bluuebunny/crossref_metadata_2025 huggingface dataset:
An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants
Authors: Wisz Michael S. , Hellinga Homme W.
Published: April 2003

Here we introduce an electrostatic model that treats the complexity of electrostatic interactions in a heterogeneous protein environment by using multiple parameters that take into account variations in protein geometry, local structure, and the type of interacting residues. The optimal values for these parameters were obtained by fitting the model to a large dataset of 260 experimentally determined pKa values distributed over 41 proteins. We obtain fits between the calculated and observed values that are significantly better than the null model. The model performs well on the groups that exhibit large pKa shifts from solution values in response to the protein environment and compares favorably with other, successful continuum models. The empirically determined values of the parameters correlate well with experimentally observed contributions of hydrogen bonds and ion pairs as well as theoretically predicted magnitudes of charge‐charge and charge‐polar interactions. The magnitudes of the dielectric constants assigned to different regions of the protein rank according to the strength of the relaxation effects expected for the core, boundary, and surface. The electrostatic interactions in this model are pairwise decomposable and can be calculated rapidly. This model is therefore well suited for the large computations required for simulating protein properties and especially for prediction of mutations for protein design. Proteins 2003;51:360–377. © 2003 Wiley‐Liss, Inc.
A novel shape complementarity scoring function for protein‐protein docking
Authors: Chen Rong , Weng Zhiping
Published: April 2003

Shape complementarity is the most basic ingredient of the scoring functions for protein‐protein docking. Most grid‐based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and the ligand within a distance cutoff. When applied to a benchmark of 49 test cases, PSC consistently ranks near‐native structures higher and produces more near‐native structures than the traditional grid‐based function, and the improvement was seen across all prediction levels and in all categories of the benchmark. Without any post‐processing or biological information about the binding site except the complementarity‐determining region of antibodies, PSC predicts the complex structure correctly for 6 test cases, and ranks at least one near‐native structure in the top 20 predictions for 18 test cases. Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (http://zlab.bu.edu/∼rong/dock). Proteins 2003;51:397–408. © 2003 Wiley‐Liss, Inc.
Molecular dynamics simulations of enhanced green fluorescent proteins: Effects of F64L, S65T and T203Y mutations on the ground‐state proton equilibria
Authors: Nifosì R. , Tozzini V.
Published: April 2003

Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y‐EGFP (E2GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (ΔGAB) upon T203Y mutation. The resulting ΔΔGAB agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E2GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single‐molecule experiments. Proteins 2003;51:378–389. © 2003 Wiley‐Liss, Inc.
Monte Carlo estimation of the number of possible protein folds: Effects of sampling bias and folds distributions
Authors: Leonov Hadas , Mitchell Joseph S.B. , Arkin Isaiah T.
Published: April 2003

The estimation of the number of protein folds in nature is a matter of considerable interest. In this study, a Monte Carlo method employing the broken stick model is used to assign a given number of proteins into a given number of folds. Subsequently, random, integer, non‐repeating numbers are generated in order to simulate the process of fold discovery. With this conceptual framework at hand, the effects of two factors upon the fold identification process were investigated: (1) the nature of folds distributions and (2) preferential sampling bias of previously identified folds. Depending on the type of distribution, dividing 100,000 proteins into 1,000 folds resulted in 10–30% of the folds having 10 proteins or less per fold, approximately 10% of the folds having 10–20 proteins per fold, 31–45% having 20–100 proteins per fold, and >30% of the folds having more than 100 proteins per fold. After randomly sampling one tenth of the proteins, 68–96% of the folds were identified. These percentages depend both on folds distribution and biased/non‐biased sampling. Only upon increasing the sampling bias for previously identified folds to 1,000, did the model result in a reduction of the number of proteins identified by an order of magnitude (approximately 9%). Thus, assuming the structures of one tenth of the population of proteins in nature have been solved, the results of the Monte Carlo simulation are more consistent with recent lower estimates of the number of folds, ≤1,000. Any deviation from this estimate would reflect significant bias in the experimental sampling of protein structure, and/or substantially nonuniform folds distribution, manifested in a large number of single‐fold proteins. Proteins 2003;51:352–359. © 2003 Wiley‐Liss, Inc.
Increased detection of structural templates using alignments of designed sequences
Authors: Larson Stefan M. , Garg Amit , Desjarlais John R. , Pande Vijay S.
Published: April 2003

Protein structure prediction by comparative modeling benefits greatly from the use of multiple sequence alignment information to improve the accuracy of structural template identification and the alignment of target sequences to structural templates. Unfortunately, this benefit is limited to those protein sequences for which at least several natural sequence homologues exist. We show here that the use of large diverse alignments of computationally designed protein sequences confers many of the same benefits as natural sequences in identifying structural templates for comparative modeling targets. A large‐scale massively parallelized application of an all‐atom protein design algorithm, including a simple model of peptide backbone flexibility, has allowed us to generate 500 diverse, non‐native, high‐quality sequences for each of 264 protein structures in our test set. PSI‐BLAST searches using the sequence profiles generated from the designed sequences (“reverse” BLAST searches) give near‐perfect accuracy in identifying true structural homologues of the parent structure, with 54% coverage. In 41 of 49 genomes scanned using reverse BLAST searches, at least one novel structural template (not found by the standard method of PSI‐BLAST against PDB) is identified. Further improvements in coverage, through optimizing the scoring function used to design sequences and continued application to new protein structures beyond the test set, will allow this method to mature into a useful strategy for identifying distantly related structural templates. Proteins 2003;51:390–396. © 2003 Wiley‐Liss, Inc.
Cooperative fluctuations of unliganded and substrate‐bound HIV‐1 protease: A structure‐based analysis on a variety of conformations from crystallography and molecular dynamics simulations
Authors: Kurt Nese , Scott Walter R.P. , Schiffer Celia A. , Haliloglu Turkan
Published: April 2003

The dynamics of HIV‐1 protease, both in unliganded and substrate‐bound forms have been analyzed by using an analytical method, Gaussian network model (GNM). The method is applied to different conformations accessible to the protein backbone in the native state, observed in crystal structures and snapshots from fully atomistic molecular dynamics (MD) simulation trajectories. The modes of motion obtained from GNM on different conformations of HIV‐1 protease are conserved throughout the MD simulations. The flaps and 40's loop of the unliganded HIV‐1 protease structure are identified as the most mobile regions. However, in the liganded structure these flaps lose mobility, and terminal regions of the monomers become more flexible. Analysis of the fast modes shows that residues important for stability are in the same regions of all the structures examined. Among these, Gly86 appears to be a key residue for stability. The contribution of residues in the active site region and flaps to the stability is more pronounced in the substrate‐bound form than in the unliganded form. The convergence of modes in GNM to similar regions of HIV‐1 protease, regardless of the conformation of the protein, supports the robustness of GNM as a potentially useful and predictive tool. Proteins 2003;51:409–422. © 2003 Wiley‐Liss, Inc.
Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects
Authors: Das Bedamati , Meirovitch Hagai
Published: April 2003

A new procedure for optimizing parameters of implicit solvation models introduced by us has been applied successfully first to cyclic peptides and more recently to three surface loops of ribonuclease A (Das and Meirovitch, Proteins 2001;43:303–314) using the simplified model Etot = EFF(ε = nr) + Σi σiAi, where σi are atomic solvation parameters (ASPs) to be optimized, Ai is the solvent accessible surface area of atom i, EFF(ε = nr) is the AMBER force‐field energy of the loop‐loop and loop‐template interactions with a distance‐dependent dielectric constant, ε = nr, where n is a parameter. The loop is free to move while the protein template is held fixed in its X‐ray structure; an extensive conformational search for energy minimized loop structures is carried out with our local torsional deformation method. The optimal ASPs and n are those for which the structure with the lowest minimized energy [Etot(n,σi)] becomes the experimental X‐ray structure, or less strictly, the energy gap between these structures is within 2–3 kcal/mol. To check if a set of ASPs can be defined, which is transferable to a large number of loops, we optimize individual sets of ASPs (based on n = 2) for 12 surface loops from which an “averaged” best‐fit set is defined. This set is then applied to the 12 loops and an independent “test” group of 8 loops leading in most cases to very small RMSD values; thus, this set can be useful for structure prediction of loops in homology modeling. For three loops we also calculate the free energy gaps to find that they are only slightly smaller than their energy counterparts, indicating that only larger n will enable reducing too large gaps. Because of its simplicity, this model allowed carrying out an extensive application of our methodology, providing thereby a large number of benchmark results for comparison with future calculations based on n > 2 as well as on more sophisticated solvation models with as yet unknown performance for loops. Proteins 2003;51:470–483. © 2003 Wiley‐Liss, Inc.
3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor
Authors: Fischer Daniel
Published: April 2003

To gain a better understanding of the biological role of proteins encoded in genome sequences, knowledge of their three‐dimensional (3D) structure and function is required. The computational assignment of folds is becoming an increasingly important complement to experimental structure determination. In particular, fold‐recognition methods aim to predict approximate 3D models for proteins bearing no sequence similarity to any protein of known structure. However, fully automated structure‐prediction methods can currently produce reliable models for only a fraction of these sequences. Using a number of semiautomated procedures, human expert predictors are often able to produce more and better predictions than automated methods. We describe a novel, fully automatic, fold‐recognition meta‐predictor, named 3D‐SHOTGUN, which incorporates some of the strategies human predictors have successfully applied. This new method is reminiscent of the so‐called cooperative algorithms of Computer Vision. The input to 3D‐SHOTGUN are the top models predicted by a number of independent fold‐recognition servers. The meta‐predictor consists of three steps: (i) assembly of hybrid models, (ii) confidence assignment, and (iii) selection. We have applied 3D‐SHOTGUN to an unbiased test set of 77 newly released protein structures sharing no sequence similarity to proteins previously released. Forty‐six correct rank‐1 predictions were obtained, 30 of which had scores higher than that of the first incorrect prediction—a significant improvement over the performance of all individual servers. Furthermore, the predicted hybrid models were, on average, more similar to their corresponding native structures than those produced by the individual servers. This opens the possibility of generating more accurate, full‐atom homology models for proteins with no sequence similarity to proteins of known structure. These improvements represent a step forward toward the wider applicability of fully automated structure‐prediction methods at genome scales. Proteins 2003;51:434–441. © 2003 Wiley‐Liss, Inc.
Role of β‐lactam carboxyl group on binding of penicillins and cephalosporins to class C β‐lactamases
Authors: Fenollar‐Ferrer Cristina , Frau Juan , Donoso Josefa , Muñoz Francisco
Published: April 2003

Molecular models for the Henry Michaelis complexes of Enterobacter cloacae, a class C β‐lactamase, with penicillin G and cephalotin have been constructed by using molecular mechanic calculations, based on the AMBER force field, to examine the molecular differentiation mechanisms between cephalosporins and penicillins in β‐lactamases. Ser318Ala and Thr316Ala mutations in both complexes and Asn346Ala and Thr316Ala/Asn346Ala double mutation in penicillin G complex have also been studied. Results confirm that Thr316, Ser318, and Asn346 play a crucial role in the substrate recognition, via their interactions with one of the oxygens of the antibiotic carboxyl group. Both mutation Ser318Ala and Thr316Ala strongly affect the correct binding of cephalotin to P99, the first mainly by precluding the discriminating salt bridge between carboxyl and serine OH groups, and the second one by the Ser318, Lys315, and Tyr150 spatial rearrangements. On the other hand, Ser318Ala mutation has little effect on penicillin G binding, but the Thr316Ala/Asn346Ala double mutation causes the departure of the antibiotic from the oxyanion hole. Molecular dynamic simulations allow us to interpret the experimental results of some class C and A β‐lactamases. Proteins 2003;51:442–452. © 2003 Wiley‐Liss, Inc.
Atomic resolution structure of prokaryotic phospholipase A2: Analysis of internal motion and implication for a catalytic mechanism
Authors: Matoba Yasuyuki , Sugiyama Masanori
Published: April 2003

We have found a secreted phospholipase A2 (PLA2, EC 3.1.1.4) from Streptomyces violaceoruber A‐2688, which is the first PLA2 identified in prokaryote, and determined its tertiary structure by NMR and X‐ray analyses. In this study, we collected the X‐ray diffraction data of the bacterial PLA2 at room temperature (297 K) using conventional MoKα radiation and refined the structure at a 1.05 Å resolution. The atomic resolution analysis led us to introduce disordered conformations and hydrogen atoms into a full anisotropic model. The molecular motion, which is expressed as the sum of rigid‐body motion and internal motion of protein, is roughly estimated as the thermal motion when the X‐ray diffraction data are collected at room temperature. In this study, we applied a TLS (rigid‐body motion in terms of translation, libration, and screw motions) model to analyze the rigid‐body motion of the bacterial PLA2 and calculated the internal motion by subtracting the estimate of the rigid‐body motion from the observed anisotropic temperature factor. We also subjected the TLS model to estimate the internal motion of the bovine pancreatic PLA2 using the anisotropic temperature factor deposited in the Protein Data Bank. Both results indicate that the localization of regions exhibiting larger internal motion in the bacterial PLA2 is almost the same as that in the bovine pancreatic PLA2, suggesting that although the tertiary structure of the bacterial PLA2 is strikingly different from that of the bovine pancreatic PLA2, the internal motion, which is associated with the calcium(II) ion‐binding, phospholipid‐binding, and allosteric interfacial activation, is commonly observed in both PLA2s. Proteins 2003;51:453–469. © 2003 Wiley‐Liss, Inc.
NAD+‐dependent DNA ligases of Mycobacterium tuberculosis and Streptomyces coelicolor
Authors: Wilkinson Adam , Sayer Heather , Bullard Desmond , Smith Andrew , Day Jonathan , Kieser Tobias , Bowater Richard
Published: April 2003

Sequencing of the genomes of Mycobacterium tuberculosis H37Rv and Streptomyces coelicolor A3(2) identified putative genes for an NAD+‐dependent DNA ligase. We have cloned both open reading frames and overexpressed the protein products in Escherichia coli. In vitro biochemical assays confirm that each of these proteins encodes a functional DNA ligase that uses NAD+ as its cofactor. Expression of either protein is able to complement E. coli GR501, which carries a temperature‐sensitive mutation in ligA. Thus, in vitro and in vivo analyses confirm predictions that ligA genes from M. tuberculosis and S. coelicolor are NAD+‐dependent DNA ligases. Proteins 2003;51:321–326. © 2003 Wiley‐Liss, Inc.
Structure‐based identification of binding sites, native ligands and potential inhibitors for G‐protein coupled receptors
Authors: Cavasotto Claudio N. , Orry Andrew J.W. , Abagyan Ruben A.
Published: April 2003

G‐protein coupled receptors (GPCRs) are the largest family of cell‐surface receptors involved in signal transmission. Drugs associated with GPCRs represent more than one fourth of the 100 top‐selling drugs and are the targets of more than half of the current therapeutic agents on the market. Our methodology based on the internal coordinate mechanics (ICM) program can accurately identify the ligand‐binding pocket in the currently available crystal structures of seven transmembrane (7TM) proteins [bacteriorhodopsin (BR) and bovine rhodopsin (bRho)]. The binding geometry of the ligand can be accurately predicted by ICM flexible docking with and without the loop regions, a useful finding for GPCR docking because the transmembrane regions are easier to model. We also demonstrate that the native ligand can be identified by flexible docking and scoring in 1.5% and 0.2% (for bRho and BR, respectively) of the best scoring compounds from two different types of compound database. The same procedure can be applied to the database of available chemicals to identify specific GPCR binders. Finally, we demonstrate that even if the sidechain positions in the bRho binding pocket are entirely wrong, their correct conformation can be fully restored with high accuracy (0.28 Å) through the ICM global optimization with and without the ligand present. These binding site adjustments are critical for flexible docking of new ligands to known structures or for docking to GPCR homology models. The ICM docking method has the potential to be used to “de‐orphanize” orphan GPCRs (oGPCRs) and to identify antagonists–agonists for GPCRs if an accurate model (experimentally and computationally validated) of the structure has been constructed or when future crystal structures are determined. Proteins 2003;51:423–433. © 2003 Wiley‐Liss, Inc.
Patch spraying: future role of electronics in limiting pesticide use
Authors: Miller Paul CH
Published: April 2003

Developments relating to the control of application equipment can deliver improvements in pesticide use by better matching applications to target requirements. This may have components relating to the spatial distribution of a weed, pest or disease or methods by which the target, particularly a crop canopy, can be described with respect to a given application. Changes in application can relate to the dose and/or volume applied, but may also concern the way in which a treatment is delivered in terms of parameters such as spray trajectory angle and droplet size distribution. For many weed species there is evidence of patchy distributions in field situations. Studies have shown that savings of typically up to 40% in herbicide use can be achieved by adopting patch spraying approaches in such situations. Weed patch detection is key to the performance of such patch spraying systems. In widely spaced rowcrops such as vegetables, there is considerable scope for developing fully automated detection systems based on image analysis, and for the development of accurate guidance systems that apply pesticides only to the crop row. In crops with a relatively high plant density, weed detection in the medium/short term is likely to be based on manual discrimination. The costs of labour for manual weed patch mapping have been estimated at less than £1.50 ha−1. Potential savings in pesticide use can also be made if applications are matched to crop canopy structure. This is most important in bush and tree crops where savings of up to 75% in pesticide use could be achieved. In crops such as cereals, studies have shown that savings in fungicide use may be possible, particularly at earlier stages of growth by adjusting spray delivery to measured canopy characteristics. Key components of the performance of application systems concern the ability to deliver over a dose rate range of more than 3:1 while maintaining control of variables such as delivery trajectory angle and spray quality. Traceability and the effective monitoring of applications is likely to be a major driver influencing the uptake of more sophisticated control systems. Methods of labelling pesticides with systems that can be read by the application unit will be an important step in the development of recording and data handling systems that will operate safely with the minimum of operator input and enable the environmental advantages of targeted pesticide application to be monitored. Copyright © 2003 Society of Chemical Industry
Growing vegetables in developing countries for local urban populations and export markets: problems confronting small‐scale producers
Authors: Dinham Barbara
Published: April 2003

Vegetables attract high applications of pesticides, and farmers in developing countries use many acutely toxic insecticides to control pests on these crops. With the liberalisation of agricultural markets in developing countries, the number of small‐scale farmers growing vegetables for both domestic and export markets is increasing. Demand for supplies of year‐round and exotic fruit and vegetables has grown in industrialised countries, but with rising quality standards and traceability requirements it is difficult for small‐scale farmers to benefit from this lucrative non‐traditional agricultural export trade. The demand is high for vegetables in the expanding cities in developing countries, and farmers in peri‐urban areas, or rural areas with good access to the cities, are in a position to find a growing market for their produce. Poor storage facilities will often mean that farmers are forced to sell at peak times when prices are low. Farmers rarely have access to training in pesticide use, and have only limited or no access to advice on the complicated management of pesticides. The Food and Agriculture Organisation of the UN is concerned about high levels of poor quality and adulterated pesticides on sale in developing countries. Surveys repeatedly show that without training, farmers are unable to make good crop decisions: recognition of pests and their predators is generally low, leading to decisions to spray to kill any insect; knowledge of product selection, application rates and timing is poor; different products are often combined in the belief that the effect will be greater; re‐entry periods after spraying and essential harvest intervals are not known; and without knowledge of alternatives, farmers will often assume that the only solution to pest problems is to spray more frequently. From a consumer's point of view, few developing countries are able to monitor pesticide residues, particularly for produce grown for home consumption: most countries do not have laboratories for even simple residue testing. Changes in European Maximum Residue Limits means that export crops will be rejected if they contain residues at the Limit of Detection of pesticides not registered in Europe. Season‐long field level training in Integrated Pest Management can help farmers to become better decision‐makers, and to greatly reduce pesticide use while reducing risks to their own health and environment, producing safer products for consumers, maintaining yields, and increasing incomes. Copyright © 2003 Society of Chemical Industry
A critical evaluation of the role of alternative oxidase in the performance of strobilurin and related fungicides acting at the Qo site of Complex III
Authors: Wood Paul M , Hollomon Derek W
Published: April 2003

Mitochondrial respiration conserves energy by linking NADH oxidation and electron‐coupled proton translocation with ATP synthesis, through a core pathway involving three large protein complexes. Strobilurin fungicides block electron flow through one of these complexes (III), and disrupt energy supply. Despite an essential need for ATP throughout fungal disease development, strobilurins are largely preventative; indeed some diseases are not controlled at all, and several pathogens have quickly developed resistance. Target‐site variation is not the only cause of these performance difficulties. Alternative oxidase (AOX) is a strobilurin‐insensitive terminal oxidase that allows electrons from ubiquinol to by‐pass Complex III. Its synthesis is constitutive in some fungi but in many others is induced by inhibition of the main pathway. AOX provides a strobilurin‐insensitive pathway for oxidation of NADH. Protons are pumped as electrons flow through Complex I, but energy conservation is less efficient than for the full respiratory chain. Salicylhydroxamic acid (SHAM) is a characteristic inhibitor of AOX, and several studies have explored the potentiation of strobilurin activity by SHAM. We present a kinetic‐based model which relates changes in the extent of potentiation during different phases of disease development to a changing importance of energy efficiency. The model provides a framework for understanding the varying efficacy of strobilurin fungicides. In many cases, AOX can limit strobilurin effectiveness once an infection is established, but is unable to interfere significantly with strobilurin action during germination. A less stringent demand for energy efficiency during early disease development could lead to insensitivity towards this class of fungicides. This is discussed in relation to Botrytis cinerea, which is often poorly controlled by strobilurins. Mutations with a similar effect may explain evidence implicating AOX in resistance development in normally well‐controlled plant pathogens, such as Venturia inaequalis. Copyright © 2003 Society of Chemical Industry
Contribution of contact toxicity and wheat condition to mortality of stored‐product insects exposed to spinosad
Authors: Toews Michael D , Subramanyam Bhadriraju
Published: April 2003

Spinosad, a reduced‐risk commercial insecticide derived from a bacterial fermentation product, possesses both contact and oral toxicities against insects. Contact toxicity of spinosad to adults of Rhyzopertha dominica (F), Sitophilus oryzae (L), and Tribolium castaneum (Herbst) was evaluated by exposure for 24 or 48 h to treated glass Petri dishes. Adults were exposed to different deposits (0.001–0.79 mg cm−2) of spinosad in 24‐h tests and to deposits of 0, 0.0016 and 0.016 mg cm−2 in 48‐h tests. Rhyzopertha dominica was most susceptible to spinosad in 24‐ and 48‐h tests, followed by S oryzae, and T castaneum. The 24‐h LD50 values were 0.0004, 0.077 and 0.189 mg cm−2 for R dominica, S oryzae, and T castaneum, respectively. All R dominica adults were dead following 48 h exposure to both spinosad deposits, whereas mortality of S oryzae and T castaneum ranged from 10 to 85% and 12 to 48%, respectively. Rhyzopertha dominica, T castaneum, and O surinamensis adults were exposed for 14 days to whole wheat, cracked wheat and wheat flour treated with 0, 0.1 and 1.0 mg kg−1 of spinosad. Rhyzopertha dominica adults were highly susceptible to spinosad, followed by O surinamensis and T castaneum. Immatures (eggs and larvae) of T castaneum and O surinamensis exposed for 14 days were more susceptible on spinosad‐treated whole wheat than on treated cracked wheat and wheat flour. This is the first report documenting contact activity of spinosad, and the effect of grain condition on spinosad toxicity, to stored‐product insects. Copyright © 2003 Society of Chemical Industry
Evaluation of probabilistic risk assessment of pesticides in the UK: chlorpyrifos use on top fruit
Authors: Crane Mark , Whitehouse Paul , Comber Sean , Watts Chris , Giddings Jeffrey , Moore Dwayne RJ , Grist Eric
Published: April 2003

The use of probabilistic risk assessment (PRA) for examining chemical impacts has become an important area of debate within the European Union. This paper describes a case study on probabilistic techniques to assess pesticide risks in the UK aquatic environment. The main aim of this paper is to demonstrate both the potential strengths and weaknesses of PRA for assessing pesticides when compared with the conventional deterministic approach, and to examine whether PRA is useful within the European regulatory context. The organophosphate insecticide, chlorpyrifos, was selected as a model compound and toxicity exposure ratios calculated using Monte Carlo analysis and different distributions of spray drift and toxicity values following application to top fruit. Chlorpyrifos is highly toxic to arthropods but less toxic to fishes. Species sensitivity followed a log‐normal distribution when fitted to all toxicity data. Toxicity data quantity had little influence on species sensitivity distribution model parameters when n was greater than 10 species. Below this, estimates were less accurate and precise, possibly because of the inclusion of data from many different sources. Estimates of chlorpyrifos exposure derived from the standard spray drift model differed substantially from measurements of chlorpyrifos in European surface waters. When a distribution based on measured concentrations was used in a PRA, the risk of acute fish mortality was low, and the risk of acute arthropod mortality was lower than in other scenarios, although not negligible. If PRA is used to assess pesticides, risk managers need further guidance on how to conduct a PRA and what constitutes ‘unacceptable risk’ under EC Directive 91/414/EEC, as judgement is required when simple trigger values are no longer used. Copyright © 2003 Society of Chemical Industry
Adsorption–desorption of metalaxyl as affecting dissipation and leaching in soils:role of mineral and organic components
Authors: Fernandes Maria C , Cox Lucía , Hermosín María C , Cornejo Juan
Published: April 2003

Adsorption–desorption studies of metalaxyl in fifteen agricultural soil samples from Southern Portugal and Spain were performed following a batch equilibration method. Very high sorption was observed on a clay soil of high content in altered illite, but, when this soil was excluded from regression analysis, organic matter (OM) was the most important single soil property affecting sorption at low concentrations of metalaxyl. At higher concentrations, no correlation was observed with any soil property. The relevance of OM on sorption was also corroborated by the increase in sorption coefficients when soil OM was increased artificially by the addition of an organic amendment. Sorption studies with the colloidal fraction of selected soils also revealed the importance of mineral surfaces in metalaxyl sorption. Sorption of metalaxyl in most of the soil samples was hysteretic. Selected soil samples were incubated in the dark, sampled periodically and extracted for their fungicide content. Metalaxyl half‐lives increased with sorption and OM content of the soil, and were specially high in the amended soil. Leaching studies in hand‐packed columns under saturated/unsaturated flow conditions showed an inverse relation between leaching and sorption. Recoveries from the soil columns were close to 80% of the metalaxyl applied, except for the soil which OM was artificially increased, in which recovery was lower and this has been attributed to the much higher irreversibility of metalaxyl sorption in the amended soil. Copyright © 2003 Society of Chemical Industry
Variations in acaricidal effect of wettable sulfur on Tetranychus urticae (Acari: Tetranychidae): effect of temperature, humidity and life stage
Authors: Auger Philippe , Guichou Sabine , Kreiter Serge
Published: April 2003

Under laboratory conditions, the acaricidal effect of wettable sulfur is influenced by climatic conditions and the stage of development of Tetranychus urticae. Its ovicidal effect results from the combined action of temperature and relative humidity (RH). Wettable sulfur becomes effective at 27.5 °C and 75% RH. Beyond this threshold, the acaricidal effect increases with rising temperature or humidity, to become complete at a temperature of 35 °C and 90% RH. Within the range of temperatures and humidities 20 °C/30% RH and 35 °C/90% RH the mortality of immatures (from protonymphs to teleiochrysalis) was total. Under similar experimental conditions, females usually died before the end of the experiment. Temperature and relative humidity increased the adulticidal potential of wettable sulfur. The fecundity of the sulfur‐treated females and the viability of their progeny was found to depend on temperature and RH. According to the same climatic conditions, eggs were less susceptible than females, which were in turn less susceptible than juvenile stages. Copyright © 2003 Society of Chemical Industry
Development of a bioassay system for monitoring susceptibility in Thrips tabaci
Authors: Rueda Alfredo , Shelton Anthony M
Published: April 2003

A system is described for collecting adult and larva of Thrips tabaci from onion foliage into insecticide‐treated vials to evaluate susceptibility to insecticides. The thrips insecticide bioassay system (TIBS) allows one to treat vials and store them for 3 weeks before thrips are collected. Depending on the population density in the field, collection of the insects for the test required from 3–6 h for one person. Assays are read after 24 h. This system was used in 1997 and 1998 in commercial onion fields in Honduras and Nicaragua, and TIBS was sensitive enough to detect differences to the insecticides tested, to thrips life stages and to different generations within an onion‐growing season. Data collected suggest that there were not serious problems with thrips insecticide resistance, with the possible exception of cypermethrin in Nicaragua which had a resistance ratio (RR) value of 26.9 for adult thrips. The largest RR values were observed at the end of the growing season, and this may be caused by the season‐long selection by insecticide sprays. The mortality of adults and larvae followed the same general pattern, but the ratio between larvae and adults differed for each chemical group. Copyright © 2003 Society of Chemical Industry
Pesticide degradation in a ‘biobed’ composting substrate
Authors: Fogg Paul , Boxall Alistair BA , Walker Allan , Jukes Andrew A
Published: April 2003

Pesticides play an important role in the success of modern farming and food production. However, the release of pesticides to the environment arising from non‐approved use, poor practice, illegal operations or misuse is increasingly recognised as contributing to water contamination. Biobeds appear to offer a cost‐effective method for treating pesticide‐contaminated waste. This study was performed to determine whether biobeds can degrade relatively complex pesticide mixtures when applied repeatedly. A pesticide mixture containing isoproturon, pendimethalin, chlorpyrifos, chlorothalonil, epoxiconazole and dimethoate was incubated in biomix and topsoil at concentrations to simulate pesticide disposal. Although the data suggest that interactions between pesticides are possible, the effects were of less significance in biomix than in topsoil. The same mixture was applied on three occasions at 30‐day intervals. Degradation was significantly quicker in biomix than in topsoil. The rate of degradation, however, decreased with each additional treatment, possibly due to the toxicity of the pesticide mixture to the microbial community. Incubations with chlorothalonil and pendimethalin carried out in sterile and non‐sterile biomix indicated that degradation, rather than irreversible adsorption to the matrix, was the main mechanism responsible for the reduction in recovered residues. Results from these experiments suggest that biobeds offer a viable means of treating pesticide waste. Copyright © 2003 Society of Chemical Industry
Pesticide buffer zones for the protection of wildlife
Authors: Burn Alastair
Published: April 2003

Buffer zones can play important roles in agricultural habitats, both in the protection of off‐crop habitats from pesticide and fertiliser drift and run‐off, and in providing important areas of non‐crop habitats. Their role in the protection of aquatic habitats from pesticide drift is a significant feature of pesticide risk management, but they are currently used only to a limited degree to protect terrestrial habitats. This paper summarises some of the evidence for the risks and impacts of pesticide drift into non‐crop habitats, and the approaches taken by the nature conservation agencies in deriving buffer zones for the protection of sites that are important for nature conservation. Biodiversity objectives need to be explicitly built into ICM programmes, and buffer zones, together with appropriate application technology, can play an important part in reducing pesticide drift in ICM systems to achieve such objectives. Copyright © 2003 Society of Chemical Industry
Pesticide usage in some vegetable crops in Great Britain: real on‐farm applications
Authors: Thomas Miles R
Published: April 2003

The last decade has seen an increasing requirement throughout the United Kingdom (UK) for accurate, timely information on pesticide usage on fresh produce such as vegetables to satisfy government legislation and provide data as part of the registration and review process of pesticides. These data, collected by the Department for Environment, Food and Rural Affair's Pesticide Usage Survey Group (PUSG), provide information on current and past usage patterns and allow the impact of use on the environment, operator and consumer to be more accurately assessed from actual usage patterns rather than worst‐case scenarios. Surveys of commercially grown carrot, Brussels sprouts and onion crops in Great Britain were undertaken at regular intervals between 1986 and 1999, using fully stratified samples of growers. Only on Brussels sprouts was there a significant decline in pesticide use over this period, but the frequency of treatments increased on all three crops, reflecting the recent introduction of more active molecules and lower dose rates. The implications for growers of EU Directive 91/44 are discussed if active ingredients are lost because they fail to achieve Annex 1 listing. © British Crown Copyright 2003. Reproduced with the permission of the Controller of Her Majesty's Stationery Office. Published for SCI by John Wiley & Sons, Ltd.
Intrinsic remediation of trichloroethene driven by tetraalkoxysilanes as co‐contaminants: Results of microcosm and field studies
Authors: Vancheeswaran Sanjay , Yu Seungho , Daley Paul , Halden Rolf U. , Williamson Kenneth J. , Ingle James D. , Semprini Lewis
Published: April 2003

Biological reduction of trichloroethene (TCE), driven by the transformation
products of tetraalkoxysilanes, was investigated in seasonal field monitorings and anaerobic groundwater
microcosms. Under anaerobic conditions, tetraalkoxysilanes such as tetrabutoxysilane (TBOS) and
tetrakis(2‐ethylbutoxy)silane (TKEBS) are abiotically hydrolyzed to their
corresponding alcohols, 1‐butanol and 2‐ethylbutanol, respectively, and silicic acid. These
alcohols are then fermented by subsurface microorganisms to their corresponding acids and hydrogen, which likely
serves as the ultimate electron donor facilitating reductive dechlorination of TCE. At Site 300, Lawrence
Livermore National Laboratory (LLNL), California, tetraalkoxysilanes are present along with TCE as
subsurface contaminants. Intrinsic transformation of TCE to cis‐dichloroethene (c‐DCE)
was observed at this site, and this was promoted by the transformation products of these tetraalkoxysilanes.
Efficient transformation of high concentrations of TCE (150–300 mg/l aqueous concentration)
was observed in anaerobic microcosms constructed with groundwater from this site. The lack of transformation of
c‐DCE to vinyl chloride (VC) and ethene in the microcosms is consistent with studies of the
microbial community in the site groundwater reported by Lowe et al. (2002).
© 2003 Wiley Periodicals, Inc.
A systematic approach to in situ bioremediation in groundwater
Authors: Faris Bart , Vlassopoulos Dimitri
Published: April 2003

In situ bioremediation (ISB) melds an understanding of microbiology, chemistry, hydrogeology, and
engineering into a strategy for planned and controlled microbial degradation of specific contaminants. ISB creates
subsurface environmental conditions, typically through reduction oxidation manipulation, which induce the
degradation of contaminants via microbial catalyzed biochemical reactions. In turn, the microbes produce enzymes
that are utilized to derive energy and that are instrumental in the degradation of target chemicals. To accomplish
this chain of events, the type of microorganisms, contaminant, and the geological conditions at the site must be
considered. Since in situ conditions are manipulated by engineered means, the most important consideration is the
ability to transmit and mix liquids in the subsurface. The Interstate Technology Regulatory Council
(ITRC)–ISB Team has recently completed a guidance document that describes a systematic approach to
ISB in groundwater. ITRC is a state‐led coalition of more than 40 states working together with industry and
stakeholders to achieve regulatory acceptance of environmental technologies. © 2003 Wiley Periodicals,
Inc.
Development of a procedure for sustainable in situ aquifer denitrification
Authors: Khan Imtiyaz A. , Spalding Roy F.
Published: April 2003

Denitrification experiments have provided data showing the pitfalls and successes in developing a sustainable
injection/extraction system in a sand and gravel aquifer. Experiments increase in complexity from continuous
injection at one well to automated‐pulsed eight well injections. In both continuous and pulsed injection of
organic carbon, 40 mg NO3‐N l−1 was reduced below the detection limit of <
0.1 mg NO3‐N l−1 in the denitrification zones. Under continuous injection,
accumulation of bacterial exudates in the vicinity of the injection well resulted in injection well clogging
within ten days. Periodic cleaning of the injection well and the adjacent gravel matrix was accomplished by using
a tool developed to circulate a cleaning solution composed of 5 percent H2O2 and 0.02
percent NaOCl; but, biofouling could not be eliminated. In the later experiments, acetate became the carbon
amendment because ethanol promoted more biomass development. A specialized pulse injection procedure was developed
to separate nitrate from acetate‐C and was successful in alleviating the proliferation of bacterial
exudates without affecting the performance of the denitrification system. Using pulsed injection, a maximum of 72
percent nitrate reduction was accomplished in the extraction well water, and denitrification was sustained for
three months without clogging. © 2003 Wiley Periodicals, Inc.
Isotope applications in environmental investigations part II: Groundwater age dating and recharge processes, and provenance of sulfur and methane
Authors: Sueker Julie K.
Published: April 2003

Measurement of the isotopic composition of solids, solutes, gases, and water complement standard
hydrogeological
investigation techniques by providing information that may not otherwise be obtainable. Groundwater age
estimates
determined from the decay of radio‐isotopes or from groundwater concentrations of anthropogenic gases
such
as chlorofluorocarbons (CFCs) and sulfur hexafluoride (SF6) are used to verify
flow
regimes and constrain or calibrate hydrologic flow models. Groundwater recharge rates are estimated by measuring
the concentrations or activities of a variety of isotopes including 2H, 3H,
18O,
and 36Cl. Excess sulfur causes salinization of water supplies and acidification of precipitation,
surface water, and groundwater. The wide range of sulfur isotopic compositions exhibited by different sulfur
species and sources allows the application of sulfur isotopes to trace sources and fate of sulfur in the
environment. Methane is a ubiquitous gas that has economic value when located in extractable reservoirs. Methane
is
also a greenhouse gas and is a potential explosion and health hazard when it accumulates in buildings and water
distribution systems. The carbon and hydrogen isotopic composition of methane can be used to determine the
provenance of methane, distinguishing between thermogenic and biogenic sources. The addition of isotopic
analyses
to environmental investigations can be a cost‐effective means of resolving intractable issues. ©
2003
Wiley Periodicals, Inc.