Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes

Plant resistance proteins (R proteins) recognize corresponding pathogen avirulence (Avr) proteins either indirectly through detection of changes in their host protein targets or through direct R-Avr protein interaction. Although indirect recognition imposes selection against Avr effector function, pathogen effector molecules recognized through direct interaction may overcome resistance through sequence diversification rather than loss of function. Here we show that the flax rust fungus AvrLS67 genes, whose products are recognized by the L5, L6, and L7 R proteins of flax, are highly diverse, with 12 sequence variants identified from six rust strains. Seven AvrL567 variants derived from Avr alleles induce necrotic responses when expressed in flax plants containing corresponding resistance genes (R genes), whereas five variants from avr alleles do not. Differences in recognition specificity between AvA567 variants and evidence for diversifying selection acting on these genes suggest they have been involved in a gene-specific arms race with the corresponding flax R genes. Yeast two-hybrid assays indicate that recognition is based on direct R-Avr protein interaction and recapitulate the interaction specificity observed in planta. Biochemical analysis of Escherichia coli-produced AvrL567 proteins shows that variants that escape recognition nevertheless maintain a conserved structure and stability, suggesting that the amino acid sequence differences directly affect the R-Avr protein interaction. We suggest that direct recognition associated with high genetic diversity at corresponding R and Avr gene loci represents an alternative outcome of plant-pathogen coevolution to indirect recognition associated with simple balanced polymorphisms for functional and nonfunctional R and Avr genes.

Spring Phenology of Butterflies : The role of seasonal variation in life-cycle regulation

Animals and plants in temperate regions must adapt their life cycle to pronounced seasonal variation. The research effort that has gone into studying these cyclical life history events, or phenological traits, has increased greatly in recent decades. As phenological traits are often correlated to temperature, they are relevant to study in terms of understanding the effect of short term environmental variation as well as long term climate change. Because of this, changes in phenology are the most obvious and among the most commonly reported responses to climate change. Moreover, phenological traits are important for fitness as they determine the biotic and abiotic environment an individual encounters. Fine-tuning of phenology allows for synchronisation at a local scale to mates, food resources and appropriate weather conditions. On a between-population scale, variation in phenology may reflect regional variation in climate. Such differences can not only give insights to life cycle adaptation, but also to how populations may respond to environmental change through time. This applies both on an ecological scale through phenotypic plasticity as well as an evolutionary scale through genetic adaptation. In this thesis I have used statistical and experimental methods to investigate both the larger geographical patterns as well as mechanisms of fine-tuning of phenology of several butterfly species. The main focus, however, is on the orange tip butterfly, Anthocharis cardamines, in Sweden and the United Kingdom. I show a contrasting effect of spring temperature and winter condition on spring phenology for three out of the five studied butterfly species. For A. cardamines there are population differences in traits responding to these environmental factors between and within Sweden and the UK that suggest adaptation to local environmental conditions. All populations show a strong negative plastic relationship between spring temperature and spring phenology, while the opposite is true for winter cold duration. Spring phenology is shifted earlier with increasing cold duration. The environmental variables show correlations, for example, during a warm year a short winter delays phenology while a warm spring speeds phenology up. Correlations between the environmental variables also occur through space, as the locations that have long winters also have cold springs. The combined effects of these two environmental variables cause a complex geographical pattern of phenology across the UK and Sweden. When predicting phenology with future climate change or interpreting larger geographical patterns one must therefore have a good enough understanding of how the phenology is controlled and take the relevant environmental factors in to account. In terms of the effect of phenological change, it should be discussed with regards to change in life cycle timing among interacting species. For example, the phenology of the host plants is important for A. cardamines fitness, and it is also the main determining factor for oviposition. In summary, this thesis shows that the broad geographical pattern of phenology of the butterflies is formed by counteracting environmental variables, but that there also are significant population differences that enable fine-tuning of phenology according to the seasonal progression and variation at the local scale.

Dynamic simulation of chemical plant

A CSSL- type modular FORTRAN package, called ACES, has been developed to assist in the simulation of the dynamic behaviour of chemical plant. ACES can be harnessed, for instance, to simulate the transients in startups or after a throughput change. ACES has benefited from two existing simulators. The structure was adapted from ICL SLAM and most plant models originate in DYFLO. The latter employs sequential modularisation which is not always applicable to chemical engineering problems. A novel device of twice- round execution enables ACES to achieve general simultaneous modularisation. During the FIRST ROUND, STATE-VARIABLES are retrieved from the integrator and local calculations performed. During the SECOND ROUND, fresh derivatives are estimated and stored for simultaneous integration. ACES further includes a version of DIFSUB, a variable-step integrator capable of handling stiff differential systems. ACES is highly formalised . It does not use pseudo steady- state approximations and excludes inconsistent and arbitrary features of DYFLO. Built- in debug traps make ACES robust. ACES shows generality, flexibility, versatility and portability, and is very convenient to use. It undertakes substantial housekeeping behind the scenes and thus minimises the detailed involvement of the user. ACES provides a working set of defaults for simulation to proceed as far as possible. Built- in interfaces allow for reactions and user supplied algorithms to be incorporated . New plant models can be easily appended. Boundary- value problems and optimisation may be tackled using the RERUN feature. ACES is file oriented; a STATE can be saved in a readable form and reactivated later. Thus piecewise simulation is possible. ACES has been illustrated and verified to a large extent using some literature-based examples. Actual plant tests are desirable however to complete the verification of the library. Interaction and graphics are recommended for future work.

Multi-party risk management helps manage cement plant construction in Thailand

Several parties (stakeholders) are involved in a construction project. The conventional Risk Management Process (RMP) manages risks from a single party perspective, which does not give adequate consideration to the needs of others. The objective of multi-party risk management is to assist decision-makers in managing risk systematically and most efficiently in a multi-party environment. Multi-party Risk Management Processes (MRMP) consist of risk identification, structuring, analysis and developing responses from all party perspectives. The MRMP has been applied to a cement plant construction project in Thailand to demonstrate its effectiveness.

A design environment for deadlock-free concurrent software

Using current software engineering technology, the robustness required for safety critical software is not assurable. However, different approaches are possible which can help to assure software robustness to some extent. For achieving high reliability software, methods should be adopted which avoid introducing faults (fault avoidance); then testing should be carried out to identify any faults which persist (error removal). Finally, techniques should be used which allow any undetected faults to be tolerated (fault tolerance). The verification of correctness in system design specification and performance analysis of the model, are the basic issues in concurrent systems. In this context, modeling distributed concurrent software is one of the most important activities in the software life cycle, and communication analysis is a primary consideration to achieve reliability and safety. By and large fault avoidance requires human analysis which is error prone; by reducing human involvement in the tedious aspect of modelling and analysis of the software it is hoped that fewer faults will persist into its implementation in the real-time environment. The Occam language supports concurrent programming and is a language where interprocess interaction takes place by communications. This may lead to deadlock due to communication failure. Proper systematic methods must be adopted in the design of concurrent software for distributed computing systems if the communication structure is to be free of pathologies, such as deadlock. The objective of this thesis is to provide a design environment which ensures that processes are free from deadlock. A software tool was designed and used to facilitate the production of fault-tolerant software for distributed concurrent systems. Where Occam is used as a design language then state space methods, such as Petri-nets, can be used in analysis and simulation to determine the dynamic behaviour of the software, and to identify structures which may be prone to deadlock so that they may be eliminated from the design before the program is ever run. This design software tool consists of two parts. One takes an input program and translates it into a mathematical model (Petri-net), which is used for modeling and analysis of the concurrent software. The second part is the Petri-net simulator that takes the translated program as its input and starts simulation to generate the reachability tree. The tree identifies `deadlock potential' which the user can explore further. Finally, the software tool has been applied to a number of Occam programs. Two examples were taken to show how the tool works in the early design phase for fault prevention before the program is ever run.

Real-time process plant fault diagnosis

Operators can become confused while diagnosing faults in process plant while in operation. This may prevent remedial actions being taken before hazardous consequences can occur. The work in this thesis proposes a method to aid plant operators in systematically finding the causes of any fault in the process plant. A computer aided fault diagnosis package has been developed for use on the widely available IBM PC compatible microcomputer. The program displays a coloured diagram of a fault tree on the VDU of the microcomputer, so that the operator can see the link between the fault and its causes. The consequences of the fault and the causes of the fault are also shown to provide a warning of what may happen if the fault is not remedied. The cause and effect data needed by the package are obtained from a hazard and operability (HAZOP) study on the process plant. The result of the HAZOP study is recorded as cause and symptom equations which are translated into a data structure and stored in the computer as a file for the package to access. Probability values are assigned to the events that constitute the basic causes of any deviation. From these probability values, the a priori probabilities of occurrence of other events are evaluated. A top-down recursive algorithm, called TDRA, for evaluating the probability of every event in a fault tree has been developed. From the a priori probabilities, the conditional probabilities of the causes of the fault are then evaluated using Bayes' conditional probability theorem. The posteriori probability values could then be used by the operators to check in an orderly manner the cause of the fault. The package has been tested using the results of a HAZOP study on a pilot distillation plant. The results from the test show how easy it is to trace the chain of events that leads to the primary cause of a fault. This method could be applied in a real process environment.

Tear protein interaction with hydrogel contact lenses

The design and synthesis of biomaterials covers a growing number of biomedical applications. The use of biomaterials in biological environment is associated with a number of problems, the most important of which is biocompatabUity. If the implanted biomaterial is not compatible with the environment, it will be rejected by the biological site. This may be manifested in many ways depending on the environment in which it is used. Adsorption of proteins takes place almost instantaneously when a biomaterial comes into contact with most biological fluids. The eye is a unique body site for the study of protein interactions with biomaterials, because of its ease of access and deceptive complexity of the tears. The use of contact lenses for either vision correction and cosmetic reasons or as a route for the controlled drug delivery, has significantly increased in recent years. It is relatively easy to introduce a contact lens Into the tear fluid and remove after a few minutes without surgery or trauma to the patient. A range of analytical techniques were used and developed to measure the proteins absorbed to some existing commercial contact lens materials and also to novel hydrogels synthesised within the research group. Analysis of the identity and quantity of proteins absorbed to biomaterials revealed the importance of many factors on the absorption process. The effect of biomaterial structure, protein nature in terms of size. shape and charge and pH of the environment on the absorption process were examined in order to determine the relative up-take of tear proteins. This study showed that both lysozyme and lactoferrin penetrate the lens matrix of ionic materials. Measurement of the mobility and activity of the protein deposited into the surface and within the matrix of ionic lens materials demonstrated that the mobility is pH dependent and, within the experimental errors, the biological activity of lysozyme remained unchanged after adsorption and desorption. The study on the effect of different monomers copolymerised with hydroxyethyl methacrylate (HEMA) on the protein up-take showed that monomers producing a positive charge on the copolymer can reduce the spoilation with lysozyme. The studies were extended to real cases in order to compare the patient dependent factors. The in-vivo studies showed that the spoilation is patient dependent as well as other factors. Studies on the extrinsic factors such as dye used in colour lenses showed that the addition of colourant affects protein absorption and, in one case, its effect is beneficial to the wearer as it reduces the quantity of the protein absorbed.

Setting parameters in MRP for the effective management of bought-out inventory in a JIT assembly environment

In recent years, UK industry has seen an explosive growth in the number of `Computer Aided Production Management' (CAPM) system installations. Of the many CAPM systems, materials requirement planning/manufacturing resource planning (MRP/MRPII) is the most widely implemented. Despite the huge investments in MRP systems, over 80 percent are said to have failed within 3 to 5 years of installation. Many people now assume that Just-In-Time (JIT) is the best manufacturing technique. However, those who have implemented JIT have found that it also has many problems. The author argues that the success of a manufacturing company will not be due to a system which complies with a single technique; but due to the integration of many techniques and the ability to make them complement each other in a specific manufacturing environment. This dissertation examines the potential for integrating MRP with JIT and Two-Bin systems to reduce operational costs involved in managing bought-out inventory. Within this framework it shows that controlling MRP is essential to facilitate the integrating process. The behaviour of MRP systems is dependent on the complex interactions between the numerous control parameters used. Methodologies/models are developed to set these parameters. The models are based on the Pareto principle. The idea is to use business targets to set a coherent set of parameters, which not only enables those business targets to be realised, but also facilitates JIT implementation. It illustrates this approach in the context of an actual manufacturing plant - IBM Havant. (IBM Havant is a high volume electronics assembly plant with the majority of the materials bought-out). The parameter setting models are applicable to control bought-out items in a wide range of industries and are not dependent on specific MRP software. The models have produced successful results in several companies and are now being developed as commercial products.

Utilising online shopping environment attributes holistically to create competitive advantage

As more consumers shop online, it becomes crucial for marketers to know how online shopping environments (OSEs) can be used to gain competitive advantage. This dissertation aims to explain theoretically how OSE attributes work together holistically to produce desirable consumer responses, applying and extending a theory from the environmental psychology literature to the online context. Firstly, the study conceptualises OSEs as virtual environments which may be perceived and experienced both cognitively and affectively through a technology-mediated interaction with a computer screen. A multi-disciplinary approach identifies key characteristics of OSEs: they involve consumers; they are more complex than their offline counterparts; they are likely first apprehended holistically; and they can elicit high levels of emotions and cognition. Secondly, the research uses a gestalt approach and extends Kaplan and Kalan’s (1982) Preference Framework, taking account of the specific characteristics of OSEs, which one visits specifically to obtain product information. The results support the proposition that OSEs are perceived in terms of their Sense-making and Exploratory attributes. Thirdly, the research explains how OSE attributes work together to produce desirable consumer responses. As hypothesised, Exploratory potential produces both Hedonic and Utilitarian value, and both kinds of value contribute to Site commitment. An unexpected result is that Sense-making potential does not produce Utilitarian value directly, but only through the mediation of Exploratory potential. The research contributes to marketing theory by: (1) identifying ways the internet has changed the nature of the shopping experience; (2) extending Kaplan and Kaplan’s Preference Framework to explain how consumers perceive OSEs holistically; (3) identifying the distinction between page-level and site-level perceptions, and (4) distinguishing between different sources of information (marketer vs. non-marketer). Managerially, the research provides a model for marketers to conceive and design retail websites whose attributes work together to create competitive advantage.

Lateral instability of slender reinforced concrete columns in a fire environment

The research concerns the development and application of an analytical computer program, SAFE-ROC, that models material behaviour and structural behaviour of a slender reinforced concrete column that is part of an overall structure and is subjected to elevated temperatures as a result of exposure to fire. The analysis approach used in SAFE-RCC is non-linear. Computer calculations are used that take account of restraint and continuity, and the interaction of the column with the surrounding structure during the fire. Within a given time step an iterative approach is used to find a deformed shape for the column which results in equilibrium between the forces associated with the external loads and internal stresses and degradation. Non-linear geometric effects are taken into account by updating the geometry of the structure during deformation. The structural response program SAFE-ROC includes a total strain model which takes account of the compatibility of strain due to temperature and loading. The total strain model represents a constitutive law that governs the material behaviour for concrete and steel. The material behaviour models employed for concrete and steel take account of the dimensional changes caused by the temperature differentials and changes in the material mechanical properties with changes in temperature. Non-linear stress-strain laws are used that take account of loading to a strain greater than that corresponding to the peak stress of the concrete stress-strain relation, and model the inelastic deformation associated with unloading of the steel stress-strain relation. The cross section temperatures caused by the fire environment are obtained by a preceding non-linear thermal analysis, a computer program FIRES-T.

Speaking out of turn? Taking the initiative in teacher-fronted classroom interaction.

Teacher-fronted interaction is generally seen to place limitations on the contributions that learners can make to classroom discourse and the conclusion is that learners are unable to experiment with, for example, turn-taking mechanisms. This article looks at teacher-fronted interaction in the language classroom from the perspective of learner talk by examining how learners might take the initiative during this apparently more rigid form of interaction. Detailed microanalysis of classroom episodes, using a conversation analysis institutional discourse approach, shows how learners orient to the institutional context to make sophisticated and effective use of turn-taking mechanisms to take the initiative and direct the interaction, even in the controlled environment of teacher-fronted talk. The article describes some of the functions of such learner initiative, examines how learners and teachers co-construct interaction and how learners can create learning opportunities for themselves. It also briefly looks at teacher reactions to such initiative. The article concludes that learner initiative in teacher-fronted interaction may constitute a significant opportunity for learning and that teachers should find ways of encouraging such interaction patterns.

Modeling naturalistic argumentation in research literatures:representation and interaction design issues

This article characterizes key weaknesses in the ability of current digital libraries to support scholarly inquiry, and as a way to address these, proposes computational services grounded in semiformal models of the naturalistic argumentation commonly found in research literatures. It is argued that a design priority is to balance formal expressiveness with usability, making it critical to coevolve the modeling scheme with appropriate user interfaces for argument construction and analysis. We specify the requirements for an argument modeling scheme for use by untrained researchers and describe the resulting ontology, contrasting it with other domain modeling and semantic web approaches, before discussing passive and intelligent user interfaces designed to support analysts in the construction, navigation, and analysis of scholarly argument structures in a Web-based environment. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 17–47, 2007.