Culture independent analysis of greyback canegrub-associated microflora and microbial community comparison using subtractive hybridisation

Greyback canegrubs cost the Australian sugarcane industry around $13 million per annum in damage and control. A novel and cost effective biocontrol bacterium could play an important role in the integrated pest management program currently in place to reduce damage and control associated costs. During the course of this project, terminal restriction fragment length polymorphism (TRFLP), 16-S rDNA cloning, suppressive subtractive hybridisation (SSH) and entomopathogen-specific PCR screening were used to investigate the little studied canegrub-associated microflora in an attempt to discover novel pathogens from putatively-diseased specimens. Microflora associated with these soil-dwelling insects was found to be both highly diverse and divergent between individual specimens. Dominant members detected in live specimens were predominantly from taxa of known insect symbionts while dominant sequences amplified from dead grubs were homologous to putativelysaprophytic bacteria and bacteria able to grow during refrigeration. A number of entomopathogenic bacteria were identified such as Photorhabdus luminescens and Pseudomonas fluorescens. Dead canegrubs prior to decomposition need to be analysed if these bacteria are to be isolated. Novel strategies to enrich putative pathogen-associated sequences (SSH and PCR screening) were shown to be promising approaches for pathogen discovery and the investigation of canegrubsassociated microflora. However, due to inter- and intra-grub-associated community diversity, dead grub decomposition and PCR-specific methodological limitations (PCR bias, primer specificity, BLAST database restrictions, 16-S gene copy number and heterogeneity), recommendations have been made to improve the efficiency of such techniques. Improved specimen collection procedures and utilisation of emerging high-throughput sequencing technologies may be required to examine these complex communities in more detail. This is the first study to perform a whole-grub analysis and comparison of greyback canegrub-associated microbial communities. This work also describes the development of a novel V3-PCR based SSH technique. This was the first SSH technique to use V3-PCR products as a starting material and specifically compare bacterial species present in a complex community.

From emotional suppression to regulated empathy : the changing face of control in the CES

Between the 1970s and the 1990s the level and type of emotionality in the Commonwealth Employment Service (the Australian national employment service) altered. Within a context of changing economic conditions and concomitant work intensification, it is argued that untenable working conditions resulted in new recruits adopting a coping strategy that led to the use rather than the suppression of emotions. The use of emotions provided workers with job satisfaction and greater control over service interactions. Management subsequently commandeered the use of emotions to complement the introduction of private sector management techniques and service delivery reforms, regaining control over worker-client interactions.

Candidate metastasis suppressor genes uncovered by array comparative genomic hybridization in a mouse allograft model of prostate cancer.

Background The purpose of this study was to identify candidate metastasis suppressor genes from a mouse allograft model of prostate cancer (NE-10). This allograft model originally developed metastases by twelve weeks after implantation in male athymic nude mice, but lost the ability to metastasize after a number of in vivo passages. We performed high resolution array comparative genomic hybridization on the metastasizing and non-metastasizing allografts to identify chromosome imbalances that differed between the two groups of tumors. Results This analysis uncovered a deletion on chromosome 2 that differed between the metastasizing and non-metastasizing tumors. Bioinformatics filters were employed to mine this region of the genome for candidate metastasis suppressor genes. Of the 146 known genes that reside within the region of interest on mouse chromosome 2, four candidate metastasis suppressor genes (Slc27a2, Mall, Snrpb, and Rassf2) were identified. Quantitative expression analysis confirmed decreased expression of these genes in the metastasizing compared to non-metastasizing tumors. Conclusion This study presents combined genomics and bioinformatics approaches for identifying potential metastasis suppressor genes. The genes identified here are candidates for further studies to determine their functional role in inhibiting metastases in the NE-10 allograft model and human prostate cancer.

Observation of the suppression of water uptake by marine particles

A 4 week intensive measurement campaign was conducted in March–April 2007 at Agnes Water, a remote coastal site on the east coast of Australia. A Volatility-Hygroscopicity-Tandem Differential Mobility Analyser (VH-TDMA) was used to investigate changes in the hygroscopic properties of ambient particles as volatile components were progressively evaporated. Nine out of 18 VH-TDMA volatility scans detected internally mixed multi-component particles in the nucleation and Aitken modes in clean marine air. Evaporation of a volatile, organic-like component in the VH-TDMA caused significant increases in particle hygroscopicity. In 3 scans the increase in hygroscopicity was so large it was explained by an increase in the absolute volume of water uptake by the particle residuals, and not merely an increase in their relative hygroscopicity. This indicates the presence of organic components that were suppressing the hygroscopic growth of mixed particles on the timescale of humidification in the VH-TDMA (6.5 secs). This observation was supported by ZSR calculations for one scan, which showed that the measured growth factors of mixed particles were up to 18% below those predicted assuming independent water uptake of the individual particle components. The observed suppression of water uptake could be due to a reduced rate of hygroscopic growth caused by the presence of organic films or organic-inorganic interactions in solution droplets that had a negative effect on hygroscopicity.

Differentiation of Rice Tungro Bacilliform Virus Strains by Restriction Analysis and DNA Hybridization

Rice tungro bacilliform virus (RTBV) is one of the two viruses that cause tungro disease. Four RTBV strains maintained in the greenhouse for 4 years, G1, G2, Ic, and L, were differentiated by restriction fragment length polymorphism (RFLP) analysis of the native viral DNA. Although strains G1 and Ic had identical restriction patterns when cleaved with Pst1, BamHI, EcoRI, and EcoRV, they can be differentiated from strains G2 and L by EcoRI and EcoRV digestion. These same endonucleases also differentiate strain G2 from strain L. When total DNA extracts from infected plants were used instead of viral DNA, and digested with EcoRV, identical restriction patterns for each strain (G2 and L) were obtained from roots, leaves, and leaf sheaths of infected plants. The restriction patterns were consistent from plant to plant, in different varieties, and at different times after inoculation. This technique can be used to differentiate RTBV strains and determine the variability of a large number of field samples.

Can hybridization cause local extinction : the case for demographic swamping of the Australian native, Senecio pinnatifolius, by the invasive, S. madagascariensis?

The outcome of interspecific hybridization between native and invasive species depends on the relative frequencies of parental taxa and viability of hybrid progeny. We investigated individual and population level consequences of hybridization between the Australian native, Senecio pinnatifolius, and the exotic S. madagascariensis, with AFLP markers and used this information to simulate the expected outcome of hybridization.A high frequency (range 8.3-75.6 %) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations indicating that sympatric populations represent tension zones. A hybridization advantage was observed for S. madagascariensis,where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Simulations indicated S. pinnatifolius could be replaced in sympatric populations if hybridization was density dependent.For this native-exotic pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. Due to asymmetric hybridization, S. pinnatifolius appears under threat from demographic swamping, and local extinction is possible where it occurs in sympatry with S. madagascariensis.

Melanoma cell invasiveness is regulated by miR-211 suppression of the BRN2 transcription factor

To identify microRNAs potentially involved in melanomagenesis, we compared microRNA expression profiles between melanoma cell lines and cultured melanocytes. The most differentially expressed microRNA between the normal and tumor cell lines was miR-211. We focused on this pigment-cell-enriched miRNA as it is derived from the microphthalmia-associated transcription factor (MITF)-regulated gene, TRPM1 (melastatin). We find that miR-211 expression is greatly decreased in melanoma cells and melanoblasts compared to melanocytes. Bioinformatic analysis identified a large number of potential targets of miR-211, including POU3F2 (BRN2). Inhibition of miR-211 in normal melanocytes resulted in increased BRN2 protein, indicating that endogenous miR-211 represses BRN2 in differentiated cells. Over-expression of miR-211 in melanoma cell lines changed the invasive potential of the cells in vitro through directly targeting BRN2 translation. We propose a model for the apparent non-overlapping expression levels of BRN2 and MITF in melanoma, mediated by miR-211 expression.

Surface plasmon hybridization and exciton coupling

We derive a semianalytical model to describe the interaction of a single photon emitter and a collection of arbitrarily shaped metal nanoparticles. The theory treats the metal nanoparticles classically within the electrostatic eigenmode method, wherein the surface plasmon resonances of collections of nanoparticles are represented by the hybridization of the plasmon modes of the noninteracting particles. The single photon emitter is represented by a quantum mechanical two-level system that exhibits line broadening due to a finite spontaneous decay rate. Plasmon-emitter coupling is described by solving the resulting Bloch equations. We illustrate the theory by studying model systems consisting of a single emitter coupled to one, two, and three nanoparticles, and we also compare the predictions of our model to published experimental data. ©2012 American Physical Society.

Chromosomal aberrations in squamous cell carcinoma and solar keratoses revealed by comparative genomic hybridization

OBJECTIVE: To identify chromosomal copy numbers of frequent genetic aberrations within squamous cell carcinomas (SCCs) and solar keratoses (SKs), and provide further evidence to support or challenge current dogma concerning the relationship between these lesions. DESIGN: Retrospective analysis of genetic aberrations in DNA from SK and SCC biopsy specimens by comparative genomic hybridization. SETTING: University-based research laboratory in Queensland, Australia. PATIENTS: Twenty-two biopsy specimens from patients with diagnosed SKs (n = 7), cutaneous SCCs (n = 10), or adjoining lesions (n = 5). MAIN OUTCOME MEASURES: Identification of frequent genetic aberrations both specific to SK and SCC and shared by these lesions to investigate their clonal relationship. RESULTS: Shared genomic imbalances were identified in SK and SCC. Frequent gains were located at chromosome arms 3q, 17q, 4p, 14q, Xq, 5p, 9q, 8q, 17p, and 20q, whereas shared regional losses were observed at 9p, 3p, 13q, 17p, 11p, 8q, and 18p. Significant loss of 18q was observed only in SCC lesions. CONCLUSIONS: Our results demonstrate that numerous chromosomal aberrations are shared by the 2 lesions, suggesting a clonal relationship between SK and SCC. Additionally, the genomic loss of 18q may be a significant event in SK progression to SCC. Finally, the type and frequency of aberrations suggests a common mode of tumorigenesis in SCC-derived tumors.