Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

Work domain analysis and sensors II: Pasteurizer II case study

In this paper we use sensor-annotated abstraction hierarchies (Reising & Sanderson, 1996, 2002a,b) to show that unless appropriately instrumented, configural displays designed according to the principles of ecological interface design (EID) might be vulnerable to misinterpretation when sensors become unreliable or are unavailable. Building on foundations established in Reising and Sanderson (2002a) we use a pasteurization process control example to show how sensor-annotated AHs help the analyst determine the impact of different instrumentation engineering policies on a configural display that is part of an ecological interface. Our analyses suggest that configural displays showing higher-order properties of a system are especially vulnerable under some conservative instrumentation configurations. However, sensor-annotated AHs can be used to indicate where corrective instrumentation might be placed. We argue that if EID is to be effectively employed in the design of displays for complex systems, then the information needs of the human operator need to be considered while instrumentation requirements are being formulated. Rasmussen's abstraction hierarchy-and particularly its extension to the analysis of information captured by sensors and derived from sensors-may therefore be a useful adjunct to up-stream instrumentation design. (C) 2002 Elsevier Science Ltd. All rights reserved.

Work domain analysis and sensors I: principles and simple example

In this paper we establish a foundation for understanding the instrumentation needs of complex dynamic systems if ecological interface design (EID)-based interfaces are to be robust in the face of instrumentation failures. EID-based interfaces often include configural displays which reveal the higher-order properties of complex systems. However, concerns have been expressed that such displays might be misleading when instrumentation is unreliable or unavailable. Rasmussen's abstraction hierarchy (AH) formalism can be extended to include representations of sensors near the functions or properties about which they provide information, resulting in what we call a sensor-annotated abstraction hierarchy. Sensor-annotated AHs help the analyst determine the impact of different instrumentation engineering policies on higher-order system information by showing how the data provided from individual sensors propagates within and across levels of abstraction in the AH. The use of sensor-annotated AHs with a configural display is illustrated with a simple water reservoir example. We argue that if EID is to be effectively employed in the design of interfaces for complex systems, then the information needs of the human operator need to be considered at the earliest stages of system development while instrumentation requirements are being formulated. In this way, Rasmussen's AH promotes a formative approach to instrumentation engineering. (C) 2002 Elsevier Science Ltd. All rights reserved.

Parallel simulation system for earthquake generation: Fault analysis modules and parallel coupling analysis

Solid earth simulations have recently been developed to address issues such as natural disasters, global environmental destruction and the conservation of natural resources. The simulation of solid earth phenomena involves the analysis of complex structures including strata, faults, and heterogeneous material properties. Simulation of the generation and cycle of earthquakes is particularly important, but such simulations require the analysis of complex fault dynamics. GeoFEM is a parallel finite-element analysis system intended for solid earth field phenomena problems. This paper describes recent development in the GeoFEM project for the simulation of earthquake generation and cycles.

Exploring complex fitness surfaces: Multiple ornamentation and polymorphism in male guppies

The sexual ornamentation used by male guppies to attract females comprises many components, each of which varies considerably among males. Although natural and sexual selection have been shown to contribute to divergence among populations in male sexual ornaments, the role of sexual selection in maintaining polymorphism within populations is less clear. We used both parametric quadratic regression and nonparametric projection pursuit regression techniques to reveal the major axes of non-linear sexual selection on male ornaments. We visualized the fitness surfaces defined by these axes using thin-plate splines to allow a direct comparison of the two methodologies. Identification of the major axes of selection and their visualization was critical in determining the form and strength of nonlinear selection. Both types of analysis revealed fitness surfaces comprising three peaks, suggesting that there is more than one way to make an attractive guppy. Disruptive selection may be an important process underlying the presence of multiple sexual ornaments and may contribute to the maintenance of the high levels of polymorphism in male sexual ornaments found in guppy populations.

Genomovar diversity amongst Burkholderia cepacia complex isolates from an Australian adult cystic fibrosis unit

In this study, a combination of recA-based PCR assays and 16S rDNA restriction fragment length polymorphism (RFLP) analysis was used to determine the genomovar diversity of clinical Burkholderia cepacia complex isolates. Twenty-eight isolates were prospectively collected from patients attending a large Australian adult cystic fibrosis (CF) unit, 22 isolates were referred from other Australian CF units and a further eight isolates originated from patients without CF. The 28 prospectively collected isolates were distributed amongst the following genomovars: Burkholderia cepacia genomovar I (28.6%), Burkholderia multivorans (21.4%), Burkholderia cepacia genomovar III (39.3%), Burkholderia vietnamiensis (3.6%) and Burkholderia ambifaria (7.1%). The results of this study highlight the usefulness of 16S rDNA RFLP typing for the identification of other Burkholderia spp. and non-fermenting gram-negative bacteria.

The use of 16s rDNA restriction fragment length polymorphism analysis for the identification of non-fermenting gram negative bacilli in a cystic fibrosis microbiology referral service

The utility of 16s rDNA restriction fragment length polymorphism (RFLP) analysis for the partial genomovar differentiation of Burkholderia cepacia complex bacterium is well documented. We compared the 16s rDNA RFLP signatures for a number of non-fermenting gram negative bacilli (NF GNB) LMG control strains and clinical isolates pertaining to the genera Burkholderia, Pseudomonas, Achromobacter (Alcaligenes), Ralstonia, Stenotrophomonas and Pandoraea. A collection of 24 control strain (LMG) and 25 clinical isolates were included in the study. Using conventional PCR, a 1.2 kbp 16s rDNA fragment was generated for each organism. Following restriction digestion and electrophoresis, each clinical isolate RFLP signature was compared to those of the control strain panel. Nineteen different RFLP signatures were detected from the 28 control strains included in the study. TwentyoneyTwenty- five of the clinical isolates could be classified by RFLP analysis into a single genus and species when compared to the patterns produced by the control strain panel. Four clinical B. pseudomallei isolates produced RFLP signatures which were indistinguishable from B. cepacia genomovars I, III and VIII. The identity of these four isolates were confirmed using B. pseudomallei specific PCR. 16s rDNA RFLP analysis can be a useful identification strategy when applied to NF GNB, particularly for those which exhibit colistin sulfate resistance. The use of this molecular based methodology has proved very useful in the setting of a CF referral laboratory particularly when utilised in conjunction with B. cepacia complex and genomovar specific PCR techniques. Species specific PCR or sequence analysis should be considered for selected isolates; especially where discrepancies between epidemiology, phenotypic and genotypic characteristics occur.

Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences

The entire internal transcribed spacer ( ITS) region, including the 5.8S subunit of the nuclear ribosomal DNA ( rDNA), was sequenced by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified fragments. The study included 40 Sporobolus ( Family Poaceae, subfamily Chloridoideae) seed collections from 14 putative species ( all 11 species from the S. indicus complex and three Australian native species). These sequences, along with those from two out-group species [ Pennisetum alopecuroides ( L.) Spreng. and Heteropogon contortus ( L.) P. Beauv. ex Roemer & Schultes, Poaceae, subfamily Panicoideae], were analysed by the parsimony method (PAUP; version 4.0b4a) to infer phylogenetic relationships among these species. The length of the ITS1, 5.8S subunit and ITS2 region were 222, 164 and 218 base pairs ( bp), respectively, in all species of the S. indicus complex, except for the ITS2 region of S. diandrus P. Beauv. individuals, which was 217 bp long. Of the 624 characters included in the analysis, 245 ( 39.3%) of the 330 variable sites contained potential phylogenetic information. Differences in sequences among the members of the S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur & Schinz and S. jacquemontii Kunth. collections were 0%, while differences ranged from 0 to 2% between these and other species of the complex. Similarly, differences in sequences among collections of S. laxus B. K. Simon, S. sessilis B. K. Simon, S. elongatus R. Br. and S. creber De Nardi were 0%, compared with differences of 1-2% between these four species and the rest of the complex. When comparing S. fertilis ( Steud.) Clayton and S. africanus (Poir.) Robyns & Tourney, differences between collections ranged from 0 to 1%. Parsimony analysis grouped all 11 species of the S. indicus complex together, indicating a monophyletic origin. For the entire data set, pair-wise distances among members of the S. indicus complex varied from 0.00 to 1.58%, compared with a range of 20.08-21.44% among species in the complex and the Australian native species studied. A strict consensus phylogenetic tree separated 11 species of the S. indicus complex into five major clades. The phylogeny, based on ITS sequences, was found to be congruent with an earlier study on the taxonomic relationship of the weedy Sporobolus grasses revealed from random amplified polymorphic DNA ( RAPD). However, this cladistic analysis of the complex was not in agreement with that created on past morphological analyses and therefore gives a new insight into the phylogeny of the S. indicus complex.

Some aspects of implementing Regulatory Impact Analysis in Brazil

In an increasingly complex society, regulatory polices emerge as an important tool in public management. Nevertheless, regulation per se is no longer enough, and the agenda for a regulatory reform is increasing. Following this context, Brazil has implemented Regulatory Impact Analysis (RIA) in its regulatory agencies. Thus, Brazilian specificities have to be considered and, in this regard, a systematic approach provides a significant contribution. This article aims to address some critical reflections about which policy-makers should ask themselves before joining the implementation of a RIA system in the Brazilian context. Through a long-term perspective, the implementation of RIA must be seen as part of a permanent change in the administrative culture, understanding that RIA should be used as a further resource in the decision-making process, rather than a final solution.

Adaptive learning in multiagent systems: a forecasting methodology based on error analysis

Electricity markets are complex environments, involving a large number of different entities, playing in a dynamic scene to obtain the best advantages and profits. MASCEM is a multi-agent electricity market simu-lator to model market players and simulate their operation in the market. Market players are entities with specific characteristics and objectives, making their decisions and interacting with other players. MASCEM pro-vides several dynamic strategies for agents’ behaviour. This paper presents a method that aims to provide market players strategic bidding capabilities, allowing them to obtain the higher possible gains out of the market. This method uses an auxiliary forecasting tool, e.g. an Artificial Neural Net-work, to predict the electricity market prices, and analyses its forecasting error patterns. Through the recognition of such patterns occurrence, the method predicts the expected error for the next forecast, and uses it to adapt the actual forecast. The goal is to approximate the forecast to the real value, reducing the forecasting error.

Cluster Analysis of Business Data

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Copper(II) aza-bis(oxazoline) complex immobilized onto ITQ-2 and MCM-22 based materials as heterogeneous catalysts for the cyclopropanation of styrene

A copper(II) chiral aza-bis(oxazoline) homogeneous catalyst (CuazaBox) was anchored onto the external surface of MCM-22 and ITQ-2 structures, as well as encapsulated into hierarchical MCM-22. The transition metal complex loading onto the porous solids was determined by ICP-AES and the materials were also characterized by elemental analysis (C, N, H, S), FTIR, XPS, TG and low temperature N-2 adsorption isotherms. The materials were tested as heterogeneous catalysts in the benchmark reaction of cyclopropanation of styrene to check the effect of the immobilization procedure on the catalytic parameters, as well as on their reutilization in several catalytic cycles. Catalyst CuazaBox anchored onto the external surface of MCM-22 and ITQ-2 materials were more active and enantioselective in the cyclopropanation of styrene than the corresponding homogeneous phase reaction run under similar experimental conditions. This is due to the propylation of the acidic aza-Box nitrogen. HMCM-22 was nevertheless the best heterogeneous catalyst. Encapsulation of CuazaBox on post-synthesis modified MCM-22 materials led to low activities and enantioselectivities. But reversal on the stereochemical course of the reaction was observed, probably due to confinement effect. (C) 2013 Elsevier Inc. All rights reserved.

SCANNERS: constraining the phase diagram of a complex scalar singlet at the LHC

We present the first version of a new tool to scan the parameter space of generic scalar potentials, SCANNERS (Coimbra et al., SCANNERS project., 2013). The main goal of SCANNERS is to help distinguish between different patterns of symmetry breaking for each scalar potential. In this work we use it to investigate the possibility of excluding regions of the phase diagram of several versions of a complex singlet extension of the Standard Model, with future LHC results. We find that if another scalar is found, one can exclude a phase with a dark matter candidate in definite regions of the parameter space, while predicting whether a third scalar to be found must be lighter or heavier. The first version of the code is publicly available and contains various generic core routines for tree level vacuum stability analysis, as well as implementations of collider bounds, dark matter constraints, electroweak precision constraints and tree level unitarity.

Cluster analysis using affinity aoefficient in order to identify religious beliefs profiles

International Scientific Forum, ISF 2013, ISF 2013, 12-14 December 2013, Tirana.

Hierarchical cluster analysis of groups of individuals : application to business data

3rd SMTDA Conference Proceedings, 11-14 June 2014, Lisbon Portugal.