Genetic Characterization of Nipah Virus, Bangladesh, 2004

Until 2004, identification of Nipah virus (NV)-like outbreaks in Bangladesh was based on serology. We describe the genetic characterization of a new strain of NV isolated during outbreaks in Bangladesh (NV-B) in 2004, which confirms that NV was the etiologic agent responsible for these outbreaks

SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

<p>Abstract</p> <p>Background</p> <p>The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation). The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations.</p> <p>Results</p> <p>SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules) as well as the regulatory relations (activation, inhibition or other modulations) of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format.</p> <p>Conclusion</p> <p>SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for each reaction, only applicable kinetic formulas are considered. This modeling scheme creates kinetics in accordance with the diagrammatic representation. In contrast most previously published tools have relied on the stoichiometry and generic modulators of a reaction, thus ignoring and potentially conflicting with the information expressed through the process diagram. Additional material and the source code can be found at the project homepage (URL found in the Availability and requirements section).</p

Crop updates 2006 - Farming Systems

This session covers nineteen papers from different authors: SOIL AND NUTRIENT MANAGEMENT 1. Inve$tigating fertili$er inve$tment, Wayne Pluske, Nutrient Management Systems 2. KASM, the potassium in Agricultural System Model,Bill Bowden and Craig Scanlan, DAWA Northam and UWA, School of Earth and Geographical Sciences 3. Long term productivity and economic benefits of subsurface acidity management from surface and subsurface liming, Stephen Davies, Chris Gazey and Peter Tozer, Department of Agriculture 4. Furrow and ridges to prevent waterlogging, Dr Derk Bakker, Department of Agriculture 5. Nitrous oxide emissions from a cropped soil in Western Australia, Louise Barton1, David Gatter2, Renee Buck1, Daniel Murphy1, Christoph Hinz1and Bill Porter2 1School of Earth and Geographical Sciences, The University of Western Australia, 2Department of Agriculture GROWER DECISIONS 6. Managing the unmanageable, Bill Bowden Department of Agriculture 7. Review of climate model summaries reported in Department of Agriculture’s Season Outlook, Meredith Fairbanks, Department of Agriculture 8. Mapping the frost risk in Western Australia, Nicolyn Short and Ian Foster, Department of Agriculture 9. .35 kg/ha.day and other myths, James Fisher, Doug Abrecht and Mario D’Antuono, Department of Agriculture 10. Gaining with growers – Lessons from a successful alliance of WA Grower Groups, Tracey M. Gianatti, Grower Group Alliance 11. WA Agribusiness Trial Network Roundup – 2005, Paul Carmody, Local Farmer Group Network, UWA 12. Drivers of no-till adoption, Frank D’Emdenabc, Rick Llewellynabdand Michael Burtonb,aCRC Australian Weed Management; bSchool of Agricultural and Resource Economics, UWA. cDepartment of Agriculture, dCSIRO Sustainable Ecosystems, Adelaide PRODUCTION SYSTEMS, PRECISION AGRICULTURE AND SUSTAINABILITY 13. Maintaining wheat and lupin yields using phase pastures and shielded sprayers to manage increasing herbicide resistance, Caroline Peek, Nadine Eva, Chris Carter and Megan Abrahams, Department of Agriculture 14. Analaysis of a wheat-pasture rotation in the 330mm annual rainfall zone using the STEP model, Andrew Blake and Caroline Peek, Department of Agriculture 15. Response to winter drought by wheat on shallow soil with low seeding rate and wide row spacing, Paul Blackwell1, Sylvain Pottier2and Bill Bowden1 1 Department of Agriculture; 2Esitpa (France) 16. How much yield variation do you need to justify zoning inputs? Michael Robertson and Greg Lyle, CSIRO Floreat, Bill Bowden, Department of Agriculture; Lisa Brennan, CSIRO Brisbane 17. Automatic guidance and wheat row position: On-row versus between-row seeding at various rates of banded P fertilisers, Tony J. Vyn1, Simon Teakle2, Peter Norris3and Paul Blackwell4,1Purdue University, USA; 2Landmark; 3Agronomy for Profit; 4 Department of Agriculture 18. Assessing the sustainability of high production systems (Avon Agricultural Systems Project), Jeff Russell and James Fisher, Department of Agriculture, Roy Murray-Prior and Deb Pritchard, Muresk Institute; Mike Collins, ex WANTFA, 19. The application of precision agriculture techniques to assess the effectiveness of raised beds on saline land in WA, Derk Bakker, Greg Hamilton, Rob Hetherington, Andrew Van Burgel and Cliff Spann, Department of Agricultur

Crop Updates 2005 - Geraldton

This session covers seventeen papers from different authors 2005 Seasonal Outlook, David Stephens and Nicola Telcik, Department of Agriculture Horses for Courses – using the best tools to manage climate risk, Cameron Weeks, Mingenew-Irwin Group / Planfarm and Richard Quinlan, Planfarm Agronomy Global influences driving Australian agriculture, Tony Harman, Australian Government Department of Agriculture, Fisheries and Forestry Wheat yield and quality improvements – where have they come from and can we have more? Wal Anderson, Department of Agriculture Rotations for nematode management, Vivien A. Vanstone, Sean J. Kelly, Helen F. Hunter and Mena C. Gilchrist, Department of Agriculture Integrate strategies to manage stripe rust risk, Ciara Beard, Geoff Thomas, Robert Loughman, Kith Jayasena and Manisha Shenkar, Department of Agriculture Frequency of herbicide resistance in wild radish populations across the WA wheatbelt, Dr Michael Walsh, Mechelle Owen and Prof. Stephen Powels, University of Western Australia The incidence and severity of wild radish resistance in the NAR – results from an in-situ survey, Rob Grima and Andrew Blake, Elders Limited Stubble management: the pros and cons of different methods, Bill Bowden, Department of Agriculture, Mike Collins WANTFA Effectiveness of Zinc Application Methods in Wheat, Luigi Moreschi, CSBP Know your Mo, Douglas Hamilton, Department of Agriculture Atrazine contamination of groundwater in the agricultural region of Western Australia, Russell Speed1, Neil Rothnie2, John Simons1, Ted Spadek2, and John Moore1, 1Department of Agriculture, 2Chemistry Centre (W.A.) Comparison of canola varieties in the Northern Agricultural Region in 2004, Graham Walton Department of Agriculture Pasture rotations are a promising option for sandplain production, Nadine Eva, Department of Agriculture Zone management can improve profit on sandplain, Bindi Webb, Damian Shepherd, Department of Agriculture, David Forrester, Davejeff Farms, casuarinas via Geraldton, Peter Tozer, Department of Agriculture Crop leftovers: what’s in stubble for sheep? Roy Butler and Keith Croker, Department of Agriculture Realising Rural Equity, Nathan Windebank, Australian Agricultural Contracts Limite

Rabies Postexposure Prophylaxis, New York, 1995–2000

The epidemiology of human rabies postexposure prophylaxis (PEP) in 4 upstate New York counties was described from data obtained from 2,216 incidences of PEP recorded by local health departments from 1995 to 2000. Overall annual incidence for the study period was 27 cases per 100,000 persons. Mean annual PEP incidence rates were highest in rural counties and during the summer months. PEP incidence was highest among patients 5–9 and 30–34 years of age. Bites accounted for most PEP (51%) and were primarily associated with cats and dogs. Bats accounted for 30% of exposures, more than any other group of animals; consequently, bats have replaced raccoons as the leading rabies exposure source to humans in this area