Quantitative Association Tests of Immune Responses to Antigens of Mycobacterium Tuberculosis: A Study of Twins in West Africa

There is now considerable evidence that host genetic factors are important in determining the outcome of infection with Mycobacterium tuberculosis (MTB). The aim of this study was to assess the role of several candidate genes in the variation observed in the immune responses to MTB antigens. In-vitro assays of T-cell proliferation, an in-vivo intradermal delayed hypersensitivity response; cytokine and antibody secretions to several mycobacterial peptide antigens were assessed in healthy, but exposed, West African twins. Candidate gene polymorphisms were typed in the NRAMP1, Vitamin D receptor, IL10, IL4, IL4 receptor and CTLA-4 genes. Variants of the loci IL10 (-1082 G/A), CTLA-4 (49 A/G) and the IL4 receptor (128 A/G) showed significant associations with immune responses to several antigens. T-cell proliferative responses and antibody responses were reduced, TNF-alpha responses were increased for subjects with the CTLA-4 G allele. The T-cell proliferative responses of subjects with IL10 GA and GG genotypes differed significantly. IL4 receptor AG and GG genotypes also showed significant differences in their T-cell proliferative responses to MTB antigens. These results yield a greater understanding of the genetic mechanisms that underlie the immune responses in tuberculosis and have implications for the design of therapeutic interventions.

Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug

Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of squashed whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.

Investigation into the ability of Gluconacetobacter sacchari to live as an endophyte in sugarcane

The relatively low numbers and sporadic pattern of incidence of the acetic acid bacterium Gluconacetobacter sacchari with the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homoptera: Pseudococcidae) over time and from different sugarcane-growing regions do not indicate that Glac. sacchari is a significant commensal of the PSMB, as has been previously proposed. This study was conducted to investigate the hypothesis that Glac. sacchari is, like its closest relative Glac. diazotrophicus, an endophyte of sugarcane (Saccharum officinarium L.). In this study, both Glac. sacchari and Glac. diazotrophicus were isolated from internal sugarcane tissue, although the detection of both species was sporadic in all sugarcane-growing regions of Queensland tested. To confirm the ability of Glac. sacchari to live endophytically, an experiment was conducted in which the roots of micropropagated sugarcane plantlets were inoculated with Glac. sacchari, and the plantlets were subsequently examined for the presence of the bacterium in the stem cells. Pure cultures of Glac. sacchari were grown from homogenized surface sterilized sugarcane stems inoculated with Glac. sacchari. Electron microscopy was used to provide further conclusive evidence that Glac. sacchari lives as an endophyte in sugarcane. Scanning electron microscopy of (SEM) sugarcane plantlet stems revealed rod-shaped cells of Glac. sacchari within a transverse section of the plantlet stem cells. The numbers of bacterial cells inside the plant cell indicated a successful infection and colonization of the plant tissue. Using transmission electron microscopy, (TEM) bacterial cells were more difficult to find, due to their spatial separation. In our study, bacteria were mostly found singularly, or in groups of up to four cells inside intercellular spaces, although bacterial cells were occasionally found inside other cells.

Molecular investigation of the microbial populations of the pink sugarcane mealybug, Saccharicoccus sacchari

In an attempt to better understand the microbial diversity and endosymbiotic microbiota of the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homoptera: Pseudococcidae), culture-independent approaches, namely PCR, a 16S rDNA clone library, and temperature gradient gel electrophoresis (TGGE) were used. Previous work has indicated that the acetic acid bacteria Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens represent only a small proportion of the microbial community of the PSMB. These findings were supported in this study by TGGE, where no bands representing G. sacchari, G. diazotrophicus, and G. liquefaciens on the acrylamide gel could be observed following electrophoresis, and by a 16S rDNA clone library study, where no clones with the sequence of an acetic acid bacterium were found. Instead, TGGE revealed that the mealybug microbial community was dominated by beta- and gamma-Proteobacteria. The dominant band in TGGE gels found in a majority of the mealybug samples was most similar, according to BLAST analysis, to the beta-symbiont of the craw mealybug Antonina crawii and to Candidatus Tremblaya princeps, an endosymbiont from the mealybug Paracoccus nothofagicola. The sequences of other dominant bands were identified as gamma-Proteobacteria, and were most closely related to uncultured bacterial clones obtained from soil samples. Mealybugs collected from different areas in Queensland, Australia, were found to produce similar TGGE profiles, although there were a few exceptions. A 16S rDNA clone library based on DNA extracted from a mealybug collected from sugarcane in the Burdekin region in Queensland, Australia, indicated very low levels of diversity among mealybug microbial populations. All sequenced clones were most closely related to the same members of the gamma-Proteobacteria, according to BLAST analysis.

Incremental model transformation for the evolution of model-driven systems

Model transformations are an integral part of model-driven development. Incremental updates are a key execution scenario for transformations in model-based systems, and are especially important for the evolution of such systems. This paper presents a strategy for the incremental maintenance of declarative, rule-based transformation executions. The strategy involves recording dependencies of the transformation execution on information from source models and from the transformation definition. Changes to the source models or the transformation itself can then be directly mapped to their effects on transformation execution, allowing changes to target models to be computed efficiently. This particular approach has many benefits. It supports changes to both source models and transformation definitions, it can be applied to incomplete transformation executions, and a priori knowledge of volatility can be used to further increase the efficiency of change propagation.

RELAX:a language to address uncertainty in self-adaptive systems requirement

Self-adaptive systems have the capability to autonomously modify their behavior at run-time in response to changes in their environment. Self-adaptation is particularly necessary for applications that must run continuously, even under adverse conditions and changing requirements; sample domains include automotive systems, telecommunications, and environmental monitoring systems. While a few techniques have been developed to support the monitoring and analysis of requirements for adaptive systems, limited attention has been paid to the actual creation and specification of requirements of self-adaptive systems. As a result, self-adaptivity is often constructed in an ad-hoc manner. In order to support the rigorous specification of adaptive systems requirements, this paper introduces RELAX, a new requirements language for self-adaptive systems that explicitly addresses uncertainty inherent in adaptive systems. We present the formal semantics for RELAX in terms of fuzzy logic, thus enabling a rigorous treatment of requirements that include uncertainty. RELAX enables developers to identify uncertainty in the requirements, thereby facilitating the design of systems that are, by definition, more flexible and amenable to adaptation in a systematic fashion. We illustrate the use of RELAX on smart home applications, including an adaptive assisted living system.

Requirements-aware systems:a research agenda for RE for self-adaptive systems

Requirements are sensitive to the context in which the system-to-be must operate. Where such context is well-understood and is static or evolves slowly, existing RE techniques can be made to work well. Increasingly, however, development projects are being challenged to build systems to operate in contexts that are volatile over short periods in ways that are imperfectly understood. Such systems need to be able to adapt to new environmental contexts dynamically, but the contextual uncertainty that demands this self-adaptive ability makes it hard to formulate, validate and manage their requirements. Different contexts may demand different requirements trade-offs. Unanticipated contexts may even lead to entirely new requirements. To help counter this uncertainty, we argue that requirements for self-adaptive systems should be run-time entities that can be reasoned over in order to understand the extent to which they are being satisfied and to support adaptation decisions that can take advantage of the systems' self-adaptive machinery. We take our inspiration from the fact that explicit, abstract representations of software architectures used to be considered design-time-only entities but computational reflection showed that architectural concerns could be represented at run-time too, helping systems to dynamically reconfigure themselves according to changing context. We propose to use analogous mechanisms to achieve requirements reflection. In this paper we discuss the ideas that support requirements reflection as a means to articulate some of the outstanding research challenges.

Requirements reflection:requirements as runtime entities

Computational reflection is a well-established technique that gives a program the ability to dynamically observe and possibly modify its behaviour. To date, however, reflection is mainly applied either to the software architecture or its implementation. We know of no approach that fully supports requirements reflection- that is, making requirements available as runtime objects. Although there is a body of literature on requirements monitoring, such work typically generates runtime artefacts from requirements and so the requirements themselves are not directly accessible at runtime. In this paper, we define requirements reflection and a set of research challenges. Requirements reflection is important because software systems of the future will be self-managing and will need to adapt continuously to changing environmental conditions. We argue requirements reflection can support such self-adaptive systems by making requirements first-class runtime entities, thus endowing software systems with the ability to reason about, understand, explain and modify requirements at runtime. © 2010 ACM.

A language for self-adaptive system requirements

Self-adaptive systems have the capability to autonomously modify their behaviour at run-time in response to changes in their environment. Such systems are now commonly built in domains as diverse as enterprise computing, automotive control systems, and environmental monitoring systems. To date, however, there has been limited attention paid to how to engineer requirements for such systems. As a result, selfadaptivity is often constructed in an ad-hoc manner. In this paper, we argue that a more rigorous treatment of requirements relating to self-adaptivity is needed and that, in particular, requirements languages for self-adaptive systems should include explicit constructs for specifying and dealing with the uncertainty inherent in self-adaptive systems. We present some initial thoughts on a new requirements language for selfadaptive systems and illustrate it using examples from the services domain. © 2008 IEEE.

A goal-based modeling approach to develop requirements of an adaptive system with environmental uncertainty

Dynamically adaptive systems (DASs) are intended to monitor the execution environment and then dynamically adapt their behavior in response to changing environmental conditions. The uncertainty of the execution environment is a major motivation for dynamic adaptation; it is impossible to know at development time all of the possible combinations of environmental conditions that will be encountered. To date, the work performed in requirements engineering for a DAS includes requirements monitoring and reasoning about the correctness of adaptations, where the DAS requirements are assumed to exist. This paper introduces a goal-based modeling approach to develop the requirements for a DAS, while explicitly factoring uncertainty into the process and resulting requirements. We introduce a variation of threat modeling to identify sources of uncertainty and demonstrate how the RELAX specification language can be used to specify more flexible requirements within a goal model to handle the uncertainty. © 2009 Springer Berlin Heidelberg.

Software engineering for self-adaptive systems:a research roadmap

The goal of this roadmap paper is to summarize the state-of-the-art and to identify critical challenges for the systematic software engineering of self-adaptive systems. The paper is partitioned into four parts, one for each of the identified essential views of self-adaptation: modelling dimensions, requirements, engineering, and assurances. For each view, we present the state-of-the-art and the challenges that our community must address. This roadmap paper is a result of the Dagstuhl Seminar 08031 on "Software Engineering for Self-Adaptive Systems," which took place in January 2008. © 2009 Springer Berlin Heidelberg.

Self-explanation in adaptive systems

The behaviour of self adaptive systems can be emergent. The difficulty in predicting the system's behaviour means that there is scope for the system to surprise its customers and its developers. Because its behaviour is emergent, a self-adaptive system needs to garner confidence in its customers and it needs to resolve any surprise on the part of the developer during testing and mainteinance. We believe that these two functions can only be achieved if a self-adaptive system is also capable of self-explanation. We argue a self-adaptive system's behaviour needs to be explained in terms of satisfaction of its requirements. Since self-adaptive system requirements may themselves be emergent, a means needs to be found to explain the current behaviour of the system and the reasons that brought that behaviour about. We propose the use of goal-based models during runtime to offer self-explanation of how a system is meeting its requirements, and why the means of meeting these were chosen. We discuss the results of early experiments in self-explanation, and set out future work. © 2012 C.E.S.A.M.E.S.

Foreword:2nd workshop requirements@run.time

The 2nd edition of the Workshop requirements@run.time was held at the 19th International Conference on Requirements Engineering (RE 2011) in the city of Trento, Italy on the 30th of August 2011. It was organized by Nelly Bencomo, Emmanuel Letier, Jon Whittle, Anthony Finkelstein, and Kris Welsh. This foreword presents a digest of the discussions and presentations that took place during the workshop. © 2011 IEEE.

Foreword:first workshop requirements@run.time

The first edition of the Workshop requirements@run.time was held at the Eighteenth International Conference on Requirements Engineering (RE 2010) in the city of Sydney, NSW, Australia on the 28th of September 2010. It was organized by Pete Sawyer, Jon Whittle, Nelly Bencomo, Daniel Berry, and Anthony Finkelstein. This foreword presents a digest of the presentations and discussions that took place during the workshop. © 2010 IEEE.

RELAX:incorporating uncertainty into the specification of self-adaptive systems

Self-adaptive systems have the capability to autonomously modify their behaviour at run-time in response to changes in their environment. Self-adaptation is particularly necessary for applications that must run continuously, even under adverse conditions and changing requirements; sample domains include automotive systems, telecommunications, and environmental monitoring systems. While a few techniques have been developed to support the monitoring and analysis of requirements for adaptive systems, limited attention has been paid to the actual creation and specification of requirements of self-adaptive systems. As a result, self-adaptivity is often constructed in an ad-hoc manner. In this paper, we argue that a more rigorous treatment of requirements explicitly relating to self-adaptivity is needed and that, in particular, requirements languages for self-adaptive systems should include explicit constructs for specifying and dealing with the uncertainty inherent in self-adaptive systems. We present RELAX, a new requirements language for selfadaptive systems and illustrate it using examples from the smart home domain. © 2009 IEEE.