work interactions could not easily be represented in a tool with a strict workflow modeling paradigm. In response, we began to develop a tool that would have the benefits of work process modeling and simulation, but be distinctively able to

  19. Modeling the role of microplastics in Bioaccumulation of organic chemicals to marine aquatic organisms. Critical Review

    NARCIS (Netherlands)

    Koelmans, A.A.

    2015-01-01

    It has been shown that ingestion of microplastics may increase bioaccumulation of organic chemicals by aquatic organisms. This paper critically reviews the literature on the effects of plastic ingestion on the bioaccumulation of organic chemicals, emphasizing quantitative approaches and mechanistic

  20. Generic Modelling of Faecal Indicator Organism Concentrations in the UK

    Directory of Open Access Journals (Sweden)

    Carl M. Stapleton

    2011-06-01

    Full Text Available To meet European Water Framework Directive requirements, data are needed on faecal indicator organism (FIO concentrations in rivers to enable the more heavily polluted to be targeted for remedial action. Due to the paucity of FIO data for the UK, especially under high-flow hydrograph event conditions, there is an urgent need by the policy community for generic models that can accurately predict FIO concentrations, thus informing integrated catchment management programmes. This paper reports the development of regression models to predict base- and high-flow faecal coliform (FC and enterococci (EN concentrations for 153 monitoring points across 14 UK catchments, using land cover, population (human and livestock density and other variables that may affect FIO source strength, transport and die-off. Statistically significant models were developed for both FC and EN, with greater explained variance achieved in the high-flow models. Both land cover and, in particular, population variables are significant predictors of FIO concentrations, with r2 maxima for EN of 0.571 and 0.624, respectively. It is argued that the resulting models can be applied, with confidence, to other UK catchments, both to predict FIO concentrations in unmonitored watercourses and evaluate the likely impact of different land use/stocking level and human population change scenarios.

  1. LSOT: A Lightweight Self-Organized Trust Model in VANETs

    Directory of Open Access Journals (Sweden)

    Zhiquan Liu

    2016-01-01

    Full Text Available With the advances in automobile industry and wireless communication technology, Vehicular Ad hoc Networks (VANETs have attracted the attention of a large number of researchers. Trust management plays an important role in VANETs. However, it is still at the preliminary stage and the existing trust models cannot entirely conform to the characteristics of VANETs. This work proposes a novel Lightweight Self-Organized Trust (LSOT model which contains trust certificate-based and recommendation-based trust evaluations. Both the supernodes and trusted third parties are not needed in our model. In addition, we comprehensively consider three factor weights to ease the collusion attack in trust certificate-based trust evaluation, and we utilize the testing interaction method to build and maintain the trust network and propose a maximum local trust (MLT algorithm to identify trustworthy recommenders in recommendation-based trust evaluation. Furthermore, a fully distributed VANET scenario is deployed based on the famous Advogato dataset and a series of simulations and analysis are conducted. The results illustrate that our LSOT model significantly outperforms the excellent experience-based trust (EBT and Lightweight Cross-domain Trust (LCT models in terms of evaluation performance and robustness against the collusion attack.

  2. Self-Organized Criticality Theory Model of Thermal Sandpile

    International Nuclear Information System (INIS)

    Peng Xiao-Dong; Qu Hong-Peng; Xu Jian-Qiang; Han Zui-Jiao

    2015-01-01

    A self-organized criticality model of a thermal sandpile is formulated for the first time to simulate the dynamic process with interaction between avalanche events on the fast time scale and diffusive transports on the slow time scale. The main characteristics of the model are that both particle and energy avalanches of sand grains are considered simultaneously. Properties of intermittent transport and improved confinement are analyzed in detail. The results imply that the intermittent phenomenon such as blobs in the low confinement mode as well as edge localized modes in the high confinement mode observed in tokamak experiments are not only determined by the edge plasma physics, but also affected by the core plasma dynamics. (paper)

  3. Dynamical quenching and annealing in self-organization multiagent models

    Science.gov (United States)

    Burgos, E.; Ceva, Horacio; Perazzo, R. P.

    2001-07-01

    We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

  4. Modeling financial markets by self-organized criticality

    Science.gov (United States)

    Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

    2015-10-01

    We present a financial market model, characterized by self-organized criticality, that is able to generate endogenously a realistic price dynamics and to reproduce well-known stylized facts. We consider a community of heterogeneous traders, composed by chartists and fundamentalists, and focus on the role of informative pressure on market participants, showing how the spreading of information, based on a realistic imitative behavior, drives contagion and causes market fragility. In this model imitation is not intended as a change in the agent's group of origin, but is referred only to the price formation process. We introduce in the community also a variable number of random traders in order to study their possible beneficial role in stabilizing the market, as found in other studies. Finally, we also suggest some counterintuitive policy strategies able to dampen fluctuations by means of a partial reduction of information.

  5. Models of charge pair generation in organic solar cells.

    Science.gov (United States)

    Few, Sheridan; Frost, Jarvist M; Nelson, Jenny

    2015-01-28

    Efficient charge pair generation is observed in many organic photovoltaic (OPV) heterojunctions, despite nominal electron-hole binding energies which greatly exceed the average thermal energy. Empirically, the efficiency of this process appears to be related to the choice of donor and acceptor materials, the resulting sequence of excited state energy levels and the structure of the interface. In order to establish a suitable physical model for the process, a range of different theoretical studies have addressed the nature and energies of the interfacial states, the energetic profile close to the heterojunction and the dynamics of excited state transitions. In this paper, we review recent developments underpinning the theory of charge pair generation and phenomena, focussing on electronic structure calculations, electrostatic models and approaches to excited state dynamics. We discuss the remaining challenges in achieving a predictive approach to charge generation efficiency.

  6. Partitioning of Nanoparticles into Organic Phases and Model Cells

    Energy Technology Data Exchange (ETDEWEB)

    Posner, J.D.; Westerhoff, P.; Hou, W-C.

    2011-08-25

    There is a recognized need to understand and predict the fate, transport and bioavailability of engineered nanoparticles (ENPs) in aquatic and soil ecosystems. Recent research focuses on either collection of empirical data (e.g., removal of a specific NP through water or soil matrices under variable experimental conditions) or precise NP characterization (e.g. size, degree of aggregation, morphology, zeta potential, purity, surface chemistry, and stability). However, it is almost impossible to transition from these precise measurements to models suitable to assess the NP behavior in the environment with complex and heterogeneous matrices. For decades, the USEPA has developed and applies basic partitioning parameters (e.g., octanol-water partition coefficients) and models (e.g., EPI Suite, ECOSAR) to predict the environmental fate, bioavailability, and toxicity of organic pollutants (e.g., pesticides, hydrocarbons, etc.). In this project we have investigated the hypothesis that NP partition coefficients between water and organic phases (octanol or lipid bilayer) is highly dependent on their physiochemical properties, aggregation, and presence of natural constituents in aquatic environments (salts, natural organic matter), which may impact their partitioning into biological matrices (bioaccumulation) and human exposure (bioavailability) as well as the eventual usage in modeling the fate and bioavailability of ENPs. In this report, we use the terminology "partitioning" to operationally define the fraction of ENPs distributed among different phases. The mechanisms leading to this partitioning probably involve both chemical force interactions (hydrophobic association, hydrogen bonding, ligand exchange, etc.) and physical forces that bring the ENPs in close contact with the phase interfaces (diffusion, electrostatic interactions, mixing turbulence, etc.). Our work focuses on partitioning, but also provides insight into the relative behavior of ENPs as either "more like

  7. The hamster flank organ model: Is it relevant to man

    International Nuclear Information System (INIS)

    Franz, T.J.; Lehman, P.A.; Pochi, P.; Odland, G.F.; Olerud, J.

    1989-01-01

    The critical role that androgens play in the etiology of acne has led to a search for topically active antiandrogens and the frequent use of the flank organ of the golden Syrian hamster as an animal model. 17-alpha-propyltestosterone (17-PT) has been identified as having potent antiandrogenic activity in the hamster model, and this report describes its clinical evaluation. Two double-blind placebo controlled studies comparing 4% 17-PT in 80% alcohol versus vehicle alone were conducted. One study examined 17-PT sebosuppressive activity in 20 subjects. The second study examined its efficacy in 44 subjects having mild to moderate acne. A third study measured in vitro percutaneous absorption of 17-PT through hamster flank and monkey skin, and human face skin in-vivo, using radioactive drug. 17-PT was found to be ineffective in reducing either the sebum excretion rate or the number of inflammatory acne lesions. Failure of 17-PT to show clinical activity was not a result of poor percutaneous absorption. Total absorption in man was 7.7% of the dose and only 1.0% in the hamster. The sebaceous gland of hamster flank organ is apparently more sensitive to antiandrogens than the human sebaceous gland

  8. Modeling temperature dependent singlet exciton dynamics in multilayered organic nanofibers

    Science.gov (United States)

    de Sousa, Leonardo Evaristo; de Oliveira Neto, Pedro Henrique; Kjelstrup-Hansen, Jakob; da Silva Filho, Demétrio Antônio

    2018-05-01

    Organic nanofibers have shown potential for application in optoelectronic devices because of the tunability of their optical properties. These properties are influenced by the electronic structure of the molecules that compose the nanofibers and also by the behavior of the excitons generated in the material. Exciton diffusion by means of Förster resonance energy transfer is responsible, for instance, for the change with temperature of colors in the light emitted by systems composed of different types of nanofibers. To study in detail this mechanism, we model temperature dependent singlet exciton dynamics in multilayered organic nanofibers. By simulating absorption and emission spectra, the possible Förster transitions are identified. Then, a kinetic Monte Carlo model is employed in combination with a genetic algorithm to theoretically reproduce time-resolved photoluminescence measurements for several temperatures. This procedure allows for the obtainment of different information regarding exciton diffusion in such a system, including temperature effects on the Förster transfer efficiency and the activation energy of the Förster mechanism. The method is general and may be employed for different systems where exciton diffusion plays a role.

  9. Towards a paradigm shift in the modeling of soil organic carbon decomposition for earth system models

    Science.gov (United States)

    He, Yujie

    Soils are the largest terrestrial carbon pools and contain approximately 2200 Pg of carbon. Thus, the dynamics of soil carbon plays an important role in the global carbon cycle and climate system. Earth System Models are used to project future interactions between terrestrial ecosystem carbon dynamics and climate. However, these models often predict a wide range of soil carbon responses and their formulations have lagged behind recent soil science advances, omitting key biogeochemical mechanisms. In contrast, recent mechanistically-based biogeochemical models that explicitly account for microbial biomass pools and enzyme kinetics that catalyze soil carbon decomposition produce notably different results and provide a closer match to recent observations. However, a systematic evaluation of the advantages and disadvantages of the microbial models and how they differ from empirical, first-order formulations in soil decomposition models for soil organic carbon is still needed. This dissertation consists of a series of model sensitivity and uncertainty analyses and identifies dominant decomposition processes in determining soil organic carbon dynamics. Poorly constrained processes or parameters that require more experimental data integration are also identified. This dissertation also demonstrates the critical role of microbial life-history traits (e.g. microbial dormancy) in the modeling of microbial activity in soil organic matter decomposition models. Finally, this study surveys and synthesizes a number of recently published microbial models and provides suggestions for future microbial model developments.

  10. Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation.

    Science.gov (United States)

    Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto; Pazos, Florencio

    2013-01-01

    Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.

  11. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan

    2017-04-05

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  12. Involvement of Multiple Gene-Silencing Pathways in a Paramutation-like Phenomenon in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Zhimin Zheng

    2015-05-01

    Full Text Available Paramutation is an epigenetic phenomenon that has been observed in a number of multicellular organisms. The epigenetically silenced state of paramutated alleles is not only meiotically stable but also “infectious” to active homologous alleles. The molecular mechanism of paramutation remains unclear, but components involved in RNA-directed DNA methylation (RdDM are required. Here, we report a multi-copy pRD29A-LUC transgene in Arabidopsis thaliana that behaves like a paramutation locus. The silent state of LUC is induced by mutations in the DNA glycosylase gene ROS1. The silent alleles of LUC are not only meiotically stable but also able to transform active LUC alleles into silent ones, in the absence of ros1 mutations. Maintaining silencing at the LUC gene requires action of multiple pathways besides RdDM. Our study identified specific factors that are involved in the paramutation-like phenomenon and established a model system for the study of paramutation in Arabidopsis.

  13. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan; Calixto, Cristiane  P.  G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten  Have, Sara; Frei  dit  Frey, Nicolas; Hirt, Heribert; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria; Brown, John  W.  S.

    2017-01-01

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  14. Intracellular Localization of Arabidopsis Sulfurtransferases1

    Science.gov (United States)

    Bauer, Michael; Dietrich, Christof; Nowak, Katharina; Sierralta, Walter D.; Papenbrock, Jutta

    2004-01-01

    Sulfurtransferases (Str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. In all organisms analyzed to date, small gene families encoding Str proteins have been identified. The gene products were localized to different compartments of the cells. Our interest concerns the localization of Str proteins encoded in the nuclear genome of Arabidopsis. Computer-based prediction methods revealed localization in different compartments of the cell for six putative AtStrs. Several methods were used to determine the localization of the AtStr proteins experimentally. For AtStr1, a mitochondrial localization was demonstrated by immunodetection in the proteome of isolated mitochondria resolved by one- and two-dimensional gel electrophoresis and subsequent blotting. The respective mature AtStr1 protein was identified by mass spectrometry sequencing. The same result was obtained by transient expression of fusion constructs with the green fluorescent protein in Arabidopsis protoplasts, whereas AtStr2 was exclusively localized to the cytoplasm by this method. Three members of the single-domain AtStr were localized in the chloroplasts as demonstrated by transient expression of green fluorescent protein fusions in protoplasts and stomata, whereas the single-domain AtStr18 was shown to be cytoplasmic. The remarkable subcellular distribution of AtStr15 was additionally analyzed by transmission electron immunomicroscopy using a monospecific antibody against green fluorescent protein, indicating an attachment to the thylakoid membrane. The knowledge of the intracellular localization of the members of this multiprotein family will help elucidate their specific functions in the organism. PMID:15181206

  15. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Claudia Voelckel

    Full Text Available BACKGROUND: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. METHODOLOGY/PRINCIPAL FINDINGS: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource. CONCLUSIONS/SIGNIFICANCE: Our comparative gene expression analyses suggest that 1 petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2 petals of A. formosa and A. thaliana may be independently derived, 3 staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4 staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.

  16. Modeling organic aerosols during MILAGRO: importance of biogenic secondary organic aerosols

    Directory of Open Access Journals (Sweden)

    A. Hodzic

    2009-09-01

    Full Text Available The meso-scale chemistry-transport model CHIMERE is used to assess our understanding of major sources and formation processes leading to a fairly large amount of organic aerosols – OA, including primary OA (POA and secondary OA (SOA – observed in Mexico City during the MILAGRO field project (March 2006. Chemical analyses of submicron aerosols from aerosol mass spectrometers (AMS indicate that organic particles found in the Mexico City basin contain a large fraction of oxygenated organic species (OOA which have strong correspondence with SOA, and that their production actively continues downwind of the city. The SOA formation is modeled here by the one-step oxidation of anthropogenic (i.e. aromatics, alkanes, biogenic (i.e. monoterpenes and isoprene, and biomass-burning SOA precursors and their partitioning into both organic and aqueous phases. Conservative assumptions are made for uncertain parameters to maximize the amount of SOA produced by the model. The near-surface model evaluation shows that predicted OA correlates reasonably well with measurements during the campaign, however it remains a factor of 2 lower than the measured total OA. Fairly good agreement is found between predicted and observed POA within the city suggesting that anthropogenic and biomass burning emissions are reasonably captured. Consistent with previous studies in Mexico City, large discrepancies are encountered for SOA, with a factor of 2–10 model underestimate. When only anthropogenic SOA precursors were considered, the model was able to reproduce within a factor of two the sharp increase in OOA concentrations during the late morning at both urban and near-urban locations but the discrepancy increases rapidly later in the day, consistent with previous results, and is especially obvious when the column-integrated SOA mass is considered instead of the surface concentration. The increase in the missing SOA mass in the afternoon coincides with the sharp drop in POA

  17. Different myrosinase and idioblast distribution in Arabidopsis and Brassica napus

    DEFF Research Database (Denmark)

    Andreasson, Erik; Jørgensen, Lise Bolt; Höglund, Anna-Stina

    2001-01-01

    Arabidopsis, Brassica napus, Myrosinase, Myrosinase Binding Protein, Glucosinolates, Myrosin Cell, Immunocytochemistry......Arabidopsis, Brassica napus, Myrosinase, Myrosinase Binding Protein, Glucosinolates, Myrosin Cell, Immunocytochemistry...

  18. Functional analysis of the Hikeshi-like protein and its interaction with HSP70 in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Koizumi, Shinya; Ohama, Naohiko; Mizoi, Junya [Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Shinozaki, Kazuo [RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 (Japan); Yamaguchi-Shinozaki, Kazuko, E-mail: akys@mail.ecc.u-tokyo.ac.jp [Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2014-07-18

    Highlights: • HKL, a Hikeshi homologous gene is identified in Arabidopsis. • HKL interacts with two HSP70 isoforms and regulates the subcellular localization of HSC70-1. • The two HSP70 translocate into nucleus in response to heat stress. • Overexpression of HKL confers thermotolerance in transgenic plants. - Abstract: Heat shock proteins (HSPs) refold damaged proteins and are an essential component of the heat shock response. Previously, the 70 kDa heat shock protein (HSP70) has been reported to translocate into the nucleus in a heat-dependent manner in many organisms. In humans, the heat-induced translocation of HSP70 requires the nuclear carrier protein Hikeshi. In the Arabidopsis genome, only one gene encodes a protein with high homology to Hikeshi, and we named this homolog Hikeshi-like (HKL) protein. In this study, we show that two Arabidopsis HSP70 isoforms accumulate in the nucleus in response to heat shock and that HKL interacts with these HSP70s. Our histochemical analysis revealed that HKL is predominantly expressed in meristematic tissues, suggesting the potential importance of HKL during cell division in Arabidopsis. In addition, we show that HKL regulates HSP70 localization, and HKL overexpression conferred thermotolerance to transgenic Arabidopsis plants. Our results suggest that HKL plays a positive role in the thermotolerance of Arabidopsis plants and cooperatively interacts with HSP70.

  19. Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

    OpenAIRE

    Wolf, Jason B.; Mutic, Joshua J.; Kover, Paula X.

    2011-01-01

    Studying the genetic basis of traits involved in ecological interactions is a fundamental part of elucidating the connections between evolutionary and ecological processes. Such knowledge allows one to link genetic models of trait evolution with ecological models describing interactions within and between species. Previous work has shown that connections between genetic and ecological processes in Arabidopsis thaliana may be mediated by the fact that quantitative trait loci (QTL) with ‘direct...

  20. Multiple paths to similar germination behavior in Arabidopsis thaliana.

    Science.gov (United States)

    Burghardt, Liana T; Edwards, Brianne R; Donohue, Kathleen

    2016-02-01

    Germination timing influences plant fitness, and its sensitivity to temperature may cause it to change as climate shifts. These changes are likely to be complex because temperatures that occur during seed maturation and temperatures that occur post-dispersal interact to define germination timing. We used the model organism Arabidopsis thaliana to determine how flowering time (which defines seed-maturation temperature) and post-dispersal temperature influence germination and the expression of genetic variation for germination. Germination responses to temperature (germination envelopes) changed as seeds aged, or after-ripened, and these germination trajectories depended on seed-maturation temperature and genotype. Different combinations of genotype, seed-maturation temperature, and after-ripening produced similar germination envelopes. Likewise, different genotypes and seed-maturation temperatures combined to produce similar germination trajectories. Differences between genotypes were most likely to be observed at high and low germination temperatures. The germination behavior of some genotypes responds weakly to maternal temperature but others are highly plastic. We hypothesize that weak dormancy induction could synchronize germination of seeds dispersed at different times. By contrast, we hypothesize that strongly responsive genotypes may spread offspring germination over several possible germination windows. Considering germination responses to temperature is important for predicting phenology expression and evolution in future climates. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  1. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

    Science.gov (United States)

    Schoof, Heiko; Zaccaria, Paolo; Gundlach, Heidrun; Lemcke, Kai; Rudd, Stephen; Kolesov, Grigory; Arnold, Roland; Mewes, H. W.; Mayer, Klaus F. X.

    2002-01-01

    Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants. PMID:11752263

  2. Infection and RNA recombination of Brome mosaic virus in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Dzianott, Aleksandra; Bujarski, Jozef J.

    2004-01-01

    Ecotypes of Arabidopsis thaliana supported the replication and systemic spread of Brome mosaic virus (BMV) RNAs. Infection was induced either by manual inoculation with viral RNA or by BMV virions, demonstrating that virus disassembly did not prevent infection. When in vitro-transcribed BMV RNAs 1-3 were used, production of subgenomic RNA4 was observed, showing that BMV RNA replication and transcription had occurred. Furthermore, inoculations of the transgenic Arabidopsis line that expressed a suppressor of RNA interference (RNAi) pathway markedly increased the BMV RNA concentrations. Inoculations with designed BMV RNA3 recombination vectors generated both homologous and nonhomologous BMV RNA-RNA recombinants. Thus, all cellular factors essential for BMV RNA replication, transcription, and RNA recombination were shown to be present in Arabidopsis. The current scope of understanding of the model Arabidopsis plant system should facilitate the identification of these factors governing the BMV life cycle

  3. Nephrology around Europe: organization models and management strategies: Spain.

    Science.gov (United States)

    de Francisco, Angel L M; Piñera, Celestino

    2011-01-01

    The main aim of this report is to present a picture of the current organization of nephrology in Spain. The Spanish health system offers almost universal coverage, a wide variety of services and a high-quality network of hospitals and primary care centers. Spain has a specialized health care training system that is highly developed, highly regulated, with the capacity to provide high-quality training in 54 different specialties. Nephrology is basically a hospital-based specialty. There are no private dialysis patients in Spain. Hemodialysis centers are 40% public, 15% private and 45% run by companies. The National Health System covers 95% of the population, and there is no cost to patients for treatment of renal disease (dialysis and transplant). We observed a clear decrease of nephrology in residents' election rankings, with position 29 out of 47 specialties in 2007. Some of the reasons for this are the complexity of the subject, no clear information at the university, reduction of professional posts and a very good public service with minimal private practice. In Spain, a model of organization for transplantation was adopted based on a decentralized transplant coordinating network. For cadaveric donors, it compares favorably with rates in other Western countries. Living donor transplantation is very low in Spain--just 10% of total renal transplantation activity. New programs due to financial constraints need to include reduced dialysis costs, greater cost-effectiveness of prescriptions, better handling of ethical issues related to the need for using a clinical score of chronic kidney disease patients to make decisions about conservative or renal replacement therapy and an action plan for improvement of organ donation and transplantation. Recovery of skills (acute kidney injury, biopsies, vascular access, etc.), research and advances in autonomous activities (imaging, surgical and medical vascular training, etc.) are some of the future educational paths needed in

  4. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

    Directory of Open Access Journals (Sweden)

    Andrea Sottoriva

    2011-05-01

    Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

  5. A geometrical model for DNA organization in bacteria.

    Directory of Open Access Journals (Sweden)

    Mathias Buenemann

    Full Text Available Recent experimental studies have revealed that bacteria, such as C. crescentus, show a remarkable spatial ordering of their chromosome. A strong linear correlation has been found between the position of genes on the chromosomal map and their spatial position in the cellular volume. We show that this correlation can be explained by a purely geometrical model. Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus together with the action of DNA compaction proteins (that organize the chromosome into topological domains are sufficient to get a linear arrangement of the chromosome along the cell axis. We develop a Monte-Carlo method that allows us to test our model numerically and to analyze the dependence of the spatial ordering on various physiologically relevant parameters. We show that the proposed geometrical ordering mechanism is robust and universal (i.e. does not depend on specific bacterial details. The geometrical mechanism should work in all bacteria that have compacted chromosomes with spatially fixed regions. We use our model to make specific and experimentally testable predictions about the spatial arrangement of the chromosome in mutants of C. crescentus and the growth-stage dependent ordering in E. coli.

  6. Modeling cooperating micro-organisms in antibiotic environment.

    Science.gov (United States)

    Book, Gilad; Ingham, Colin; Ariel, Gil

    2017-01-01

    Recent experiments with the bacteria Paenibacillus vortex reveal a remarkable strategy enabling it to cope with antibiotics by cooperating with a different bacterium-Escherichia coli. While P. vortex is a highly effective swarmer, it is sensitive to the antibiotic ampicillin. On the other hand, E. coli can degrade ampicillin but is non-motile when grown on high agar percentages. The two bacterial species form a shared colony in which E. coli is transported by P. vortex and E. coli detoxifies the ampicillin. The paper presents a simplified model, consisting of coupled reaction-diffusion equations, describing the development of ring patterns in the shared colony. Our results demonstrate some of the possible cooperative movement strategies bacteria utilize in order to survive harsh conditions. In addition, we explore the behavior of mixed colonies under new conditions such as antibiotic gradients, synchronization between colonies and possible dynamics of a 3-species system including P. vortex, E. coli and a carbon producing algae that provides nutrients under illuminated, nutrient poor conditions. The derived model was able to simulate an asymmetric relationship between two or three micro-organisms where cooperation is required for survival. Computationally, in order to avoid numerical artifacts due to symmetries within the discretizing grid, the model was solved using a second order Vectorizable Random Lattices method, which is developed as a finite volume scheme on a random grid.

  7. Modeling cooperating micro-organisms in antibiotic environment.

    Directory of Open Access Journals (Sweden)

    Gilad Book

    Full Text Available Recent experiments with the bacteria Paenibacillus vortex reveal a remarkable strategy enabling it to cope with antibiotics by cooperating with a different bacterium-Escherichia coli. While P. vortex is a highly effective swarmer, it is sensitive to the antibiotic ampicillin. On the other hand, E. coli can degrade ampicillin but is non-motile when grown on high agar percentages. The two bacterial species form a shared colony in which E. coli is transported by P. vortex and E. coli detoxifies the ampicillin. The paper presents a simplified model, consisting of coupled reaction-diffusion equations, describing the development of ring patterns in the shared colony. Our results demonstrate some of the possible cooperative movement strategies bacteria utilize in order to survive harsh conditions. In addition, we explore the behavior of mixed colonies under new conditions such as antibiotic gradients, synchronization between colonies and possible dynamics of a 3-species system including P. vortex, E. coli and a carbon producing algae that provides nutrients under illuminated, nutrient poor conditions. The derived model was able to simulate an asymmetric relationship between two or three micro-organisms where cooperation is required for survival. Computationally, in order to avoid numerical artifacts due to symmetries within the discretizing grid, the model was solved using a second order Vectorizable Random Lattices method, which is developed as a finite volume scheme on a random grid.

  8. Spectrophotometry and organic matter on Iapetus. 1: Composition models

    Science.gov (United States)

    Wilson, Peter D.; Sagan, Carl

    1995-01-01

    Iapetus shows a greater hemispheric albedo asymmetry than any other body in the solar system. Hapke scattering theory and optical constants measured in the laboratory are used to identify possible compositions for the dark material on the leading hemisphere of Iapetus. The materials considered are poly-HCN, kerogen, Murchison organic residue, Titan tholin, ice tholin, and water ice. Three-component mixtures of these materials are modeled in intraparticle mixture of 25% poly-HCN, 10% Murchison residue, and 65% water ice is found to best fit the spectrum, albedo, and phase behavior of the dark material. The Murchison residue and/or water ice can be replaced by kerogen and ice tholin, respectively, and still produce very good fits. Areal and particle mixtures of poly-HCN, Titan tholin, and either ice tholin or Murchison residue are also possible models. Poly-HCN is a necessary component in almost all good models. The presence of poly-HCN can be further tested by high-resolution observations near 4.5 micrometers.

  9. Self-Organized Criticality in an Anisotropic Earthquake Model

    Science.gov (United States)

    Li, Bin-Quan; Wang, Sheng-Jun

    2018-03-01

    We have made an extensive numerical study of a modified model proposed by Olami, Feder, and Christensen to describe earthquake behavior. Two situations were considered in this paper. One situation is that the energy of the unstable site is redistributed to its nearest neighbors randomly not averagely and keeps itself to zero. The other situation is that the energy of the unstable site is redistributed to its nearest neighbors randomly and keeps some energy for itself instead of reset to zero. Different boundary conditions were considered as well. By analyzing the distribution of earthquake sizes, we found that self-organized criticality can be excited only in the conservative case or the approximate conservative case in the above situations. Some evidence indicated that the critical exponent of both above situations and the original OFC model tend to the same result in the conservative case. The only difference is that the avalanche size in the original model is bigger. This result may be closer to the real world, after all, every crust plate size is different. Supported by National Natural Science Foundation of China under Grant Nos. 11675096 and 11305098, the Fundamental Research Funds for the Central Universities under Grant No. GK201702001, FPALAB-SNNU under Grant No. 16QNGG007, and Interdisciplinary Incubation Project of SNU under Grant No. 5

  10. In Vivo RNAi-Based Screens: Studies in Model Organisms

    Directory of Open Access Journals (Sweden)

    Miki Yamamoto-Hino

    2013-11-01

    Full Text Available RNA interference (RNAi is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results.

  11. ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

    Science.gov (United States)

    Krishnakumar, Vivek; Contrino, Sergio; Cheng, Chia-Yi; Belyaeva, Irina; Ferlanti, Erik S; Miller, Jason R; Vaughn, Matthew W; Micklem, Gos; Town, Christopher D; Chan, Agnes P

    2017-01-01

    ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and functional annotation from the Araport11 update, the Col-0 genome sequence, RNA-seq and array expression, co-expression, protein interactions, homologs, pathways, publications, alleles, germplasm and phenotypes. The data are collected from a wide variety of public resources. Users can browse gene-specific data through Gene Report pages, identify and create gene lists based on experiments or indexed keywords, and run GO enrichment analysis to investigate the biological significance of selected gene sets. Developed by the Arabidopsis Information Portal project (Araport, https://www.araport.org/), ThaleMine uses the InterMine software framework, which builds well-structured data, and provides powerful data query and analysis functionality. The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services. Here we describe recent developments in ThaleMine including new features and extensions, and discuss future improvements. InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data. ThaleMine is the first InterMine developed for a plant model. As additional new plant InterMines are developed by the legume and other plant research communities, the potential of cross-organism integrative data analysis will be further enabled. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. Azolla--a model organism for plant genomic studies.

    Science.gov (United States)

    Qiu, Yin-Long; Yu, Jun

    2003-02-01

    The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

  13. Giant plasma membrane vesicles: models for understanding membrane organization.

    Science.gov (United States)

    Levental, Kandice R; Levental, Ilya

    2015-01-01

    The organization of eukaryotic membranes into functional domains continues to fascinate and puzzle cell biologists and biophysicists. The lipid raft hypothesis proposes that collective lipid interactions compartmentalize the membrane into coexisting liquid domains that are central to membrane physiology. This hypothesis has proven controversial because such structures cannot be directly visualized in live cells by light microscopy. The recent observations of liquid-liquid phase separation in biological membranes are an important validation of the raft hypothesis and enable application of the experimental toolbox of membrane physics to a biologically complex phase-separated membrane. This review addresses the role of giant plasma membrane vesicles (GPMVs) in refining the raft hypothesis and expands on the application of GPMVs as an experimental model to answer some of key outstanding problems in membrane biology. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Corporate Social Responsibility And Islamic Business Organizations: A Proposed Model

    Directory of Open Access Journals (Sweden)

    Rusnah Muhamad

    2008-01-01

    Full Text Available The issue of corporate social responsibility (CSR has been of growing concern among business communities in recent years. Various corporate leaders maintain that business is considered to contribute fully to the society if it is effi cient, profi table and socially responsible. Islam is considered as addin (a way of life, thus, providing comprehensive guidelines in every aspects of the believers’ life. It is the aim of this paper to propose an Islamic model of corporate social responsibility based on human relationships with the God (hablun min’Allah; with other fellow human being (hablun min’an-nas and with the environment.Keywords : Corporate Social Responsibility, Islamic Business Organization

  15. Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.

    Science.gov (United States)

    van Baarlen, Peter; van Belkum, Alex; Thomma, Bart P H J

    2007-02-01

    Relatively simple eukaryotic model organisms such as the genetic model weed plant Arabidopsis thaliana possess an innate immune system that shares important similarities with its mammalian counterpart. In fact, some human pathogens infect Arabidopsis and cause overt disease with human symptomology. In such cases, decisive elements of the plant's immune system are likely to be targeted by the same microbial factors that are necessary for causing disease in humans. These similarities can be exploited to identify elementary microbial pathogenicity factors and their corresponding targets in a green host. This circumvents important cost aspects that often frustrate studies in humans or animal models and, in addition, results in facile ethical clearance.

  16. A NEW ORGANIZATIONAL FORM: STARFISH ORGANIZATION IN BUSINESS MODEL PERSPECTIVE

    OpenAIRE

    Aygul Turan; Aysegul Ozbebek Tunc

    2013-01-01

    As we moved into new economy, decentralization is a very powerful strategy day by day. A large number of traditional organizations are decentralized- some of them decentralize a part of the organization, some of them decentralize whole of the organizations- because of being a winner of the competition. As a decentralized organization, starfish organization is a new concept of the organizational science literature. In this framework, we focus on the starfish organization’s structure. The aim o...

  17. System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max.

    Directory of Open Access Journals (Sweden)

    Yungang Xu

    Full Text Available Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN, a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max, due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs, in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional

  18. Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

    Science.gov (United States)

    Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

    2018-04-20

    Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

  19. An auxin responsive CLE gene regulates shoot apical meristem development in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Hongyan eGuo

    2015-05-01

    Full Text Available Plant hormone auxin regulates most, if not all aspects of plant growth and development, including lateral root formation, organ pattering, apical dominance and tropisms. Peptide hormones are peptides with hormone activities. Some of the functions of peptide hormones in regulating plant growth and development are similar to that of auxin, however, the relationship between auxin and peptide hormones remains largely unknown. Here we report the identification of OsCLE48, a rice (Oryza sativa CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION gene, as an auxin response gene, and the functional characterization of OsCLE48 in Arabidopsis and rice. OsCLE48 encodes a CLE peptide hormone that is similar to Arabidopsis CLEs. RT-PCR analysis showed that OsCLE48 was induced by exogenously application of IAA (indole-3-acetic acid, a naturally occurred auxin. Expression of integrated OsCLE48p:GUS reporter gene in transgenic Arabidopsis plants was also induced by exogenously IAA treatment. These results indicate that OsCLE48 is an auxin responsive gene. Histochemical staining showed that GUS activity was detected in all the tissue and organs of the OsCLE48p:GUS transgenic Arabidopsis plants. Expression of OsCLE48 under the control of the 35S promoter in Arabidopsis inhibited shoot apical meristem development. Expression of OsCLE48 under the control of the CLV3 native regulatory elements almost completely complemented clv3-2 mutant phenotypes, suggesting that OsCLE48 is functionally similar to CLV3. On the other hand, expression of OsCLE48 under the control of the 35S promoter in Arabidopsis has little, if any effects on root apical meristem development, and transgenic rice plants overexpressing OsCLE48 are morphologically indistinguishable from wild type plants, suggesting that the functions of some CLE peptides may not be fully conserved in Arabidopsis and rice.

  20. Modeling Organic Contaminant Desorption from Municipal Solid Waste Components

    Science.gov (United States)

    Knappe, D. R.; Wu, B.; Barlaz, M. A.

    2002-12-01

    Approximately 25% of the sites on the National Priority List (NPL) of Superfund are municipal landfills that accepted hazardous waste. Unlined landfills typically result in groundwater contamination, and priority pollutants such as alkylbenzenes are often present. To select cost-effective risk management alternatives, better information on factors controlling the fate of hydrophobic organic contaminants (HOCs) in landfills is required. The objectives of this study were (1) to investigate the effects of HOC aging time, anaerobic sorbent decomposition, and leachate composition on HOC desorption rates, and (2) to simulate HOC desorption rates from polymers and biopolymer composites with suitable diffusion models. Experiments were conducted with individual components of municipal solid waste (MSW) including polyvinyl chloride (PVC), high-density polyethylene (HDPE), newsprint, office paper, and model food and yard waste (rabbit food). Each of the biopolymer composites (office paper, newsprint, rabbit food) was tested in both fresh and anaerobically decomposed form. To determine the effects of aging on alkylbenzene desorption rates, batch desorption tests were performed after sorbents were exposed to toluene for 30 and 250 days in flame-sealed ampules. Desorption tests showed that alkylbenzene desorption rates varied greatly among MSW components (PVC slowest, fresh rabbit food and newsprint fastest). Furthermore, desorption rates decreased as aging time increased. A single-parameter polymer diffusion model successfully described PVC and HDPE desorption data, but it failed to simulate desorption rate data for biopolymer composites. For biopolymer composites, a three-parameter biphasic polymer diffusion model was employed, which successfully simulated both the initial rapid and the subsequent slow desorption of toluene. Toluene desorption rates from MSW mixtures were predicted for typical MSW compositions in the years 1960 and 1997. For the older MSW mixture, which had a

  1. Development of a statistical shape model of multi-organ and its performance evaluation

    International Nuclear Information System (INIS)

    Nakada, Misaki; Shimizu, Akinobu; Kobatake, Hidefumi; Nawano, Shigeru

    2010-01-01

    Existing statistical shape modeling methods for an organ can not take into account the correlation between neighboring organs. This study focuses on a level set distribution model and proposes two modeling methods for multiple organs that can take into account the correlation between neighboring organs. The first method combines level set functions of multiple organs into a vector. Subsequently it analyses the distribution of the vectors of a training dataset by a principal component analysis and builds a multiple statistical shape model. Second method constructs a statistical shape model for each organ independently and assembles component scores of different organs in a training dataset so as to generate a vector. It analyses the distribution of the vectors of to build a statistical shape model of multiple organs. This paper shows results of applying the proposed methods trained by 15 abdominal CT volumes to unknown 8 CT volumes. (author)

  2. Elimination kinetic model for organic chemicals in earthworms.

    NARCIS (Netherlands)

    Dimitrova, N.; Dimitrov, S.; Georgieva, D.; van Gestel, C.A.M.; Hankard, P.; Spurgeon, D.J.; Li, H.; Mekenyan, O.

    2010-01-01

    Mechanistic understanding of bioaccumulation in different organisms and environments should take into account the influence of organism and chemical depending factors on the uptake and elimination kinetics of chemicals. Lipophilicity, metabolism, sorption (bioavailability) and biodegradation of

  3. KICS: A Model of Motivational Leadership in Organizations

    Directory of Open Access Journals (Sweden)

    John N. N. Ugoani

    2015-09-01

    Full Text Available This pure research gave birth to a Model of Motivational Leadership – KICS: which embraces knowledge, intelligence, collaboration and synergy. It is a synergistic  proposition based on the theory of emotional intelligence as the index of competencies needed for effective leadership. It opened with a general discussion on traditional models of leadership, then the roles of knowledge, intelligence, collaboration and synergy as they relate to motivational leadership. Issues of emotional intelligence clusters and synthesis of the model’s elements were discussed, emphasizing how KICS-based motivational leadership skills can be developed and sustained. Motivational leadership entails exciting people’s imaginations and inspiring them to move in a desired direction. It takes more than simple power to motivate and lead in organizations. Realizing that unity and cohesiveness are built from personal bonds, the best leaders ensure to deepen their rapport with employees and colleagues which enhances organizational performance. This pure research argues that the synergy of related emotional intelligence competencies can lead to motivational leadership behaviour. Knowledge is critical to leadership because there are different types of leadership and different situations require different kinds of knowledge, and the person possessing the knowledge demanded by a certain situation in most cases, tends to become the best leader. A knowledgeable person is one who is trained to consider his actions to undertake them deliberately, in a disciplined manner. Added to this ability is the intelligence to endure in a chosen course in the face of distraction, confusion and difficulty, all combined in producing a motivational leader. Knowledge tends to be procedural in nature and to operate outside of focal awareness. It also reflects the structure of the situation more closely than it does in the structure of formal disciplinary knowledge. The survey research design

  4. DNA is structured as a linear "jigsaw puzzle" in the genomes of Arabidopsis, rice, and budding yeast.

    Science.gov (United States)

    Liu, Yun-Hua; Zhang, Meiping; Wu, Chengcang; Huang, James J; Zhang, Hong-Bin

    2014-01-01

    Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear "jigsaw puzzle". Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice.

  5. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  6. Reference: 255 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ases, AtIPK1 and AtIPK2beta, for the later steps of phytate synthesis in Arabidopsis thaliana. Coincident disruption...olyphosphate kinases in phosphate signaling biology. Generation of phytate-free seeds in Arabidopsis through disruption

  7. Arabidopsis CDS blastp result: AK108458 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK108458 002-143-D05 At4g35000.1 L-ascorbate peroxidase 3 (APX3) identical to ascorbat...e peroxidase 3 [Arabidopsis thaliana] GI:2444019, L-ascorbate peroxidase [Arabidopsis thaliana] gi|152379...1|emb|CAA66926; similar to ascorbate peroxidase [Gossypium hirsutum] gi|1019946|gb|AAB52954 2e-35 ...

  8. Arabidopsis CDS blastp result: AK070842 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK070842 J023074O14 At4g35000.1 L-ascorbate peroxidase 3 (APX3) identical to ascorbat...e peroxidase 3 [Arabidopsis thaliana] GI:2444019, L-ascorbate peroxidase [Arabidopsis thaliana] gi|1523791...|emb|CAA66926; similar to ascorbate peroxidase [Gossypium hirsutum] gi|1019946|gb|AAB52954 1e-112 ...

  9. Evaluation of approaches focused on modelling of organic carbon stocks using the RothC model

    Science.gov (United States)

    Koco, Štefan; Skalský, Rastislav; Makovníková, Jarmila; Tarasovičová, Zuzana; Barančíková, Gabriela

    2014-05-01

    The aim of current efforts in the European area is the protection of soil organic matter, which is included in all relevant documents related to the protection of soil. The use of modelling of organic carbon stocks for anticipated climate change, respectively for land management can significantly help in short and long-term forecasting of the state of soil organic matter. RothC model can be applied in the time period of several years to centuries and has been tested in long-term experiments within a large range of soil types and climatic conditions in Europe. For the initialization of the RothC model, knowledge about the carbon pool sizes is essential. Pool size characterization can be obtained from equilibrium model runs, but this approach is time consuming and tedious, especially for larger scale simulations. Due to this complexity we search for new possibilities how to simplify and accelerate this process. The paper presents a comparison of two approaches for SOC stocks modelling in the same area. The modelling has been carried out on the basis of unique input of land use, management and soil data for each simulation unit separately. We modeled 1617 simulation units of 1x1 km grid on the territory of agroclimatic region Žitný ostrov in the southwest of Slovakia. The first approach represents the creation of groups of simulation units based on the evaluation of results for simulation unit with similar input values. The groups were created after the testing and validation of modelling results for individual simulation units with results of modelling the average values of inputs for the whole group. Tests of equilibrium model for interval in the range 5 t.ha-1 from initial SOC stock showed minimal differences in results comparing with result for average value of whole interval. Management inputs data from plant residues and farmyard manure for modelling of carbon turnover were also the same for more simulation units. Combining these groups (intervals of initial

  10. The prisoner as model organism: malaria research at Stateville Penitentiary

    Science.gov (United States)

    Comfort, Nathaniel

    2009-01-01

    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner’s time on the project was counted as part of his sentence, and because serving on the project could shorten one’s sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such ‘mixed mechanisms’ in his Discipline and punish. His shining example of such a ‘transparent’ and subtle style of punishment was the panopticon, Jeremy Bentham’s architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham’s model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. PMID:19720327

  11. Multiwall carbon nanotubes modulate paraquat toxicity in Arabidopsis thaliana.

    Science.gov (United States)

    Fan, Xiaoji; Xu, Jiahui; Lavoie, Michel; Peijnenburg, W J G M; Zhu, Youchao; Lu, Tao; Fu, Zhengwei; Zhu, Tingheng; Qian, Haifeng

    2018-02-01

    Carbon nanotubes can be either toxic or beneficial to plant growth and can also modulate toxicity of organic contaminants through surface sorption. The complex interacting toxic effects of carbon nanotubes and organic contaminants in plants have received little attention in the literature to date. In this study, the toxicity of multiwall carbon nanotubes (MWCNT, 50 mg/L) and paraquat (MV, 0.82 mg/L), separately or in combination, were evaluated at the physiological and the proteomic level in Arabidopsis thaliana for 7-14 days. The results revealed that the exposure to MWCNT had no inhibitory effect on the growth of shoots and leaves. Rather, MWCNT stimulated the relative electron transport rate and the effective photochemical quantum yield of PSII value as compared to the control by around 12% and lateral root production up to nearly 4-fold as compared to the control. The protective effect of MWCNT on MV toxicity on the root surface area could be quantitatively explained by the extent of MV adsorption on MWCNT and was related to stimulation of photosynthesis, antioxidant protection and number and area of lateral roots which in turn helped nutrient assimilation. The influence of MWCNT and MV on photosynthesis and oxidative stress at the physiological level was consistent with the proteomics analysis, with various over-expressed photosynthesis-related proteins (by more than 2 folds) and various under-expressed oxidative stress related proteins (by about 2-3 folds). This study brings new insights into the interactive effects of two xenobiotics (MWCNT and MV) on the physiology of a model plant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Towards Increased Relevance: Context-Adapted Models of the Learning Organization

    Science.gov (United States)

    Örtenblad, Anders

    2015-01-01

    Purpose: The purposes of this paper are to take a closer look at the relevance of the idea of the learning organization for organizations in different generalized organizational contexts; to open up for the existence of multiple, context-adapted models of the learning organization; and to suggest a number of such models.…

  13. On agent cooperation : the relevance of cognitive plausibility for multiagent simulation models of organizations

    NARCIS (Netherlands)

    van den Broek, J.

    2001-01-01

    Human organizations and computational multiagent systems both are social systems because they are both made up of a large number of interacting parts. Since human organizations are arrangements of distributed real intelligence, any DAI model is in some sense a model of an organization. This

  14. On agent cooperation : The relevance of cognitive plausibility for multiagent simulation models of organizations

    NARCIS (Netherlands)

    Broek, J. van den

    2001-01-01

    Human organizations and computational multiagent systems both are social systems because they are both made up of a large number of interacting parts. Since human organizations are arrangements of distributed real intelligence, any DAI model is in some sense a model of an organization. This

  15. Modelling and Optimization of Organization of Workplaces in a Foundry

    Directory of Open Access Journals (Sweden)

    Kukla S.

    2016-09-01

    Full Text Available The paper presents a practical example of improvement of foundry production systems in terms of post-finishing of nodular iron castings produced in the conditions of bulk production for automotive industry. The attention was paid to high labour-intensive efforts, which are difficult to be subjected to mechanization and automation. The times of actions related to grinding processing of castings in three grinding positions connected with a belt conveyor were estimated with the use of a time study method. A bottleneck as well as limiting factors were specified in a system. A number of improvements were proposed, aimed at improving work organization on the castings post-finishing line. An analysis of work ergonomics at the workplace was made in order to eliminate unnecessary and onerous for the employee actions. A model of production system using the Arena software, on which a simulation experiment was conducted, was drawn up in order to visualize the analysed phenomena. The effects of the project were shown on graphs comparing times, costs, work ergonomics and overall efficiency of production equipment indicator.

  16. Drug repurposing for aging research using model organisms.

    Science.gov (United States)

    Ziehm, Matthias; Kaur, Satwant; Ivanov, Dobril K; Ballester, Pedro J; Marcus, David; Partridge, Linda; Thornton, Janet M

    2017-10-01

    Many increasingly prevalent diseases share a common risk factor: age. However, little is known about pharmaceutical interventions against aging, despite many genes and pathways shown to be important in the aging process and numerous studies demonstrating that genetic interventions can lead to a healthier aging phenotype. An important challenge is to assess the potential to repurpose existing drugs for initial testing on model organisms, where such experiments are possible. To this end, we present a new approach to rank drug-like compounds with known mammalian targets according to their likelihood to modulate aging in the invertebrates Caenorhabditis elegans and Drosophila. Our approach combines information on genetic effects on aging, orthology relationships and sequence conservation, 3D protein structures, drug binding and bioavailability. Overall, we rank 743 different drug-like compounds for their likelihood to modulate aging. We provide various lines of evidence for the successful enrichment of our ranking for compounds modulating aging, despite sparse public data suitable for validation. The top ranked compounds are thus prime candidates for in vivo testing of their effects on lifespan in C. elegans or Drosophila. As such, these compounds are promising as research tools and ultimately a step towards identifying drugs for a healthier human aging. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

  17. Changes in endogenous abscisic acid levels during dormancy release and maintenance of mature seeds: studies with the Cape Verde Islands ecotype, the dormant model of Arabidopsis thaliana.

    Science.gov (United States)

    Ali-Rachedi, Sonia; Bouinot, Denise; Wagner, Marie-Hélène; Bonnet, Magda; Sotta, Bruno; Grappin, Philippe; Jullien, Marc

    2004-07-01

    Mature seeds of the Cape Verde Islands (Cvi) ecotype of Arabidopsis thaliana (L.) Heynh. show a very marked dormancy. Dormant (D) seeds completely fail to germinate in conditions that are favourable for germination whereas non-dormant (ND) seeds germinate easily. Cvi seed dormancy is alleviated by after-ripening, stratification, and also by nitrate or fluridone treatment. Addition of gibberellins to D seeds does not suppress dormancy efficiently, suggesting that gibberellins are not directly involved in the breaking of dormancy. Dormancy expression of Cvi seeds is strongly dependent on temperature: D seeds do not germinate at warm temperatures (20-27 degrees C) but do so easily at a low temperature (13 degrees C) or when a fluridone treatment is given to D seeds sown at high temperature. To investigate the role of abscisic acid (ABA) in dormancy release and maintenance, we measured the ABA content in both ND and D seeds imbibed using various dormancy-breaking conditions. It was found that dry D seeds contained higher amounts of ABA than dry ND after-ripened seeds. During early imbibition in standard conditions, there was a decrease in ABA content in both seeds, the rate of which was slower in D seeds. Three days after sowing, the ABA content in D seeds increased specifically and then remained at a high level. When imbibed with fluridone, nitrate or stratified, the ABA content of D seeds decreased and reached a level very near to that of ND seeds. In contrast, gibberellic acid (GA3) treatment caused a transient increase in ABA content. When D seeds were sown at low optimal temperature their ABA content also decreased to the level observed in ND seeds. The present study indicates that Cvi D and ND seeds can be easily distinguished by their ability to synthesize ABA following imbibition. Treatments used here to break dormancy reduced the ABA level in imbibed D seeds to the level observed in ND seeds, with the exception of GA3 treatment, which was active in promoting

  18. Organics.

    Science.gov (United States)

    Chian, Edward S. K.; DeWalle, Foppe B.

    1978-01-01

    Presents water analysis literature for 1978. This review is concerned with organics, and it covers: (1) detergents and surfactants; (2) aliphatic and aromatic hydrocarbons; (3) pesticides and chlorinated hydrocarbons; and (4) naturally occurring organics. A list of 208 references is also presented. (HM)

  19. Organizers.

    Science.gov (United States)

    Callison, Daniel

    2000-01-01

    Focuses on "organizers," tools or techniques that provide identification and classification along with possible relationships or connections among ideas, concepts, and issues. Discusses David Ausubel's research and ideas concerning advance organizers; the implications of Ausubel's theory to curriculum and teaching; "webbing," a…

  20. COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis.

    Science.gov (United States)

    Schindelman, G; Morikami, A; Jung, J; Baskin, T I; Carpita, N C; Derbyshire, P; McCann, M C; Benfey, P N

    2001-05-01

    To control organ shape, plant cells expand differentially. The organization of the cellulose microfibrils in the cell wall is a key determinant of differential expansion. Mutations in the COBRA (COB) gene of Arabidopsis, known to affect the orientation of cell expansion in the root, are reported here to reduce the amount of crystalline cellulose in cell walls in the root growth zone. The COB gene, identified by map-based cloning, contains a sequence motif found in proteins that are anchored to the extracellular surface of the plasma membrane through a glycosylphosphatidylinositol (GPI) linkage. In animal cells, this lipid linkage is known to confer polar localization to proteins. The COB protein was detected predominately on the longitudinal sides of root cells in the zone of rapid elongation. Moreover, COB RNA levels are dramatically upregulated in cells entering the zone of rapid elongation. Based on these results, models are proposed for the role of COB as a regulator of oriented cell expansion.

  1. Overexpression of four Arabidopsis thaliana NHLgenes in soybean (Glycine max) roots and their effect over resistance to the soybean cyst nematode (Heterodera glycines)

    Science.gov (United States)

    In the US, the soybean cyst nematode (SCN) is the most destructive pathogen of soybean. Currently grown soybean varieties are not resistant to all field populations of SCN. We genetically engineered soybean roots so they expressed genes from the model plant, Arabidopsis. When the Arabidopsis genes, ...

  2. Composition and function of P bodies in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Luis David Maldonado-Bonilla

    2014-05-01

    Full Text Available mRNA accumulation is tightly regulated by diverse molecular pathways. The identification and characterization of enzymes and regulatory proteins involved in controlling the fate of mRNA offers the possibility to broaden our understanding of posttranscriptional gene regulation. Processing bodies (P bodies, PB are cytoplasmic protein complexes involved in degradation and translational arrest of mRNA. Composition and dynamics of these subcellular structures have been studied in animal systems, yeasts and in the model plant Arabidopsis. Their assembly implies the aggregation of specific factors related to decapping, deadenylation and exoribonucleases that operate synchronously to regulate certain mRNA targets during development and adaptation to stress. Although the general function of PB along with the flow of genetic information is understood, several questions still remain open. This review summarizes data on the composition, potential molecular roles, and biological significance of PB and potentially related proteins in Arabidopsis.

  3. Modeling the current and future role of particulate organic nitrates in the southeastern United States

    Science.gov (United States)

    Organic nitrates are an important aerosol constituent in locations where biogenic hydrocarbon emissions mix with anthropogenic NOx sources. While regional and global chemical transport models may include a representation of organic aerosol from monoterpene reactions with nitrate ...

  4. DESIGNING A DATA GOVERNANCE MODEL BASED ON SOFT SYSTEM METHODOLOGY (SSM) IN ORGANIZATION

    OpenAIRE

    Hanung Nindito Prasetyo; Kridanto surendro

    2015-01-01

    Today, many emerging various models of data governance like DAMA, DGI and the latest is a model from IBM. Model DAMA International is a data governance model designed by industry associations. The model requires the fulfillment of the entire artifact in a matrix that has been determined that too many components that must be built in data governance in an organization. While the data governance model is built from the data DGI consulting organization which requires the development of data gove...

  5. Mature and emerging organic markets: Modelling consumer attitude and behaviour with Partial Least Square Approach

    OpenAIRE

    von Meyer-Höfer, Marie; von der Wense, Vera; Padilla Bravo, Carlos; Spiller, Achim

    2013-01-01

    Although the organic food sector has been the subject of research for around 20 years, little is known about consumer behaviour when comparing developed and emerging organic food markets using causal research models. Thus, by developing a behavioural model based on the Theory of Planned Behaviour (TPB), the aim of this research article is to investigate the main determinants of organic food consumption in a mature (Germany) and an emerging (Chile) organic market. Subjects aged 18 or above wer...

  6. COMPARATIVE ANALYSIS OF THE ORGANIZATIONAL MODELS IN ORGANIC FARMING

    Directory of Open Access Journals (Sweden)

    Alexandra MUSCĂNESCU

    2013-10-01

    Full Text Available As regards to organic farming, organic farms have a lot of shortcomings in ensuring smooth organization of production due to climatic factors or crop sensitivity and action of pests and diseases, but especially to the high cost of inputs, reduced subsidies and difficulties in obtaining fair prices on the market. Understanding how the organizational structure of the business can compete to ensure efficiency at farm level is an important means to resolve these deficiencies. In this context, this paper aims to identify the characteristics of the organization of organic crop farms starting from an interview-based analysis of two large crop specialised farms in Tulcea and Calaraşi Counties. The information obtained through this method of investigation has been translated into a SWOT analysis and represented the basis for comparison with information gathered from other interviews from two organic farms in Scotland. The main conclusions we reached highlight two types of organization systems, one without integration and another with supply chain integration, very similar to the Scottish ones, but also showing a very obvious difference in the mentality of the farm owners; Romanians focusing on meeting the conditions for certification and maintenance of crops in organic, and the Scots at finding new markets.

  7. Modelling the subgenual organ of the honeybee, Apis mellifera

    DEFF Research Database (Denmark)

    Storm, Jesper; Kilpinen, Ole

    1998-01-01

    In a recent study on the honeybee (Apis mellifera), the subgenual organ was observed moving inside the leg during sinusoidal vibrations of the leg (Kilpinen and Storm 1997). The subgenual organ of the honeybee is suspended in a haemolymph channel in the tibia of each leg. When the leg accelerates...

  8. Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis

    NARCIS (Netherlands)

    Xuan, Wei; Band, Leah R.; Kumpf, Robert P.; Rybel, De Bert

    2016-01-01

    The plant root cap, surrounding the very tip of the growing root, perceives and transmits environmental signals to the inner root tissues. In Arabidopsis thaliana, auxin released by the root cap contributes to the regular spacing of lateral organs along the primary root axis. Here, we show that

  9. Overexpression of DOSOC1, an ortholog of Arabidopsis SOC1, promotes flowering in the orchid Dendrobium Chao Parya Smile.

    Science.gov (United States)

    Ding, Lihua; Wang, Yanwen; Yu, Hao

    2013-04-01

    SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) encodes a MADS-box protein that plays an essential role in integrating multiple flowering signals to regulate the transition from vegetative to reproductive development in the model plant Arabidopsis. Although SOC1-like genes have been isolated in various angiosperms, its orthologs in Orchidaceae, one of the largest families of flowering plants, are so far unknown. To investigate the regulatory mechanisms of flowering time control in orchids, we isolated a SOC1-like gene, DOSOC1, from Dendrobium Chao Praya Smile. DOSOC1 was highly expressed in reproductive organs, including inflorescence apices, pedicels, floral buds and open flowers. Its expression significantly increased in whole plantlets during the transition from vegetative to reproductive development, which usually occurred after 8 weeks of culture in Dendrobium Chao Praya Smile. In the shoot apex at the floral transitional stage, DOSOC1 was particularly expressed in emerging floral meristems. Overexpression of DOSOC1 in wild-type Arabidopsis plants resulted in early flowering, which was coupled with the up-regulation of two other flowering promoters, AGAMOUS-LIKE 24 and LEAFY. In addition, overexpression of DOSOC1 was able partially to complement the late-flowering phenotype of Arabidopsis soc1-2 loss-of-function mutants. Furthermore, we successfully created seven 35S:DOSOC1 transgenic Dendrobium orchid lines, which consistently exhibited earlier flowering than wild-type orchids. Our results suggest that SOC1-like genes play an evolutionarily conserved role in promoting flowering in the Orchidaceae family, and that DOSOC1 isolated from Dendrobium Chao Praya Smile could serve as an important target for genetic manipulation of flowering time in orchids.

  10. Current developments in soil organic matter modeling and the expansion of model applications: a review

    International Nuclear Information System (INIS)

    Campbell, Eleanor E; Paustian, Keith

    2015-01-01

    Soil organic matter (SOM) is an important natural resource. It is fundamental to soil and ecosystem functions across a wide range of scales, from site-specific soil fertility and water holding capacity to global biogeochemical cycling. It is also a highly complex material that is sensitive to direct and indirect human impacts. In SOM research, simulation models play an important role by providing a mathematical framework to integrate, examine, and test the understanding of SOM dynamics. Simulation models of SOM are also increasingly used in more ‘applied’ settings to evaluate human impacts on ecosystem function, and to manage SOM for greenhouse gas mitigation, improved soil health, and sustainable use as a natural resource. Within this context, there is a need to maintain a robust connection between scientific developments in SOM modeling approaches and SOM model applications. This need forms the basis of this review. In this review we first provide an overview of SOM modeling, focusing on SOM theory, data-model integration, and model development as evidenced by a quantitative review of SOM literature. Second, we present the landscape of SOM model applications, focusing on examples in climate change policy. We conclude by discussing five areas of recent developments in SOM modeling including: (1) microbial roles in SOM stabilization; (2) modeling SOM saturation kinetics; (3) temperature controls on decomposition; (4) SOM dynamics in deep soil layers; and (5) SOM representation in earth system models. Our aim is to comprehensively connect SOM model development to its applications, revealing knowledge gaps in need of focused interdisciplinary attention and exposing pitfalls that, if avoided, can lead to best use of SOM models to support policy initiatives and sustainable land management solutions. (topical review)

  11. A review of modelling the interaction between natural organic matter and metal cations

    International Nuclear Information System (INIS)

    Falck, W.E.

    1989-01-01

    This report reviews techniques available to model the interaction between natural organic matter (mainly fulvic and humic acids) and metal cations and protons. A comprehensive overview over the properties of natural organic matter is given and experimental techniques are presented briefly. Two major concepts of modelling have been identified: discrete ligand models and continuous distribution model. Different modelling approaches like Discrete Ligand Models (s.s.), Random-Structure Model, Affinity Spectra, Statistical Distribution Models, Continuous Stability Function Models and surface sorption models and their advantages/disadvantages are discussed. (author)

  12. Participatory plant breeding and organic agriculture: A synergistic model for organic variety development in the United States

    Directory of Open Access Journals (Sweden)

    Adrienne C. Shelton

    2016-12-01

    Full Text Available Abstract Organic farmers require improved varieties that have been adapted to their unique soils, nutrient inputs, management practices, and pest pressures. One way to develop adapted varieties is to situate breeding programs in the environment of intended use, such as directly on organic farms, and in collaboration with organic farmers. This model is a form of participatory plant breeding, and was originally created in order to meet the needs of under-served, small-scale farmers in developing countries. A robust body of literature supports the quantitative genetic selection theory of participatory plant breeding, and helps to explain its increasing prevalence among organic breeding projects in the United States. The history of the organic farming movement in the United States highlights the cultural relevance of engaging organic farmers in the breeding process, complementing the biological rationale for participatory plant breeding. In addition, limited private investment in organic plant breeding encourages the involvement of plant breeders at public institutions. This paper synthesizes the biological, cultural, and economic justifications for utilizing participatory plant breeding as an appropriate methodology for organic cultivar development.

  13. Stage-structured matrix models for organisms with non-geometric development times

    Science.gov (United States)

    Andrew Birt; Richard M. Feldman; David M. Cairns; Robert N. Coulson; Maria Tchakerian; Weimin Xi; James M. Guldin

    2009-01-01

    Matrix models have been used to model population growth of organisms for many decades. They are popular because of both their conceptual simplicity and their computational efficiency. For some types of organisms they are relatively accurate in predicting population growth; however, for others the matrix approach does not adequately model...

  14. 76 FR 34712 - Medicare Program; Pioneer Accountable Care Organization Model; Extension of the Submission...

    Science.gov (United States)

    2011-06-14

    ... stakeholders to develop initiatives to test innovative payment and service delivery models to reduce program...] Medicare Program; Pioneer Accountable Care Organization Model; Extension of the Submission Deadlines for... of the Pioneer Accountable Care Organization Model letters of intent to June 30, 2011 and the...

  15. Organizations

    DEFF Research Database (Denmark)

    Hatch, Mary Jo

    and considers many more. Mary Jo Hatch introduces the concept of organizations by presenting definitions and ideas drawn from the a variety of subject areas including the physical sciences, economics, sociology, psychology, anthropology, literature, and the visual and performing arts. Drawing on examples from......Most of us recognize that organizations are everywhere. You meet them on every street corner in the form of families and shops, study in them, work for them, buy from them, pay taxes to them. But have you given much thought to where they came from, what they are today, and what they might become...... prehistory and everyday life, from the animal kingdom as well as from business, government, and other formal organizations, Hatch provides a lively and thought provoking introduction to the process of organization....

  16. PROCESS DOCUMENTATION: A MODEL FOR KNOWLEDGE MANAGEMENT IN ORGANIZATIONS.

    Science.gov (United States)

    Haddadpoor, Asefeh; Taheri, Behjat; Nasri, Mehran; Heydari, Kamal; Bahrami, Gholamreza

    2015-10-01

    Continuous and interconnected processes are a chain of activities that turn the inputs of an organization to its outputs and help achieve partial and overall goals of the organization. These activates are carried out by two types of knowledge in the organization called explicit and implicit knowledge. Among these, implicit knowledge is the knowledge that controls a major part of the activities of an organization, controls these activities internally and will not be transferred to the process owners unless they are present during the organization's work. Therefore the goal of this study is identification of implicit knowledge and its integration with explicit knowledge in order to improve human resources management, physical resource management, information resource management, training of new employees and other activities of Isfahan University of Medical Science. The project for documentation of activities in department of health of Isfahan University of Medical Science was carried out in several stages. First the main processes and related sub processes were identified and categorized with the help of planning expert. The categorization was carried out from smaller processes to larger ones. In this stage the experts of each process wrote down all their daily activities and organized them into general categories based on logical and physical relations between different activities. Then each activity was assigned a specific code. The computer software was designed after understanding the different parts of the processes, including main and sup processes, and categorization, which will be explained in the following sections. The findings of this study showed that documentation of activities can help expose implicit knowledge because all of inputs and outputs of a process along with the length, location, tools and different stages of the process, exchanged information, storage location of the information and information flow can be identified using proper

  17. Organic chemistry in the atmosphere. [laboratory modeling of Titan atmosphere

    Science.gov (United States)

    Sagan, C.

    1974-01-01

    The existence of an at least moderately complex organic chemistry on Titan is stipulated based on clear evidence of methane, and at least presumptive evidence of hydrogen in its atmosphere. The ratio of methane to hydrogen is the highest of any atmosphere in the solar system. Irradiation of hydrogen/methane mixtures produces aromatic and aliphatic hydrocarbons. A very reasonable hypothesis assumes that the red cloud cover of Titan is made of organic chemicals. Two-carbon hydrocarbons experimentally produced from irradiated mixtures of methane, ammonia, water, and hydrogen bear out the possible organic chemistry of the Titanian environment.

  18. Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution

    OpenAIRE

    Putman, Nathan F.; He, Ruoying

    2013-01-01

    Ocean circulation models are widely used to simulate organism transport in the open sea, where challenges of directly tracking organisms across vast spatial and temporal scales are daunting. Many recent studies tout the use of ‘high-resolution’ models, which are forced with atmospheric data on the scale of several hours and integrated with a time step of several minutes or seconds. However, in many cases, the model's outputs that are used to simulate organism movement have been averaged to co...

  19. A phase model of intergenerational learning in organizations

    NARCIS (Netherlands)

    Gerpott, F.H.; Lehmann-Willenbrock, N.; Voelpel, S.C.

    Demographic changes challenge organizations to qualify employees across all career stages and to ensure the transfer of company-specific knowledge between experienced and young workers. Human resource development programs for employees from different generations may help address these challenges.

  20. Public attitudes to financial incentive models for organs

    DEFF Research Database (Denmark)

    Hoeyer, Klaus; Schicktanz, Silke; Deleuran, Ida

    2013-01-01

    Waiting lists for organs have stimulated interest in the use of financial incentives for organ donation (FIs), but the literature does not contain an adequate overview of studies of public attitudes toward this mode of procurement. We conducted a literature review of international peer......-reviewed research published between 2002 and 2012 on how members of the public position themselves toward FIs. We identified and analyzed 23 studies using MEDLINE, PsycINFO, Sociological Abstracts and cross-reference search. The search included whole organs, donation, quantitative and empirical qualitative social...... scientific studies on, public attitudes (excluding professionals and medical students). The review reveals a broad divergence of public opinions on financial incentives. However, quantitative studies showed a low overall level of acceptance of payment for organs in living donation (LD); only a slightly...

  1. Modelling and mapping the topsoil organic carbon content for Tanzania

    Science.gov (United States)

    Kempen, Bas; Kaaya, Abel; Ngonyani Mhaiki, Consolatha; Kiluvia, Shani; Ruiperez-Gonzalez, Maria; Batjes, Niels; Dalsgaard, Soren

    2014-05-01

    Soil organic carbon (SOC), held in soil organic matter, is a key indicator of soil health and plays an important role in the global carbon cycle. The soil can act as a net source or sink of carbon depending on land use and management. Deforestation and forest degradation lead to the release of vast amounts of carbon from the soil in the form of greenhouse gasses, especially in tropical countries. Tanzania has a high deforestation rate: it is estimated that the country loses 1.1% of its total forested area annually. During 2010-2013 Tanzania has been a pilot country under the UN-REDD programme. This programme has supported Tanzania in its initial efforts towards reducing greenhouse gas emission from forest degradation and deforestation and towards preserving soil carbon stocks. Formulation and implementation of the national REDD strategy requires detailed information on the five carbon pools among these the SOC pool. The spatial distribution of SOC contents and stocks was not available for Tanzania. The initial aim of this research, was therefore to develop high-resolution maps of the SOC content for the country. The mapping exercise was carried out in a collaborative effort with four Tanzanian institutes and data from the Africa Soil Information Service initiative (AfSIS). The mapping exercise was provided with over 3200 field observations on SOC from four sources; this is the most comprehensive soil dataset collected in Tanzania so far. The main source of soil samples was the National Forest Monitoring and Assessment (NAFORMA). The carbon maps were generated by means of digital soil mapping using regression-kriging. Maps at 250 m spatial resolution were developed for four depth layers: 0-10 cm, 10-20 cm, 20-30 cm, and 0-30 cm. A total of 37 environmental GIS data layers were prepared for use as covariates in the regression model. These included vegetation indices, terrain parameters, surface temperature, spectral reflectances, a land cover map and a small

  2. A sustainable business model for public service organizations?

    OpenAIRE

    S.P. Osborne; Z. Radnor; I. Vidal; T. Kinder

    2014-01-01

    The current global economic recession presents significant challenges to public service organizations (PSOs) that deliver public services to local communities – irrespective of whether these organizations are situated in the public, private, or third sectors. Governments around the world have responded to this recession by a range of strategies intended to reduce public spending and generate growth. This is not the place to debate such strategies – this task has been undertaken...

  3. Modelling the fate of persistent organic pollutants in Europe: parameterisation of a gridded distribution model

    International Nuclear Information System (INIS)

    Prevedouros, Konstantinos; MacLeod, Matthew; Jones, Kevin C.; Sweetman, Andrew J.

    2004-01-01

    A regionally segmented multimedia fate model for the European continent is described together with an illustrative steady-state case study examining the fate of γ-HCH (lindane) based on 1998 emission data. The study builds on the regionally segmented BETR North America model structure and describes the regional segmentation and parameterisation for Europe. The European continent is described by a 5 deg. x 5 deg. grid, leading to 50 regions together with four perimetric boxes representing regions buffering the European environment. Each zone comprises seven compartments including; upper and lower atmosphere, soil, vegetation, fresh water and sediment and coastal water. Inter-regions flows of air and water are described, exploiting information originating from GIS databases and other georeferenced data. The model is primarily designed to describe the fate of Persistent Organic Pollutants (POPs) within the European environment by examining chemical partitioning and degradation in each region, and inter-region transport either under steady-state conditions or fully dynamically. A test case scenario is presented which examines the fate of estimated spatially resolved atmospheric emissions of lindane throughout Europe within the lower atmosphere and surface soil compartments. In accordance with the predominant wind direction in Europe, the model predicts high concentrations close to the major sources as well as towards Central and Northeast regions. Elevated soil concentrations in Scandinavian soils provide further evidence of the potential of increased scavenging by forests and subsequent accumulation by organic-rich terrestrial surfaces. Initial model predictions have revealed a factor of 5-10 underestimation of lindane concentrations in the atmosphere. This is explained by an underestimation of source strength and/or an underestimation of European background levels. The model presented can further be used to predict deposition fluxes and chemical inventories, and it

  4. Modeling the Structure and Effectiveness of Intelligence Organizations: Dynamic Information Flow Simulation

    National Research Council Canada - National Science Library

    Behrman, Robert; Carley, Kathleen

    2003-01-01

    This paper describes the Dynamic Information Flow Simulation (DIFS), an abstract model for analyzing the structure and function of intelligence support organizations and the activities of entities within...

  5. Strigolactones suppress adventitious rooting in Arabidopsis and pea.

    Science.gov (United States)

    Rasmussen, Amanda; Mason, Michael Glenn; De Cuyper, Carolien; Brewer, Philip B; Herold, Silvia; Agusti, Javier; Geelen, Danny; Greb, Thomas; Goormachtig, Sofie; Beeckman, Tom; Beveridge, Christine Anne

    2012-04-01

    Adventitious root formation is essential for the propagation of many commercially important plant species and involves the formation of roots from nonroot tissues such as stems or leaves. Here, we demonstrate that the plant hormone strigolactone suppresses adventitious root formation in Arabidopsis (Arabidopsis thaliana) and pea (Pisum sativum). Strigolactone-deficient and response mutants of both species have enhanced adventitious rooting. CYCLIN B1 expression, an early marker for the initiation of adventitious root primordia in Arabidopsis, is enhanced in more axillary growth2 (max2), a strigolactone response mutant, suggesting that strigolactones restrain the number of adventitious roots by inhibiting the very first formative divisions of the founder cells. Strigolactones and cytokinins appear to act independently to suppress adventitious rooting, as cytokinin mutants are strigolactone responsive and strigolactone mutants are cytokinin responsive. In contrast, the interaction between the strigolactone and auxin signaling pathways in regulating adventitious rooting appears to be more complex. Strigolactone can at least partially revert the stimulatory effect of auxin on adventitious rooting, and auxin can further increase the number of adventitious roots in max mutants. We present a model depicting the interaction of strigolactones, cytokinins, and auxin in regulating adventitious root formation.

  6. Role of methyl salicylate on oviposition deterrence in Arabidopsis thaliana.

    Science.gov (United States)

    Groux, Raphaël; Hilfiker, Olivier; Gouhier-Darimont, Caroline; Peñaflor, Maria Fernanda Gomes Villalba; Erb, Matthias; Reymond, Philippe

    2014-07-01

    Plants attacked by herbivores have evolved different strategies that fend off their enemies. Insect eggs deposited on leaves have been shown to inhibit further oviposition through visual or chemical cues. In some plant species, the volatile methyl salicylate (MeSA) repels gravid insects but whether it plays the same role in the model species Arabidopsis thaliana is currently unknown. Here we showed that Pieris brassicae butterflies laid fewer eggs on Arabidopsis plants that were next to a MeSA dispenser or on plants with constitutively high MeSA emission than on control plants. Surprisingly, the MeSA biosynthesis mutant bsmt1-1 treated with egg extract was still repellent to butterflies when compared to untreated bsmt1-1. Moreover, the expression of BSMT1 was not enhanced by egg extract treatment but was induced by herbivory. Altogether, these results provide evidence that the deterring activity of eggs on gravid butterflies is independent of MeSA emission in Arabidopsis, and that MeSA might rather serve as a deterrent in plants challenged by feeding larvae.

  7. Approaching the sequential and three-dimensional organization of Archaea, Bacteria and Eukarya genomes. Dynamic Organization of Nuclear Function

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Göker (Markus); R. Lohner (Rudolf); J. Langowski (Jörg)

    2002-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  8. Multi-element bioimaging of Arabidopsis thaliana roots

    DEFF Research Database (Denmark)

    Persson, Daniel Olof; Chen, Anle; Aarts, Mark G.M.

    2016-01-01

    Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventio......Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using...... omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images...... looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion...

  9. The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development.

    Science.gov (United States)

    Wang, Xiping; Feng, Suhua; Nakayama, Naomi; Crosby, W L; Irish, Vivian; Deng, Xing Wang; Wei, Ning

    2003-05-01

    The COP9 signalosome (CSN) is involved in multiple developmental processes. It interacts with SCF ubiquitin ligases and deconjugates Nedd8/Rub1 from cullins (deneddylation). CSN is highly expressed in Arabidopsis floral tissues. To investigate the role of CSN in flower development, we examined the expression pattern of CSN in developing flowers. We report here that two csn1 partially deficient Arabidopsis strains exhibit aberrant development of floral organs, decline of APETALA3 (AP3) expression, and low fertility in addition to defects in shoot and inflorescence meristems. We show that UNUSUAL FLORAL ORGANS (UFO) forms a SCF(UFO) complex, which is associated with CSN in vivo. Genetic interaction analysis indicates that CSN is necessary for the gain-of-function activity of the F-box protein UFO in AP3 activation and in floral organ transformation. Compared with the previously reported csn5 antisense and csn1 null mutants, partial deficiency of CSN1 causes a reduction in the level of CUL1 in the mutant flowers without an obvious defect in CUL1 deneddylation. We conclude that CSN is an essential regulator of Arabidopsis flower development and suggest that CSN regulates Arabidopsis flower development in part by modulating SCF(UFO)-mediated AP3 activation.

  10. Application of several activity coefficient models to water-organic-electrolyte aerosols of atmospheric interest

    Directory of Open Access Journals (Sweden)

    T. Raatikainen

    2005-01-01

    Full Text Available In this work, existing and modified activity coefficient models are examined in order to assess their capabilities to describe the properties of aqueous solution droplets relevant in the atmosphere. Five different water-organic-electrolyte activity coefficient models were first selected from the literature. Only one of these models included organics and electrolytes which are common in atmospheric aerosol particles. In the other models, organic species were solvents such as alcohols, and important atmospheric ions like NH4+ could be missing. The predictions of these models were compared to experimental activity and solubility data in aqueous single electrolyte solutions with 31 different electrolytes. Based on the deviations from experimental data and on the capabilities of the models, four predictive models were selected for fitting of new parameters for binary and ternary solutions of common atmospheric electrolytes and organics. New electrolytes (H+, NH4+, Na+, Cl-, NO3- and SO42- and organics (dicarboxylic and some hydroxy acids were added and some modifications were made to the models if it was found useful. All new and most of the existing parameters were fitted to experimental single electrolyte data as well as data for aqueous organics and aqueous organic-electrolyte solutions. Unfortunately, there are very few data available for organic activities in binary solutions and for organic and electrolyte activities in aqueous organic-electrolyte solutions. This reduces model capabilities in predicting solubilities. After the parameters were fitted, deviations from measurement data were calculated for all fitted models, and for different data types. These deviations and the calculated property values were compared with those from other non-electrolyte and organic-electrolyte models found in the literature. Finally, hygroscopic growth factors were calculated for four 100 nm organic-electrolyte particles and these predictions were compared to

  11. Table of 3D organ model IDs and organ names (PART-OF Tree) - BodyParts3D | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us BodyParts3D Table of 3D organ model IDs and organ names (PART-OF Tree) Data detail Data name Table of 3D org...an model IDs and organ names (PART-OF Tree) DOI 10.18908/lsdba.nbdc00837-002 Description of ...data contents List of downloadable 3D organ models in a tab-delimited text file format, describing the correspondence between 3D org...an model IDs and organ names available in PART-OF Tree. D...atabase Site Policy | Contact Us Table of 3D organ model IDs and organ names (PART-OF Tree) - BodyParts3D | LSDB Archive ...

  12. Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm.

    Science.gov (United States)

    Zhang, Yunhua; Dai, Li; Liu, Ying; Zhang, YuHang; Wang, ShaoPeng

    2017-01-01

    Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.

  13. Mechanically, the shoot apical meristem of Arabidopsis behaves like a shell inflated by a pressure of about 1 MPa

    Directory of Open Access Journals (Sweden)

    Léna eBeauzamy

    2015-11-01

    Full Text Available In plants, the shoot apical meristem contains the stem cells and is responsible for the generation of all aerial organs. Mechanistically, organogenesis is associated with an auxin-dependent local softening of the epidermis. This has been proposed to be sufficient to trigger outgrowth, because the epidermis is thought to be under tension and stiffer than internal tissues in all the aerial part of the plant. However, this has not been directly demonstrated in the shoot apical meristem. Here we tested this hypothesis in Arabidopsis using indentation methods and modeling. We considered two possible scenarios: either the epidermis does not have unique properties and the meristem behaves as a homogeneous linearly-elastic tissue, or the epidermis is under tension and the meristem exhibits the response of a shell under pressure. Large indentation depths measurements with a large tip (~size of the meristem were consistent with a shell-like behavior. This also allowed us to deduce a value of turgor pressure, estimated at 0.82 ± 0.16 MPa. Indentation with atomic force microscopy provided local measurements of pressure in the epidermis, further confirming the values obtained from large deformations. Altogether, our data demonstrate that the Arabidopsis shoot apical meristem behaves like a shell under a MPa range pressure and support a key role for the epidermis in shaping the shoot apex.

  14. Multi-scale modeling of spin transport in organic semiconductors

    Science.gov (United States)

    Hemmatiyan, Shayan; Souza, Amaury; Kordt, Pascal; McNellis, Erik; Andrienko, Denis; Sinova, Jairo

    In this work, we present our theoretical framework to simulate simultaneously spin and charge transport in amorphous organic semiconductors. By combining several techniques e.g. molecular dynamics, density functional theory and kinetic Monte Carlo, we are be able to study spin transport in the presence of anisotropy, thermal effects, magnetic and electric field effects in a realistic morphologies of amorphous organic systems. We apply our multi-scale approach to investigate the spin transport in amorphous Alq3 (Tris(8-hydroxyquinolinato)aluminum) and address the underlying spin relaxation mechanism in this system as a function of temperature, bias voltage, magnetic field and sample thickness.

  15. Isolation and characterization of a floral homeotic gene in Fraxinus nigra causing earlier flowering and homeotic alterations in transgenic Arabidopsis

    Science.gov (United States)

    Jun Hyung Lee; Paula M. Pijut

    2017-01-01

    Reproductive sterility, which can be obtained by manipulating floral organ identity genes, is an important tool for gene containment of genetically engineered trees. In Arabidopsis, AGAMOUS (AG) is the only C-class gene responsible for both floral meristem determinacy and floral organ identity, and its mutations produce...

  16. Similarity-based search of model organism, disease and drug effect phenotypes

    KAUST Repository

    Hoehndorf, Robert; Gruenberger, Michael; Gkoutos, Georgios V; Schofield, Paul N

    2015-01-01

    Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions

  17. Reference: 21 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ication of a number of mutant lines with altered Chl fluorescence characteristics. Analysis of photosynthesis...cation of mutants of Arabidopsis defective in acclimation of photosynthesis to th

  18. Reference: 789 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ylakoid membranes. Microarray analysis of the chl27-t mutant showed repression of numerous nuclear genes involved in photosynthesis...d CHL27 proteins. Role of Arabidopsis CHL27 protein for photosynthesis, chloroplast development and gene exp

  19. Reference: 306 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understa...nd how DNA is endoreduplicated and how this process is r

  20. Reference: 150 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ridization, Pht1;4 was found mainly expressed in inorgan...physiological characterization of Arabidopsis pht1;4 high affinity phosphate transporter mutants. Using GUS-gene trap and in situ hyb

  1. Arabidopsis CDS blastp result: AK099152 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK099152 J023070H02 At4g01900.1 P II nitrogen sensing protein (GLB I) identical to P II nitrogen... sensing protein GLB I (GI:7268574) [Arabidopsis thaliana]; similar to nitrogen regulatory prot

  2. Arabidopsis CDS blastp result: AK068407 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK068407 J013149B08 At4g01900.1 P II nitrogen sensing protein (GLB I) identical to P II nitrogen... sensing protein GLB I (GI:7268574) [Arabidopsis thaliana]; similar to nitrogen regulatory prot

  3. Arabidopsis CDS blastp result: AK241043 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 2e-41 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  4. Arabidopsis CDS blastp result: AK243135 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 7e-43 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  5. Reference: 346 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available th a function in purine turnover in Arabidopsis. To our knowledge this is the fir...ock in allantoate catabolism. AtAAH transcript was detected in all tissues examined by RT-PCR, consistent wi

  6. Reference: 510 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available in support of PSII activity, whereas the interaction of PsbO2 with PSII regulates the turnover... its degradation. The Arabidopsis PsbO2 protein regulates dephosphorylation and turnover of the photosystem

  7. Reference: 278 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available functional ERA1 gene, which encodes the beta-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects...gnaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsi

  8. Arabidopsis CDS blastp result: AK287673 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287673 J065121E18 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-17 ...

  9. Arabidopsis CDS blastp result: AK241272 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241272 J065132I19 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  10. Arabidopsis CDS blastp result: AK241712 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241712 J065197H24 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-27 ...

  11. Arabidopsis CDS blastp result: AK106306 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK106306 002-101-C10 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 3e-89 ...

  12. Arabidopsis CDS blastp result: AK287726 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287726 J065138E17 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  13. Arabidopsis CDS blastp result: AK109848 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK109848 002-148-F05 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-73 ...

  14. Arabidopsis CDS blastp result: AK242387 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242387 J080051E14 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 2e-45 ...

  15. Arabidopsis CDS blastp result: AK240892 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240892 J065030K10 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-88 ...

  16. Arabidopsis CDS blastp result: AK242957 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242957 J090089I15 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-28 ...

  17. Arabidopsis CDS blastp result: AK287621 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287621 J065066I09 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-85 ...

  18. Reference: 627 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available omal processing protease (GPP) from the fat-storing cotyledons of watermelon (Citrullus vulgaris) by column ...ptidase, and a Lon-protease. Specific antibodies against the peroxisomal Deg-protease from Arabidopsis (Deg15) identify the watermelo

  19. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  20. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  1. Arabidopsis CDS blastp result: AK110467 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110467 002-166-G08 At3g03050.1 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-7 (gi:962

  2. Arabidopsis CDS blastp result: AK066835 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066835 J013087I16 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-171 ...

  3. Arabidopsis CDS blastp result: AK102695 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102695 J033103F21 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  4. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At3g03050.1 68416.m00301 cellulose synthase family protein (CslD3) similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose syntha

  5. Arabidopsis CDS blastp result: AK100523 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK100523 J023100P04 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  6. Arabidopsis CDS blastp result: AK065259 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK065259 J013002J18 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  7. Arabidopsis CDS blastp result: AK102134 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102134 J033085F12 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  8. The fifth international conference on Arabidopsis research

    Energy Technology Data Exchange (ETDEWEB)

    Hangarter, R.; Scholl, R.; Davis, K.; Feldmann, K.

    1993-12-31

    This volume contains abstracts of oral and poster presentations made in conjunction with the Fifth International Conference on Arabidopsis Research held August 19--22, 1993 at the Ohio State University, Columbus, Ohio.

  9. Models of Purposive Human Organization: A Comparative Study

    Science.gov (United States)

    1984-02-01

    develop techniques for organizational diagnosis with the D-M model, to be followed by intervention by S-T methodology. 2. Introduction 2.1. Background In...relational and object data for Dinnat-Murphree model construction. 2. Develop techniques for organizational diagnosis with the Dinnat-Murphree model

  10. The Learning Organization: A Model for Educational Change.

    Science.gov (United States)

    Brown, Rexford

    1997-01-01

    Analyzes public school bureaucracy and ways to reform institutions into learning communities that value shared knowledge and learning experiences. Describes how a bureaucratic organizational structure impairs learning. Proposes the "learning organization" in which adults learn alongside students, planning is decentralized, families are…

  11. Mitochondrial damage and ageing using skin as a model organ.

    Science.gov (United States)

    Hudson, Laura; Bowman, Amy; Rashdan, Eyman; Birch-Machin, Mark A

    2016-11-01

    Ageing describes the progressive functional decline of an organism over time, leading to an increase in susceptibility to age-related diseases and eventually to death, and it is a phenomenon observed across a wide range of organisms. Despite a vast repertoire of ageing studies performed over the past century, the exact causes of ageing remain unknown. For over 50 years it has been speculated that mitochondria play a key role in the ageing process, due mainly to correlative data showing an increase in mitochondrial dysfunction, mitochondrial DNA (mtDNA) damage, and reactive oxygen species (ROS) with age. However, the exact role of the mitochondria in the ageing process remains unknown. The skin is often used to study human ageing, due to its easy accessibility, and the observation that the ageing process is able to be accelerated in this organ via environmental insults, such as ultra violet radiation (UVR). This provides a useful tool to investigate the mechanisms regulating ageing and, in particular, the role of the mitochondria. Observations from dermatological and photoageing studies can provide useful insights into chronological ageing of the skin and other organs such as the brain and liver. Moreover, a wide range of diseases are associated with ageing; therefore, understanding the cause of the ageing process as well as regulatory mechanisms involved could provide potentially advantageous therapeutic targets for the prevention or treatment of such diseases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  12. Lifetimes of organic photovoltaics: photooxidative degradation of a model compound

    DEFF Research Database (Denmark)

    Norrman, K.; Alstrup, J.; Jørgensen, M.

    2006-01-01

    A poly phenylene vinylene (PPV-type) oligomer used in organic photovoltaics was designed to facilitate the interpretation of mass spectral data. A film of the oligomer was subjected to various degrees of illumination (1000 W m(-2), AM1.5) in air resulting in photooxidation of the material...

  13. Modelling conventional and organic farming : a literature review

    NARCIS (Netherlands)

    Acs, S.; Berentsen, P.B.M.; Huirne, R.B.M.

    2005-01-01

    Literature shows a significant development of organic farming in Europe but with considerable differences between countries. These depend on general agricultural policy (the set of regulations and laws), specific policy incentives, and also on differences in consumer behaviour. This paper reviews

  14. Mechanistic modelling of the vertical soil organic matter profile

    NARCIS (Netherlands)

    Braakhekke, M.C.

    2014-01-01

    Soil organic matter (SOM) constitutes a large global pool of carbon that may play a considerable role for future climate. The vertical distribution of SOM in the profile may be important due to depth-dependence of physical, chemical, and biological conditions, and links to physical processes

  15. Modeling organic aerosol concentrations and properties during winter 2014 in the northwestern Mediterranean region

    OpenAIRE

    Chrit, Mounir; Sartelet, Karine; Sciare, Jean; Majdi, Marwa; Nicolas, José; Petit, Jean-Eudes; Dulac, François

    2018-01-01

    Organic aerosols are measured at a remote site (Ersa) on Corsica Cape in the northwestern Mediterranean basin during the Chemistry-Aerosol Mediterranean Experiment (CharMEx) winter campaign of 2014, when high organic concentrations from anthropogenic origin are observed. This work aims at representing the observed organic aerosol concentrations and properties (oxidation state) using the air-quality model Polyphemus with a surrogate approach for secondary organic aerosol (SOA) formation. Becau...

  16. Modelling the Impact of Organization Structure and Whistle Blowers on Intra-Organizational Corruption Contagion

    OpenAIRE

    Nekovee, Maziar; Pinto, Jonathan

    2017-01-01

    We complement the rich conceptual work on organizational corruption by quantitatively modelling the spread of corruption within organizations. We systematically vary four organizational culture-related parameters, i.e., organization structure, location of bad apple, employees propensity to become corrupted (corruption probability), and number of whistle-blowers. Our simulation studies find that in organizations with flatter structures, corruption permeates the organization at a lower threshol...

  17. Plausible carrier transport model in organic-inorganic hybrid perovskite resistive memory devices

    Science.gov (United States)

    Park, Nayoung; Kwon, Yongwoo; Choi, Jaeho; Jang, Ho Won; Cha, Pil-Ryung

    2018-04-01

    We demonstrate thermally assisted hopping (TAH) as an appropriate carrier transport model for CH3NH3PbI3 resistive memories. Organic semiconductors, including organic-inorganic hybrid perovskites, have been previously speculated to follow the space-charge-limited conduction (SCLC) model. However, the SCLC model cannot reproduce the temperature dependence of experimental current-voltage curves. Instead, the TAH model with temperature-dependent trap densities and a constant trap level are demonstrated to well reproduce the experimental results.

  18. Model to the evolution of the organic matter in the pampa's soil. Relation with cultivation systems

    International Nuclear Information System (INIS)

    Andriulo, Adrian; Mary, Bruno; Guerif, Jerome; Balesdent, Jerome

    1996-08-01

    The objective of the work is to present a model to describe the evolution of the organic matter in soils of the Argentine's pampa. This model can be utilised to evaluate the evolution of the soil's fertility in the agricultural production at this moment. Three kinds of assay were done. The determination of organic carbon made possible to prove the Henin-Dupuis model and a derived model

  19. Reference: 398 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available modulate the photosynthetic potential of plant cells. Identification of genes required for light-induced chloroplast movement... is beginning to define the molecular machinery that controls these movement...s. In this work, we describe plastid movement impaired 2 (pmi2), a mutant in Arabidopsis (Arabi...dopsis thaliana) that displays attenuated chloroplast movements under intermediate and high light intensitie...s while maintaining a normal movement response under low light intensities. In wi

  20. Reference: 170 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available rice A et al. 2005 Mar. Plant Cell 17(3):791-803. Environmental time cues, such as photocycles (light/dark) and thermocycles...h is known about entrainment of the Arabidopsis thaliana clock to photocycles, th...e determinants of thermoperception and entrainment to thermocycles are not known. The Arabidopsis PSEUDO-RES... an oscillation after entrainment to thermocycles and to reset its clock in response to cold pulses and thus

  1. Maize and Arabidopsis ARGOS Proteins Interact with Ethylene Receptor Signaling Complex, Supporting a Regulatory Role for ARGOS in Ethylene Signal Transduction[OPEN

    Science.gov (United States)

    Shi, Jinrui; Wang, Hongyu; Habben, Jeffrey E.

    2016-01-01

    The phytohormone ethylene regulates plant growth and development as well as plant response to environmental cues. ARGOS genes reduce plant sensitivity to ethylene when overexpressed in transgenic Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). A previous genetic study suggested that the endoplasmic reticulum and Golgi-localized maize ARGOS1 targets the ethylene signal transduction components at or upstream of CONSTITUTIVE TRIPLE RESPONSE1, but the mechanism of ARGOS modulating ethylene signaling is unknown. Here, we demonstrate in Arabidopsis that ZmARGOS1, as well as the Arabidopsis ARGOS homolog ORGAN SIZE RELATED1, physically interacts with Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1), an ethylene receptor interacting protein that regulates the activity of ETHYLENE RESPONSE1. The protein-protein interaction was also detected with the yeast split-ubiquitin two-hybrid system. Using the same yeast assay, we found that maize RTE1 homolog REVERSION-TO-ETHYLENE SENSITIVITY1 LIKE4 (ZmRTL4) and ZmRTL2 also interact with maize and Arabidopsis ARGOS proteins. Like AtRTE1 in Arabidopsis, ZmRTL4 and ZmRTL2 reduce ethylene responses when overexpressed in maize, indicating a similar mechanism for ARGOS regulating ethylene signaling in maize. A polypeptide fragment derived from ZmARGOS8, consisting of a Pro-rich motif flanked by two transmembrane helices that are conserved among members of the ARGOS family, can interact with AtRTE1 and maize RTL proteins in Arabidopsis. The conserved domain is necessary and sufficient to reduce ethylene sensitivity in Arabidopsis and maize. Overall, these results suggest a physical association between ARGOS and the ethylene receptor signaling complex via AtRTE1 and maize RTL proteins, supporting a role for ARGOS in regulating ethylene perception and the early steps of signal transduction in Arabidopsis and maize. PMID:27268962

  2. From Learning Object to Learning Cell: A Resource Organization Model for Ubiquitous Learning

    Science.gov (United States)

    Yu, Shengquan; Yang, Xianmin; Cheng, Gang; Wang, Minjuan

    2015-01-01

    This paper presents a new model for organizing learning resources: Learning Cell. This model is open, evolving, cohesive, social, and context-aware. By introducing a time dimension into the organization of learning resources, Learning Cell supports the dynamic evolution of learning resources while they are being used. In addition, by introducing a…

  3. Peningkatan Keterampilan Pengambilan Keputusan Dan Penguasaan Konsep IPA Melalui Model Pembelajaran Advance Organizer Di Sekolah Dasar

    OpenAIRE

    Badarudin

    2017-01-01

    Peningkatan Keterampilan Pengambilan Keputusan dan Penguasaan Konsep IPA melalui Model Pembelajaran Advance Organizer di Sekolah Dasar. Penelitian ini bertujuan untuk mengetahui perbedaan peningkatan keterampilan pengambilan keputusan dan pemahaman konsep IPA siswa sebagai dampak dari implementasi model Advance Organizer. Penelitian ini menggunakan metode kuasi eksperimen dengan desain Non equivalent (Pre-Test and Post- Test) Control Groups Design. Subyek penelitian adalah siswa kelas V pada ...

  4. Modeling the Current and Future Roles of Particulate Organic Nitrates in the Southeastern United States.

    Science.gov (United States)

    Pye, Havala O T; Luecken, Deborah J; Xu, Lu; Boyd, Christopher M; Ng, Nga L; Baker, Kirk R; Ayres, Benjamin R; Bash, Jesse O; Baumann, Karsten; Carter, William P L; Edgerton, Eric; Fry, Juliane L; Hutzell, William T; Schwede, Donna B; Shepson, Paul B

    2015-12-15

    Organic nitrates are an important aerosol constituent in locations where biogenic hydrocarbon emissions mix with anthropogenic NOx sources. While regional and global chemical transport models may include a representation of organic aerosol from monoterpene reactions with nitrate radicals (the primary source of particle-phase organic nitrates in the Southeast United States), secondary organic aerosol (SOA) models can underestimate yields. Furthermore, SOA parametrizations do not explicitly take into account organic nitrate compounds produced in the gas phase. In this work, we developed a coupled gas and aerosol system to describe the formation and subsequent aerosol-phase partitioning of organic nitrates from isoprene and monoterpenes with a focus on the Southeast United States. The concentrations of organic aerosol and gas-phase organic nitrates were improved when particulate organic nitrates were assumed to undergo rapid (τ = 3 h) pseudohydrolysis resulting in nitric acid and nonvolatile secondary organic aerosol. In addition, up to 60% of less oxidized-oxygenated organic aerosol (LO-OOA) could be accounted for via organic nitrate mediated chemistry during the Southern Oxidants and Aerosol Study (SOAS). A 25% reduction in nitrogen oxide (NO + NO2) emissions was predicted to cause a 9% reduction in organic aerosol for June 2013 SOAS conditions at Centreville, Alabama.

  5. Democracy versus dictatorship in self-organized models of financial markets

    Science.gov (United States)

    D'Hulst, R.; Rodgers, G. J.

    2000-06-01

    Models to mimic the transmission of information in financial markets are introduced. As an attempt to generate the demand process, we distinguish between dictatorship associations, where groups of agents rely on one of them to make decision, and democratic associations, where each agent takes part in the group decision. In the dictatorship model, agents segregate into two distinct populations, while the democratic model is driven towards a critical state where groups of agents of all sizes exist. Hence, both models display a level of organization, but only the democratic model is self-organized. We show that the dictatorship model generates less-volatile markets than the democratic model.

  6. Neotropical electric fishes (Gymnotiformes as model organisms for bioassays

    Directory of Open Access Journals (Sweden)

    Milena Ferreira

    2015-04-01

    Full Text Available Electric fishes (Gymnotiformes inhabit Central and South America and form a relatively large group with more than 200 species. Besides a taxonomic challenge due to their still unresolved systematic, wide distribution and the variety of habitats they occupy, these fishes have been intensively studied due to their peculiar use of bioelectricity for electrolocation and communication. Conventional analysis of cells, tissues and organs have been complemented with the studies on the electric organ discharges of these fishes. This review compiles the results of 13 bioassays developed during the last 50 years, which used the quickness, low costs and functionality of the bioelectric data collection of Gymnotiformes to evaluate the effects of environmental contaminants and neuroactive drugs.

  7. Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery

    Directory of Open Access Journals (Sweden)

    Baldwin Samantha

    2011-02-01

    Full Text Available Abstract Background Arabidopsis thaliana is a useful model organism for deciphering the genetic determinants of seed size; however the small size of its seeds makes measurements difficult. Bulk seed weights are often used as an indicator of average seed size, but details of individual seed is obscured. Analysis of seed images is possible but issues arise from variations in seed pigmentation and shadowing making analysis laborious. We therefore investigated the use of a consumer level scanner to facilitate seed size measurements in conjunction with open source image-processing software. Results By using the transmitted light from the slide scanning function of a flatbed scanner and particle analysis of the resulting images, we have developed a method for the rapid and high throughput analysis of seed size and seed size distribution. The technical variation due to the approach was negligible enabling us to identify aspects of maternal plant growth that contribute to biological variation in seed size. By controlling for these factors, differences in seed size caused by altered parental genome dosage and mutation were easily detected. The method has high reproducibility and sensitivity, such that a mutant with a 10% reduction in seed size was identified in a screen of endosperm-expressed genes. Our study also generated average seed size data for 91 Arabidopsis accessions and identified a number of quantitative trait loci from two recombinant inbred line populations, generated from Cape Verde Islands and Burren accessions crossed with Columbia. Conclusions This study describes a sensitive, high-throughput approach for measuring seed size and seed size distribution. The method provides a low cost and robust solution that can be easily implemented into the workflow of studies relating to various aspects of seed development.

  8. Organisms modeling: The question of radial basis function networks

    Directory of Open Access Journals (Sweden)

    Muzy Alexandre

    2014-01-01

    Full Text Available There exists usually a gap between bio-inspired computational techniques and what biologists can do with these techniques in their current researches. Although biology is the root of system-theory and artifical neural networks, computer scientists are tempted to build their own systems independently of biological issues. This publication is a first-step re-evalution of an usual machine learning technique (radial basis funtion(RBF networks in the context of systems and biological reactive organisms.

  9. A double moral hazard model of organization design

    OpenAIRE

    Berkovitch, Elazar; Israel, Ronen; Spiegel, Yossi

    2007-01-01

    We develop a theory of organization design in which the firm's structure is chosen to mitigate moral hazard problems in the selection and the implementation of projects. For a given set of projects, the 'divisional structure' which gives each agent the full responsibility over a subset of projects is in general more efficient than the functional structure under which projects are implemented by teams of agents, each of whom specializes in one task. However, the ex post efficiency of the divis...

  10. Arabidopsis NATA1 Acetylates Putrescine and Decreases Defense-Related Hydrogen Peroxide Accumulation1[OPEN

    Science.gov (United States)

    Preuss, Aileen S.

    2016-01-01

    Biosynthesis of the polyamines putrescine, spermidine, and spermine is induced in response to pathogen infection of plants. Putrescine, which is produced from Arg, serves as a metabolic precursor for longer polyamines, including spermidine and spermine. Polyamine acetylation, which has important regulatory functions in mammalian cells, has been observed in several plant species. Here we show that Arabidopsis (Arabidopsis thaliana) N-ACETYLTRANSFERASE ACTIVITY1 (NATA1) catalyzes acetylation of putrescine to N-acetylputrescine and thereby competes with spermidine synthase for a common substrate. NATA1 expression is strongly induced by the plant defense signaling molecule jasmonic acid and coronatine, an effector molecule produced by DC3000, a Pseudomonas syringae strain that initiates a virulent infection in Arabidopsis ecotype Columbia-0. DC3000 growth is reduced in nata1 mutant Arabidopsis, suggesting a role for NATA1-mediated putrescine acetylation in suppressing antimicrobial defenses. During infection by P. syringae and other plant pathogens, polyamine oxidases use spermidine and spermine as substrates for the production of defense-related H2O2. Compared to wild-type Columbia-0 Arabidopsis, the response of nata1mutants to P. syringae infection includes reduced accumulation of acetylputrescine, greater abundance of nonacetylated polyamines, elevated H2O2 production by polyamine oxidases, and higher expression of genes related to pathogen defense. Together, these results are consistent with a model whereby P. syringae growth is improved in a targeted manner through coronatine-induced putrescine acetylation by NATA1. PMID:27208290

  11. Models for governing relationships in healthcare organizations: Some empirical evidence.

    Science.gov (United States)

    Romiti, Anna; Del Vecchio, Mario; Grazzini, Maddalena

    2018-01-01

    Recently, most European countries have undergone integration processes through mergers and strategic alliances between healthcare organizations. The present paper examined three cases within the Italian National Health Service in order to determine how different organizations, within differing institutional contexts, govern an healthcare integration process. Furthermore, we explored the possibility that the governance mode, usually seen as alternatives (i.e., merger or alliance), could be considered as a separate step in the development of a more suitable integration process. Multiple case studies were used to compare different integration approaches. Specifically, three cases were considered, of which two were characterized by collaborative processes and the other by a merger. Semi-structured interviews were conducted with managers involved in the processes. Each case presents different governing modes, structures, and mechanisms for achieving integration. The role played by the institutional context also led to different results with unique advantages and disadvantages. Three main conclusions are discussed: (a) Alliances and mergers can be interpreted as different steps in a path leading to a better integration; (b) The alignment between institutional/political time horizon and the time needed for the organizations to achieve an integration process lead to a better integration; (c) Trust plays an important role in integration process operating at different levels that of institutional and organizational level and that built between people.

  12. The pattern of polymorphism in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    2005-07-01

    Full Text Available We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

  13. Dynamic root uptake model for neutral lipophilic organics

    DEFF Research Database (Denmark)

    Trapp, Stefan

    2002-01-01

    and output to stem with the transpiration stream plus first-order metabolism and dilution by exponential growth. For chemicals with low or intermediate lipophilicity (log Kow , 2), there was no relevant difference between dynamic model and equilibrium approach. For lipophilic compounds, the dynamic model...

  14. Modeling cadmium in the feed chain and cattle organs

    NARCIS (Netherlands)

    Fels-Klerx, van der H.J.; Romkens, P.F.A.M.; Franz, E.; Raamsdonk, van L.W.D.

    2011-01-01

    The objectives of this study were to estimate cadmium contamination levels in different scenarios related to soil characteristics and assumptions regarding cadmium accumulation in the animal tissues, using quantitative supply chain modeling. The model takes into account soil cadmium levels, soil pH,

  15. Computational Modeling of Cultural Dimensions in Adversary Organizations

    Science.gov (United States)

    2010-01-01

    theatre of operations. 50 51 Chapter 5 Adversary Modeling Applications 5.1 Modeling Uncertainty in Adversary Behavior: Attacks in...Underestimate the Strength of Coalition Power 1 1 (= True) 1 1 1 -- Coalition Deploys Forces to Indonesia 1 1 2 1 2 -- Thai can Conduct Unilateral NEO 1 1

  16. Sulfinylated Azadecalins act as functional mimics of a pollen germination stimulant in Arabidopsis pistils

    Science.gov (United States)

    Qin, Yuan; Wysocki, Ronald J; Somogyi, Arpad; Feinstein, Yelena; Franco, Jessica Y; Tsukamoto, Tatsuya; Dunatunga, Damayanthi; Levy, Clara; Smith, Steven; Simpson, Robert; Gang, David; Johnson, Mark A; Palanivelu, Ravishankar

    2011-01-01

    SUMMARY Polarized cell elongation is triggered by small molecule cues during development of diverse organisms. During plant reproduction, pollen interactions with the stigma result in the polar outgrowth of a pollen tube, which delivers sperm cells to the female gametophyte to effect double fertilization. In many plants, pistils stimulate pollen germination. However, in Arabidopsis, the effect of pistils on pollen germination and the pistil factors that stimulate pollen germination remain poorly characterized. Here, we demonstrate that stigma, style, and ovules in Arabidopsis pistils stimulate pollen germination. We isolated an Arabidopsis pistil extract fraction that stimulates Arabidopsis pollen germination, and employed ultrahigh resolution ESI FT-ICR and MS/MS techniques to accurately determine the mass (202.126 daltons) of a compound that is specifically present in this pistil extract fraction. Using the molecular formula (C10H19NOS) and tandem mass spectral fragmentation patterns of the m/z (mass to charge ratio) 202.126 ion, we postulated chemical structures, devised protocols, synthesized N-Methanesulfinyl 1- and 2-azadecalins that are close structural mimics of the m/z 202.126 ion, and showed that they are sufficient to stimulate Arabidopsis pollen germination in vitro (30 µM stimulated ~50% germination) and elicit accession-specific response. Although N-Methanesulfinyl 2-azadecalin stimulated pollen germination in three species of Lineage I of Brassicaceae, it did not induce a germination response in Sisymbrium irio (Lineage II of Brassicaceae) and tobacco, indicating that activity of the compound is not random. Our results show that Arabidopsis pistils promote germination by producing azadecalin-like molecules to ensure rapid fertilization by the appropriate pollen. PMID:21801250

  17. Ames Culture Chamber System: Enabling Model Organism Research Aboard the international Space Station

    Science.gov (United States)

    Steele, Marianne

    2014-01-01

    Understanding the genetic, physiological, and behavioral effects of spaceflight on living organisms and elucidating the molecular mechanisms that underlie these effects are high priorities for NASA. Certain organisms, known as model organisms, are widely studied to help researchers better understand how all biological systems function. Small model organisms such as nem-atodes, slime mold, bacteria, green algae, yeast, and moss can be used to study the effects of micro- and reduced gravity at both the cellular and systems level over multiple generations. Many model organisms have sequenced genomes and published data sets on their transcriptomes and proteomes that enable scientific investigations of the molecular mechanisms underlying the adaptations of these organisms to space flight.

  18. Arabidopsis seedling flood-inoculation technique: a rapid and reliable assay for studying plant-bacterial interactions

    Directory of Open Access Journals (Sweden)

    Uppalapati Srinivasa R

    2011-10-01

    Full Text Available Abstract Background The Arabidopsis thaliana-Pseudomonas syringae model pathosystem is one of the most widely used systems to understand the mechanisms of microbial pathogenesis and plant innate immunity. Several inoculation methods have been used to study plant-pathogen interactions in this model system. However, none of the methods reported to date are similar to those occurring in nature and amicable to large-scale mutant screens. Results In this study, we developed a rapid and reliable seedling flood-inoculation method based on young Arabidopsis seedlings grown on MS medium. This method has several advantages over conventional soil-grown plant inoculation assays, including a shorter growth and incubation period, ease of inoculation and handling, uniform infection and disease development, requires less growth chamber space and is suitable for high-throughput screens. In this study we demonstrated the efficacy of the Arabidopsis seedling assay to study 1 the virulence factors of P. syringae pv. tomato DC3000, including type III protein secretion system (TTSS and phytotoxin coronatine (COR; 2 the effector-triggered immunity; and 3 Arabidopsis mutants affected in salicylic acid (SA- and pathogen-associated molecular pattern (PAMPs-mediated pathways. Furthermore, we applied this technique to study nonhost resistance (NHR responses in Arabidopsis using nonhost pathogens, such as P. syringae pv. tabaci, pv. glycinea and pv. tomato T1, and confirmed the functional role of FLAGELLIN-SENSING 2 (FLS2 in NHR. Conclusions The Arabidopsis seedling flood-inoculation assay provides a rapid, efficient and economical method for studying Arabidopsis-Pseudomonas interactions with minimal growth chamber space and time. This assay could also provide an excellent system for investigating the virulence mechanisms of P. syringae. Using this method, we demonstrated that FLS2 plays a critical role in conferring NHR against nonhost pathovars of P. syringae, but not to

  19. Modeling the surface tension of complex, reactive organic-inorganic mixtures

    Science.gov (United States)

    Schwier, A. N.; Viglione, G. A.; Li, Z.; McNeill, V. Faye

    2013-11-01

    Atmospheric aerosols can contain thousands of organic compounds which impact aerosol surface tension, affecting aerosol properties such as heterogeneous reactivity, ice nucleation, and cloud droplet formation. We present new experimental data for the surface tension of complex, reactive organic-inorganic aqueous mixtures mimicking tropospheric aerosols. Each solution contained 2-6 organic compounds, including methylglyoxal, glyoxal, formaldehyde, acetaldehyde, oxalic acid, succinic acid, leucine, alanine, glycine, and serine, with and without ammonium sulfate. We test two semi-empirical surface tension models and find that most reactive, complex, aqueous organic mixtures which do not contain salt are well described by a weighted Szyszkowski-Langmuir (S-L) model which was first presented by Henning et al. (2005). Two approaches for modeling the effects of salt were tested: (1) the Tuckermann approach (an extension of the Henning model with an additional explicit salt term), and (2) a new implicit method proposed here which employs experimental surface tension data obtained for each organic species in the presence of salt used with the Henning model. We recommend the use of method (2) for surface tension modeling of aerosol systems because the Henning model (using data obtained from organic-inorganic systems) and Tuckermann approach provide similar modeling results and goodness-of-fit (χ2) values, yet the Henning model is a simpler and more physical approach to modeling the effects of salt, requiring less empirically determined parameters.

  20. Modeling equilibrium adsorption of organic micropollutants onto activated carbon

    KAUST Repository

    De Ridder, David J.; Villacorte, Loreen O.; Verliefde, Arne R. D.; Verberk, Jasper Q J C; Heijman, Bas G J; Amy, Gary L.; Van Dijk, Johannis C.

    2010-01-01

    to these properties occur in parallel, and their respective dominance depends on the solute properties as well as carbon characteristics. In this paper, a model based on multivariate linear regression is described that was developed to predict equilibrium carbon

  1. Fruit tree model for uptake of organic compounds from soil

    DEFF Research Database (Denmark)

    Trapp, Stefan; Rasmussen, D.; Samsoe-Petersen, L.

    2003-01-01

    -state, and an example calculation is given. The Fruit Tree Model is compared to the empirical equation of Travis and Arms (T&A), and to results from fruits, collected in contaminated areas. For polar compounds, both T&A and the Fruit Tree Model predict bioconcentration factors fruit to soil (BCF, wet weight based......) of > 1. No empirical data are available to support this prediction. For very lipophilic compounds (log K-OW > 5), T&A overestimates the uptake. The conclusion from the Fruit Tree Model is that the transfer of lipophilic compounds into fruits is not relevant. This was also found by an empirical study...... with PCDD/F. According to the Fruit Tree Model, polar chemicals are transferred efficiently into fruits, but empirical data to verify these predictions are lacking....

  2. Integrated corporate structure life cycle management modeling and organization

    OpenAIRE

    Naumenko, M.; Morozova, L.

    2011-01-01

    Integrated business structure presented as complementary pool of its participants skills. The methodical approach to integrated business structure life cycle modeling proposed. Recommendations of enterprises life cycles stages correlate are submitted.

  3. A QUADTREE ORGANIZATION CONSTRUCTION AND SCHEDULING METHOD FOR URBAN 3D MODEL BASED ON WEIGHT

    OpenAIRE

    C. Yao; G. Peng; Y. Song; M. Duan

    2017-01-01

    The increasement of Urban 3D model precision and data quantity puts forward higher requirements for real-time rendering of digital city model. Improving the organization, management and scheduling of 3D model data in 3D digital city can improve the rendering effect and efficiency. This paper takes the complexity of urban models into account, proposes a Quadtree construction and scheduling rendering method for Urban 3D model based on weight. Divide Urban 3D model into different rendering weigh...

  4. Integrating centralized and decentralized organization structures: an education and development model.

    Science.gov (United States)

    Sheriff, R; Banks, A

    2001-01-01

    Organization change efforts have led to critically examining the structure of education and development departments within hospitals. This qualitative study evaluated an education and development model in an academic health sciences center. The model combines centralization and decentralization. The study results can be used by staff development educators and administrators when organization structure is questioned. This particular model maximizes the benefits and minimizes the limitations of centralized and decentralized structures.

  5. Modeling of iodine radiation chemistry in the presence of organic compounds

    International Nuclear Information System (INIS)

    Taghipour, Fariborz; Evans, Greg J.

    2002-01-01

    A kinetic-based model was developed that simulates the radiation chemistry of iodine in the presence of organic compounds. The model's mechanistic description of iodine chemistry and generic semi-mechanistic reactions for various classes of organics, provided a reasonable representation of experimental results. The majority of the model and experimental results of iodine volatilization rates were in agreement within an order of magnitude

  6. Modeling the acid-base chemistry of organic solutes in Adirondack, New York, lakes

    Science.gov (United States)

    Driscoll, Charles T.; Lehtinen, Michael D.; Sullivan, Timothy J.

    1994-02-01

    Data from the large and diverse Adirondack Lake Survey were used to calibrate four simple organic acid analog models in an effort to quantify the influence of naturally occurring organic acids on lake water pH and acid-neutralizing capacity (ANC). The organic acid analog models were calibrated to observations of pH, dissolved organic carbon (DOC), and organic anion (An-) concentrations from a reduced data set representing 1128 individual lake samples, expressed as 41 observations of mean pH, in intervals of 0.1 pH units from pH 3.9 to 7.0. Of the four organic analog approaches examined, including the Oliver et al. (1983) model, as well as monoprotic, diprotic, and triprotic representations, the triprotic analog model yielded the best fit (r2 = 0.92) to the observed data. Moreover, the triprotic model was qualitatively consistent with observed patterns of change in organic solute charge density as a function of pH. A low calibrated value for the first H+ dissociation constant (pKal = 2.62) and the observation that organic anion concentrations were significant even at very low pH (acidic functional groups. Inclusion of organic acidity in model calculations resulted in good agreement between measured and predicted values of lake water pH and ANC. Assessments to project the response of surface waters to future changes in atmospheric deposition, through the use of acidification models, will need to include representations of organic acids in model structure to make accurate predictions of pH and ANC.

  7. Two models for absorption by coloured dissolved organic matter (CDOM

    Directory of Open Access Journals (Sweden)

    Jill N. Schwarz

    2002-06-01

    Full Text Available The standard exponential model for CDOM absorption has been applied to data from diverse waters. Absorption at 440 nm (ag440 ranged between close to zero and 10 m-1, and the slope of the semilogarithmic absorption spectrum over a minimum range of 400 to 440 nm (s440 ranged between < 0.01 and 0.04 nm-1. No relationship was found between ag440 or s440 and salinity. Except in the southern Baltic, s440 was found to have a broad distribution (0.0165 ± 0.0035, suggesting that it should be introduced as an additional variable in bio-optical models when ag440 is large. An alternative model for CDOM absorption was applied to available high quality UV-visible absorption spectra from the Wisla river (Poland. This model assumes that the CDOM absorption spectrum comprises distinct Gaussian absorption bands in the UV, similar to those of benzene. Five bands were fit to the data. The mean central energy of all bands was higher in early summer (E~7.2, 6.6, 6.4, 6.2 and 5.5 eV or 172, 188, 194, 200 and 226 nm than in winter. The higher energy bands were found to decay in both height and width with increasing salinity, while lower energy bands broadened with increasing salinity. s440 was found to be correlated with shape parameters of the bands centred at 6.4 and 5.5 eV. While the exponential model is convenient for optical modelling and remote sensing applications, these results suggest that the Gaussian model offers a deeper understanding of chemical interactions affecting CDOM molecular structure.

  8. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy.

    Directory of Open Access Journals (Sweden)

    Alex Costa

    Full Text Available Selective Plane Illumination Microscopy (SPIM is an imaging technique particularly suited for long term in-vivo analysis of transparent specimens, able to visualize small organs or entire organisms, at cellular and eventually even subcellular resolution. Here we report the application of SPIM in Calcium imaging based on Förster Resonance Energy Transfer (FRET. Transgenic Arabidopsis plants expressing the genetically encoded-FRET-based Ca(2+ probe Cameleon, in the cytosol or nucleus, were used to demonstrate that SPIM enables ratiometric fluorescence imaging at high spatial and temporal resolution, both at tissue and single cell level. The SPIM-FRET technique enabled us to follow nuclear and cytosolic Ca(2+ dynamics in Arabidopsis root tip cells, deep inside the organ, in response to different stimuli. A relevant physiological phenomenon, namely Ca(2+ signal percolation, predicted in previous studies, has been directly visualized.

  9. Self-organized critical model for protein folding

    Science.gov (United States)

    Moret, M. A.

    2011-09-01

    The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the fractal behavior of 5526 protein structures present in the Brookhaven Protein Data Bank. Power laws of protein mass, volume and solvent-accessible surface area are measured independently. The present findings indicate that self-organized criticality is an alternative explanation for the protein folding. Also we note that the protein packing is an independent and constant value because the self-similar behavior of the volumes and protein masses have the same fractal dimension. This power law guarantees that a protein is a complex system. From the analyzed data, q-Gaussian distributions seem to fit well this class of systems.

  10. Presenting a comprehensive market oriented model and evaluating its impact on organization performance

    Directory of Open Access Journals (Sweden)

    Mohammad Taqi Amini

    2013-08-01

    Full Text Available Like other innovative strategies, companies have paid more attention to market oriented strategies in recent years. This has been focused by organizations for improved effectiveness and the organization performance accelerated a lot in business competition. In responding to this fact, organizations are trying to formulate many of the issues familiar to large organizations, which have involved with market oriented strategy planning. This paper reviews key elements in market-oriented strategy planning with regard to competitiveness and performance in large organizations and outlines a comprehensive model for strategy planning in profit organizations. These elements include environment, top management, organization structure and market oriented strategy. Professional question of this study has a particularly important role in formulating relations of this model. These elements are well positioned to evaluate the impact of market-oriented strategy planning on organizations and their expected impacts on organization performance. A well-organized questionnaire to help organizations with their planning is proposed in this survey. Based on the proposed questionnaire, data obtained from Tehran food industry experts and analyzed by using SEM method. Results accepted eight hypotheses and rejected one.

  11. Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1

    Directory of Open Access Journals (Sweden)

    Sandhu Devinder

    2009-08-01

    Full Text Available Abstract Background Systemic acquired resistance (SAR is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR genes. Arabidopsis non-expressor of PR1 (NPR1 is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Results Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i PR-1 was induced following INA treatment and (ii BGL2 following infection with Pseudomonas syringae pv. tomato (Pst, and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Conclusion Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential

  12. Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1.

    Science.gov (United States)

    Sandhu, Devinder; Tasma, I Made; Frasch, Ryan; Bhattacharyya, Madan K

    2009-08-05

    Systemic acquired resistance (SAR) is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA) is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR) genes. Arabidopsis non-expressor of PR1 (NPR1) is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA) or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i) PR-1 was induced following INA treatment and (ii) BGL2 following infection with Pseudomonas syringae pv. tomato (Pst), and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential for oligomer-monomer transition of Arabidopsis NPR1

  13. An Incremental Model for Cloud Adoption: Based on a Study of Regional Organizations

    Directory of Open Access Journals (Sweden)

    Emre Erturk

    2017-11-01

    Full Text Available Many organizations that use cloud computing services intend to increase this commitment. A survey was distributed to organizations in Hawke’s Bay, New Zealand to understand their adoption of cloud solutions, in comparison with global trends and practices. The survey also included questions on the benefits and challenges, and which delivery model(s they have adopted and are planning to adopt. One aim is to contribute to the cloud computing literature and build on the existing adoption models. This study also highlights additional aspects applicable to various organizations (small, medium, large and regional. Finally, recommendations are provided for related future research projects.

  14. Scanning tunneling spectroscopy on organic semiconductors : experiment and model

    NARCIS (Netherlands)

    Kemerink, M.; Alvarado, S.F.; Müller, P.; Koenraad, P.M.; Salemink, H.W.M.; Wolter, J.H.; Janssen, R.A.J.

    2004-01-01

    Scanning-tunneling spectroscopy expts. performed on conjugated polymer films are compared with three-dimensional numerical model calcns. for charge injection and transport. It is found that if a sufficiently sharp tip is used, the field enhancement near the tip apex leads to a significant increase

  15. A Social Information Processing Model of Media Use in Organizations.

    Science.gov (United States)

    Fulk, Janet; And Others

    1987-01-01

    Presents a model to examine how social influence processes affect individuals' attitudes toward communication media and media use behavior, integrating two research areas: media use patterns as the outcome of objectively rational choices and social information processing theory. Asserts (in a synthesis) that media characteristics and attitudes are…

  16. Modeling charge transfer at organic donor-acceptor semiconductor interfaces

    NARCIS (Netherlands)

    Cakir, Deniz; Bokdam, Menno; de Jong, Machiel Pieter; Fahlman, M.; Brocks, G.

    2012-01-01

    We develop an integer charge transfer model for the potential steps observed at interfaces between donor and acceptor molecular semiconductors. The potential step can be expressed as the difference between the Fermi energy pinning levels of electrons on the acceptor material and holes on the donor

  17. Modeling equilibrium adsorption of organic micropollutants onto activated carbon

    KAUST Repository

    De Ridder, David J.

    2010-05-01

    Solute hydrophobicity, polarizability, aromaticity and the presence of H-bond donor/acceptor groups have been identified as important solute properties that affect the adsorption on activated carbon. However, the adsorption mechanisms related to these properties occur in parallel, and their respective dominance depends on the solute properties as well as carbon characteristics. In this paper, a model based on multivariate linear regression is described that was developed to predict equilibrium carbon loading on a specific activated carbon (F400) for solutes reflecting a wide range of solute properties. In order to improve prediction accuracy, groups (bins) of solutes with similar solute properties were defined and solute removals were predicted for each bin separately. With these individual linear models, coefficients of determination (R2) values ranging from 0.61 to 0.84 were obtained. With the mechanistic approach used in developing this predictive model, a strong relation with adsorption mechanisms is established, improving the interpretation and, ultimately, acceptance of the model. © 2010 Elsevier Ltd.

  18. From Bench to Bountiful Harvests: A Road Map for the Next Decade of Arabidopsis Research[OA

    Science.gov (United States)

    Lavagi, Irene; Estelle, Mark; Weckwerth, Wolfram; Beynon, Jim; Bastow, Ruth M.

    2012-01-01

    In the face of an increasing world population and climate instability, the demands for food and fuel will continue to rise. Plant science will be crucial to help meet these exponentially increasing requirements for food and fuel supplies. Fundamental plant research will play a major role in providing key advances in our understanding of basic plant processes that can then flow into practical advances through knowledge sharing and collaborations. The model plant Arabidopsis thaliana has played a major role in our understanding of plant biology, and the Arabidopsis community has developed many tools and resources to continue building on this knowledge. Drawing from previous experience of internationally coordinated projects, The international Arabidopsis community, represented by the Multinational Arabidopsis Steering Committee (MASC), has drawn up a road map for the next decade of Arabidopsis research to inform scientists and decision makers on the future foci of Arabidopsis research within the wider plant science landscape. This article provides a summary of the MASC road map. PMID:22751212

  19. A nanosized Ag–silica hybrid complex prepared by γ-irradiation activates the defense response in Arabidopsis

    International Nuclear Information System (INIS)

    Chu, Hyosub; Kim, Hwa-Jung; Su Kim, Joong; Kim, Min-Soo; Yoon, Byung-Dae; Park, Hae-Jun; Kim, Cha Young

    2012-01-01

    Silver nanoparticles have antimicrobial activity against many pathogenic microbes. Here, the preparation of a nanosized Ag–silica hybrid complex (NSS) prepared by γ-irradiation is described. The effects of both NSS and reduced Ag nanoparticles (Ag 0 ) on the growth of the model plant Arabidopsis thaliana were tested. The application of 1–10 ppm NSS complex improved Arabidopsis growth in soil, whereas 100 ppm NSS resulted in weakly curled leaves. In addition, supplementation of Murashige and Skoog (MS) growth medium with 1 ppm NSS promoted the root growth of Arabidopsis seedlings, but root growth was inhibited by supplementation with 10 ppm NSS. To investigate whether the NSS complex could induce plant defense responses, the expression of pathogenesis-related (PR) genes that are implicated in systemic acquired resistance (SAR) in Arabidopsis plants was examined. PR1, PR2 and PR5 were significantly up-regulated by each application of 10 ppm NSS complex or Ag 0 to the rosette leaves. Furthermore, pretreatment with the NSS complex induced more pathogen resistance to the virulent pathogen Pseudomonas syringae pv. tomato DC3000 (Pst) compared to water treatment in Arabidopsis plants. - Research highlights: ► We describe the preparation of silver nanoparticles using γ-irradiation technique. ► We examine the effects of silver nanoparticles on the growth of Arabidopsis. ► Silver nanoparticles induced the expression of SAR marker genes. ► Silver nanoparticles exhibited enhanced disease resistance to the bacterial pathogen.

  20. Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis

    Science.gov (United States)

    Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metad...

  1. Sleep and Development in Genetically Tractable Model Organisms.

    Science.gov (United States)

    Kayser, Matthew S; Biron, David

    2016-05-01

    Sleep is widely recognized as essential, but without a clear singular function. Inadequate sleep impairs cognition, metabolism, immune function, and many other processes. Work in genetic model systems has greatly expanded our understanding of basic sleep neurobiology as well as introduced new concepts for why we sleep. Among these is an idea with its roots in human work nearly 50 years old: sleep in early life is crucial for normal brain maturation. Nearly all known species that sleep do so more while immature, and this increased sleep coincides with a period of exuberant synaptogenesis and massive neural circuit remodeling. Adequate sleep also appears critical for normal neurodevelopmental progression. This article describes recent findings regarding molecular and circuit mechanisms of sleep, with a focus on development and the insights garnered from models amenable to detailed genetic analyses. Copyright © 2016 by the Genetics Society of America.

  2. Phragmites australis as a model organism for studying plant invasions

    Czech Academy of Sciences Publication Activity Database

    Meyerson, L. A.; Cronin, J. T.; Pyšek, Petr

    2016-01-01

    Roč. 18, č. 9 (2016), s. 2421-2431 ISSN 1387-3547 R&D Projects: GA ČR(CZ) GA14-15414S Grant - others:AV ČR(CZ) AP1002 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:67985939 Keywords : common reed * model species * global climate change Subject RIV: EH - Ecology, Behaviour Impact factor: 2.473, year: 2016

  3. ORCHIDEE-SOM: modeling soil organic carbon (SOC) and dissolved organic carbon (DOC) dynamics along vertical soil profiles in Europe

    Science.gov (United States)

    Camino-Serrano, Marta; Guenet, Bertrand; Luyssaert, Sebastiaan; Ciais, Philippe; Bastrikov, Vladislav; De Vos, Bruno; Gielen, Bert; Gleixner, Gerd; Jornet-Puig, Albert; Kaiser, Klaus; Kothawala, Dolly; Lauerwald, Ronny; Peñuelas, Josep; Schrumpf, Marion; Vicca, Sara; Vuichard, Nicolas; Walmsley, David; Janssens, Ivan A.

    2018-03-01

    Current land surface models (LSMs) typically represent soils in a very simplistic way, assuming soil organic carbon (SOC) as a bulk, and thus impeding a correct representation of deep soil carbon dynamics. Moreover, LSMs generally neglect the production and export of dissolved organic carbon (DOC) from soils to rivers, leading to overestimations of the potential carbon sequestration on land. This common oversimplified processing of SOC in LSMs is partly responsible for the large uncertainty in the predictions of the soil carbon response to climate change. In this study, we present a new soil carbon module called ORCHIDEE-SOM, embedded within the land surface model ORCHIDEE, which is able to reproduce the DOC and SOC dynamics in a vertically discretized soil to 2 m. The model includes processes of biological production and consumption of SOC and DOC, DOC adsorption on and desorption from soil minerals, diffusion of SOC and DOC, and DOC transport with water through and out of the soils to rivers. We evaluated ORCHIDEE-SOM against observations of DOC concentrations and SOC stocks from four European sites with different vegetation covers: a coniferous forest, a deciduous forest, a grassland, and a cropland. The model was able to reproduce the SOC stocks along their vertical profiles at the four sites and the DOC concentrations within the range of measurements, with the exception of the DOC concentrations in the upper soil horizon at the coniferous forest. However, the model was not able to fully capture the temporal dynamics of DOC concentrations. Further model improvements should focus on a plant- and depth-dependent parameterization of the new input model parameters, such as the turnover times of DOC and the microbial carbon use efficiency. We suggest that this new soil module, when parameterized for global simulations, will improve the representation of the global carbon cycle in LSMs, thus helping to constrain the predictions of the future SOC response to global

  4. WHETHER OPEN INNOVATION IS A BETTER CHOICE AS A MODEL OF INNOVATION FOR ORGANIZATIONS?

    OpenAIRE

    KANBUR, AYSUN; A. H. MOHAMED, Ibrahim

    2018-01-01

    This studypresents a review of innovation models and by taking consideration andexamining these models it is aimed to understand whether the model based onopen innovation is a better choice among all the other models. Fororganizations, innovation models generally demonstrate how to work in aninnovative point of view. Companies of today’s business life are striving todevelop their capabilities and their activities to become innovative companies.Many of the organizations try to find the most su...

  5. Fully coupled opto-electronic modelling of organic solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Reinke, Nils A.; Haeusermann, Roger; Huber, Evelyne; Moos, Michael [ZHAW, Institute of Comp. Physics (Germany); Flatz, Thomas [Fluxim AG (Switzerland); Ruhstaller, Beat [ZHAW, Institute of Comp. Physics (Germany); Fluxim AG (Switzerland)

    2009-07-01

    Record solar power conversion efficiencies of up to 5.5 % for single junction organic solar cells (OSC) are encouraging but still inferior to values of inorganic solar cells. For further progress, a detailed analysis of the mechanisms that limit the external quantum efficiency is crucial. It is widely believed that the device physics of OSCs can be reduced to the processes, which take place at the donor/acceptor-interface. Neglecting transport, trapping and ejection of charge carriers at the electrodes raises the question of the universality of such a simplification. In this study we present a fully coupled opto-electronic simulator, which calculates the spatial and spectral photon flux density inside the OSC, the formation of the charge transfer state and its dissociation into free charge carriers. Our simulator solves the drift- diffusion equations for the generated charge carriers as well as their ejection at the electrodes. Our results are in good agreement with both steady-state and transient OSC characteristics. We address the influence of physical quantities such as the optical properties, film-thicknesses, the recombination rate and charge carrier mobilities on performance figures. For instance the short circuit current can be enhanced by 15% to 25% when using a silver instead of an aluminium cathode. Our simulations lead to rules of thumb, which help to optimise a given OSC structure.

  6. 76 FR 29249 - Medicare Program; Pioneer Accountable Care Organization Model: Request for Applications

    Science.gov (United States)

    2011-05-20

    ... Affordable Care Act, to test innovative payment and service delivery models that reduce spending under.... This Model will test the effectiveness of a combination of the following: Payment arrangements that...] Medicare Program; Pioneer Accountable Care Organization Model: Request for Applications AGENCY: Centers for...

  7. An Introduction to Topic Modeling as an Unsupervised Machine Learning Way to Organize Text Information

    Science.gov (United States)

    Snyder, Robin M.

    2015-01-01

    The field of topic modeling has become increasingly important over the past few years. Topic modeling is an unsupervised machine learning way to organize text (or image or DNA, etc.) information such that related pieces of text can be identified. This paper/session will present/discuss the current state of topic modeling, why it is important, and…

  8. Herbivore-induced volatile production by Arabidopsis thaliana leads to attraction of the parasitoid Cotesia rubecula: chemical, behavioral, and gene-expression analysis

    NARCIS (Netherlands)

    Poecke, R.M.P.; Posthumus, M.A.; Dicke, M.

    2001-01-01

    Many plant species defend themselves against herbivorous insects indirectly by producing volatiles in response to herbivory. These volatiles attract carnivorous enemies of the herbivores. Research on the model plant Arabidopsis thaliana (L.) Heynh. has contributed considerably to the unraveling of

  9. Modeling the World Health Organization Disability Assessment Schedule II using non-parametric item response models.

    Science.gov (United States)

    Galindo-Garre, Francisca; Hidalgo, María Dolores; Guilera, Georgina; Pino, Oscar; Rojo, J Emilio; Gómez-Benito, Juana

    2015-03-01

    The World Health Organization Disability Assessment Schedule II (WHO-DAS II) is a multidimensional instrument developed for measuring disability. It comprises six domains (getting around, self-care, getting along with others, life activities and participation in society). The main purpose of this paper is the evaluation of the psychometric properties for each domain of the WHO-DAS II with parametric and non-parametric Item Response Theory (IRT) models. A secondary objective is to assess whether the WHO-DAS II items within each domain form a hierarchy of invariantly ordered severity indicators of disability. A sample of 352 patients with a schizophrenia spectrum disorder is used in this study. The 36 items WHO-DAS II was administered during the consultation. Partial Credit and Mokken scale models are used to study the psychometric properties of the questionnaire. The psychometric properties of the WHO-DAS II scale are satisfactory for all the domains. However, we identify a few items that do not discriminate satisfactorily between different levels of disability and cannot be invariantly ordered in the scale. In conclusion the WHO-DAS II can be used to assess overall disability in patients with schizophrenia, but some domains are too general to assess functionality in these patients because they contain items that are not applicable to this pathology. Copyright © 2014 John Wiley & Sons, Ltd.

  10. For the Arts To Have Meaning...A Model of Adult Education in Performing Arts Organizations.

    Science.gov (United States)

    Kitinoja, L.; Heimlich, J. E.

    A model of adult education appears to function in the outreach programs of three Columbus (Ohio) performing arts organizations. The first tier represents the arts organization's board of trustees, and the second represents the internal administration of the company. Two administrative bodies are arbitrarily labelled as education and marketing,…

  11. Basic model for the prediction of 137Cs concentration in the organisms of detritus food chain

    International Nuclear Information System (INIS)

    Tateda, Yuzuru

    1997-01-01

    In order to predict 137 Cs concentrations in marine organisms for monitoring, a basic model for the prediction of nuclide levels in marine organisms of detritus food chain was studied. The equilibrated values of ( 137 Cs level in organism)/( 137 Cs level in seawater) derived from calculation agreed with the observed data, indicating validity of modeling conditions. The result of simulation by this basic model showed the following conclusions. 1) ''Ecological half-life'' of 137 Cs in organisms of food chain were 35 and 130 days for detritus feeder and benthic teleosts, respectively, indicating that there was no difference of the ecological half lives in organisms between in detritus food chain and in other food chains. 2) The 137 Cs concentration in organisms showed a peak at 18 and 100 days in detritus and detritus feeder, respectively, after the introduction of 137 Cs into environmental seawater. Their concentration ratios to 137 Cs peak level in seawater were within a range of 2.7-3.8, indicating insignificant difference in the response to 137 Cs change in seawater between in the organisms of detritus food chain and of other food chain. 3) The basic model studies makes it available that the prediction of 137 Cs level in organisms of food chain can be simulated in coastal ecosystem. (author)

  12. Risk management in organic coffee supply chains : testing the usefulness of critical risk models

    NARCIS (Netherlands)

    Brusselaers, J.F.; Benninga, J.; Hennen, W.H.G.J.

    2011-01-01

    This report documents the findings of the analysis of the supply chain of organic coffee from Uganda to the Netherlands using a Chain Risk Model (CRM). The CRM considers contamination of organic coffee with chemicals as a threat for the supply chain, and analyses the consequences of contamination in

  13. Indonesian Private University Lecturer Performance Improvement Model to Improve a Sustainable Organization Performance

    Science.gov (United States)

    Suryaman

    2018-01-01

    Lecturer performance will affect the quality and carrying capacity of the sustainability of an organization, in this case the university. There are many models developed to measure the performance of teachers, but not much to discuss the influence of faculty performance itself towards sustainability of an organization. This study was conducted in…

  14. Modelling energy level alignment at organic interfaces and density functional theory

    DEFF Research Database (Denmark)

    Flores, F.; Ortega, J.; Vazquez, Patricia

    2009-01-01

    A review of our theoretical understanding of the band alignment at organic interfaces is presented with particular emphasis on the metal/organic (MO) case. The unified IDIS (induced density of interface states) and the ICT (integer charge transfer) models are reviewed and shown to describe qualit...

  15. The model selection in the process of teambuilding for the management of the organization

    OpenAIRE

    Sergey Petrov

    2010-01-01

    Improving competitiveness of organizations necessary for their success in a market economy is no longer possible only due to material resources. This implies need for qualitatively new approach to human capital. The author reviews approaches to team building and suggests team management model based on situations-cases in which the organized one way or another team reaches goal.

  16. A Unifying Organ Model of Pancreatic Insulin Secretion.

    Directory of Open Access Journals (Sweden)

    Andrea De Gaetano

    Full Text Available The secretion of insulin by the pancreas has been the object of much attention over the past several decades. Insulin is known to be secreted by pancreatic β-cells in response to hyperglycemia: its blood concentrations however exhibit both high-frequency (period approx. 10 minutes and low-frequency oscillations (period approx. 1.5 hours. Furthermore, characteristic insulin secretory response to challenge maneuvers have been described, such as frequency entrainment upon sinusoidal glycemic stimulation; substantial insulin peaks following minimal glucose administration; progressively strengthened insulin secretion response after repeated administration of the same amount of glucose; insulin and glucose characteristic curves after Intra-Venous administration of glucose boli in healthy and pre-diabetic subjects as well as in Type 2 Diabetes Mellitus. Previous modeling of β-cell physiology has been mainly directed to the intracellular chain of events giving rise to single-cell or cell-cluster hormone release oscillations, but the large size, long period and complex morphology of the diverse responses to whole-body glucose stimuli has not yet been coherently explained. Starting with the seminal work of Grodsky it was hypothesized that the population of pancreatic β-cells, possibly functionally aggregated in islets of Langerhans, could be viewed as a set of independent, similar, but not identical controllers (firing units with distributed functional parameters. The present work shows how a single model based on a population of independent islet controllers can reproduce very closely a diverse array of actually observed experimental results, with the same set of working parameters. The model's success in reproducing a diverse array of experiments implies that, in order to understand the macroscopic behaviour of the endocrine pancreas in regulating glycemia, there is no need to hypothesize intrapancreatic pacemakers, influences between different

  17. Optimising the anaerobic co-digestion of urban organic waste using dynamic bioconversion mathematical modelling

    DEFF Research Database (Denmark)

    Fitamo, Temesgen Mathewos; Boldrin, Alessio; Dorini, G.

    2016-01-01

    Mathematical anaerobic bioconversion models are often used as a convenient way to simulate the conversion of organic materials to biogas. The aim of the study was to apply a mathematical model for simulating the anaerobic co-digestion of various types of urban organic waste, in order to develop...... in a continuously stirred tank reactor. The model's outputs were validated with experimental results obtained in thermophilic conditions, with mixed sludge as a single substrate and urban organic waste as a co-substrate at hydraulic retention times of 30, 20, 15 and 10 days. The predicted performance parameter...... (methane productivity and yield) and operational parameter (concentration of ammonia and volatile fatty acid) values were reasonable and displayed good correlation and accuracy. The model was later applied to identify optimal scenarios for an urban organic waste co-digestion process. The simulation...

  18. Organization-and-technological model of medical care delivered to patients with arterial hypertension

    Directory of Open Access Journals (Sweden)

    Kiselev A.R.

    2014-09-01

    Full Text Available Organization-and-technological model of medical care delivered to patients with arterial hypertension based on IDEF0 methodology and corresponded with clinical guidelines is presented.

  19. Organization-and-technological model of medical care delivered to patients with chronic heart failure

    Directory of Open Access Journals (Sweden)

    Kiselev A.R.

    2014-09-01

    Full Text Available Organization-and-technological model of medical care delivered to patients with chronic heart failure based on IDEF0 methodology and corresponded with clinical guidelines is presented.

  20. QSAR models for the removal of organic micropollutants in four different river water matrices

    KAUST Repository

    Sudhakaran, Sairam; Calvin, James; Amy, Gary L.

    2012-01-01

    Ozonation is an advanced water treatment process used to remove organic micropollutants (OMPs) such as pharmaceuticals and personal care products (PPCPs). In this study, Quantitative Structure Activity Relationship (QSAR) models, for ozonation

  1. Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

    DEFF Research Database (Denmark)

    Jin, Biao; Rolle, Massimo

    2016-01-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework ...

  2. Modeling space-charge-limited currents in organic semiconductors: Extracting trap density and mobility

    KAUST Repository

    Dacuñ a, Javier; Salleo, Alberto

    2011-01-01

    We have developed and have applied a mobility edge model that takes drift and diffusion currents to characterize the space-charge-limited current in organic semiconductors into account. The numerical solution of the drift-diffusion equation allows

  3. Organization-and-technological model of medical care delivered to patients with coronary heart disease

    Directory of Open Access Journals (Sweden)

    Popova Y.V.

    2014-09-01

    Full Text Available Organization-and-technological model of medical care delivered to patients with coronary heart disease based on IDEF0 methodology and corresponded with clinical guidelines is presented.

  4. Effects of Some Neurobiological Factors in a Self-organized Critical Model Based on Neural Networks

    International Nuclear Information System (INIS)

    Zhou Liming; Zhang Yingyue; Chen Tianlun

    2005-01-01

    Based on an integrate-and-fire mechanism, we investigate the effect of changing the efficacy of the synapse, the transmitting time-delayed, and the relative refractoryperiod on the self-organized criticality in our neural network model.

  5. Predicting The Exit Time Of Employees In An Organization Using Statistical Model

    Directory of Open Access Journals (Sweden)

    Ahmed Al Kuwaiti

    2015-08-01

    Full Text Available Employees are considered as an asset to any organization and each organization provide a better and flexible working environment to retain its best and resourceful workforce. As such continuous efforts are being taken to avoid or extend the exitwithdrawal of employees from the organization. Human resource managers are facing a challenge to predict the exit time of employees and there is no precise model existing at present in the literature. This study has been conducted to predict the probability of exit of an employee in an organization using appropriate statistical model. Accordingly authors designed a model using Additive Weibull distribution to predict the expected exit time of employee in an organization. In addition a Shock model approach is also executed to check how well the Additive Weibull distribution suits in an organization. The analytical results showed that when the inter-arrival time increases the expected time for the employees to exit also increases. This study concluded that Additive Weibull distribution can be considered as an alternative in the place of Shock model approach to predict the exit time of employee in an organization.

  6. Functional water flow pathways and hydraulic regulation in the xylem network of Arabidopsis.

    Science.gov (United States)

    Park, Joonghyuk; Kim, Hae Koo; Ryu, Jeongeun; Ahn, Sungsook; Lee, Sang Joon; Hwang, Ildoo

    2015-03-01

    In vascular plants, the xylem network constitutes a complex microfluidic system. The relationship between vascular network architecture and functional hydraulic regulation during actual water flow remains unexplored. Here, we developed a method to visualize individual xylem vessels of the 3D xylem network of Arabidopsis thaliana, and to analyze the functional activities of these vessels using synchrotron X-ray computed tomography with hydrophilic gold nanoparticles as flow tracers. We show how the organization of the xylem network changes dynamically throughout the plant, and reveal how the elementary units of this transport system are organized to ensure both long-distance axial water transport and local lateral water transport. Xylem vessels form distinct clusters that operate as functional units, and the activity of these units, which determines water flow pathways, is modulated not only by varying the number and size of xylem vessels, but also by altering their interconnectivity and spatial arrangement. Based on these findings, we propose a regulatory model of water transport that ensures hydraulic efficiency and safety. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  7. Model of lifetime prediction - Study of the behaviour of polymers and organic matrix composites

    International Nuclear Information System (INIS)

    Colin, X.

    2009-01-01

    The team 'Aging of Organic Materials' of the Process and Engineering Laboratory in Mechanics and Materials (Arts et Metiers, ParisTech) has developed the model of lifetime prediction for the prediction of the behaviour of polymers and organic composites. This model has already given evidence of a real predictive mean for various industrial applications, as for instance the prediction of a rupture under the coupled effect of a mechanical load and a chemical degradation. (O.M.)

  8. Development and evaluation of a skin organ model for the analysis of radiation effects

    International Nuclear Information System (INIS)

    Meineke, V.; Mueller, K.; Ridi, R.; Cordes, N.; Beuningen, D. van; Koehn, F.M.; Ring, J.; Mayerhofer, A.

    2004-01-01

    Background and purpose: the reaction of tissues to ionizing radiation involves alterations in cell-cell and cell-matrix interactions mediated by cellular adhesion molecules. The aim of this study was to develop and evaluate an artificial skin organ model for the analysis of radiation effects. Material and methods: a human co-culture system consisting of the spontaneously immortalized keratinocyte cell line HaCaT and primary HDFa fibroblasts embedded into a collagen sponge was established. This skin organ model has been characterized and evaluated for its suitability for radiobiological investigations. For that purpose, expression of β 1 -integrin following irradiation was compared in the skin organ model and in HaCaT monolayer cells (FACScan and immunohistochemistry). Furthermore, the influence of ionizing radiation on DNA fragmentation was investigated in the skin organ model (TUNEL assay). Results: the novel skin organ model showed characteristics of human skin as demonstrated by cytokeratin and Ki-67 immunoreactivity and by electron microscopy. A single dose of 5 Gy X-irradiation induced an upregulation of β 1 -integrin expression both in the skin organ model and in HaCaT cells. Following irradiation, β 1 -integrin immunoreactivity was intensified in the upper layers of the epidermis equivalent whereas it was almost absent in the deeper layers. Additionally, irradiation of the skin organ model also caused a marked increase of DNA fragmentation. Conclusion: these results demonstrate that the novel skin organ model is suitable to investigate cellular radiation effects under three-dimensional conditions. This allows to investigate radiation effects which cannot be demonstrated in monolayer cell cultures. (orig.)

  9. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Moreau Hervé

    2008-10-01

    Full Text Available Abstract Background The Wuschel related homeobox (WOX family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. Results The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Conclusion Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most

  10. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  11. Lampreys as Diverse Model Organisms in the Genomics Era.

    Science.gov (United States)

    McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

    2015-11-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

  12. CONCEPTUAL MODELLING AND ORGANIZATION OF SECURITY MECHANISMS IN DISTRIBUTED SYSTEMS

    Directory of Open Access Journals (Sweden)

    T. Galibus

    2016-01-01

    Full Text Available We analyze the existing DS from the point of security and construct a two-level hierarchy of models. Such approach allows us to separate the abstraction (architecture level and the concrete (component level of ISS. The core set of methods, i. e. authentication and key exchange protocols, corresponds to the abstraction level and is defined as security infrastructure (SI. The final security parameters optimization and additional mechanisms such as authorization, routing and data auditing of the protection mechanisms are configured on the component level of the DS. In addition, we outline the systematic step-by-step ISS configuration method.

  13. Models for the mechanism for activating copper-zinc superoxide dismutase in the absence of the CCS Cu chaperone in Arabidopsis.

    Science.gov (United States)

    Huang, Chien-Hsun; Kuo, Wen-Yu; Jinn, Tsung-Luo

    2012-03-01

    Copper-zinc superoxide dismutase (CuZnSOD; CSD) is an important antioxidant enzyme for oxidative stress protection. To date, two activation pathways have been identified in many species. One requiring the CCS, Cu chaperone for SOD, to insert Cu and activate CSD (referred to as CCS-dependent pathway), and the other works independently of CCS (referred to as CCS-independent pathway). In our previous study, we suggest an unidentified factor will work with glutathione (GSH) for CSD activation in the absence of the CCS. Here, two models of the CCS-independent mechanism are proposed. The role of the unidentified factor may work as a scaffold protein, which provides a platform for the CSD protein and Cu-GSH to interact, or as a Cu carrier, which itself can bind Cu and interact with CSD proteins. We also suggest that the CSD protein conformation at C-terminal is important in providing a docking site for unidentified factor to access.

  14. Multiple organ definition in CT using a Bayesian approach for 3D model fitting

    Science.gov (United States)

    Boes, Jennifer L.; Weymouth, Terry E.; Meyer, Charles R.

    1995-08-01

    Organ definition in computed tomography (CT) is of interest for treatment planning and response monitoring. We present a method for organ definition using a priori information about shape encoded in a set of biometric organ models--specifically for the liver and kidney-- that accurately represents patient population shape information. Each model is generated by averaging surfaces from a learning set of organ shapes previously registered into a standard space defined by a small set of landmarks. The model is placed in a specific patient's data set by identifying these landmarks and using them as the basis for model deformation; this preliminary representation is then iteratively fit to the patient's data based on a Bayesian formulation of the model's priors and CT edge information, yielding a complete organ surface. We demonstrate this technique using a set of fifteen abdominal CT data sets for liver surface definition both before and after the addition of a kidney model to the fitting; we demonstrate the effectiveness of this tool for organ surface definition in this low-contrast domain.

  15. Plausible carrier transport model in organic-inorganic hybrid perovskite resistive memory devices

    Directory of Open Access Journals (Sweden)

    Nayoung Park

    2018-04-01

    Full Text Available We demonstrate thermally assisted hopping (TAH as an appropriate carrier transport model for CH3NH3PbI3 resistive memories. Organic semiconductors, including organic-inorganic hybrid perovskites, have been previously speculated to follow the space-charge-limited conduction (SCLC model. However, the SCLC model cannot reproduce the temperature dependence of experimental current-voltage curves. Instead, the TAH model with temperature-dependent trap densities and a constant trap level are demonstrated to well reproduce the experimental results.

  16. Relevance of the ICRP biokinetic model for dietary organically bound tritium

    International Nuclear Information System (INIS)

    Trivedi, A.

    1999-10-01

    Ingested dietary tritium can participate in metabolic processes, and become synthesized into organically bound tritium in the tissues and organs. The distribution and retention of the organically bound tritium throughout the body are much different than tritium in the body water. The International Commission on Radiological Protection (ICRP) Publication 56 (1989) has a biokinetic model to calculate dose from the ingestion of organically bound dietary tritium. The model predicts that the dose from the ingestion of organically bound dietary tritium is about 2.3 times higher than from the ingestion of the same activity of tritiated water. Under steady-state conditions, the calculated dose rate (using the first principle approach) from the ingestion of dietary organically bound tritium can be twice that from the ingestion of tritiated water. For an adult, the upper-bound dose estimate for the ingestion of dietary organically bound tritium is estimated to be close to 2.3 times higher than that of tritiated water. Therefore, given the uncertainty in the dose calculation with respect to the actual relevant dose, the ICRP biokinetic model for organically bound tritium is sufficient for dosimetry for adults. (author)

  17. A CONSOLIDATED MODEL OF ANALYSIS OF THE RELATIONS BETWEEN POLITICS AND MANAGEMENT WITHIN PUBLIC ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Catalina Maria GEORGESCU

    2011-01-01

    Full Text Available An interdisciplinary approach which combines the theoretical, empirical andconceptual dimensions, the present study tries to offer a new workperspective on the assessment and modeling of the relation between themanagement of public organizations and the political environment. Thetheoretical research was centered on reviewing the literature on the relationbetween the management of public organizations and the politicalenvironment. The empirical research was materialized by modeling with theregression technique of several aspects integrated to the relations betweenthe management of human resources within public organizations in theeducation field and the external political environment.

  18. A Simulation Model of Combined Biogas, Bioethanol and Protein Fodder Co-Production in Organic Farming

    DEFF Research Database (Denmark)

    Oleskowicz-Popiel, Piotr; Thomsen, Mette Hedegaard; Thomsen, Anne Belinda

    2009-01-01

    In order to evaluate new strategies for the production of renewable energy within sustainable organic agriculture, a process-simulation model for a 100 ha organic farm was developed. Data used for the model was obtained from laboratory trials, literature data, consultancy with experts, and results...... ha organic farm with ethanol or biogas, respectively. This calculation was based on the assumption that the electrical efficiency of CHP (combined heat and power) unit was 38%. A variety of different scenarios can be simulated to mirror the farmer's needs....

  19. Laos Organization Name Using Cascaded Model Based on SVM and CRF

    Directory of Open Access Journals (Sweden)

    Duan Shaopeng

    2017-01-01

    Full Text Available According to the characteristics of Laos organization name, this paper proposes a two layer model based on conditional random field (CRF and support vector machine (SVM for Laos organization name recognition. A layer of model uses CRF to recognition simple organization name, and the result is used to support the decision of the second level. Based on the driving method, the second layer uses SVM and CRF to recognition the complicated organization name. Finally, the results of the two levels are combined, And by a subsequent treatment to correct results of low confidence recognition. The results show that this approach based on SVM and CRF is efficient in recognizing organization name through open test for real linguistics, and the recalling rate achieve 80. 83%and the precision rate achieves 82. 75%.

  20. A Topographically and anatomically unified phantom model for organ dose determination in radiation hygiene

    International Nuclear Information System (INIS)

    Servomaa, A.; Rannikko, S.; Ermakov, I.; Masarskyi, L.; Saltukova, L.

    1989-08-01

    The effective dose equivalent is used as a risk-related factor for assessing radiation impact on patients. In order to assess the effective dose equivalent, data on organ doses in several organs are needed. For calculation of the collective effective dose equivalent, data on the sex and size distribution of the exposed population are also needed. A realistic phantom model based on the Alderson-Rando anatomical phantom has been developed for these purposes. The phantom model includes 22 organs and takes into account the deflections due to sex, height, weight and other anatomical features. Coordinates of the outer contours of inner organs are given in different slabs of the phantom. The images of cross sections of different slabs realistically depict the distribution of the organs in the phantom. Statistics about height and weight distribution as a function of the age of the Finnish population are also given. (orig.)