Invasion of pests resistant to Bt toxins can lead to inherent non-uniqueness in genetically modified Bt-plant dynamics: mathematical modeling

Genetically modified crops are effective pest management tools for worldwide growers. However, there is a concern that pests may develop resistance to Bt-toxins produced by genetically modified Bt-plants. We study the impact of the Bt-resistant pests on Bt-crops. Furthermore, the dynamics of the Bt-plant-Bt-susceptible insects-Bt-resistant insects system is analysed and it is shown that throughout the insect reproduction period the plant biomass dynamics resulting from invasion of Bt-resistant insects is non-unique. Namely, the chaotic attractor and the limit cycle, which are responsible for the plant and insect biomass dynamics, are shown to coexist. As a result, the Bt-plant-Bt-resistant insect system can manifest either chaotic or regular oscillations of plant and insect biomass depending on spatial patterns resulting from invasion of Bt resistant insects into the Bt plant-Bt susceptible insect system. We show that the non-uniqueness of the system dynamics under unfavorable environmental conditions, such as in the so-called zones of risky agriculture in many developing countries and industrialized countries, can lead to essential decrease in the plant biomass.     

A priori prediction of disease invasion dynamics in a novel environment

Directly transmitted infectious diseases spread through wildlife populations as travelling waves away from the sites of original introduction. These waves often become distorted through their interaction with environmental and population heterogeneities and by long-distance translocation of infected individuals. Accurate a priori predictions of travelling waves of infection depend upon understanding and quantifying these distorting factors. We assess the effects of anisotropies arising from the orientation of rivers in relation to the direction of disease-front propagation and the damming effect of mountains on disease movement in natural populations. The model successfully predicts the local and large-scale prevaccination spread of raccoon rabies through New York State, based on a previous spatially heterogeneous model of raccoon-rabies invasion across the state of Connecticut. Use of this model provides a rare example of a priori prediction of an epidemic invasion over a naturally heterogeneous landscape. Model predictions matched to data can also be used to evaluate the most likely points of disease introduction. These results have general implications for predicting future pathogen invasions and evaluating potential containment strategies.     

Uncertainty and predictability in population dynamics of a bitrophic ecological model: Mixed-mode oscillations,bistability and sensitivity to parameters

We consider a two-trophic ecological model comprising of two predators competing for their common prey. We cast the model into the framework of a singular perturbed system of equations in one fast variable (prey population density) and two slow variables (predator population densities), mimicking the common observation that the per-capita productivity rate decreases from bottom to top along the trophic levels in Nature. We assume that both predators exhibit Holling II functional response with one of the predators (territorial) having a density dependent mortality rate. Depending on the system parameters, the model exhibits small, intermediate and/or large fluctuations in the population densities. The large fluctuations correspond to periodic population outbreaks followed by collapses (commonly known as cycles of “boom and bust”). The small fluctuations arise due to a singular Hopf bifurcation in the system, and are ecologically more desirable. However, more interestingly, the system exhibits mixed-mode oscillations (which are concatenations of the large amplitude oscillations and the small amplitude oscillations) that indicate the adaptability of the species to prolong the time gap between successive cycles of boom and bust. Numerical simulations are carried out to demonstrate the extreme sensitivity of the system to initial conditions (chaos and bistability of limit cycles are observed) as well as to the system parameters (here we only show the sensitivity to the density dependent mortality rate of the territorial predator). This model throws light at the uncertainties in long term behaviors that are associated with a real ecological system. We show that even very small changes in the system parameters due to natural or human-induced causes can lead to a complete different ecological phenomenon, thus affecting the predictability of the density of the prey population. In this paper, we explain the mechanisms behind the irregular fluctuations in the population sizes in an attempt to understand the dynamics occurring in a natural population and also comment on the inherent uncertainties associated with the system.     

Quantitative analysis of glioma cell invasion by confocal laser scanning microscopy in a novel brain slice model

To quantitatively analyze the spatial extent of glioma cell migration in an organotypic brain slice culture, we developed a new invasion model with the aid of confocal laser scanning microscopy (CLSM). CLSM allowed not only for three-dimensional visualization of the invasive pattern of human T98G glioma cells in the living brain slice but also for serial analysis of the invasive process over several weeks. Twenty-four hours after the T98G glioma spheroid was initiated to coculture with a brain slice, the glioma cells detached themselves from the spheroid and spontaneously continued to migrate on the surface of the brain slice, while they diffusely invaded into the slice by migrating to a deeper site. Immunohistochemical analysis revealed that these migrating glioma cells much more strongly immunostained for matrix metalloproteinase (MMP)-2 and -9 than the tumor spheroid which remained at the implanted site. Treatment of the T98G glioma spheroid with 1,10-phenanthroline, a specific inhibitor of MMPs, significantly inhibited not only the cell migration on the surface of the brain slice but also the invasion of the glioma cells into the slice. The present version of the glioma invasion model using CLSM makes it possible to spatially and serially analyze the extent of glioma cell invasion in the living brain slice for several weeks, making it a very useful tool for investigating the cellular and molecular mechanisms of glioma invasion under conditions most analogous to those of normal brains in vivo.     

Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

Background  

Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model.     

Mechanisms and diversity of resistance to insect pests in wild relatives of groundnut

The levels of resistance to insect pests in cultivated groundnut (Arachis hypogaea) germplasm are quite low, and therefore, we screened 30 accessions of Arachis spp. and 12 derived lines for resistance to insect pests under field and greenhouse conditions. Accessions belonging to Arachis cardenasii, Arachis duranensis, Arachis kempff-mercadoi, Arachis monticola, Arachis stenosperma, Arachis paraguariensis, Arachis pusilla, and Arachis triseminata showed multiple resistance to the leaf miner Aproaerema modicella, Helicoverpa armigera, Empoasca kerri, and to rust, Puccnia arachidis Speg., and late leaf spot, Cercosporidium personatum (Berk. et Curt.). Arachis cardenasii (ICG 8216), Arachis ipaensis (ICG 8206), A. paraguariensis (ICG 8130), and Arachis appressipila (ICG 8946) showed resistance to leaf feeding and antibiosis to Spodoptera litura under no-choice conditions. Six lines, derived from wild relatives, showed resistance to H. armigera and S. litura, and/or leaf miner. Plant morphological characteristics such as main stem thickness, hypanthium length, leaflet shape and length, leaf hairiness, standard petal length and petal markings, basal leaflet width, main stem thickness and hairiness, stipule adnation length and width, and peg length showed significant correlation and/or regression coefficients with damage by H. armigera, S. litura, and leafhoppers, and these traits can possibly be used as markers to select for resistance to these insect pests. Principal component analysis placed the Arachis spp. accessions into five groups, and these differences can be exploited to diversify resistance to the target insect pests in groundnut.     

江苏棉区种植转基因抗虫棉GK22对棉田害虫、杂草种群的影响

2001年在江苏选择南京、盐城两地,试验观察转Bt基因抗虫棉GK22的种植,对棉田害虫及杂草种群变动的影响,结果是：咀嚼式口器害虫的棉铃虫（Helicover pa armigera),红铃虫（Pectinophora goosypiella),玉米螟（Ostrinia nubilalis),金刚钻（Earias cupreoviridis),棉不造桥虫（Anomis flava),棉大卷叶虫（Adoxophyes orana)等虫口数量,蕾铃被害均表现出较好的控制效果,处理区咀嚼式口器害虫的幼虫总 量,比对照区分别减少92．51％,78．4％,其中：棉铃虫幼虫数量分别减少88．3％,72．9％,蕾铃被害虫减少87．5％,90．7％,74．11％,55．85％,红铃虫虫花减少74．4％,51．64％,铃内活虫减少90％,100％,玉米螟虫口减少72．7％,100％,金钢钻,造桥虫,卷叶虫虫口减少93％以上,对刺吸式口器盲蝽象（Adelphocoris suturalis),棉蚜（Aphis gossyppii),棉红叶螨（Tetranychus cinnabariuns)等害虫,试验区和对照区种群消长动态趋势基本一致,差异不显,两试对杂草种类及数量调查,抗虫棉区和对照区差异亦不明显。     

Species assembly in model ecosystems, I: Analysis of the population model and the invasion dynamics

Recently we have introduced a simplified model of ecosystem assembly (Capitán et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper analysis of the model, obtaining analytical results and introducing some approximations which allow us to reconstruct the results of our previous work. In particular, we show that the population dynamics equations of a very general class of trophic-level structured food-web have an unique interior equilibrium point which is globally stable. We show analytically that communities found as end states of the assembly process are pyramidal and we find that the equilibrium abundance of any species at any trophic level is approximately inversely proportional to the number of species in that level. We also find that the per capita growth rate of a top predator invading a resident community is key to understand the appearance of complex end states reported in our previous work. The sign of these rates allows us to separate regions in the space of parameters where the end state is either a single community or a complex set containing more than one community. We have also built up analytical approximations to the time evolution of species abundances that allow us to determine, with high accuracy, the sequence of extinctions that an invasion may cause. Finally we apply this analysis to obtain the communities in the end states. To test the accuracy of the transition probability matrix generated by this analytical procedure for the end states, we have compared averages over those sets with those obtained from the graph derived by numerical integration of the Lotka-Volterra equations. The agreement is excellent.     

Computational model of hepatitis B virus DNA polymerase: Molecular dynamics and docking to understand resistant mutations

Hepatitis B virus (HBV) DNA polymerase (HDP) is a pharmacological target of intense interest. Of the seven agents approved in USA for the treatment of HBV infections, five are HDP inhibitors. However, resistance development against HDP inhibitors, such as lamivudine and adefovir, has severely hurt their efficacy to treat HBV. As a step toward understanding the mechanism of resistance development and for gaining detailed insights about the active site of the enzyme, we have built a homology model of HDP which is an advance over previously reported ones. Validation using various techniques, including PROSTAT, PROCHECK, and Verify‐3D profile, proved the model to be stereochemically significant. The stability of the model was studied using a 5 ns molecular dynamics simulation. The model was found to be sufficiently stable after the initial 2.5 ns with overall root mean squared deviation (RMSD) of 4.13 Å. The homology model matched the results of experimental mutation studies of HDP reported in the literature, including those of antiviral‐resistant mutations. Our model suggests the significant role of conserved residues, such as rtLys32, in binding of the inhibitors, contrary to previous studies. The model provides an explanation for the inactivity of some anti‐HIV molecules which are inactive against HDP. Conformational changes which occurred in certain binding pocket amino acids helped to explain the better binding of some of the inhibitors in comparison to the substrates.     

Asymptotic analysis of a TMDD model: when a reaction contributes to the destruction of its product

The multi-scale dynamics of a two-compartment with first order absorption Target-Mediated Drug Disposition (TMDD) pharmacokinetics model is analysed, using the Computational Singular Perturbation (CSP) algorithm. It is shown that the process evolves along two Slow Invariant Manifolds (SIMs), on which the most intense components of the model are equilibrated, so that the less intensive are the driving ones. The CSP tools allow for the identification of the components of the TMDD model that (i) constrain the evolution of the process on the SIMs, (ii) drive the system along the SIMs and (iii) generate the fast time scales. Among others, such diagnostics identify (i) the factors that determine the start and the duration of the period in which the ligand-receptor complex acts and (ii) the processes that determine its degradation rate. The counterintuitive influence of the process that transfers the ligand from the tissue to the main compartment, as it is manifested during the final stage of the process, is studied in detail.

     

转Bt基因棉花主要抗虫黄酮类化合物时空动态的HPLC分析

棉花植株中的黄酮类化台物是重要的抗病虫害物质。运用高效液相色谱技术,对转Bt基因棉花主要抗虫黄酮类化合物的种类、含量和时空动态进行了初步探讨。结果表明,棉花组织中主要抗虫黄酮类化台物(包括异斛皮苷、芳香苷和槲皮素等)能够用HPLC方法检测并进行定量;异树皮苷、芳香苷和树皮素的含量均以花瓣中最高,花萼、苞叶和棉铃中较少;棉花生长中后期顶端嫩叶中抗虫黄酮类化合物的含量明显高于苗期．不同组织不同生长期的主要抗虫黄酮类化合物含量有一定的差异,所起的抗虫作用也有所不同．     

Bt毒蛋白在转Bt基因棉中的表达及其在害虫-天敌间的转移

以常规棉泗棉3号作为对照,采用酶联免疫生测法（ELISA）和室内生物测定法,研究了转Bt基因棉新棉33B和GK-12不同组织器官中Cry1Ac或Cry1Ab毒蛋白的表达及其向靶标害虫（棉铃虫）、非靶标害虫（棉蚜）以及天敌（龟纹瓢虫）的传递和影响。研究结果表明,新棉33B各组织器官中Bt毒蛋白的表达量较高,为79.7～1 390.0 ng/g鲜重,GK-012较低为165～2640 ng/g鲜重。在花盛期,新棉33B各组织器官中Bt毒蛋白的表达量依次为：柱头、花 >子房、花瓣>群尖;而5～7叶期的初展嫩叶、现蕾初期的幼蕾及花铃期的幼铃表达量相当,而且与花盛期群尖的表达量没有明显区别。同样处于花盛期的GK-12,其各组织器官中Bt毒蛋白的表达量依次为：花药>柱头>花瓣>群尖>子房;而5～7叶期的初展嫩叶、现蕾初期的幼蕾及花铃期的幼铃表达量相当,而且与花盛期群尖的表达量没有明显差异。常规对照棉的幼铃、花药、柱头以及子房中痕量Bt毒蛋白的存在可能与传粉昆虫等的活动有关。在转Bt基因棉田采集的棉蚜和棉铃虫老龄幼虫,其体内均可检测到Bt毒蛋白;在新棉33B棉田采集的龟纹瓢虫幼虫和成虫体内也可检测出Bt毒素。当以Bt棉田的棉蚜饲喂龟纹瓢虫时,龟纹瓢虫的生长发育、存活以及繁殖等基本没有受到影响。     

HDX-analyzer: a novel package for statistical analysis of protein structure dynamics

BACKGROUND: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2. IMPLEMENTATION AND RESULTS: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme. CONCLUSION: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.     

Complex dynamics occur in a single-locus, multiallelic model of general frequency-dependent selection

We examine the characteristics of non-equilibrium dynamics produced by a simple well-known model of frequency-dependent selection at a single diploid locus. An examination of the parameter space of this “pairwise-interaction model” (PIM) revealed non-equilibrium dynamics for polymorphisms of 3, 4 and 5 alleles; both allele-frequency cycling and aperiodic trajectories were detected. We measured the number, cycle length and domains of attraction of the various attractors produced by the model. The domains of attraction tended to be smaller, and the cycles longer, for systems with larger number of alleles. Fitnesses that parametrized negative frequency-dependent selection were more likely to allow cycling, and these cycles also had larger domains of attraction. Aperiodic trajectories were detected only in cases with 4 or 5 alleles. The genetic cycles produced by the model do not have periods as short as those predicted in ecological models with cycling (such as predator–prey population cycles, etc.). Consequently, in a real-world system, PIM allele-frequency cycling is likely to be indistinguishable from stable equilibria when observed over short time scales.     

Complex dynamics occur in a single-locus,multiallelic model of general frequency-dependent selection

We examine the characteristics of non-equilibrium dynamics produced by a simple well-known model of frequency-dependent selection at a single diploid locus. An examination of the parameter space of this “pairwise-interaction model” (PIM) revealed non-equilibrium dynamics for polymorphisms of 3, 4 and 5 alleles; both allele-frequency cycling and aperiodic trajectories were detected. We measured the number, cycle length and domains of attraction of the various attractors produced by the model. The domains of attraction tended to be smaller, and the cycles longer, for systems with larger number of alleles. Fitnesses that parametrized negative frequency-dependent selection were more likely to allow cycling, and these cycles also had larger domains of attraction. Aperiodic trajectories were detected only in cases with 4 or 5 alleles. The genetic cycles produced by the model do not have periods as short as those predicted in ecological models with cycling (such as predator–prey population cycles, etc.). Consequently, in a real-world system, PIM allele-frequency cycling is likely to be indistinguishable from stable equilibria when observed over short time scales.     

Diversity and analysis of sequences encoded by arcelin genes from Indian wild pulses resistant to bruchids

Wild pulse accessions are considered a vital source of genes for insect resistance for crop improvement programmes. Wild pulses resistant to infestation towards the bruchid insect pest, Callosobruchus maculatus from South India were chosen to screen the existence of potent insecticidal protein, arcelin from APA locus (Arcelin/Phytohemagglutinin/α-Amylase inhibitor) to ascertain their nature and functional diversity without any specific indication for insect resistant factors. The DNA sequence coding for arcelin from various species of wild pulses were amplified, sequenced and deduced to their protein sequences. These protein sequences were examined physico-chemically using several bioinformatics tools and docked with various sugars to resolve the nature of arcelin molecules. Results indicated the presence of significant differences in the properties of arcelin molecules from various species of Indian wild pulses with their amino acid sequences, several physico-chemical properties and binding ability with sugars. The differences observed on these arcelin molecules from diverse wild pulses are predicted to provide a prospective insect pest control factors.     

Pyramiding Bt genes for increasing resistance of cotton to two major lepidopteran pests: Spodoptera litura and Heliothis armigera

To more effectively control two major cotton insects (cotton bollworm and Spodoptera litura) and improve the efficacy of the pest resistance management, novel transgenic plants expressing Bacillus thuringiensis Cry9C gene were generated, and gene stacking strategy was incorporated. Initially, a binary plasmid vector harboring Cry9C gene was introduced into an elite cotton cultivar Simian-3 by Agrobacterium-mediated transformation. Integration and expression of the Cry9C genes in three transgenic lines were confirmed by PCR and RT-PCR. Among these transgenic lines, T0 generation of line 16 (L-16) with normal phenotypes were selected by ELISA assays for its highest expression level of Cry9C. In T1 population of L-16, the expression level of Cry9C ranged from 29 to 45 μg/g fresh leaf. The following insect bioassays demonstrated that transgenic S3-35S::Cry9C cotton plants exhibited moderate toxicity to Heliothis armigera but strong toxicity to S. litura compared with the transgenic plants expressing Cry 1Ac gene. For incorporation of gene staking strategy, Cry9C gene and Cry 2A or Cry 1Ac were pyramided, respectively by sexual crossing. The expression of Cry9C protein in all F1 progenies had a similar level as the parent plants indicating the high heritability of Bt genes in transgenic progenies. Progenies from both Cry9C × Cry 2A and Cry9C × Cry 1Ac exhibited higher resistance to S. litura compared with their parents. Together our data demonstrated that our newly generated transgenic plants represent a reservoir of novel insect-resistant materials in cotton breeding, and the successful incorporation of gene pyramiding technology can provide a new solution of developing multiple resistance management strategies.     

Multi-dimensional sensitivity analysis and ecological implications of a nutrient uptake model

Mechanistic models of nutrient uptake are essential to the study of plant-soil interactions. In these models, uptake rates depend on the supply of the nutrient through the soil and the uptake capacity of the roots. The behaviour of the models is complex, although only six to ten parameters are used. Our goal was to demonstrate a comprehensive and efficient method of exploring a steady-state uptake model with variation in parameters across a range of values described in the literature. We employed two analytical techniques: the first a statistical analysis of variance, and the second a graphical representation of the simulated response surface. The quantitative statistical technique allows objective comparison of parameter and interaction sensitivity. The graphical technique uses a judicious arrangement of figures to present the shape of the response surface in five dimensions. We found that the most important parameters controlling uptake per unit length of root are the average dissolved nutrient concentration and the maximal rate of nutrient uptake. Root radius is influential if rates are expressed per unit root length; on a surface area basis, this parameter is less important. The next most important parameter is the effective diffusion coefficient, especially in the uptake of phosphorus. The interactions of parameters were extremely important and included three and four dimensional effects. For example, limitation by maximal nutrient influx rate is approached more rapidly with increasing nutrient solution concentration when the effective diffusion coefficient is high. We also note the ecological implications of the response surface. For example, in nutrient-limited conditions, the rate of uptake is best augmented by extending root length; when nutrients are plentiful increasing uptake kinetics will have greater effect.