Identification of TFG (TRK-fused gene) as a putative metastatic melanoma tumor suppressor gene

High density SNP arrays can be used to identify DNA copy number changes in tumors such as homozygous deletions of tumor suppressor genes and focal amplifications of oncogenes. Illumina Human CNV370 Bead chip arrays were used to assess the genome for unbalanced chromosomal events occurring in 39 cell lines derived from stage III metastatic melanomas. A number of genes previously recognized to have an important role in the development and progression of melanoma were identified including homozygous deletions of CDKN2A (13 of 39 samples), CDKN2B (10 of 39), PTEN (3 of 39), PTPRD (3 of 39), TP53 (1 of 39), and amplifications of CCND1 (2 of 39), MITF (2 of 39), MDM2 (1 of 39), and NRAS (1 of 39). In addition, a number of focal homozygous deletions potentially targeting novel melanoma tumor suppressor genes were identified. Because of their likely functional significance for melanoma progression, FAS, CH25H, BMPR1A, ACTA2, and TFG were investigated in a larger cohort of melanomas through sequencing. Nonsynonymous mutations were identified in BMPR1A (1 of 43), ACTA2 (3 of 43), and TFG (5 of 103). A number of potentially important mutation events occurred in TFG including the identification of a mini mutation ‘‘hotspot’’ at amino acid residue 380 (P380S and P380L) and the presence of multiple mutations in two melanomas. Mutations in TFG may have important clinical relevance for current therapeutic strategies to treat metastatic melanoma.

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants. © 2013 Loss-Morais et al.; licensee BioMed Central Ltd.

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

The velocity synchronous discrete Fourier transform for order tracking in the field of rotating machinery

Diagnostics of rotating machinery has developed significantly in the last decades, and industrial applications are spreading in different sectors. Most applications are characterized by varying velocities of the shaft and in many cases transients are the most critical to monitor. In these variable speed conditions, fault symptoms are clearer in the angular/order domains than in the common time/frequency ones. In the past, this issue was often solved by synchronously sampling data by means of phase locked circuits governing the acquisition; however, thanks to the spread of cheap and powerful microprocessors, this procedure is nowadays rarer; sampling is usually performed at constant time intervals, and the conversion to the order domain is made by means of digital signal processing techniques. In the last decades different algorithms have been proposed for the extraction of an order spectrum from a signal sampled asynchronously with respect to the shaft rotational velocity; many of them (the so called computed order tracking family) use interpolation techniques to resample the signal at constant angular increments, followed by a common discrete Fourier transform to shift from the angular domain to the order domain. A less exploited family of techniques shifts directly from the time domain to the order spectrum, by means of modified Fourier transforms. This paper proposes a new transform, named velocity synchronous discrete Fourier transform, which takes advantage of the instantaneous velocity to improve the quality of its result, reaching performances that can challenge the computed order tracking.

The Impacts of Climate Change on Australia’s Food Production and Export

The global food system is undergoing unprecedented change. With population increases, demands for food globally will continue to rise at the same time that agricultural environments are compromised through urban encroachment, climate change and environmental degradation. Australia has long identified itself as an agricultural exporting nation—but what will its capacity be in feeding an increasing global population as it also comes to terms with extreme climatic events such as the floods, fires and droughts, and reduced water availability, experienced in recent decades? This chapter traces the history of Australian agricultural exports and evaluates its food production and export capacity against scientific predictions of climate change impacts. With the federal government forecasting declines in the production of wheat, beef, dairy and sugar, Australia’s key export commodities may well be compromised. Calls to produce more food using new technologies are likely to generate significant environmental problems. Yet, a radical reconfiguration of Australian agriculture which incorporates alternative approaches, such as agro-ecology, is rarely considered by government and industry.

Expression, regulation and putative nutrient-sensing function of taste GPCRs in the heart

G protein-coupled receptors (GPCRs) are critical for cardiovascular physiology. Cardiac cells express >100 nonchemosensory GPCRs, indicating that important physiological and potential therapeutic targets remain to be discovered. Moreover, there is a growing appreciation that members of the large, distinct taste and odorant GPCR families have specific functions in tissues beyond the oronasal cavity, including in the brain, gastrointestinal tract and respiratory system. To date, these chemosensory GPCRs have not been systematically studied in the heart. We performed RT-qPCR taste receptor screens in rodent and human heart tissues that revealed discrete subsets of type 2 taste receptors (TAS2/Tas2) as well as Tas1r1 and Tas1r3 (comprising the umami receptor) are expressed. These taste GPCRs are present in cultured cardiac myocytes and fibroblasts, and are enriched in myocytes, which we corroborated using in situ hybridization. Tas1r1 gene-targeted mice (Tas1r1Cre/Rosa26tdRFP) strikingly recapitulated these data. In vivo taste receptor expression levels were developmentally regulated in the postnatal period. Intriguingly, several Tas2rs were upregulated in cultured rat myocytes and in mouse heart in vivo following starvation. The discovery of taste GPCRs in the heart opens an exciting new field of cardiac research. We predict that these taste receptors may function as nutrient sensors in the heart.

Export readiness index : construction and analysis

The internationalisation process of firms has attracted much research interest since the 1970s. It is noted, however, that a significant research gap exists in studies with a primary focus on the pre-internationalisation behaviour of firms. This paper proposes the incorporation of a pre-internationalisation phase into the traditional Uppsala model of firm internationalisation to address the issue of export readiness. Through extensive literature review, the concepts fundamental to the ability of an Uppsala type firm to begin internationalisation through an export entry mode are identified: exposure to stimuli factors, attitudinal commitment of decision makers towards exporting, the firm’s resource capabilities, as well as the moderating effect of lateral rigidity. The concept of export readiness is operationalised in this study through the construction of an export readiness index (ERI) using exploratory and confirmatory factor analysis. The index is then applied to some representative cases and tested using logistic regression to establish its validity as a diagnostic tool. The proposed ERI presents not only a more practical approach towards analysing firms’ export readiness but has also major public policy implications as a possible tool for government export promotion agencies.

Internet marketing and export market growth in Chile

Previous studies show that the Internet positively influences firms’ export activities from developed markets. However, the literature is vague as to whether the Internet has an impact on the export performance of firms from emerging markets. This study tests a conceptual model that includes the effect of Internet marketing capabilities on export market growth in an emerging market. Drawing on a cross-national sample of 204 export firms from a Latin American country (Chile), findings indicate that Internet marketing capabilities positively influence the availability of export information, which in turn impacts the development of business network relationships and export market growth.

Causes of rigidity in SMEs' export commencement decision

Today, small-medium sized enterprises (SMEs) collectively contribute to the largest percentage of job creation in OECD countries. SMEs have become increasingly international since the turn of the century despite being smaller in size in comparison to large multinational firms, and notably, exporting is the most favoured mode of international market entry utilised by SMEs in their internationalisation strategy. Governments around the world have acknowledged the importance of export promotion and have employed policies that are targeted at increasing the export activity of SMEs. However, in many countries, the involvement of SMEs in export operations remains rather low. Within Australia, for example, only about one-third of local SMEs are exporting and this raises an important question as to why there is such a huge percentage of non-exporters. Much scholarly research that focuses on this problem has concentrated on the broad concept of 'export barriers' that act as obstacles to a firm's export development. This paper takes a different approach to previous studies and proposes that a firm's resistance to commence exporting can be better understood through an analysis of the behavioural decision process during its pre-export state. Using a sample of Australian SMEs, the factors that are important in preventing a firm’s initial export commencement decision are categorised and discussed through the use of factor analysis.

Corporatizing the 'intellectual machinery' of government : the case of educational policy in Australia

This article analyses what it describes as the corporatization of the ‘intellectual machinery’ of government: the theories, knowledges, research and ‘know how’ utilized by political authorities to render the world thinkable, programmable and subject to intervention. Through an analysis of two key nodal points in national policy on teacher professional standards in Australia over the last decade, the article discloses a shift in the relation between expertise and politics. This is manifested, it is argued, in an increased reliance by policy authorities on corporatized forms of research produced by national and international private consulting firms, Think Tanks, and ‘policy entrepreneurs’ and a concomitant decrease in their reliance on free research produced largely by academics in institutions of higher education. The article seeks to account for this shift in terms of the ‘advanced liberal’ formula for rule which now characterizes government in contemporary Western polities.

Method for planning and executing obstacle-free paths for rotating excavation machinery

This invention concerns the control of rotating excavation machinery, for instance to avoid collisions with obstacles. In a first aspect the invention is a control system for autonomous path planning in excavation machinery, comprising: A map generation subsystem to receive data from an array of disparate and complementary sensors to generate a 3-Dimensional digital terrain and obstacle map referenced to a coordinate frame related to the machine's geometry, during normal operation of the machine. An obstacle detection subsystem to find and identify obstacles in the digital terrain and obstacle map, and then to refine the map by identifying exclusion zones that are within reach of the machine during operation. A collision detection subsystem that uses knowledge of the machine's position and movements, as well as the digital terrain and obstacle map, to identify and predict possible collisions with itself or other obstacles, and then uses a forward motion planner to predict collisions in a planned path. And, a path planning subsystem that uses information from the other subsystems to vary planned paths to avoid obstacles and collisions. In other aspects the invention is excavation machinery including the control system; a method for control of excavation machinery; and firmware and software versions of the control system.

Identification of a putative cellulase gene in the giant freshwater prawn, Macrobrachium rosenbergii (De Man, 1879)

Nutrition plays an important role in the development of all organisms and in particular that of farmed aquatic species where costs associated with feed can often exceed 60% of total production costs. Crustacean species in addition, have the added metabolic requirement for regular moulting to allow normal growth and this requires large amounts of energy in the form of sugars (glucose). The current study explored the capacity of the giant freshwater prawn to produce endogenous cellulose-degrading enzymes capable of extracting nutrients (simple sugars) from plant sources in formulated feeds used in the prawn aquaculture industry. We identified a putative cellulase cDNA fragment in the target organism of 1576 base pairs in length of non-microbial origin that after protein modelling exhibited a TM-score of 0.916 with a described cellulase reported from another crustacean species. The functional role of cellulase enzymes is to hydrolyse cellulose to glucose and the fragment identified in GFP was highly expressed in the hepatopancreas, the site of primary food digestion and absorption in crustaceans. Hepatopancreatic tissue from Macrobrachium rosenbergii also showed active digestion of cellulose to glucose following an endoglucanase assay. Cellulase gene(s) are present in the genomes of many invertebrate taxa and play an active role in the conversion of cellulose to available energy. Identification and characterization of endogenous cellulase gene(s) in giant freshwater prawn can assist development of the culture industry because the findings confirm that potentially greater levels of low-cost plant-material could be included in artificial formulated diets in the future without necessarily compromising individual growth performance. Ultimately, this development may contribute to more efficient, cost-effective production systems for freshwater prawn culture stocks that meet the animal's basic nutritional requirements and that also support good individual growth rates.

Race against time: The export of essential medicines to Rwanda

This article considers the significance of the first export of essential medicines under the WTO General Council Decision 2003. In July 2007, Rwanda became the first country to provide a notification under the WTO General Council Decision 2003 of its intent to import a fixed-dose, triple combination HIV/AIDS drug manufactured by the Canadian generic pharmaceuticalmanufacturer Apotex, Inc. In September 2007, Apotex was granted the first compulsory licence application under Canada's Access to Medicines Regime. This article considers the convoluted and protracted negotiations between the Government of Rwanda, Apotex and three patent holders, GlaxoSmithKline, Boehringer Ingleheim Canada and Shire BioChemical, Inc. It questions the efficiency of this process. This article considers the review of the Jean Chretien Pledge to Africa Act 2004 (Canada). It is critical of the refusal of the Conservative Government of Canada to make any amendments to the legislation to improve the cost-effective delivery of essential medicines. This article queries the proposed Hong Kong Amendment to the TRIPS Agreement 1994, given the concerns of the Africa Group. It is submitted that it is undesirable to codify the WTO General Council Decision 2003, given its failure to provide a speedy, efficient and cost-effective delivery of essential medicines.

Export of radioactive cesium from agricultural fields under simulated rainfall in Fukushima

In this study, we investigated the impact of rainfall on runoff, soil erosion and consequently on the discharge of radioactive cesium in agricultural fields in Fukushima prefecture using a rainfall simulator. Simulated heavy rainfalls (50 mm h-1) generated significant runoff and soil erosion. The average concentration of radioactive cesium (the sum of 134Cs and 137Cs) in the runoff sediments was [similar]3500 Bq kg-1 dry soil, more than double the concentrations measured in the field soils which should be considered in studies using the 137Cs loss to estimate long-term soil erosion. However, the estimated mass of cesium discharged through one runoff event was less than 2% of the cesium inventory in the field. This suggested that cesium discharge via soil erosion is not a significant factor in reducing the radioactivity of contaminated soils in Fukushima prefecture. However, the eroded sediment carrying radioactive cesium will deposit into the river systems and potentially pose a radioactivity risk for aquatic living organisms.

Heat shock protein 70 on Neuro2a cells is a putative receptor for Japanese encephalitis virus

Japanese encephalitis virus (JEV) envelope (E) protein has been shown to play a critical role in attachment to cells. However, the receptor interacting with envelope protein has not been conclusively identified. Using mouse neuroblastoma (Neuro2a) cells and purified JEV-E protein in `Virus Overlay Protein Binding Assay' followed by MALDI-TOF analysis, we identified `heat shock protein 70' (Hsp70) as a possible receptor for JEV. Indirect immunofluorescence and flow-cytometry analysis demonstrated localization of Hsp70 on Neuro2a cell surface. Co-immunoprecipitation followed by Western blot analysis reconfirmed the interaction between Hsp70 and JEV-E protein. Further, anti-Hsp70 polyclonal-antibodies were able to block JEV entry into Neuro2a cells. Additionally, using the bioinformatic tool - FTDOCK, clocking between the proteins was performed. Amongst six interacting structural poses studied one pose involving RGD motif on JEV-E and leucine(539) on Hsp70 displayed stable interaction. These observations indicate that Hsp70 serves as putative receptor for JEV in Neuro2A cells.