A custom-built insulin resistance gene chip

Objectives/Aim—Microarray (gene chip) technology offers a powerful new tool for analyzing the expression of large numbers of genes in many experimental samples. The aim of this study was to design, construct, and use a gene chip to measure the expression levels of key genes in metabolic pathways related to insulin resistance.
Methods—We selected genes that were implicated in the development of insulin resistance, including genes involved in insulin signaling; glucose uptake, oxidation, and storage; fat uptake, oxidation, and storage; cytoskeletal components; and transcription factors. The key regulatory genes in the pathways were identified, along with other recently identified candidate genes such as calpain-10. A total of 242 selected genes (including 32 internal control elements) were sequence-verified, purified, and arrayed on aldehyde-coated slides.
Results—Where more than 1 clone containing the gene of interest was available, we chose those containing the genes in the 5' orientation and an insert size of around 1.5 kb. Of the 262 clones purchased, 56 (21%) were found to contain sequences other than those expected. In addition, 2 (1%) did not grow under standard conditions and were assumed to be nonviable. In these cases, alternate clones containing the gene of interest were chosen as described above. The current version of the Insulin Resistance Gene Chip contains 210 genes of interest, plus 48 control elements. A full list of the genes is available at http://www.hbs.deakin.edu.au/mru/research/gene_chip_tech/genechip_three.htm/.
Conclusions—The human Insulin Resistance Gene Chip that we have constructed will be a very useful tool for investigating variation in the expression of genes relevant to insulin resistance under various experimental conditions. Initially, the gene chip will be used in studies such as exercise interventions, fasting, euglycemic-hyperinsulinemic clamps, and administration of antidiabetic agents

Interobserver reproducibility of histopathologic prognostic variables in primary cutaneous melanomas

Background: The prognosis for patients with localized primary cutaneous melanoma is known to depend principally on tumor thickness, and to a lesser extent on ulcerative state and Clark level. We have recently found in an analysis of 3661 patients that tumor mitotic rate (TMR) is also an important prognostic parameter, ranking second only to tumor thickness. However, few studies have assessed the accuracy and reproducibility with which these features of a melanoma are recorded by histopathologists.
Aim: To assess interobserver reproducibility of major pathologic prognostic parameters in cutaneous melanoma.
Methods: Single hematoxylin and eosin-stained slides of 69 dermally invasive primary cutaneous melanomas were circulated among six pathologists with differing experience in the assessment of melanocytic tumors. The observers independently determined the tumor thickness, Clark level of invasion, ulcerative state, and TMR for each lesion. Intraclass correlation coefficients and kappa scores for multiple ratings per subject were calculated.
Results: The intraclass correlation coefficients were 0.96 for tumor thickness and 0.76 for TMR. The kappa scores were 0.83 for ulcerative state and 0.60 for Clark level. These results indicated excellent agreement among the pathologists for measurements of tumor thickness, ulcerative state, and TMR and fair to good agreement for Clark level.
Conclusions: Appropriately trained and experienced histopathologists can assess prognostically important features of melanomas accurately and reproducibly. Given our recent finding of the significance of TMR in determining prognosis, it is important that this feature be assessed by a standardized method and documented for all primary cutaneous melanomas.

One-step coating of fluoro-containing silica nanoparticles for universal generation of surface superhydrophobicity

Stable superhydrophobic surfaces with water contact angles over 170 degrees and sliding angles below 7 degrees were produced by simply coating a particulate silica sol solution of co-hydrolysed TEOS/fluorinated alkyl silane with NH₃^.H₂O on various substrates, including textile fabrics (e.g. polyester, wool and cotton), electrospun nanofibre mats, filter papers, glass slides, and silicon wafers.

Developing the Deakin online teaching and learning repository

Slides for a report on the development of the Deakin online teaching and learning repository and the proposal to create a modern Deakin version of the 1991Najaden Collection of papers on collaborative learning through computer conferencing. The collection will be called Audio, Video, Disco - Look, Listen, Learn and contain 'best of breed' papers about Deakin's past and future as a distance edcuation - flexible learning university, from the Deakin online teaching and learning repository.

Mimicry and the eye of the beholder

Recent experiments (Dittrich et al. (Proc. R. Soc. Lond. B 251, 195 (1993))) suggest that pigeon perception of wasp mimicry by hoverflies is similar to that of humans and of computer-based image matching. However, the relations are nonlinear and may explain why some species are abundant despite their being poor mimics to the human eye. We suggest that these discrepancies between pigeon and human categorization may lie in the differences between avian and primate colour vision. As pigeon categorization and computer image analysis were both assessed by using colour slides designed for human vision, they lacked the natural colour information available to wild birds, in particular that from ultraviolet (uv) wavelengths.

A new approach to the investigation of allergenic respirable particles using a modified Anderson Impactor

Pollen allergens have been shown to occur in fine particles much smaller than pollen grains. As such allergenic particles have a high probability of entering the lower human airways, it is important to further investigate their origin and their biological and immunological properties. Accordingly, we have modified the particle collection surface of an Andersen Impactor using adhesive coated microscope slides to enable identification by high resolution microscopic analysis and immunodetection of allergenic particulates.

Au-Ag三角纳米环单层膜的原位转化制备及SERS效应

A gold-silver nanoframe monolayer nanostructure was obtained on the glass slide using the in-situ sacrificial template reaction. First the silver nanoprisms(~79.2 nm edge length) were prepared as the sacrificial template and were assembled on the slides through electrostatic interactions. The chloroautric acid in-situ reacted with the silver nanoprisms as oxidant. We evaluated the effect of oxidation reaction time on the morphologies and the LSPR properties of the prepared nanoframes. The thickness of gold-silver framework can be adjusted from 29.3 nm to 16.2 nm. We applied the gold-silver framework monolayer as a new surface-enhanced Raman scattering(SERS) substrate for determining 4-aminothiophenol.

Active content for preparation of teaching materials

Teaching materials such as study guides have implicit structure that can be exploited to explicitly assist in the learning and teaching process. Document technologies specific to the teaching context generate visible structures and linkages in a consistent manner across multiple course materials. We describe techniques that:

• Create, manage and validate links between the learning objectives, content related to each objective and corresponding assessment task.

• Explicitly present relationships between concepts, as a concept map, related to unit content and external study resources.

• Treat various study resources (study guide, presentation slides) as consistent views.

• Facilitate the use of external media to support multiple modalities.

The process creates teaching content as a single master document which is annotated to: identify learning outcomes associated with topics and exercises, relationships between concepts covered, references to external resources and media, as well as summary points and keywords. Different views of this master document produce the range of course documentation.

Examples of documents include: a study guide with learning outcomes linked to content, concept maps providing a graphical view of key relationships, and presentation slides that generate visual mnemonics for important topics.

While this structure simplifies formatting of learning materials it also offers additional benefits to the teacher. Reports are generated showing that all outcomes are covered and assessed.   Explicitly annotating and visualizing concepts allows the lecturer to ensure that all elements fall within a single scaffold. Simplified access to external media encourages alternative presentation modalities and produces presentations that are easily adapted to new themes.

Cellulose nanofibre textured SERS substrate

Poor reproducibility limits the wide uptake of low-cost surface enhanced Raman spectroscopy (SERS) substrates. This study reports a relatively low-cost and reproducible cellulose nanofibre (CNF) textured SERS substrate. Utilizing a layer of CNFs deposited onto glass slides, nanoscale roughness was achieved, which facilitated effective aggregation of gold nanoparticles (AuNPs) to form a novel CNF textured SERS substrate. This substrate meets the critical roughness requirements to control the distribution of AuNPs to provide 'hot spots' for SERS detection, offering significant signal enhancement. The reproducibility and accuracy of low-cost cellulosic SERS substrates were significantly improved on a model SERS molecule of 4-aminothiophenol.

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears

BACKGROUND: Acute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. Here, we performed sequencing-based genomic DNA methylation profiling of eight paediatric ALL patients using archived bone marrow smear microscope slides. FINDINGS: SOLiD™ sequencing data was collected from Methyl-Binding Domain (MBD) enriched fractions of genomic DNA. The primary tumour and remission bone marrow sample was analysed from eight patients. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS (Model-based Analysis for ChIP-Seq) and HOMER (Hypergeometric Optimization of Motif EnRichment). In total, 3.67 gigabases (Gb) were sequenced, 2.74 Gb were aligned to the reference genome (average 74.66% alignment efficiency). This dataset enables the interrogation of differential DNA methylation associated with paediatric ALL. Preliminary results reveal concordant regions of enrichment indicative of a DNA methylation signature. CONCLUSION: Our dataset represents one of the first SOLiD™MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears. Differential DNA methylation between cancer and equivalent disease-free tissue can be identified and correlated with existing and published genomic studies. Given the rarity of paediatric haematopoietic malignancies, relative to adult counterparts, our demonstration of the utility of archived bone marrow smear samples to high-throughput methylation sequencing approaches offers tremendous potential to explore the role of DNA methylation in the aetiology of cancer.