Efficient Parallel Statistical Model Checking of Biochemical Networks

We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture

Crop Updates - 2003 Weeds

This session covers Thirty four papers from different authors INTRODUCTION INTEGRATED WEED MANAGEMENT IWM system studies/demonstration sites Six years of IWM investigation – what does it tell us? Bill Roy, Agricultural Consulting and Research Services Pty Ltd Long term herbicide resistance site, the final chapter, Peter Newman and Glen Adam, Department of Agriculture Management of skeleton weed (chondrilla juncea) in a cropping rotation in Western Australia, J. R. Peirce and B. J. Rayner, Department of Agriculture WEED BIOLOGY AND COMPETITION Annual ryegrass seedbanks: The good, the bad and the ugly, Kathryn J. Steadman1, Amanda J. Ellery2 and Sally C. Peltzer3 , 1WA Herbicide Resistance Initiative, UWA, 2CSIRO Plant Industry, 3 Department of Agriculture Annual ryegrass seeds after-ripen faster during a hot summer, Kathryn J. Steadman1, Gavin P. Bignell1 and Amanda J. Ellery2, 1WA Herbicide Resistance Initiative, UWA, 2CSIRO Plant Industry Predicting annual ryegrass dormancy from climatic variables, Amanda Ellery, Andrew Moore, Sandy Nedelkos, Ross Chapman, CSIRO Plant Industry Removing dormancy in annual ryegrass seeds for early herbicide resistance testing, Kathryn J. Steadman and Mechelle J. Owen, WA Herbicide Resistance Initiative, UWA Annual ryegrass germination responds to nitrogen, Amanda Ellery1, Simone Dudley1 and Robert Gallagher2, 1CSIRO Plant Industry, 2Washington State University The agro-ecology of Malva parviflora (small flowered mallow), Pippa J. Michael, Kathryn J. Steadman and Julie A. Plummer, Western Australia Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia The looming threat of wild radish, Peter Newman, Department of Agriculture IWM TOOLS Double knock, how close can we go? Peter Newman and Glen Adam, Department of Agriculture Double knock herbicide effect on annual ryegrass, Catherine Borger, Abul Hashem and Nerys Wilkins, Department of Agriculture Tactical techniques for managing Annual Ryegrass, Sally Peltzer1, Alex Douglas1, Fran Hoyle1, Paul Matson1 and Michael Walsh2 Department of Agriculture and 2Western Australian Herbicide Resistance Initiative. Weed control through soil inversion, Sally Peltzer, Alex Douglas and Paul Matson, Department of Agriculture The burning issues of annual ryegrass seed control, Darren Chitty and Michael Walsh, Western Australian Herbicide Resistance Initiative, UWA No sign of chaff-cart resistant ryegrass! David Ferris, WA Herbicide Resistance Initiative UWA PACKAGES AND MODELLING Conserving glyphosate susceptibility – modelling past, present and future us. Paul Neve1, Art Diggle2, Patrick Smith3 and Stephen Powles1 ,1Western Australian Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia, 2Department of Agriculture, 3CSIRO Sustainable Ecosystems WEEDEM: A program for predicting weed emergence in Western Australia, Michael Walsh,1 David Archer2, James Eklund2 and Frank Forcella2, 1Western Australia Herbicide Resistance Initiative, UWA, 2USDA-Agricultural Research Service, 803 Iowa Avenue, Morris, MN 56267, USA Weed and herbicide management for long term profit: A workshop, Alister Draper1 and Rick Llewellyn12, 1WA Herbicide Resistance Initiative, 2School of Agricultural and Resource Economics, University of Western Australia HERBICIDE RESISTANCE Alternative herbicides for control of triazine and diflufenican multiple resistant wild radish, Aik Cheam1, Siew Lee1, David Nicholson1 and Mike Clarke2 1Department of Agriculture, Western Australia, 2Bayer CropScience Resistance of wild mustard biotype to ALS-inhibiting herbicides in WA Wheatbelt, Abul Hashem, Department of Agriculture Glyphosate-resistant ryegrass biotypes in the WA wheatbelt, Abul Hashem, Catherine Borger and Nerys Wilkins, Department of Agriculture Implications of herbicide rates for resistance management, Paul Neve, Western Australian Herbicide Resistance Initiative, University of Western Australia Putting a price on herbicide resistance, Rick Llewellyn, School of Agricultural and Resource Economics/WA Herbicide Resistance Initiative, University of Western Australia Herbicide resistance from over the fence: Mobility and management, Debbie Allena, Rick Llewellynb, aUniversity of Western Australia, 4th year student, 2002. Mingenew-Irwin Group, bSchool of Agricultural and Resource Economics/Western Australia Herbicide Resistance Initiative, University of Western Australia HERBICIDE TOLERANCE Herbicide tolerance of new barley varieties, Harmohinder S. Dhammu and Terry Piper, Department of Agriculture Herbicide tolerance of new lupins, Harmohinder S. Dhammu, Terry Piper and David Nicholson, Department of Agriculture Herbicide tolerance of new field pea varieties, Harmohinder S. Dhammu, Terry Piper and David Nicholson, Department of Agriculture Herbicide tolerance of new lentil varieties, H.S. Dhammu, T.J. Piper and L.E. Young, Department of Agriculture HERBICIDES – NEW PRODUCTS/PRODUCT USES; USE Kill half leaf ryegrass with Spray.Seed® at night, Peter Newman and Glenn Adam, Department of Agriculture CLEARFIELD™ wheat to control hard-to-kill weeds, Abul Hashem, Catherine Borger and Nerys Wilkins, Department of Agriculture Diuron, a possible alternative to simazine pre-emergent in lupins, Peter Newman and Glenn Adam, Department of Agriculture Dual Gold® soft on barley, soft on weeds in dry conditions, Peter Newman and Glenn Adam, Department of Agriculture Dual Gold® soft on lupins, soft on ryegrass in dry conditions, Peter Newman and Glenn Adam, Department of Agricultur

Precautionary Effect and Variations of the Value of Information

For a sequential, two-period decision problem with uncertainty and under broad conditions (non-finite sample set, endogenous risk, active learning and stochastic dynamics), a general sufficient condition is provided to compare the optimal initial decisions with or without information arrival in the second period. More generally the condition enables the comparison of optimal decisions related to different information structures. It also ties together and clarifies many conditions for the so-called irreversibility effect that are scattered in the environmental economics literature. A numerical illustration with an integrated assessment model of climate-change economics is provided

Correction: Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

[This corrects the article DOI: 10.1371/journal.pone.0170941.]

Brassinosteroid leaf unrolling QTL mapping in durum wheat

Brassinosteroids are a newly reported class of plant growth phytohormones found in plants throughout the plant kingdom. Functioning at very low concentrations, they play an essential role in improving biomass yield and stress tolerance. There are no reports in the literature of the genetic variability of responsiveness of brassinosteroids in wheat; most studies on brassinosteroids have focused on the physiological effects of exogenous addition of brassinosteroids. Our aim was to study the genetic variation in the responsiveness of a doubled haploid durum wheat population to three brassinosteroid concentrations using the leaf unrolling test, which is a simple bioassay to test brassinosteroid activity. An F1-derived doubled haploid population of 77 individuals from the cross Strongfield/Blackbird was used to construct a genetic map of 427 molecular marker loci. The leaf unrolling test was performed on the parents and doubled haploid genotypes of the population using 0.2, 2 and 20 nM brassinosteroid concentrations. The results indicated significant differences in leaf unrolling between the two parents, doubled haploid genotypes, treatments and genotype-by-treatment combinations. Transgressive segregation beyond Strongfield of leaf unrolling was observed for all concentrations, with the strongest response at 20 nM. Putative quantitative trait loci were revealed in the intervals Xgwm2-Xbarc45 on chromosome 3A and Xwmc643a-Xwmc625a on chromosome 3B. Additional quantitative trait loci were associated with markers Xwmc48a, Xwmc511, Xwmc89a and Xgwmc692 on chromosome 4B, and Xwmc17 on chromosome 7A. This work should enhance the understanding of the relationship between stress tolerance and productivity, and responsiveness to brassinosteroids

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

<div><p>Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.</p></div