Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ~16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome

Invasive species are a major threat to global biodiversity but can also serve as valuable model systems to examine important evolutionary processes. While the ecological aspects of invasions have been well documented, the genetic basis of adaptive change during the invasion process has been hampered by a lack of genomic resources for the majority of invasive species. Here we report the first larval transcriptomic resource for the Northern Pacific Seastar, Asterias amurensis, an invasive marine predator in Australia. Approximately 117.5 million 100 base-pair (bp) paired-end reads were sequenced from a single RNA-Seq library from a pooled set of full-sibling A. amurensis bipinnaria larvae. We evaluated the efficacy of a pre-assembly error correction pipeline on subsequent de novo assembly. Error correction resulted in small but important improvements to the final assembly in terms of mapping statistics and core eukaryotic genes representation. The error-corrected de novo assembly resulted in 115,654 contigs after redundancy clustering. 41,667 assembled contigs were homologous to sequences from NCBI's non-redundant protein and UniProt databases. We assigned Gene Ontology, KEGG Orthology, Pfam protein domain terms and predicted protein-coding sequences to > 36,000 contigs. The final transcriptome dataset generated here provides functional information for 18,319 unique proteins, comprising at least 11,355 expressed genes. Furthermore, we identified 9,739 orthologs to P. miniata proteins, evaluated our annotation pipeline and generated a list of 150 candidate genes for responses to several environmental stressors that may be important for adaptation of A. amurensis in the invasive range. Our study has produced a large set of A. amurensis RNA contigs with functional annotations that can serve as a resource for future comparisons to other echinoderm transcriptomes and gene expression studies. Our data can be used to study the genetic basis of adaptive change and other important evolutionary processes during a successful invasion.

Immune-microbiota interactions: dysbiosis as a global health issue

Throughout evolution, microbial genes and metabolites have become integral to virtually all aspects of host physiology, metabolism and even behaviour. New technologies are revealing sophisticated ways in which microbial communities interface with the immune system, and how modern environmental changes may be contributing to the rapid rise of inflammatory noncommunicable diseases (NCDs) through declining biodiversity. The implications of the microbiome extend to virtually every branch of medicine, biopsychosocial and environmental sciences. Similarly, the impact of changes at the immune-microbiota interface are directly relevant to broader discussions concerning rapid urbanization, antibiotics, agricultural practices, environmental pollutants, highly processed foods/beverages and socioeconomic disparities--all implicated in the NCD pandemic. Here, we make the argument that dysbiosis (life in distress) is ongoing at a micro- and macro-scale and that as a central conduit of health and disease, the immune system and its interface with microbiota is a critical target in overcoming the health challenges of the twenty-first century.

Incorporation of group 14 elements into siloxane-bridged paracyclophanes cyclo-[p,p´-Me2SiC6H4EMe2C6H4SiMe2O]2 (E = C, Si, Ge, Sn)§

The bis(arylene silanes) p,p'-HMe₂SiC₆H₄EMe₂C₆H₄SiMe₂H (E = C (10), Si (11), Ge (12), Sn(13)) were prepared by the in situ Grignard reaction of p,p'-BrC₆H₄CMe₂C₆H₄Br, Mg turnings, and HSiMe₂Cl (for 10) and the Grignard reaction using p-HMe₂SiC₆H₄Br, Mg turnings, and Me₂ECl₂ (E = Si for 11, Ge for 12, Sn for 13). The oxidation of 10-13 using Pearlman's catalyst, Pd(OH)₂/C, in aqueous THF provided the bis(arylene silanols) p,p'-HOMe₂SiC₆H₄EMe₂C₆H₄SiMe₂OH (E = C (14), Si (15), Ge (16), Sn(17)). The HCl-catalyzed condensation of 14-17 in highly diluted solutions of acetone/water afforded the siloxane-bridged paracyclophanes cyclo-[p,p'-Me₂SiC₆H₄EMe₂C₆H₄SiMe₂O]₂ (6-9) that incorporate the group 14 elements E = C, Si, Ge, and Sn. Compounds 6-17 were investigated by multinuclear solution and solid-state NMR spectroscopy and 6 and 9 also by X-ray crystallography.

Elements of a model of effective teachers

Much research in teacher education has concentrated on individual elements of effective teaching such as the best way to teach content. There has been less emphasis on understanding the complex process of effective teaching in its entirety. Teacher educators are in the business of creating effective teachers and as such need a clear, evidence based model of an effective teacher. We believe that current models of effective teachers are limited because they fail to give sufficient emphasis to many important aspects of effective teachers and fail to integrate these components into a coherent whole and so provide a language for discussion of and a conceptual framework for developing teacher education.

This paper discusses the elements needed for a model of an effective teacher. This model emphasises not only the domains of effective teaching which receive most of the attention in teacher education and evaluation, namely content knowledge, pedagogical knowledge and, more recently, pedagogical content knowledge but also takes into account the teacher's personal knowledge and knowledge of context. We suggest that it is not just this knowledge that teachers have in these domains but the way this knowledge overlaps and interacts both within the teacher and with the teacher's physical, social, intellectual and emotional environment.

An examination of the effective teacher challenges not only teacher educators to rethink the way we educate both preservice and inservice teachers; but also the way we assess, judge and reward teachers.

Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology

Discovery of cis-regulatory elements in gene promoters is a highly challenging research issue in computational molecular biology. This paper presents a novel approach to searching putative cis-regulatory elements in human promoters by first finding 8-mer sequences of high statistical significance from gene promoters of humans, mice, and Drosophila melanogaster, respectively, and then identifying the most conserved ones across the three species (phylogenetic footprinting). In this study, a conservation analysis on both closely related species (humans and mice) and distantly related species (humans/mice and Drosophila) is conducted not only to examine more candidates but also to improve the prediction accuracy. We have found 124 putative cis-regulatory elements and grouped these into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters reveals that SP1, EGR, and NRF-1 are the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis also shows that many GO categories of transcription factors binding to these cis-regulatory elements match the GO categories of genes whose promoters contain these elements. Compared with previous research, the contribution of this study lies not only in the finding of new cis-regulatory elements, but also in its pioneering exploration on the coexistence of discovered elements and the GO relationship between transcription factors and regulated genes. This exploration verifies the putative cis-regulatory elements that have been found from this study and also gives new insight on the regulation mechanisms of gene expression.

Effect of alloying elements on the microstructure property relationship in thermomechanically processed C-Mn-Si TRIP steels

The effect of additions of Nb, Al and Mo to Fe-C-Mn-Si TRIP steel on the final microstructure and mechanical properties after simulated  thermomechanical processing (TMP) has been studied. The laboratory simulations of discontinuous cooling during TMP were performed using a hot rolling mill. All samples were characterised using optical microscopy and image analysis. The volume fraction of retained austenite was ascertained using a heat tinting technique and X-ray diffraction measurements. Room temperature mechanical properties were determined by a tensile test. From this a comprehensive understanding of the structural aspect of the bainite transformation in these types of TRIP steels has been developed. The  results have shown that the final microstructures of thermomechanically processed TRIP steels comprise 50 % of polygonal ferrite, 7 - 12 % of retained austenite, non-carbide bainitic structure and martensite. All steels exhibited a good combination of ultimate tensile strength and total elongation. The microstructure-property examination revealed the relationship between the composition of TRIP steels and their mechanical properties. It has been shown that the addition of Mo to the C-Si-Mn-Nb TRIP steel increases the ultimate tensile strength up to 1020 MPa. The stability of the retained austenite of the Nb-Mo steel was degraded, which led to a decrease in the elongation (24 %). The results have demonstrated that the addition of Al to C-Si-Mn-Nb steel leads to a good combination of strength (∼ 940 MPa) and elongation (∼ 30 %) due to the formation of refined acicular ferrite and granular bainite structure with ∼7 - 8 % of stable retained austenite. Furthermore, it has been found that the addition of Al increases the volume fraction of bainitic ferrite laths. The investigations have shown an interesting result that, in the Nb-Mo-Al steel, Al has a more pronounced effect on the microstructure in comparison with Mo. It has been found that the bainitic structure of the Nb-Mo-Al steel appears to be more granular than in the Nb-Mo steel. Moreover, the volume fraction of the retained austenite increased (12 %) with decreasing bainitic ferrite content. The results have demonstrated that this steel has the best mechanical properties (1100 MPa and 28 % elongation). It has been concluded that the combined effect of Nb, Mo, and Al addition on the dispersion of the bainite, martensite and retained austenite in the ferrite matrix and the morphology of these phases is different than effect of Nb, Mo and Al, separately.

A usability instrument for evaluating websites-navigation elements

Many small businesses websites have become an important advertising medium. However little consideration is given to how these websites might be made more effective. Many factors impact on website effectiveness, including navigation. Research here describes a usability instrument developed for evaluating small business websites and uses navigation as an example of its application. The research found that the quality of navigation does have an impact on ease-of-use of a site, user's emotional response and frustration levels and a user's intention to return to that website. The research also established the statistically significant elements that contribute to navigation.

Describing elements of mathematics lessons that accommodate diversity in student background

We are researching actions that teachers can take to improve mathematics learning for all students. Structural elements of the lessons being trialled include making aspects of pedagogy explicit to seek to overcome differences in familiarity with schooling processes, and sequencing tasks with the potential to engage students. This article reports research on teachers building learning communities by preparing variations to set tasks in order to address differences in students’ backgrounds.

Effect of alloying elements on the microstructure-property relationship in thermomechanically processed C-Mn-Si TRIP steels

The effect of additions of Nb, Al and Mo to Fe-C-Mn-Si TRIP steel on the final microstructure and mechanical properties after simulated thermomechanical processing (TMP) has been studied. The laboratory simulations of discontinuous cooling during TMP were performed using a hot rolling mill. All samples were characterised using optical microscopy and image analysis. The volume fraction of retained austenite was ascertained using a heat tinting technique and X-ray diffraction measurements. Room temperature mechanical properties were determined by a tensile test. From this a comprehensive understanding of the structural aspect of the bainite transformation in these types of TRIP steels has been developed. The results have shown that the final microstructures of thermomechanically processed TRIP steels comprise 50 % of polygonal ferrite, 7 - 12 % of retained austenite, non-carbide bainitic structure and martensite. All steels exhibited a good combination of ultimate tensile strength and total elongation. The microstructure-property examination revealed the relationship between the composition of TRIP steels and their mechanical properties. It has been shown that the addition of Mo to the C-Si-Mn-Nb TRIP steel increases the ultimate tensile strength up to 1020 MPa. The stability of the retained austenite of the Nb-Mo steel was degraded, which led to a decrease in the elongation (24 %). The results have demonstrated that the addition of Al to C-Si-Mn-Nb steel leads to a good combination of strength (∼ 940 MPa) and elongation (∼ 30 %) due to the formation of refined acicular ferrite and granular bainite structure with ∼7 - 8 % of stable retained austenite. Furthermore, it has been found that the addition of Al increases the volume fraction of bainitic ferrite laths. The investigations have shown an interesting result that, in the Nb-Mo-Al steel, Al has a more pronounced effect on the microstructure in comparison with Mo. It has been found that the bainitic structure of the Nb-Mo-Al steel appears to be more granular than in the Nb-Mo steel. Moreover, the volume fraction of the retained austenite increased (12 %) with decreasing bainitic ferrite content. The results have demonstrated that this steel has the best mechanical properties (1100 MPa and 28 % elongation). It has been concluded that the combined effect of Nb, Mo, and Al addition on the dispersion of the bainite, martensite and retained austenite in the ferrite matrix and the morphology of these phases is different than effect of Nb, Mo and Al, separately.

Depth-profile analysis of elements by glow discharge optical emmission specrometry

Glow-discharge optical emission spectrometry (GD-OES) is a powerful tool for the rapid analysis of elements in the surface of solids. One may employ GD-OES to determine quantitatively the bulk concentration of elements in a sample. With further calibration, one may also obtain elemental concentrations as a function of depth into the sample. This allows depth profiling on a host of advanced materials: treated metals, coated metals and other materials, multi-layers, painted surfaces, hard samples coated with polymers, thin films, and many others.

A consortium of institutions in Victoria, led by Deakin University, has purchased a new glow-discharge optical emission spectrometer. This instrument has the ability to perform elemental depth profiling on a wide range of materials. This technique, the first of its kind in Australia, is of particular interest to those working on metals, ceramics, glasses, coatings, semi-conductors, and multi-layers. We present here an overview of depth profiling by GD-OES and some examples of its use.

Implementing elements of Schon's reflective practitioner in an undergraduate public relations program

While the internship unit in a public relations degree is often viewed as the foremost area of experiential learning it can fail to deliver significant learning outcomes for student and teacher. This paper explores the use of other activity-based learning (ABL) methods as implemented in the Deakin University public relations undergraduate degree. The paper applies Donald Schon's concept of the reflective practitioner to learning undertaken in an internship unit and compares this application to two other units where ABL is used and the focus is on creating a client-professional relationship. For the purpose of this paper information was analysed using the 2006 on-campus cohort only. The cohort was further refined to include those students who successfully completed the degree of BA in public relations. Student internship evaluation forms and unit records were viewed to gain statistical information.