Evaluation of individual protein errors in silver-stained two-dimensional gels

The relationship between spot volume and variation for all protein spots observed on large format 2D gels when utilising silver stain technology and a model system based on mammalian NSO cell extracts is reported. By running multiple gels we have shown that the reproducibility of data generated in this way is dependent on individual protein spot volumes, which in turn are directly correlated with the coefficient of variation. The coefficients of variation across all observed protein spots were highest for low abundant proteins which are the primary contributors to process error, and lowest for more abundant proteins. Using the relationship between spot volume and coefficient of variation we show it is necessary to calculate variation for individual protein spot volumes. The inherent limitations of silver staining therefore mean that errors in individual protein spot volumes must be considered when assessing significant changes in protein spot volume and not global error. (C) 2003 Elsevier Science (USA). All rights reserved.

5 '-Untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation

Upstream AUGs (uAUGs) and upstream open reading frames (uORFs) are common features of mRNAs that encode regulatory proteins and have been shown to profoundly influence translation of the main ORF. In this study, we employed a series of artificial 5'-untranslated regions (5'-UTRs) containing one or more uAUGs/uORFs to systematically assess translation initiation at the main AUG by leaky scanning and reinitiation mechanisms. Constructs containing either one or two uAUGs in varying contexts but without an in-frame stop codon upstream of the main AUG were used to analyse the leaky scanning mechanism. This analysis largely confirmed the ranking of different AUG contextual sequences that was determined previously by Kozak. In addition, this ranking was the same for both the first and second uAUGs, although the magnitude of initiation efficiency differed. Moreover, similar to10% of ribosomes exhibited leaky scanning at uAUGs in the most favourable context and initiated at a downstream AUG. A second group of constructs containing different numbers of uORFs, each with optimal uAUGs, were used to measure the capacity for reinitiation. We found significant levels of initiation at the main ORF even in constructs containing four uORFs, with nearly 10% of ribosomes capable of reinitiating five times. This study shows that for mRNAs containing multiple uORFs/uAUGs, ribosome reinitiation and leaky scanning are efficient mechanisms for initiation at their main AUGs.

Global changes in gene expression observed at the transition from growth to stationary phase in Listeria monocytogenes ScottA batch culture

Listeria monocytogenes is a food-borne Gram-positive bacterium that is responsible for a variety of infections (worldwide) annually. The organism is able to survive a variety of environmental conditions and stresses, however, the mechanisms by which L. monocytogenes adapts to environmental change are yet to be fully elucidated. An understanding of the mechanism(s) by which L. monocytogenes survives unfavourable environmental conditions will aid in developing new food processing methods to control the organism in foodstuffs. We have utilized a proteomic approach to investigate the response of L. monocytogenes batch cultures to the transition from exponential to stationary growth phase. Proteomic analysis showed that batch cultures of L. monocytogenes perceived stress and began preparations for stationary phase much earlier (approximately A(600) = 0.75, mid-exponential) than predicted by growth characteristics alone. Global analysis of the proteome revealed that the expression levels of more than 50% of all proteins observed changed significantly over a 7-9 h period during this transition phase. We have highlighted ten proteins in particular whose expression levels appear to be important in the early onset of the stationary phase. The significance of these findings in terms of functionality and the mechanistic picture are discussed.

A full cost environmental accounting experiment

A lack of appropriate measurement techniques has constrained full cost environmental accounting (FCEA) experimentation. Yet, there has been little research on the applicability of valuation techniques recently developed by environmental economists within FLEA frameworks. This paper examines a reporting experiment using these valuation techniques that was undertaken by an Australian Government Department managing publicly owned forests. The FCEA experiment was ultimately not successful. However, the implementation experiences of the Department including the reactions of its managers and stakeholders provide an opportunity to critically reflect on the experimental outcomes to extend the current empirical knowledge of corporate social responsibility reporting. Such critical reflection has not been common in past FCEA experimentation. © 2005 Elsevier Ltd. All rights reserved.

A new approach to control of MIMO processes with static nonlinearities using an extended IMC framework

In this paper, a new control design method is proposed for stable processes which can be described using Hammerstein-Wiener models. The internal model control (IMC) framework is extended to accommodate multiple IMC controllers, one for each subsystem. The concept of passive systems is used to construct the IMC controllers which approximate the inverses of the subsystems to achieve dynamic control performance. The Passivity Theorem is used to ensure the closed-loop stability. (c) 2005 Elsevier Ltd. All rights reserved.

Identification of MIMO Hammerstein systems using cardinal spline functions

A new approach to identify multivariable Hammerstein systems is proposed in this paper. By using cardinal cubic spline functions to model the static nonlinearities, the proposed method is effective in modelling processes with hard and/or coupled nonlinearities. With an appropriate transformation, the nonlinear models are parameterized such that the nonlinear identification problem is converted into a linear one. The persistently exciting condition for the transformed input is derived to ensure the estimates are consistent with the true system. A simulation study is performed to demonstrate the effectiveness of the proposed method compared with the existing approaches based on polynomials. (C) 2006 Elsevier Ltd. All rights reserved.

Coadaptation: A unifying principle in evolutionary thermal biology

Over the last 50 yr, thermal biology has shifted from a largely physiological science to a more integrated science of behavior, physiology, ecology, and evolution. Today, the mechanisms that underlie responses to environmental temperature are being scrutinized at levels ranging from genes to organisms. From these investigations, a theory of thermal adaptation has emerged that describes the evolution of thermoregulation, thermal sensitivity, and thermal acclimation. We review and integrate current models to form a conceptual model of coadaptation. We argue that major advances will require a quantitative theory of coadaptation that predicts which strategies should evolve in specific thermal environments. Simply combining current models, however, is insufficient to understand the responses of organisms to thermal heterogeneity; a theory of coadaptation must also consider the biotic interactions that influence the net benefits of behavioral and physiological strategies. Such a theory will be challenging to develop because each organism's perception of and response to thermal heterogeneity depends on its size, mobility, and life span. Despite the challenges facing thermal biologists, we have never been more pressed to explain the diversity of strategies that organisms use to cope with thermal heterogeneity and to predict the consequences of thermal change for the diversity of communities.

Embedding defeasible logic into logic programming

Defeasible reasoning is a simple but efficient approach to nonmonotonic reasoning that has recently attracted considerable interest and that has found various applications. Defeasible logic and its variants are an important family of defeasible reasoning methods. So far no relationship has been established between defeasible logic and mainstream nonmonotonic reasoning approaches. In this paper we establish close links to known semantics of logic programs. In particular, we give a translation of a defeasible theory D into a meta-program P(D). We show that under a condition of decisiveness, the defeasible consequences of D correspond exactly to the sceptical conclusions of P(D) under the stable model semantics. Without decisiveness, the result holds only in one direction (all defeasible consequences of D are included in all stable models of P(D)). If we wish a complete embedding for the general case, we need to use the Kunen semantics of P(D), instead.

Extending the theory of Owicki and Gries with a logic of progress

This paper describes a logic of progress for concurrent programs. The logic is based on that of UNITY, molded to fit a sequential programming model. Integration of the two is achieved by using auxiliary variables in a systematic way that incorporates program counters into the program text. The rules for progress in UNITY are then modified to suit this new system. This modification is however subtle enough to allow the theory of Owicki and Gries to be used without change.

Efficient experimental designs when most treatments are unreplicated

In early generation variety trials, large numbers of new breeders' lines (varieties) may be compared, with each having little seed available. A so-called unreplicated trial has each new variety on just one plot at a site, but includes several replicated control varieties, making up around 10% and 20% of the trial. The aim of the trial is to choose some (usually around one third) good performing new varieties to go on for further testing, rather than precise estimation of their mean yields. Now that spatial analyses of data from field experiments are becoming more common, there is interest in an efficient layout of an experiment given a proposed spatial analysis and an efficiency criterion. Common optimal design criteria values depend on the usual C-matrix, which is very large, and hence it is time consuming to calculate its inverse. Since most varieties are unreplicated, the variety incidence matrix has a simple form, and some matrix manipulations can dramatically reduce the computation needed. However, there are many designs to compare, and numerical optimisation lacks insight into good design features. Some possible design criteria are discussed, and approximations to their values considered. These allow the features of efficient layouts under spatial dependence to be given and compared. (c) 2006 Elsevier Inc. All rights reserved.

Logic of Violations: A gentzen systems for reasoning with contrary-to-duty obligations

In this paper we present a Gentzen system for reasoning with contrary-to-duty obligations. The intuition behind the system is that a contrary-to-duty is a special kind of normative exception. The logical machinery to formalise this idea is taken from substructural logics and it is based on the definition of a new non-classical connective capturing the notion of reparational obligation. Then the system is tested against well-known contrary-to-duty paradoxes.