Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

Plant breeders use many different breeding methods to develop superior cultivars. However, it is difficult, cumbersome, and expensive to evaluate the performance of a breeding method or to compare the efficiencies of different breeding methods within an ongoing breeding program. To facilitate comparisons, we developed a QU-GENE module called QuCim that can simulate a large number of breeding strategies for self-pollinated species. The wheat breeding strategy Selected Bulk used by CIMMYT's wheat breeding program was defined in QuCim as an example of how this is done. This selection method was simulated in QuCim to investigate the effects of deviations from the additive genetic model, in the form of dominance and epistasis, on selection outcomes. The simulation results indicate that the partial dominance model does not greatly influence genetic advance compared with the pure additive model. Genetic advance in genetic systems with overdominance and epistasis are slower than when gene effects are purely additive or partially dominant. The additive gene effect is an appropriate indicator of the change in gene frequency following selection when epistasis is absent. In the absence of epistasis, the additive variance decreases rapidly with selection. However, after several cycles of selection it remains relatively fixed when epistasis is present. The variance from partial dominance is relatively small and therefore hard to detect by the covariance among half sibs and the covariance among full sibs. The dominance variance from the overdominance model can be identified successfully, but it does not change significantly, which confirms that overdominance cannot be utilized by an inbred breeding program. QuCim is an effective tool to compare selection strategies and to validate some theories in quantitative genetics.

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA Microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design microarray probes with high specificities and sensitivities. Highly specific probes correspond to probes having unique DNA sequences; whereas highly sensitive probes correspond to those with melting temperature within a desired range and having no secondary structure. The selection of these probes from a set of functional DNA sequences (exons) constitutes a computationally expensive discrete non-linear search problem. We delegate the search task to a simple yet effective Evolution Strategy algorithm. The computational efficiency is also greatly improved by making use of an available bioinformatics tool.

Cloning and expression of the large zebrafish protocadherin gene, Fat

The cadherin superfamily members play an important role in mediating cell-cell contact and adhesion (Takeichi, M., 1991. Cadherin cell adhesion receptors as a morphogenetic regulator. Science 251, 1451-1455). A distinct subfamily, neither belonging to the classical or protocadherins includes Fat, the largest member of the cadherin super-family. Fat was originally identified in Drosophila. Subsequently, orthologues of Fat have been described in man (Dunne, J., Hanby, A. M., Poulsom, R., Jones, T. A., Sheer, D., Chin, W. G., Da, S. M., Zhao, Q., Beverley, P. C., Owen, M. J., 1995. Molecular cloning and tissue expression of FAT, the human homologue of the Drosophila fat gene that is located on chromosome 4q34-q35 and encodes a putative adhesion molecule. Genomics 30, 207-223), rat (Ponassi, M., Jacques, T. S., Ciani, L., ffrench, C. C., 1999. Expression of the rat homologue of the Drosophila fat tumour suppressor gene. Mech. Dev. 80, 207-212) and mouse (Cox, B., Hadjantonakis, A. K., Collins, J. E., Magee, A. I., 2000. Cloning and expression throughout mouse development of mfat 1, a homologue of the Drosophila tumour suppressor gene fat [In Process Citation]. Dev. Dyn. 217, 233-240). In Drosophila, Fat has been shown to play an important role in both planar cell polarity and cell boundary formation during development. In this study we describe the characterization of zebrafish Fat, the first non-mammalian, vertebrate Fat homologue to be identified. The Fat protein has 64% amino acid identity and 80% similarity to human FAT and an identical domain structure to other vertebrate Fat proteins. During embryogenesis fat mRNA is expressed in the developing brain, specialised epithelial surfaces the notochord, ears, eyes and digestive tract, a pattern similar but distinct to that found in mammals. (c) 2005 Elsevier B.V. All rights reserved.

Unimolecular Rovibrational Bound and Resonance States for Large Angular Momentum: J=20 Calculations for HO2

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-> H+O-2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.

Isolation of polymorphic tetranucleotide microsatellite for the large-billed scrubwren (Sericomis magnirostris)

We isolated 12 polymorphic microsatellite markers for the large-billed scrubwren Sericornis magnirostris from genomic libraries enriched for (AAGG)(n) and (AACC)(n) repetitive elements and characterized them in 11 individuals. The number of alleles ranged from four to 15 per locus with the observed heterozygosity ranging from 0.14 to 0.91. These markers will be useful to address questions concerning population genetic structure and models of speciation.

Prediction of protein B-factor profiles

The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.

The impact of leadership and change management strategy on organizational culture and individual acceptance of change during a merger

This article reports a longitudinal study that examined mergers between three large multi-site public-sector organizations. Both qualitative and quantitative methods of analysis are used to examine the effect of leadership and change management strategies on acceptance of cultural change by individuals. Findings indicate that in many cases the change that occurs as a result of a merger is imposed on the leaders themselves, and it is often the pace of change that inhibits the successful re-engineering of the culture. In this respect, the success or otherwise of any merger hinges on individual perceptions about the manner in which the process is handled and the direction in which the culture is moved. Communication and a transparent change process are important, as this will often determine not only how a leader will be regarded, but who will be regarded as a leader. Leaders need to be competent and trained in the process of transforming organizations to ensure that individuals within the organization accept the changes prompted by a merger.

Australia's National Mental Health Strategy and deinstitutionalization: some empirical results

Objective: To determine the role of the National Mental Health Strategy in the deinstitutionalization of patients in psychiatric hospitals in Queensland. Method: Regression analysis (using the maximum likelihood method) has been applied to relevant time-series datasets on public psychiatric institutions in Queensland. In particular, data on both patients and admissions per 10 000 population are analysed in detail from 1953-54 to the present, although data are presented from 1883-84. Results: These Queensland data indicate that deinstitutionalization was a continuing process from the 1950s to the present. However, it is clear that the experience varied from period to period. For example, the fastest change (in both patients and admissions) took place in the period 1953-54 to 1973-74, followed by the period 1974-75 to 1984-85. Conclusions: In large part, the two policies associated with deinstitutionalization, namely a discharge policy ('opening the back door') and an admission policy ('closing the front door') had been implemented before the advent of the National Mental Health Strategy in January 1993. Deinstitutionalization was most rapid in the 30-year period to the early 1980s: the process continued in the 1990s, but at a much slower rate. Deinstitutionalization was, in large part, over before the Strategy was developed and implemented.

The influence of natural body sway on neuromuscular responses to an unpredictable surface translation

Previous research has shown that the postural configuration adopted by a subject, such as active leaning, influences the postural response to an unpredictable support surface translation. While those studies have examined large differences in postural conditions, it is of additional interest to examine the effects of naturally occurring changes in standing posture. Thus, it was hypothesized that the normal postural sway observed during quiet standing would affect the responses to an unpredictable support surface translation. Seventeen young adults stood quietly on a moveable platform and were perturbed in either the forward or backward direction when the location of the center of pressure (COP) was either 1.5 standard deviations anterior or posterior to the mean baseline COP signal. Postural responses, in the form of electromyographic (EMG) latencies and amplitudes, were recorded from lower limb and trunk muscles. When the location of the COP at the time of the translation was in the opposite, as compared to the same, direction as the upcoming translation, there was a significantly earlier onset of the antagonists (10-23%, i.e. 15-45 ms) and a greater EMG amplitude (14-39%) in four of the six recorded muscles. Stepping responses were most frequently observed during trials where the position of the COP was opposite to the direction of the translation. The results support the hypothesis that postural responses to unpredictable support surface translations are influenced by the normal movements of postural sway. The results may help to explain the large variability of postural responses found between past studies.

Strategy-making process and firm performance in small firms

This paper argues that individual small firms just like large firms, place differing emphasis on strategy-making and may employ different modes of strategy-making. It offers a typology of the different modes of strategy-making that seem most likely to exist in small firms, and hypothesises how this typology relates to performance. It then describes the results of an empirical study of the strategy-making processes of small firms. The structural equation analysis of the data from 477 small firms with less than 100 employees indicates among other results that the simplistic, adaptive, intrapreneurial and participative modes of strategy-making exist in these small firms. Of these modes, the simplistic mode exhibits the strongest relationship with firm performance.

Statistical racing techniques for improved empirical evaluation of evolutionary algorithms

In empirical studies of Evolutionary Algorithms, it is usually desirable to evaluate and compare algorithms using as many different parameter settings and test problems as possible, in border to have a clear and detailed picture of their performance. Unfortunately, the total number of experiments required may be very large, which often makes such research work computationally prohibitive. In this paper, the application of a statistical method called racing is proposed as a general-purpose tool to reduce the computational requirements of large-scale experimental studies in evolutionary algorithms. Experimental results are presented that show that racing typically requires only a small fraction of the cost of an exhaustive experimental study.

The co-evolutionary dynamics of IS engagement

In this paper we consider the co-evolutionary dynamics of IS engagement where episodic change of implementation increasingly occurs within the context of linkages and interdependencies between systems and processes within and across organisations. Although there are many theories that interpret the various motors of change be it lifecycle, teleological, dialectic or evolutionary, our paper attempts to move towards a unifying view of change by studying co-evolutionary dynamics from a complex systems perspective. To understand how systems and organisations co-evolve in practice and how order emerges, or fails to emerge, we adopt complex adaptive systems theory to incorporate evolutionary and teleological motors, and actor-network theory to incorporate dialectic motors. We illustrate this through the analysis of the implementation of a novel academic scheduling system at a large research-intensive Australian university.

Actor-network theory as a theoretical lens and research strategy for investigating firm internationalisation

Totally generalisable theories of firm internationalisation in the post-industrial era of international business, where national barriers are becoming less significant and technology becoming more influential, appear to be illusory. Stepwise or evolutionary models that predict gradual internationalisation are under challenge from empirical evidence of rapid internationalisation such as the phenomenon of the “born global” firm. Similarly, equilibrium models such as the eclectic paradigm have been criticised for being static and unable to account for process and path dependency. In this paper, the information and knowledge assumptions implied in theories of firm internationalisation are outlined and discussed. From this discussion, we suggest that actor-network theory, with its balance between description and explanation, may be a useful theoretical and empirical tool for investigating the complex and heterogeneous process of firm internationalisation whilst creating opportunities for further theory building.

Learning to play Pac-Man: An evolutionary, rule-based approach

Pac-Man is a well-known, real-time computer game that provides an interesting platform for research. We describe an initial approach to developing an artificial agent that replaces the human to play a simplified version of Pac-Man. The agent is specified as a simple finite state machine and ruleset. with parameters that control the probability of movement by the agent given the constraints of the maze at some instant of time. In contrast to previous approaches, the agent represents a dynamic strategy for playing Pac-Man, rather than a pre-programmed maze-solving method. The agent adaptively "learns" through the application of population-based incremental learning (PBIL) to adjust the agents' parameters. Experimental results are presented that give insight into some of the complexities of the game, as well as highlighting the limitations and difficulties of the representation of the agent.