The Ikaros gene family

Ikaros-related transcription factors are essential for adaptive immunity. Evolutionary analysis suggested derivation from a precursor similar to the 'atypical' Pegasus protein, and possibly related to invertebrate Hunchback. Pegasus was shown to regulate neural, gut and blood cell development in zebrafish, with Ikaros identified as one of several potential gene targets.

Analysis of cultural conflict in the development of web-enabled information systems

The advent of the World Wide Web (WWW) and the emergence of Internet commerce have given rise to the web as a medium of information exchange. In recent years, the phenomenon has affected the realm of transaction processing systems, as organizations are moving from designing web pages for marketing purposes, to web-based applications that support business-to-business (WEB) and business-to-consumer (B2C) interactions, integrated with databases and other back-end systems (Isakowitz, Bieber et al., 1998). Furthermore, web-enabled applications are increasingly being used to facilitate transactions even between various business units within a single enterprise. Examples of some of the more popular web-enabled applications in use today include airline reservation systems, internet banking, student enrollment systems in universities, and Human Resource (HR) and payroll systems. The prime motive behind the adoption of web-enabled applications are productivity gains due to reduced processing time, decrease in the usage of paper-based documentation and conventional modes of communication (such as letters, fax, or telephone), and improved quality of services to clients. Indeed, web-based solutions are commonly referred to as customer-centric (Li, 2000), which means that they provide user interfaces that do not necessitate high level of computer proficiency. Thus, organizations implement such systems to streamline routine transactions and gain strategic benefits in the process (Nambisan & Wang, 1999), though the latter are to be expected in the long-term. Notwithstanding the benefits of web technology adoption, the web has ample share of challenges for initiators and developers. Many of these challenges are associated with the unique nature of web-enabled applications. Research in the area of web-enabled information systems has revealed several differences with traditional applications. These differences exist with regards to system development methodology, stakeholder involvement, tasks, and technology (Nazareth, 1998). According to Fraternali (1999), web applications are commonly developed using an evolutionary prototyping approach, whereby the simplified version of the application is deployed as a pilot first, in order to gather user feedback. Thus, web-enabled applications typically undergo continuous refinement and evolution (Ginige, 1998; Nazareth, 1998; Siau, 1998; Standing, 2001). Prototype-based development also leads web-enabled information systems to have much shorter development life cycles, but which, unlike traditional applications, are regrettably developed in a rather adhoc fashion (Carstensen & Vogelsang, 2001). However, the principal difference between the two kinds of applications lies in the broad and diverse group of stakeholders associated with web-based information systems (Gordijn, Akkermans, et al., 2000; Russo, 2000; Earl & Khan, 2001; Carter, 2002; Hasselbring, 2002; Standing, 2002; Stevens & Timbrell, 2002). Stakeholders, or organizational members participating in a common business process (Freeman, 1984), vary in their computer competency, business knowledge, language and culture. This diversity is capable of causing conflict between different stakeholder groups with regards to the establishment of system requirements (Pouloudi & Whitley, 1997; Stevens & Timbrell, 2002). Since, web-based systems transcend organizational, departmental, and even national boundaries, the issue of culture poses a significant challenge to the web systems’ initiators and developers (Miles & Snow, 1992; Kumar & van Dissel, 1996; Pouloudi & Whitley, 1996; Li & Williams, 1999).

Proactive versus reactive business ethics performance: a conceptual framework of profile analysis and case illustrations

The topic of this paper focuses on proactive versus reactive business ethics performance in the marketplace. The internal perception of a corporation and the external perception of the same corporation are used as generic determinants of business ethics performance. In turn, they are underpinned by evolutionary and contextual issues in the marketplace. The authors provide a generic conceptual framework of proactive and reactive business ethics performance. Case illustrations underpin the positives and negatives of proactive and reactive business ethics in the marketplace. A profile analysis process of proactive and reactive business ethics performance is also outlined. The gap between the internal and external perceptions of a corporation’s actions becomes crucial to achieve successful business ethics performance in the marketplace. Therefore, a corporation’s current business ethics performance should always be regarded as an on-the-spot-account that is either proactive or reactive. An important insight of this research is that business ethics performance requires the ongoing re-connection with reality by corporations.

Evolutionary relationships among bluetongue and related orbiviruses

Polymerase chain reaction (PCR) sequencing of specific viral gene segments was used to investigate the phylogenetic relationships among the orbiviruses. Sequence comparisons of the bluetongue virus (BTV) RNA3 from different regions of the world (North America, South Africa, India, Indonesian, Malaysia, Australia and the Caribbean region) showed that geographic separation had resulted in significant divergence, consistent with the evolution of distinct viral populations. There were at least 3 topotypes (Gould, 1987); the Australasian, African - American and another topotype represented by BTV 15 isolated in Australia in 1986. The topotypes of BTV had RNA3 nucleotide sequences that differed by approximately 20 per cent. Analysis of BTV-specific gene segments from animal and insect specimens showed that bluetongue viruses had entered northern Australia from South East Asia, possibly by wind-borne vectors. Nucleotide sequence comparisons were used to show the close genetic relationship between BTV 2 (Ona-A strain) from Florida and BTV 12 from Jamaica, and to investigate the reassortment of BTV genome segments in nature. The mutation rates of the BTV RNA2 and RNA3 segments were estimated to be of the order of 10(-4) nucleotide changes/site/year, similar in magnitude to that reported for other RNA viruses.

Adventures of punctuated equilibria : a struggle for authority in the evolutionary sciences

The theory of ‘punctuated equilibria’ was formulated by two paleontologists, Niles Eldredge and Stephen Gould, in 1972 and has been the focus of considerable controversy within the evolutionary sciences ever since. The primary intentions of this thesis are to relate the history of punctuated equilibria and to examine how it has affected evolutionary science. Several modes of analysis have been used to illuminate the history: The sociological perspectives of Pierre Bourdieu and Bruno Latour (who see scientific debate as a ‘struggle for authority’); Rhetorical analysis of some of the key documents; Communication with practising scientists via questionnaires and correspondence; Citation Analysis. Chapter 1 gives a short summary of the history and introduces the methods and socio-philosophical perspectives used to illuminate the history. Chapters 3 and 4 examine the rhetorical process by which Eldredge and Gould constructed the ‘punctuationist revolution’. Chapters 2, 3, 5 and 6 relate the history of punctuated equilibria.

Advanced graph mining methods for protein analysis

As one of the primary substances in a living organism, protein defines the character of each cell by interacting with the cellular environment to promote the cell’s growth and function [1]. Previous studies on proteomics indicate that the functions of different proteins could be assigned based upon protein structures [2,3]. The knowledge on protein structures gives us an overview of protein fold space and is helpful for the understanding of the evolutionary principles behind structure. By observing the architectures and topologies of the protein families, biological processes can be investigated more directly with much higher resolution and finer detail. For this reason, the analysis of protein, its structure and the interaction with the other materials is emerging as an important problem in bioinformatics. However, the determination of protein structures is experimentally expensive and time consuming, this makes scientists largely dependent on sequence rather than more general structure to infer the function of the protein at the present time. For this reason, data mining technology is introduced into this area to provide more efficient data processing and knowledge discovery approaches.

Unlike many data mining applications which lack available data, the protein structure determination problem and its interaction study, on the contrary, could utilize a vast amount of biologically relevant information on protein and its interaction, such as the protein data bank (PDB) [4], the structural classification of proteins (SCOP) databases [5], CATH databases [6], UniProt [7], and others. The difficulty of predicting protein structures, specially its 3D structures, and the interactions between proteins as shown in Figure 6.1, lies in the computational complexity of the data. Although a large number of approaches have been developed to determine the protein structures such as ab initio modelling [8], homology modelling [9] and threading [10], more efficient and reliable methods are still greatly needed.

In this chapter, we will introduce a state-of-the-art data mining technique, graph mining, which is good at defining and discovering interesting structural patterns in graphical data sets, and take advantage of its expressive power to study protein structures, including protein structure prediction and comparison, and protein-protein interaction (PPI). The current graph pattern mining methods will be described, and typical algorithms will be presented, together with their applications in the protein structure analysis.

The rest of the chapter is organized as follows: Section 6.2 will give a brief introduction of the fundamental knowledge of protein, the publicly accessible protein data resources and the current research status of protein analysis; in Section 6.3, we will pay attention to one of the state-of-the-art data mining methods, graph mining; then Section 6.4 surveys several existing work for protein structure analysis using advanced graph mining methods in the recent decade; finally, in Section 6.5, a conclusion with potential further work will be summarized.

The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts

Computer simulations were used to test the effect of increasing phylogenetic topological inaccuracy on the results obtained from correlation tests of independent contrasts. Predictably, increasing the number of disruptions in the tree increases the likelihood of significant error in the r values produced and in the statistical conclusions drawn from the analysis. However, the position of the disruption in the tree is important: Disruptions closer to the tips of the tree have a greater effect than do disruptions that are close to the root of the tree. Independent contrasts derived from inaccurate topologies are more likely to lead to erroneous conclusions when there is a true significant relationship between the variables being tested (i.e., they tend to be conservative). The results also suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data. Therefore, the use of random phylogenies is not beneficial in the absence of knowledge of the true phylogeny.

Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera : Noctuidae) and of its relationship to H. zea

Background
Helicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea.

Results
We obtained partial (511 bp) mitochondrial DNA (mtDNA) Cytochrome Oxidase-I (COI) sequences for 249 individuals of H. armigera sampled from Australia, Burkina Faso, Uganda, China, India and Pakistan which were associated with various host plants. Single nucleotide polymorphisms (SNPs) within the partial COI gene differentiated H. armigera populations into 33 mtDNA haplotypes. Shared haplotypes between continents, low F-statistic values and low nucleotide diversity between countries (0.0017 – 0.0038) suggests high mobility in this pest. Phylogenetic analysis of four major Helicoverpa pest species indicates that H. punctigera is basal to H. assulta, which is in turn basal to H. armigera and H. zea. Samples from North and South America suggest that H. zea is also a single species across its distribution. Our data reveal short genetic distances between H. armigera and H. zea which seem to have been established via a founder event from H. armigera stock at around 1.5 million years ago.

Conclusion
Our mitochondrial DNA sequence data supports the single species status of H. armigera across Africa, Asia and Australia. The evidence for inter-continental gene flow observed in this study is consistent with published evidence of the capacity of this species to migrate over long distances. The finding of high genetic similarity between Old World H. armigera and New World H. zea emphasises the need to consider work on both pests when building pest management strategies for either.

An evolutionary-based similarity reasoning scheme for monotonic multi-input fuzzy inference systems

In this paper, an Evolutionary-based Similarity Reasoning (ESR) scheme for preserving the monotonicity property of the multi-input Fuzzy Inference System (FIS) is proposed. Similarity reasoning (SR) is a useful solution for undertaking the incomplete rule base problem in FIS modeling. However, SR may not be a direct solution to designing monotonic multi-input FIS models, owing to the difficulty in getting a set of monotonically-ordered conclusions. The proposed ESR scheme, which is a synthesis of evolutionary computing, sufficient conditions, and SR, provides a useful solution to modeling and preserving the monotonicity property of multi-input FIS models. A case study on Failure Mode and Effect Analysis (FMEA) is used to demonstrate the effectiveness of the proposed ESR scheme in undertaking real world problems that require the monotonicity property of FIS models.

Comparative analysis of classic brain component sizes in relation to flightiness in birds

Increased encephalization has been linked to a range of behavioural traits and scenarios. However, studies of whole brain size in this context have been criticised for ignoring the role of specific brain areas in controlling behaviour. In birds, the response to potential threats is one such behaviour that may relate to the way in which the brain processes sensory information. We used a phylogenetic generalised least squares (PGLS) analyses, based on five different phylogenetic hypotheses, to analyse the relationship of relative sizes of whole brain and brain components with Flight-Initiation Distance (FID), the distance at which birds flee from an approaching human, for 41 bird species. Starting distance (the distance at which an approach to a bird commences), body mass and eye size have elsewhere been shown to be positively associated with FID, and consequently were included as covariates in our analysis. Starting distance and body mass were by far the strongest predictors of FID. Of all brain components, cerebellum size had the strongest predictor weight and was negatively associated with FID but the confidence intervals on the average estimate included zero and the overall predictor weight was low. Models featuring individual brain components were generally more strongly weighted than models featuring whole brain size. The PGLS analyses estimated there to be no phylogenetic signal in the regression models, and hence produced results equivalent to ordinary least squares regression analysis. However analyses that assumed strong phylogenetic signal produced substantially different results with each phylogeny, and overall suggest a negative relationship between forebrain size and FID. Our analyses suggest that the evolutionary assumptions of the comparative analysis, and consideration of starting distance make a profound difference to the interpretation of the effect of brain components on FID in birds.

Epidemiological and evolutionary inference of the transmission network of the 2014 highly pathogenic Avian Influenza H5N2 outbreak in British Columbia, Canada

The first North American outbreak of highly pathogenic avian influenza (HPAI) involving a virus of Eurasian A/goose/Guangdong/1/1996 (H5N1) lineage began in the Fraser Valley of British Columbia, Canada in late November 2014. A total of 11 commercial and 1 non-commercial (backyard) operations were infected before the outbreak was terminated. Control measures included movement restrictions that were placed on a total of 404 individual premises, 150 of which were located within a 3 km radius of an infected premise(s) (IP). A complete epidemiological investigation revealed that the source of this HPAI H5N2 virus for 4 of the commercial IPs and the single non-commercial IP likely involved indirect contact with wild birds. Three IPs were associated with the movement of birds or service providers and localized/environmental spread was suspected as the source of infection for the remaining 4 IPs. Viral phylogenies, as determined by Bayesian Inference and Maximum Likelihood methods, were used to validate the epidemiologically inferred transmission network. The phylogenetic clustering of concatenated viral genomes and the median-joining phylogenetic network of the viruses supported, for the most part, the transmission network that was inferred by the epidemiologic analysis.

GIS-based dynamic modelling and analysis of flash floods considering land-use planning

Flood inundation is a common natural disaster and a growing development challenge for many cities and thousands of small towns around the world. Soil features have frequently altered with the rapid development of urbanised regions, which has led to more frequent and longer duration of flooding in urban flood-prone regions. Thus, this paper presents a geographic information system (GIS)-based methodology for measuring and visualising the effects on urban flash floods generated by land-use changes over time. The measurement is formulated with a time series in order to perform a dynamic analysis. A catchment mesh is introduced into a hydrological model for reflecting the spatial layouts of infrastructure and structures over different construction periods. The Geelong Waurn Ponds campus of Deakin University is then selected as a case study. Based on GIS simulation and mapping technologies, this research illustrates the evolutionary process of flash floods. The paper then describes flood inundation for different built environments and presents a comparison by quantifying the flooding extents for infrastructure and structures. The results reveal that the GIS-based estimation model can examine urban flash floods in different development phases and identify the change of flooding extents in terms of land-use planning. This study will bring benefits to urban planners in raising awareness of flood impact and the approach proposed here could be used for flood mitigation through future urban planning.

What are we missing about marine invasions? Filling in the gaps with evolutionary genomics

Research on invasion biology has been largely dominated by studies on the ecological effects of invasion events, although recently, evolutionary processes have been shown to be important to invasion success. This is largely attributed to novel genomic tools that provide new opportunities to unravel the natural history, taxonomy, and invasion pathways of invasive species, as well as the genetic basis of adaptive traits that allow them to expand within and beyond their native range. Despite these advances and the growing literature of genomic research on terrestrial pests, these tools have not been widely applied to marine invasive species. This is in part due to the perception that high levels of dispersal and connectivity in many invasive marine species can limit the opportunity for local adaptation. However, there is growing evidence that even in species with high dispersal potential, significant site-specific adaptation can occur. We review how these “omic” tools provide unprecedented opportunities to characterise the role of adaptive variation, physiological tolerance, and epigenetic processes in determining the success of marine invaders. Yet, rapid range expansion in invasions can confound the analysis of genomic data, so we also review how data should be properly analysed and carefully interpreted under such circumstances. Although there are a limited number of studies pioneering this research in marine systems, this review highlights how future studies can be designed to integrate ecological and evolutionary information. Such datasets will be imperative for the effective management of marine pests.

Transmissible cancers in an evolutionary context.

Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for the prevention and treatment of both contagious and non-communicable cancers.