Modeling Symmetric Macromolecular Structures in Rosetta3

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems

1992: Abilene Christian College Bible Lectures - Full Text

CORINTH REVISITED: Studies in I Corinthians Being the Abilene Christian University Annual Bible Lectures 1992 Published by ACU PRESS 1634 Campus Court Abilene, Texas 7960

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu

Black Hole Spectroscopy: Testing General Relativity through Gravitational Wave Observations

Assuming that general relativity is the correct theory of gravity in the strong field limit, can gravitational wave observations distinguish between black hole and other compact object sources? Alternatively, can gravitational wave observations provide a test of one of the fundamental predictions of general relativity? Here we describe a definitive test of the hypothesis that observations of damped, sinusoidal gravitational waves originated from a black hole or, alternatively, that nature respects the general relativistic no-hair theorem. For astrophysical black holes, which have a negligible charge-to-mass ratio, the black hole quasi-normal mode spectrum is characterized entirely by the black hole mass and angular momentum and is unique to black holes. In a different theory of gravity, or if the observed radiation arises from a different source (e.g., a neutron star, strange matter or boson star), the spectrum will be inconsistent with that predicted for general relativistic black holes. We give a statistical characterization of the consistency between the noisy observation and the theoretical predictions of general relativity, together with a numerical example.Comment: 19 pages, 7 figure

Effects of canagliflozin on myocardial infarction:a post hoc analysis of the CANVAS Program and CREDENCE trial

AIMS: Given the benefits of sodium glucose co-transporter 2 inhibition (SGLT2i) in protecting against heart failure in diabetic patients, we sought to explore the potential impact of SGLT2i on the clinical features of patients presenting with myocardial infarction (MI) through a post-hoc analysis of CANVAS Program and CREDENCE trial.METHODS AND RESULTS: Individuals with type 2 diabetes and history or high risk of cardiovascular disease (CANVAS Program) or type 2 diabetes and chronic kidney disease (CREDENCE) were included. The intervention was Canagliflozin 100 or 300 mg (combined in the analysis) or placebo. MI events were adjudicated as ST-elevation myocardial infarction (STEMI), non-STEMI as well as type 1 MI or type 2 MI. 421 first MI events in the CANVAS Program and 178 first MI events in the CREDENCE trial were recorded (83 fatal, 128 STEMI, 431 non-STEMI, and 40 unknown). No benefit of canagliflozin compared with placebo on time to first MI event was observed (HR 0.89; 95% CI 0.75, 1.05). Canagliflozin was associated with lower risk for non-STEMI (HR 0.78; 95% CI 0.65, 0.95) but suggested a possible increase in STEMI (HR 1.55; 95% CI 1.06, 2.27), with no difference in risk of type 1 or type 2 MI. There was no change in fatal MI (HR 1.22, 95% CI 0.78, 1.93).CONCLUSIONS: Canagliflozin was not associated with a reduction in overall MI in the pooled CANVAS Program and CREDENCE trial population. The possible differential effect on STEMI and Non-STEMI observed in the CANVAS cohort warrants further investigation.</p

The Head-On Collision of Two Equal Mass Black Holes Peter Anninos

We study the head-on collision of two equal mass, nonrotating black holes. Various initial configurations are investigated, including holes which are initially surrounded by a common apparent horizon to holes that are separated by about $20M$, where $M$ is the mass of a single black hole. We have extracted both $\ell = 2$ and $\ell=4$ gravitational waveforms resulting from the collision. The normal modes of the final black hole dominate the spectrum in all cases studied. The total energy radiated is computed using several independent methods, and is typically less than $0.002 M$. We also discuss an analytic approach to estimate the total gravitational radiation emitted in the collision by generalizing point particle dynamics to account for the finite size and internal dynamics of the two black holes. The effects of the tidal deformations of the horizons are analysed using the membrane paradigm of black holes. We find excellent agreement between the numerical results and the analytic estimates.Comment: 33 pages, NCSA 94-048, WUGRAV-94-

Pan-European rural monitoring network shows dominance of NH3 gas and NH4NO3 aerosol in inorganic atmospheric pollution load

A comprehensive European dataset on monthly atmospheric NH3, acid gases (HNO3, SO2, HCl), and aerosols (NH4+, NO3-, SO42-, Cl−, Na+, Ca2+, Mg2+) is presented and analysed. Speciated measurements were made with a low-volume denuder and filter pack method (DEnuder for Long-Term Atmospheric sampling, DELTA®) as part of the EU NitroEurope (NEU) integrated project. Altogether, there were 64 sites in 20 countries (2006–2010), coordinated between seven European laboratories. Bulk wet-deposition measurements were carried out at 16 co-located sites (2008–2010). Inter-comparisons of chemical analysis and DELTA® measurements allowed an assessment of comparability between laboratories. The form and concentrations of the different gas and aerosol components measured varied between individual sites and grouped sites according to country, European regions, and four main ecosystem types (crops, grassland, forests, and semi-natural). The smallest concentrations (with the exception of SO42- and Na+) were in northern Europe (Scandinavia), with broad elevations of all components across other regions. SO2 concentrations were highest in central and eastern Europe, with larger SO2 emissions, but particulate SO42- concentrations were more homogeneous between regions. Gas-phase NH3 was the most abundant single measured component at the majority of sites, with the largest variability in concentrations across the network. The largest concentrations of NH3, NH4+ and NO-3 were at cropland sites in intensively managed agricultural areas (e.g. Borgo Cioffi in Italy), and the smallest were at remote semi-natural and forest sites (e.g. Lompolojänkkä, Finland), highlighting the potential for NH3 to drive the formation of both NH4+ and NO3- aerosol. In the aerosol phase, NH4+ was highly correlated with both NO3- and SO42-, with a near-1:1 relationship between the equivalent concentrations of NH4+ and sum(NO3- + SO42-) of which around 60 % was as NH4NO3. Distinct seasonality was also observed in the data, influenced by changes in emissions, chemical interactions, and the influence of meteorology on partitioning between the main inorganic gases and aerosol species. Springtime maxima in NH3 were attributed to the main period of manure spreading, while the peak in summer and trough in winter were linked to the influence of temperature and rainfall on emissions, deposition, and gas–aerosol-phase equilibrium. Seasonality in SO2 was mainly driven by emissions (combustion), with concentrations peaking in winter, except in southern Europe, where the peak occurred in summer. Particulate SO42− showed large peaks in concentrations in summer in southern and eastern Europe, contrasting with much smaller peaks occurring in early spring in other regions. The peaks in particulate SO42- coincided with peaks in NH3 concentrations, attributed to the formation of the stable (NH4)2SO4. HNO3 concentrations were more complex, related to traffic and industrial emissions, photochemistry, and HNO3:NH4NO3 partitioning. While HNO3 concentrations were seen to peak in the summer in eastern and southern Europe (increased photochemistry), the absence of a spring peak in HNO3 in all regions may be explained by the depletion of HNO3 through reaction with surplus NH3 to form the semi-volatile aerosol NH4NO3. Cooler, wetter conditions in early spring favour the formation and persistence of NH4NO3 in the aerosol phase, consistent with the higher springtime concentrations of NH4+ and NO3−. The seasonal profile of NO3- was mirrored by NH4+, illustrating the influence of gas–aerosol partitioning of NH4NO3 in the seasonality of these components. Gas-phase NH3 and aerosol NH4NO3 were the dominant species in the total inorganic gas and aerosol species measured in the NEU network. With the current and projected trends in SO2, NOx , and NH3 emissions, concentrations of NH3 and NH4NO3 can be expected to continue to dominate the inorganic pollution load over the next decades, especially NH3, which is linked to substantial exceedances of ecological thresholds across Europe. The shift from (NH4)2SO4 to an atmosphere more abundant in NH4NO3 is expected to maintain a larger fraction of reactive N in the gas phase by partitioning to NH3 and HNO3 in warm weather, while NH4NO3 continues to contribute to exceedances of air quality limits for PM2.5

Crop Updates 2000 - Weeds

This session covers thirty six papers from different authors: INTRODUCTION, Vanessa Stewart Agriculture Western Australia INTEGRATED WEED MANAGEMENT Effect of seeding density, row spacing and Trifluralin on the competitive ability of Annual Ryegrass in a minimum tillage system, David Minkey, Abul Hashem, Glen Riethmuller and Martin Harries, Agriculture Western Australia High wheat seeding rates coupled with narrow row spacing increases yield and suppresses grass, Peter Newman1 and Cameron Weeks2,1Agronomist, Elders Limited 2Mingenew/Irwin Group Resistant ryegrass management in a wheat – lupin rotation, Abul Hashem, Harmohinder S. Dhammu, Aik Cheam, David Bowran and Terry Piper, Agriculture Western Australia Integrated weed management – Will it work with my rotation? Alexandra Wallace, Agriculture Western Australia Long term herbicide resistance trial – Mingenew, Peter Newman Elders, Cameron Weeks Mingenew-Irwin Group Is two years enough? Bill Roy, Agricultural Consulting and Research Services The fate of ryegrass seed when sheep graze chaff cart heaps, Keith L. Devenish1 and Lisa J. Leaver2 1 Agriculture Western Australia, 2Curtin University of Technology, Muresk Institute of Agriculture Can blanket wiping and crop topping prevent seed set of resistant wild radish and mustard? StAbul Hashem, Harmohinder Dhammu, Vanessa Stewart, Brad Rayner and Mike Collins, Agriculture Western Australia The value of green manuring in the integrated management of ryegrass, Marta Monjardino1,2, David Pannell2, Stephen Powles1 ,1Western Australia Herbicide Resistance Initiative, 2Agricultural and Resource Economics, University of Western Australia Some ways of increasing wheat competitiveness against ryegrass,, Mike Collins Centre for Cropping Systems, Agriculture Western Australia WEED BIOLOGY Understanding and driving weed seed banks to very low levels, Sally Peltzer, Agriculture Western Australi HERBICIDE RESISTANCE Cross resistance of chlorsulfuron-resistant wild radish to imidazolinones, Abul Hashem, Harmohinder Dhammu and David Bowran, Agriculture Western Australia Investigation of suspected triazine resistant ryegrass populations for cross-resistance and multiple resistance to herbicides, Michael Walsh, Charles Boyle and Stephen Powles, Western Australian Herbicide Resistance Initiative, University of Western Australia Genetics and fitness of glyphosate resistant ryegrass, S. Powles1, P. Neve1, D. Lorraine-Colwill2, C. Preston2 ,1WAHRI, University of Western Australia 2 CRC Weed Management Systems, University of Adelaide Managing herbicide resistance – the effect of local extinction of resistance genes, Art Diggle1, Paul B. Neve2, Stephen B. Powles2 ,1Agriculture Western Australia, 2WAHRI, Faculty of Agriculture, University of Western Australia The double knock - the best strategy for conserving glyphosate susceptibility? Paul B. Neve1, Art Diggle2, Stephen B. Powles1,1WAHRI, Faculty of Agriculture, University of Western Australia, 2Agriculture Western Australia Wild radish had evolved resistance to triazines, Abul Hashem, Harmohinder S. Dhammu, David Bowran and Aik Cheam, Agriculture Western Australia Ryegrass resistance in Western Australia – where and how much? Rick Llewellyn and Stephen Powles, Western Australian Herbicide Resistance Initiative, Faculty of Agriculture, University of Western Australia Wild radish herbicide resistance survey, Michael Walsh, Ryan Duane and Stephen Powles, Western Australian Herbicide Resistance Initiative, University of Western Australia Knockdown resistance in the Western Australian wheatbelt – a proposed survey, Paul B. Neve1, Abul Hashem2, Stephen B. Powles1,1Western Australian Herbicide Resistance Initiative, University of Western Australia, 2Agriculture Western Australia Diflufenican resistant wild radish, Aik Cheam, Siew Lee, David Bowran, David Nicholson and Abul Hashem, Agriculture Western Australi Multiple resistance to triazines and diflufenican further complicates wild radish control, Aik Cheam, Siew Lee, David Bowran, David Nicholson and Abul Hashem, Agriculture Western Australia HERBICIDE TOLERANCE 25. Herbicide tolerance of lupins, Terry Piper, Weed Science Group, Agriculture Western Australia 26. Tanjil lupins will tolerate metribuzin under the right conditions, Peter Newman, Agronomist Elders Limited and Cameron Weeks, Mingenew/Irwin Group 27. Herbicide damage does not mean lower yield in Lupins, Peter Carlton, Trials Coordinator, Elders Limited 28. Herbicide tolerance of new pea varieties, Dr Terry Piper, Agriculture Western Australia 29. Herbicide tolerance of (waterlogged) wheat, Dr Terry Piper, Agriculture Western Australia 30. Wheat tolerance trials – Mingenew 1999, Peter Newman1, Cameron Weeks2 and Stewart Smith3,1Elders, Mingenew, 2Mingenew-Irwin Group,3Agriculture Western Australia ISSUES OF TRIFLURALIN USE 31. Trifluralin works better on ryegrass when no-tilling into thick wheat stubbles as granules, or mixed with limesand, Bill Crabtree, WANTFA Scientific Officer 32. Increasing trifluralin rate did not compensate for delaying incorporation, Bill Crabtree, WANTFA Scientific Officer 33. Poor emergence survey, 1999, Terry Piper, Weed Science Group, Agriculture Western Australia HERBICIDES – ISSUES AND OPTIONS 34. AFFINITY 400DF – A new herbicide with a new mode of action (Group G) for Broadleaf Weed Control in Cereals, Gordon Cumming, Technical Officer, Crop Care Australasia 35 Herbicide screening for Marshmallow, David Minkey1 and David Cameron2,1Agriculture Western Australia, 2Elders Ltd, Merredin 36. The control of Capeweed in Clearfield Production System for Canola, Mike Jackson and Scott Paton, Cyanamid Agriculture Pty Ltd 37.Effect of herbicides Tordonä 75D and Lontrelä,used for eradication of Skeleton Weed, on production of Lupins I the following seasons, John R. Peirce and Brad J. Rayner, Agriculture Western Australia INDUSTRY PROTECTION 38. Graingaurd – Opportunities for agribusiness to help protect the West Australian grains industry, Greg Shea, Executive Officer, GrainGuard Agriculture Western Australi

Glastir Monitoring & Evaluation Programme. First year annual report

The Welsh Government has commissioned a comprehensive new ecosystem monitoring and evaluation programme to monitor the effects of Glastir, its new land management scheme, and to monitor progress towards a range of international biodiversity and environmental targets. A random sample of 1 km squares stratified by landcover types will be used both to monitor change at a national level in the wider countryside and to provide a backdrop against which intervention measures are assessed using a second sample of 1 km squares located in areas eligible for enhanced payments for advanced interventions. Modelling in the first year has forecast change based on current understanding, whilst a rolling national monitoring programme based on an ecosystem approach will provide an evidence-base for on-going, adaptive development of the scheme by Welsh Government. To our knowledge, this will constitute the largest and most in-depth ecosystem monitoring and evaluation programme of any member state of the European Union