A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models.

A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models. © 2014 Springer Science+Business Media New York.

Genetically modified insect resistance in cotton: some farm level economic impacts in India

The paper explores the impact of insect-resistant Bacillus thuringiensis (Bt) cotton on costs and returns over the first two seasons of its commercial release in three sub-regions of Maharashtra State, India. It is the first such research conducted in India based on farmers' own practices rather than trial plots. Data were collected for a total of 7793 cotton plots in 2002 and 1577 plots in 2003. Results suggest that while the cost of cotton seed was much higher for farmers growing Bt cotton relative to those growing non-Bt cotton, the costs of bollworm spray were much lower. While Bt plots had greater costs (seed plus insecticide) than non-Bt plots, the yields and revenue from Bt plots were much higher than those of non-Bt plots (some 39% and 63% higher in 2002 and 2003, respectively). Overall, the gross margins of Bt plots were some 43% (2002) and 73% (2003) higher than those of non-Bt plots, although there was some variation between the three sub-regions of the state. The results suggest that Bt cotton has provided substantial benefits for farmers in India over the 2 years, but there are questions as to whether these benefits are sustainable. (c) 2004 Elsevier Ltd. All rights reserved.

Genetically modified insect resistance in cotton: some farm level economic impacts in India

The paper explores the impact of insect-resistant Bacillus thuringiensis (Bt) cotton on costs and returns over the first two seasons of its commercial release in three sub-regions of Maharashtra State, India. It is the first such research conducted in India based on farmers' own practices rather than trial plots. Data were collected for a total of 7793 cotton plots in 2002 and 1577 plots in 2003. Results suggest that while the cost of cotton seed was much higher for farmers growing Bt cotton relative to those growing non-Bt cotton, the costs of bollworm spray were much lower. While Bt plots had greater costs (seed plus insecticide) than non-Bt plots, the yields and revenue from Bt plots were much higher than those of non-Bt plots (some 39% and 63% higher in 2002 and 2003, respectively). Overall, the gross margins of Bt plots were some 43% (2002) and 73% (2003) higher than those of non-Bt plots, although there was some variation between the three sub-regions of the state. The results suggest that Bt cotton has provided substantial benefits for farmers in India over the 2 years, but there are questions as to whether these benefits are sustainable. (c) 2004 Elsevier Ltd. All rights reserved.

Association of plant hairs and insect resistance : an annotated bibliography /

"September 1975."

The role of abscisic acid and water stress in root herbivore-induced leaf resistance

Herbivore-induced systemic resistance occurs in many plants and is commonly assumed to be adaptive. The mechanisms triggered by leaf-herbivores that lead to systemic resistance are largely understood, but it remains unknown how and why root herbivory also increases resistance in leaves. To resolve this, we investigated the mechanism by which the root herbivore Diabrotica virgifera induces resistance against lepidopteran herbivores in the leaves of Zea mays. Diabrotica virgifera infested plants suffered less aboveground herbivory in the field and showed reduced growth of Spodoptera littoralis caterpillars in the laboratory. Root herbivory did not lead to a jasmonate-dependent response in the leaves, but specifically triggered water loss and abscisic acid (ABA) accumulation. The induction of ABA by itself was partly responsible for the induction of leaf defenses, but not for the resistance against S. littoralis. Root-herbivore induced hydraulic changes in the leaves, however, were crucial for the increase in insect resistance. We conclude that the induced leaf resistance after root feeding is the result of hydraulic changes, which reduce the quality of the leaves for chewing herbivores. This finding calls into question whether root-herbivore induced leaf-resistance is an evolved response. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

Insect herbivory, plant defense, and early Cenozoic climate change

Insect damage on fossil leaves from the Central Rocky Mountains, United States, documents the response of herbivores to changing regional climates and vegetation during the late Paleocene (humid, warm temperate to subtropical, predominantly deciduous), early Eocene (humid subtropical, mixed deciduous and evergreen), and middle Eocene (seasonally dry, subtropical, mixed deciduous and thick-leaved evergreen). During all three time periods, greater herbivory occurred on taxa considered to have short rather than long leaf life spans, consistent with studies in living forests that demonstrate the insect resistance of long-lived, thick leaves. Variance in herbivory frequency and diversity was highest during the middle Eocene, indicating the increased representation of two distinct herbivory syndromes: one for taxa with deciduous, palatable foliage, and the other for hosts with evergreen, thick-textured, small leaves characterized by elevated insect resistance. Leaf galling, which is negatively correlated with moisture today, apparently increased during the middle Eocene, whereas leaf mining decreased.

Nucleopolyhedrovirus introduction in Australia

Nucleopolyhedrovirus (NPV) has become an integral part of integrated pest management (IPM) in many Australian agricultural and horticultural crops. This is the culmination of years of work conducted by researchers at the Queensland Department of Primary Industries and Fisheries (QDPI&F) and Ag Biotech Australia Pty Ltd. In the early 1970’s researchers at QDPI&F identified and isolated a virus in Helicoverpa armigera populations in the field. This NPV was extensively studied and shown to be highly specific to Helicoverpa and Heliothis species. Further work showed that when used appropriately the virus could be used effectively to manage these insects in crops such as sorghum, cotton, chickpea and sweet corn. A similar virus was first commercially produced in the USA in the 1970’s. This product, Elcar®, was introduced into Australia in the late 1970’s by Shell Chemicals with limited success. A major factor contributing to the poor adoption of Elcar was the concurrent enormous success of the synthetic pyrethroids. The importance of integrated pest management was probably also not widely accepted at that time. Gradual development of insect resistance to synthetic pyrethroids and other synthetic insecticides in Australia and the increased awareness of the importance of IPM meant that researchers once again turned their attentions to environmentally friendly pest management tools such NPV and beneficial insects. In the 1990’s a company called Rhone-Poulenc registered an NPV for use in Australian sorghum, chickpea and cotton. This product, Gemstar®, was imported from the USA. In 2000 Ag Biotech Australia established an in-vivo production facility in Australia to produce commercial volumes of a product similar to the imported product. This product was branded, ViVUS®, and was first registered and sold commercially in Australia in 2003. The initial production of ViVUS used a virus identical to the American product but replicating it in an Australian Helicoverpa species, H. armigera. Subsequent research collaboration between QDPI&F and Ag Biotech reinvigorated interest in the local virus strain. This was purified and the production system adapted to produce it on a commercial scale. This new version of ViVUS, which was branded ViVUS Gold®, was first registered and sold commercially in 2004. Widespread insect resistance to insecticides and a greater understanding of integrated pest management is leading to increased adoption of technologies such NPV in Australian agriculture.

Construction timbers in Queensland. Book 1 and Book 2: Properties and specifications for satisfactory performance of construction timbers in Queensland. Class 1 and Class 10 buildings (houses, carports, garages, greenhouses and sheds). 2013 edition.

This publication lists the more important wood properties of commercial timbers used for construction in Queensland. It also provides requirements and conditions of use for these timbers to provide appropriate design service life in various construction applications. The correct specification of timber considers a range of timber properties including, but not limited to, stress grade; durability class; moisture content and insect resistance. For the specification of timber sizes and spans, relevant Australian Standards and design manuals should be consulted—e.g. Australian Standard AS 1684 series Residential timber—framed construction parts 2 and 3 (Standards Australia 2006a;b.) Book 1 explains the terms used; with reference to nomenclature; origin and timber properties presented under specific column headings in the schedules (Book 2). It also explains target design life; applications and decay hazard zones; presented in the Book 2 Schedules. Book 2 consists of reference tables; presented as schedules A; B and C: • Schedule A contains commercial mixtures of unidentified timbers and of some Australian and imported softwoods. Index numbers 1–10 • Schedule B contains Australian-grown timber species; including both natural forests and plantations. Index numbers 11–493 • Schedule C contains timbers imported into Australia from overseas. Index numbers 494–606 Each schedule has two parts presenting data in tables. • Part 1: Nomenclature, origin and properties of imported timber species • Part 2: Approved uses for commercial mixtures of imported timber species The recommendations made in this publication assume that good building practice will be carried out.

Molecular modeling of Bt Cry1Ac (DI–DII)–ASAL (Allium sativum lectin)–fusion protein and its interaction with aminopeptidase N (APN) receptor of Manduca sexta

Genetic engineering of Bacillus thuringiensis (Bt) Cry proteins has resulted in the synthesis of various novel toxin proteins with enhanced insecticidal activity and specificity towards different insect pests. In this study, a fusion protein consisting of the DI–DII domains of Cry1Ac and garlic lectin (ASAL) has been designed in silico by replacing the DIII domain of Cry1Ac with ASAL. The binding interface between the DI–DII domains of Cry1Ac and lectin has been identified using protein–protein docking studies. Free energy of binding calculations and interaction profiles between the Cry1Ac and lectin domains confirmed the stability of fusion protein. A total of 18 hydrogen bonds was observed in the DI–DII–lectin fusion protein compared to 11 hydrogen bonds in the Cry1Ac (DI–DII–DIII) protein. Molecular mechanics/Poisson–Boltzmann (generalized-Born) surface area [MM/PB (GB) SA] methods were used for predicting free energy of interactions of the fusion proteins. Protein–protein docking studies based on the number of hydrogen bonds, hydrophobic interactions, aromatic–aromatic, aromatic–sulphur, cation–pi interactions and binding energy of Cry1Ac/fusion proteins with the aminopeptidase N (APN) of Manduca sexta rationalised the higher binding affinity of the fusion protein with the APN receptor compared to that of the Cry1Ac–APN complex, as predicted by ZDOCK, Rosetta and ClusPro analysis. The molecular binding interface between the fusion protein and the APN receptor is well packed, analogously to that of the Cry1Ac–APN complex. These findings offer scope for the design and development of customized fusion molecules for improved pest management in crop plants.

陆地棉抗虫基因工程研究

以陆地棉（Gossypium hirsutum L.）栽培品种新陆早4号、系550、冀资492、衡无89-30、邯93-2、冀资123等为材料，进行了组织培养及植株再生研究，建立了一套陆地棉体细胞植株再生速成体系。通过调整激素种类与比例以及改善培养条件，降低了畸形胚发生频率（从80%降为41%），并可将畸形苗转化为正常苗（转化率约为78%）;通过水培和嫁接，结合试管扦插、扩繁技术，解决了棉花生根及移栽难题，为农杆菌介导法转化棉花奠定了基础。 用绿色荧光蛋白基因（gfp）作为报告基因，构建了pBGb1m（含Bt和gfp二价基因）、pBGbf（含Bt-gfp融合基因）和pBGbfg（含Bt-gfp融合基因和gna基因）等三种植物表达载体。通过农杆菌介导法转化烟草，转基因再生植株经过荧光、虫试、PCR、Southern blot和Western blot等检测，表明三种植物表达载体能够在转基因植物中有效表达，同时，绿色荧光蛋白（GFP）的检测表现出了简便、经济、快速、可靠等优点，为大量棉花转基因苗的检测提供了一种有效方法。 采用花粉管通道法将携带细胞间隙定位信号肽的Bt基因的pBin438-S1m质粒导入棉花品种冀资492，经过田间卡那霉素筛选、虫试、PCR、PCR-Southern blot和Southern blot检测，证明Bt基因已整合至棉花基因组中，而且可能是以单拷贝形式插入。 同时，通过农杆菌介导法将三种植物表达载体（pBGb1m、pBGbf和pBGbfg）转化陆地棉栽培品种新陆早4号、冀资492、衡无89-30和邯93-2等材料，获得了大量转化再生棉株。经过PCR和PCR-Southern blot检测，转基因阳性植株为转为再生植株总数的89.45%。目前，虫试、Southern blot及Western blot正在进行之中。