Culturally and Linguistically Diverse School Environments – Exploring the Unknown

Abstract: Australian education policies aspire to meet the unique needs of all students including those from linguistically diverse backgrounds; however, a first step in achieving this aim is clear identification of such students. Many children from previous migrant families and new arrivals to Australia come from homes where at least one parent speaks a language other than English. This exploratory research utilises survey and interview responses from students and staff in five Queensland state high schools. Results showed that 79.5% of the 2,484 students surveyed were from English-only homes with only 10.5% classified as having English as Another Language/Dialect. The remaining 10% were also from bi/multilingual homes. While early identification of bi/multilingual students allows for appropriate assessment and strategic support, staff responses highlighted limited preservice training and/or understanding of how to support these students. Only 4.7% of staff surveyed had received any academic training, and 10.4% professional development, about teaching students from diverse backgrounds who, in the surveyed schools, accounted for 20.5% of the student cohort

phyloXML: XML for evolutionary biology and comparative genomics

<p>Abstract</p> <p>Background</p> <p>Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.</p> <p>Results</p> <p>We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data.</p> <p>Conclusion</p> <p>PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at <url>http://www.phyloxml.org</url>.</p

High Density Microarray Analysis Reveals New Insights into Genetic Footprints of Listeria monocytogenes Strains Involved in Listeriosis Outbreaks

Listeria monocytogenes, a foodborne bacterial pathogen, causes invasive and febrile gastroenteritis forms of listeriosis in humans. Both invasive and febrile gastroenteritis listeriosis is caused mostly by serotypes 1/2a, 1/2b and 4b strains. The outbreak strains of serotype 1/2a and 4b could be further classified into several epidemic clones but the genetic bases for the diverse pathophysiology have been unsuccessful. DNA microarray provides an important tool to scan the entire genome for genetic signatures that may distinguish the L. monocytogenes strains belonging to different outbreaks. We have designed a pan-genomic microarray chip (Listeria GeneChip) containing sequences from 24 L. monocytogenes strains. The chip was designed to identify the presence/absence of genomic sequences, analyze transcription profiles and identify SNPs. Analysis of the genomic profiles of 38 outbreak strains representing 1/2a, 1/2b and 4b serotypes, revealed that the strains formed distinct genetic clusters adhering to their serotypes and epidemic clone types. Although serologically 1/2a and 1/b strains share common antigenic markers microarray analysis revealed that 1/2a strains are further apart from the closely related 1/2b and 4b strains. Within any given serotype and epidemic clone type the febrile gastroenteritis and invasive strains can be further distinguished based on several genetic markers including large numbers of phage genome, and intergenic sequences. Our results showed that the microarray-based data can be an important tool in characterization of L. monocytogenes strains involved in both invasive and gastroenteritis outbreaks. The results for the first time showed that the serotypes and epidemic clones are based on extensive pan-genomic variability and the 1/2b and 4bstrains are more closely related to each other than the 1/2a strains. The data also supported the hypothesis that the strains causing these two diverse outbreaks are genotypically different and this finding might be important in understanding the pathophysiology of this organism

Evaluating major curriculum change:the effect on student confidence

Aim: The aim of this study was to evaluate the effect of major curriculum change within a UK dental school on final-year student self-rated confidence levels. Methods: Final-year dental students graduating in each year between 2007 and 2012 completed the same course evaluation questionnaire, which assessed their confidence in relation to a range of clinical procedures using a Likert-type scale. This period spanned the introduction of a new curriculum and allowed analysis of differences in self-rated confidence between students graduating from the old (2007 and 2008) and new (2009–2012) curricula, across thirty key procedures. Results: New curriculum students showed significantly higher self-confidence ratings in nineteen of the thirty procedures, compared with those on the old curriculum. For the remaining eleven procedures there was no significant difference between the two curricula. The proportion of students on the outcomes-based curriculum rating themselves as 'confident” was statistically significantly higher in seven out of the thirty procedures, when compared with the traditional curriculum, and unchanged or nonsignificantly increased in the remainder. Discussion and conclusions: The relationship between specific curricular innovations and student confidence is considered, as is the usefulness of self-rated confidence in curriculum evaluation. Curriculum change appeared to have a positive effect on student confidence across a range of procedures

Expression of eEF1A2 is associated with clear cell histology in ovarian carcinomas: overexpression of the gene is not dependent on modifications at the EEF1A2 locus

The tissue-specific translation elongation factor eEF1A2 is a potential oncogene that is overexpressed in human ovarian cancer. eEF1A2 is highly similar (98%) to the near-ubiquitously expressed eEF1A1 (formerly known as EF1-α) making analysis with commercial antibodies difficult. We wanted to establish the expression pattern of eEF1A2 in ovarian cancer of defined histological subtypes at both the RNA and protein level, and to establish the mechanism for the overexpression of eEF1A2 in tumours. We show that while overexpression of eEF1A2 is seen at both the RNA and protein level in up to 75% of clear cell carcinomas, it occurs at a lower frequency in other histological subtypes. The copy number at the EEF1A2 locus does not correlate with expression level of the gene, no functional mutations were found, and the gene is unmethylated in both normal and tumour DNA, showing that overexpression is not dependent on genetic or epigenetic modifications at the EEF1A2 locus. We suggest that the cause of overexpression of eEF1A2 may be the inappropriate expression of a trans-acting factor. The oncogenicity of eEF1A2 may be related either to its role in protein synthesis or to potential non-canonical functions

Digitise This! A Quick and Easy Remote Sensing Method to Monitor the Daily Extent of Dredge Plumes

Technological advancements in remote sensing and GIS have improved natural resource managers’ abilities to monitor large-scale disturbances. In a time where many processes are heading towards automation, this study has regressed to simple techniques to bridge a gap found in the advancement of technology. The near-daily monitoring of dredge plume extent is common practice using Moderate Resolution Imaging Spectroradiometer (MODIS) imagery and associated algorithms to predict the total suspended solids (TSS) concentration in the surface waters originating from floods and dredge plumes. Unfortunately, these methods cannot determine the difference between dredge plume and benthic features in shallow, clear water. This case study at Barrow Island, Western Australia, uses hand digitising to demonstrate the ability of human interpretation to determine this difference with a level of confidence and compares the method to contemporary TSS methods. Hand digitising was quick, cheap and required very little training of staff to complete. Results of ANOSIM R statistics show remote sensing derived TSS provided similar spatial results if they were thresholded to at least 3 mg L-1. However, remote sensing derived TSS consistently provided false-positive readings of shallow benthic features as Plume with a threshold up to TSS of 6 mg L-1, and began providing false-negatives (excluding actual plume) at a threshold as low as 4 mg L-1. Semi-automated processes that estimate plume concentration and distinguish between plumes and shallow benthic features without the arbitrary nature of human interpretation would be preferred as a plume monitoring method. However, at this stage, the hand digitising method is very useful and is more accurate at determining plume boundaries over shallow benthic features and is accessible to all levels of management with basic training

Genetic parameters for social effects on survival in cannibalistic layers: Combining survival analysis and a linear animal model

<p>Abstract</p> <p>Background</p> <p>Mortality due to cannibalism in laying hens is a difficult trait to improve genetically, because censoring is high (animals still alive at the end of the testing period) and it may depend on both the individual itself and the behaviour of its group members, so-called associative effects (social interactions). To analyse survival data, survival analysis can be used. However, it is not possible to include associative effects in the current software for survival analysis. A solution could be to combine survival analysis and a linear animal model including associative effects. This paper presents a two-step approach (2STEP), combining survival analysis and a linear animal model including associative effects (LAM).</p> <p>Methods</p> <p>Data of three purebred White Leghorn layer lines from Institut de Sélection Animale B.V., a Hendrix Genetics company, were used in this study. For the statistical analysis, survival data on 16,780 hens kept in four-bird cages with intact beaks were used. Genetic parameters for direct and associative effects on survival time were estimated using 2STEP. Cross validation was used to compare 2STEP with LAM. LAM was applied directly to estimate genetic parameters for social effects on observed survival days.</p> <p>Results</p> <p>Using 2STEP, total heritable variance, including both direct and associative genetic effects, expressed as the proportion of phenotypic variance, ranged from 32% to 64%. These results were substantially larger than when using LAM. However, cross validation showed that 2STEP gave approximately the same survival curves and rank correlations as LAM. Furthermore, cross validation showed that selection based on both direct and associative genetic effects, using either 2STEP or LAM, gave the best prediction of survival time.</p> <p>Conclusion</p> <p>It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens.</p

Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression

Theoretical and empirical studies have sought to explain the formation and maintenance of social relationships within groups. The resulting dominance hierarchies have significant fitness and survival consequences dependent upon social status. We hypothesised that each position or rank within a group has a distinctive brain gene expression profile that correlates with behavioural phenotype. Furthermore, transitions in rank position should determine which genes shift in expression concurrent with the new dominance status. We used a custom cDNA microarray to profile brain transcript expression in a model species, the rainbow trout, which forms tractable linear hierarchies. Dominant, subdominant and submissive individuals had distinctive transcript profiles with 110 gene probes identified using conservative statistical analyses. By removing the dominant, we characterised the changes in transcript expression in sub-dominant individuals that became dominant demonstrating that the molecular transition occurred within 48 hours. A strong, novel candidate gene, ependymin, which was highly expressed in both the transcript and protein in subdominants relative to dominants, was tested further. Using antibody injection to inactivate ependymin in pairs of dominant and subdominant zebrafish, the subdominant fish exhibited a substantial increase in aggression in parallel with an enhanced competitive ability. This is the first study to characterise the molecular signatures of dominance status within groups and the first to implicate ependymin in control of aggressive behaviour. It also provides evidence for indirect genetic effect models in which genotype/phenotype of an individual is influenced by conspecific interactions within a group. The variation in the molecular profile of each individual within a group may offer a new explanation of intraspecific variation in gene expression within undefined groups of animals and provides new candidates for empirical study

The role of SPARC in extracellular matrix assembly

SPARC is a collagen-binding matricellular protein. Expression of SPARC in adult tissues is frequently associated with excessive deposition of collagen and SPARC-null mice fail to generate a robust fibrotic response to a variety of stimuli. This review summarizes recent advancements in the characterization of the binding of SPARC to collagens and describes the results of studies that implicate a function for SPARC in the regulation of the assembly of basal lamina and fibrillar collagen in the ECM. Potential cellular mechanisms that underlie SPARC activity in ECM deposition are also explored

27 years of benthic and coral community dynamics on turbid, highly urbanised reefs off Singapore

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states within a decade. In contrast, there was a net decline in coral cover and continuing shifts in community structure at deeper reef slope sites (6–7 m). There was no evidence of phase shifts to macroalgal dominance but coral habitats at deeper sites were replaced by unstable substrata such as fine sediments and rubble. The persistence of coral dominance at chronically disturbed shallow sites is likely due to an abundance of coral taxa which are tolerant to environmental stress. In addition, high turbidity may interact antagonistically with other disturbances to reduce the impact of thermal stress and limit macroalgal growth rates