Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Principal preparation and training : a look at China and its issues

Purpose: The purpose of this paper is to provide an understanding of principal preparation and training in China by providing a background discussion of principal preparation in a number of countries. As an illustration, it provides an overview of the curriculum used in the initial preparation of school principals at Beijing Normal University.-----Design/methodology/approach: The paper draws mainly on writing and research from China, Australia and the USA to explore principal preparation and training in China.-----Findings: In addition to providing a rich description of principal preparation in China, the paper's main findings comprise seven key challenges that confront China as it endeavours to provide quality principal preparation. These challenges include China's diversity and uneven social, cultural and educational development; limited resources in some regions throughout China; the place and importance of study tours for principal preparation; the teaching approach used to train principals; the process used for assessing principal learning during their training programs; the limited transfer of learning from the classroom to the school environment; and the timing of training for principals.-----Practical implications: Each of the challenges arising here raises important practical implications for developers of principal training programs.-----Originality/value: The paper paints a picture of principal preparation in China and raises a number of issues and challenges with which it continues to grapple. Of note is that China is not alone in facing some of these ongoing concerns.

Preservice teachers’ perceptions of their middle schooling teacher preparation

The middle schooling movement in Australia has gained momentum in the past 10 to 15 years (Pendergast & Bahr, 2005) with much of the literature recognising that preservice teachers need to graduate with theoretical and pedagogical knowledge to engage middle years students (Education Queensland, 2004). This qualitative study analysed the responses of preservice teachers towards their completion of a four-year Bachelor of Education primary degree that included a middle years pathway (or electives). The study aims to investigate the final years’ perceptions of their confidence and preparedness to teach in the middle-school context as a result of their university learning. Data were gathered using open-ended one-to-one interviews of approximately 45 minutes duration. Seven of the twenty-two final-year preservice teachers were involved in the study that represented 32% of the cohort. Results indicated the need for increased school-based units, the importance of pedagogical approaches employed by the lecturer and the preference for further linkages between middle school theories and middle school teaching practices. Those who provide teacher education courses need to consider the importance of how they deliver middle years courses as well as the content of the course. Furthermore, teacher education institutions need to evaluate and re-shape their courses to ensure preservice teachers are provided with real-world experiences related to both the literature and the profession.

Skin preparation with alcohol versus alcohol followed by any antiseptic for preventing bacteraemia or contamination of blood for transfusion (Review)

Background: Blood for transfusion may become contaminated at any point between collection and transfusion and may result in bacteraemia (the presence of bacteria in the blood),severe illness or even death for the blood recipient. Donor arm skin is one potential source of blood contamination, so it is usual to cleanse the skin with an antiseptic before blood donation. One-step and two-step alcohol based antiseptic regimens are both commonly advocated but there is uncertainty as to which is most effective.----- Objectives: To assess the effects of cleansing the skin of blood donors with alcohol in a one-step compared with alcohol in a two-step procedure to prevent contamination of collected blood or bacteraemia in the recipient.----- Search strategy: We searched the Cochrane Wounds Group Specialised Register (March 10 2009); The Cochrane Central Register of Controlled Trials(CENTRAL) The Cochrane Library 2009, Issue 1; Ovid MEDLINE - (1950 to February Week 4 2009); Ovid EMBASE - (1980 to 2009 Week 9); and EBSCO CINAHL - (1982 to February Week 4 2009). We also searched the reference lists of key papers.----- Selection criteria: All randomised trials (RCTs) comparing alcohol based donor skin cleansing in a one-step versus a two-step process that includes alcohol and any other antiseptic for pre-venepuncture skin cleansing were considered. Quasi randomised trials were to have been considered in the absence of RCTs.----- Data collection and analysis: Two review authors independently assessed studies for inclusion.----- Main results: No studies (RCTs or quasi RCTs) met the inclusion criteria. Authors’ conclusions We did not identify any eligible studies for inclusion in this review. It is therefore unclear whether a two-step, alcohol followed by antiseptic skin cleansing process prior to blood donation confers any reduction in the risk of blood contamination or bacteraemia in blood recipients, or conversely whether a one-step process increases risk above that associated with a two-step process.

Prevention of postnatal distress or depression : an evaluation of an intervention at preparation for parenthood classes.

Determined the effectiveness of a psychosocial intervention, provided to expectant couples in routine antenatal classes, on the postpartum psychosocial adjustment of women and men. Preparation for Parenthood programs were randomly allocated to one of three conditions: usual service ('control'), experimental ('empathy'), or non-specific control ('baby-play'). The latter condition controlled for the non-specific effects of the intervention, these being: the provision of an extra class; asking couples to consider the early postpartum weeks; and receiving booster information after the antenatal class, and again shortly after the birth. Women and men were categorised into three levels of self-esteem, as measured antenatally: low, medium and high. 268 participants were recruited antenatally. Interview data and self-report information was collected from 202 of these women at 6 weeks postpartum, and 180 women at 6 months postpartum. The intervention consisted of a session focusing on psychosocial issues related to becoming first-time parents. Participants discussed possible postpartum concerns in separate gender groups for part of the session, and then discussed these issues with their partners

Internationalisation and international students : creating an internationalised learning context for international students’ study preparation via CMC

Australian universities have been phenomenally internationalised because of significant numbers of international students in their student cohorts. The international students make up 17.3 percent (OECD 2007) of all the university enrolment, and some universities have much more international student enrolments than the average. From a truly internationalisation perspective, however, there is far more demand of integration with Australian students and international students, the internationalising learning content and context. There have not been much discussion and effort of understanding and practicing of internationalising the learning context from international students’ cultural background and internationalised learning environment. There are many factors which interfere with internationalisation in the learning context such as English proficiency, culture difference and academic staff unawareness. This paper argues the concepts of cultural dimensions and the characteristics of CMC (Computer-Mediated Communication) in a multicultural learning context of Australian higher education. This paper aims to develop a framework of international students’ preparation program for their Western university study based on technology-driven learning models, especially targeting those students who have an Asian cultural background. The program is expected to help international students bridge the gap of cultural differences and better preparation for their active participation and engagement in a new learning environment in order to realise truly internationalisation in Australian higher education

Investigation of highly regulated promoters for the production of recombinant proteins in plants

Plants have been identified as promising expression systems for the commercial production of recombinant proteins. Plant-based protein production or “biofarming” offers a number of advantages over traditional expression systems in terms of scale of production, the capacity for post-translation processing, providing a product free of contaminants and cost effectiveness. A number of pharmaceutically important and commercially valuable proteins, such as antibodies, biopharmaceuticals and industrial enzymes are currently being produced in plant expression systems. However, several challenges still remain to improve recombinant protein yield with no ill effect on the host plant. The ability for transgenic plants to produce foreign proteins at commercially viable levels can be directly related to the level and cell specificity of the selected promoter driving the transgene. The accumulation of recombinant proteins may be controlled by a tissue-specific, developmentally-regulated or chemically-inducible promoter such that expression of recombinant proteins can be spatially- or temporally- controlled. The strict control of gene expression is particularly useful for proteins that are considered toxic and whose expression is likely to have a detrimental effect on plant growth. To date, the most commonly used promoter in plant biotechnology is the cauliflower mosaic virus (CaMV) 35S promoter which is used to drive strong, constitutive transgene expression in most organs of transgenic plants. Of particular interest to researchers in the Centre for Tropical Crops and Biocommodities at QUT are tissue-specific promoters for the accumulation of foreign proteins in the roots, seeds and fruit of various plant species, including tobacco, banana and sugarcane. Therefore this Masters project aimed to isolate and characterise root- and seed-specific promoters for the control of genes encoding recombinant proteins in plant-based expression systems. Additionally, the effects of matching cognate terminators with their respective gene promoters were assessed. The Arabidopsis root promoters ARSK1 and EIR1 were selected from the literature based on their reported limited root expression profiles. Both promoters were analysed using the PlantCARE database to identify putative motifs or cis-acting elements that may be associated with this activity. A number of motifs were identified in the ARSK1 promoter region including, WUN (wound-inducible), MBS (MYB binding site), Skn-1, and a RY core element (seed-specific) and in the EIR1 promoter region including, Skn-1 (seed-specific), Box-W1 (fungal elicitor), Aux-RR core (auxin response) and ABRE (ABA response). However, no previously reported root-specific cis-acting elements were observed in either promoter region. To confirm root specificity, both promoters, and truncated versions, were fused to the GUS reporter gene and the expression cassette introduced into Arabidopsis via Agrobacterium-mediated transformation. Despite the reported tissue-specific nature of these promoters, both upstream regulatory regions directed constitutive GUS expression in all transgenic plants. Further, similar levels of GUS expression from the ARSK1 promoter were directed by the control CaMV 35S promoter. The truncated version of the EIR1 promoter (1.2 Kb) showed some differences in the level of GUS expression compared to the 2.2 Kb promoter. Therefore, this suggests an enhancer element is contained in the 2.2 Kb upstream region that increases transgene expression. The Arabidopsis seed-specific genes ATS1 and ATS3 were selected from the literature based on their seed-specific expression profiles and gene expression confirmed in this study as seed-specific by RT-PCR analysis. The selected promoter regions were analysed using the PlantCARE database in order to identify any putative cis elements. The seed-specific motifs GCN4 and Skn-1 were identified in both promoter regions that are associated with elevated expression levels in the endosperm. Additionaly, the seed-specific RY element and the ABRE were located in the ATS1 promoter. Both promoters were fused to the GUS reporter gene and used to transform Arabidopsis plants. GUS expression from the putative promoters was consitutive in all transgenic Arabidopsis tissue tested. Importantly, the positive control FAE1 seed-specific promoter also directed constitutive GUS expression throughout transgenic Arabidopsis plants. The constitutive nature seen in all of the promoters used in this study was not anticipated. While variations in promoter activity can be caused by a number of influencing factors, the variation in promoter activity observed here would imply a major contributing factor common to all plant expression cassettes tested. All promoter constructs generated in this study were based on the binary vector pCAMBIA2300. This vector contains the plant selection gene (NPTII) under the transcriptional control of the duplicated CaMV 35S promoter. This CaMV 35S promoter contains two enhancer domains that confer strong, constitutive expression of the selection gene and is located immediately upstream of the promoter-GUS fusion. During the course of this project, Yoo et al. (2005) reported that transgene expression is significantly affected when the expression cassette is located on the same T-DNA as the 35S enhancer. It was concluded, the trans-acting effects of the enhancer activate and control transgene expression causing irregular expression patterns. This phenomenon seems the most plausible reason for the constitutive expression profiles observed with the root- and seed-specific promoters assessed in this study. The expression from some promoters can be influenced by their cognate terminator sequences. Therefore, the Arabidopsis ARSK1, EIR1, ATS1 and ATS3 terminator sequences were isolated and incorporated into expression cassettes containing the GUS reporter gene under the control of their cognate promoters. Again, unrestricted GUS activity was displayed throughout transgenic plants transformed with these reporter gene fusions. As previously discussed constitutive GUS expression was most likely due to the trans-acting effect of the upstream CaMV 35S promoter in the selection cassette located on the same T-DNA. The results obtained in this study make it impossible to assess the influence matching terminators with their cognate promoters have on transgene expression profiles. The obvious future direction of research continuing from this study would be to transform pBIN-based promoter-GUS fusions (ie. constructs containing no CaMV 35S promoter driving the plant selection gene) into Arabidopsis in order to determine the true tissue specificity of these promoters and evaluate the effects of their cognate 3’ terminator sequences. Further, promoter truncations based around the cis-elements identified here may assist in determining whether these motifs are in fact involved in the overall activity of the promoter.

Preparation of future weather data to study the impact of climate change on buildings

The dynamic interaction between building systems and external climate is extremely complex, involving a large number of difficult-to-predict variables. In order to study the impact of climate change on the built environment, the use of building simulation techniques together with forecast weather data are often necessary. Since most of building simulation programs require hourly meteorological input data for their thermal comfort and energy evaluation, the provision of suitable weather data becomes critical. In this paper, the methods used to prepare future weather data for the study of the impact of climate change are reviewed. The advantages and disadvantages of each method are discussed. The inherent relationship between these methods is also illustrated. Based on these discussions and the analysis of Australian historic climatic data, an effective framework and procedure to generate future hourly weather data is presented. It is shown that this method is not only able to deal with different levels of available information regarding the climate change, but also can retain the key characters of a “typical” year weather data for a desired period.

Rhetoric of landscape architecture and interior design discourses : preparation for cross-disciplinary practice

The rhetoric of the pedagogic discourses of landscape architectural students and interior design students is described as part of a doctoral study undertaken to document practices and orientations prior to cross-disciplinary collaboration. We draw on the theoretical framework of Basil Bernstein, an educational sociologist, and the rhetorical method of Kenneth Burke, a literary dramatist, to study the grammars of ‘landscape’ representation employed within these disciplinary examples. We investigate how prepared final year students are for working in a cross-disciplinary manner. The discursive interactions of their work, as illustrated by four examples of drawn images and written text, are described. Our findings suggest that we need to concern ourselves aspects of our pedagogic discourse that brings uniqueness and value to our disciplines ,as well as that shared discourses between disciplines.

Grafted fluoropolymers as supports for solid-phase organic chemistry : preparation and characterization

Solid-phase organic chemistry has rapidly expanded in the last decade, and, as a consequence, so has the need for the development of supports that can withstand the extreme conditions required to facilitate some reactions. The authors here prepare a thermally stable, grafted fluoropolymer support (see Figure for an example) in three solvents, and found that the penetration of the graft was greatest in dichloromethane.

Thermogravimetric analysis of selected coal-bearing strata kaolinite

Two kinds of coal-bearing kaolinite from China were analysed by X-ray diffraction (XRD), Thermogravimetric analysis-mass spectrometry (TG-MS), infrared emission spectroscopy. Thermal decomposition occurs in a series of steps attributed to (a) desorption of water at 68 °C for Datong coal bearing strata kaolinite and 56 °C for Xiaoxian with mass losses of 0.36 % and 0.51 % (b) decarbonization at 456 °C for Datong coal bearing strata kaolinite and 431 °C for Xiaoxian kaolinite, (c) dehydroxylation takes place in two steps at 589 and 633 °C for Datong coal bearing strata kaolinite and at 507 °C and 579 °C for Xiaoxian kaolinite. This mineral were further characterised by infrared emission spectroscopy (IES). Well defined hydroxyl stretching bands at around 3695, 3679, 3652 and 3625 cm-1 are observed. At 650 °C all intensity in these bands is lost in harmony with the thermal analysis results. Characteristic functional groups from coal are observed at 1918, 1724 and 1459 cm-1. The intensity of these bands decrease by thermal treatment and is lost by 700 °C.