Common origins of MDA-MB-435 cells from various sources with those shown to have melanoma properties

Recently, the tissue origin of MDA-MB-435 cell line has been the subject of considerable debate. In this study, we set out to determine whether MDA-MB-435-DTP cells shown to express melanoma-specific genes were identical to various other MDA-MB-435 cell stocks worldwide. CGH-microarray, genetic polymorphism genotyping, microsatellite fingerprint analysis and/or chromosomal number confirmed that the MDA-MB-435 cells maintained at the Lombardi Comprehensive Cancer Center (MDA-MB-435-LCC) are almost identical to the MDA-MB-435-DTP cells, and showed a very similar profile to those obtained from the same original source (MD Anderson Cancer Center) but maintained independently (MDA-MB-435-PMCC). Gene expression profile analy-sis confirmed common expression of genes among different MDA-MB-435-LCC cell stocks, and identified some unique gene products in MDA-MB-435-PMCC cells. RT-PCR analysis confirmed the expression of the melanoma marker tyrosinase across multiple MDA-MB-435 cell stocks. Collectively, our results show that the MDA-MB-435 cells used widely have identical origins to those that exhibit a melanoma-like gene expression signature, but exhibit a small degree of genotypic and phenotypic drift.

LCC15-MB cells are MDA-MB-435 : a review of misidentified breast and prostate cell lines

Current stocks of the LCC15-MB cell line, which we originally isolated from a human breast-bone metastasis, were found to be genetically matched to the MDA-MB-435 cell line from the Lombardi Cancer Center (MDA-MB-435-LCC) using comparative genomic hybridisation, DNA microsatellite analysis and chromosomal number. LCC15-MB stocks used for our previously published studies as well as the earliest available LCC15-MB cells also showed identity to MDA-MB-435-LCC cells. The original karyotype reported for LCC15-MB cells was considerably different to that of MDA-MB-435 cells, indicating that the original LCC15-MB cells were lost to contamination by MDA-MB-435-LCC cells. Chromosome number is the simplest test to distinguish original LCC 15-MB cells (n ∼ 75) from MDA-MB-435 (n ∼ 52). Collectively, our results prove that LCC15-MB cells currently available are MDA-MB-435 cells and we suggest their re-designation as MDA-MB-435-LCC15 cells. We also review the known misclassification of breast and prostate cancer cell lines to date and have initiated a register maintained at http://www.svi.edu.au/cell_lines_registry.doc.

A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery

The striped catfish (Pangasianodon hypophthalmus) culture industry in the Mekong Delta in Vietnam has developed rapidly over the past decade. The culture industry now however, faces some significant challenges, especially related to climate change impacts notably from predicted extensive saltwater intrusion into many low topographical coastal provinces across the Mekong Delta. This problem highlights a need for development of culture stocks that can tolerate more saline culture environments as a response to expansion of saline water-intruded land. While a traditional artificial selection program can potentially address this need, understanding the genomic basis of salinity tolerance can assist development of more productive culture lines. The current study applied a transcriptomic approach using Ion PGM technology to generate expressed sequence tag (EST) resources from the intestine and swim bladder from striped catfish reared at a salinity level of 9 ppt which showed best growth performance. Total sequence data generated was 467.8 Mbp, consisting of 4,116,424 reads with an average length of 112 bp. De novo assembly was employed that generated 51,188 contigs, and allowed identification of 16,116 putative genes based on the GenBank non-redundant database. GO annotation, KEGG pathway mapping, and functional annotation of the EST sequences recovered with a wide diversity of biological functions and processes. In addition, more than 11,600 simple sequence repeats were also detected. This is the first comprehensive analysis of a striped catfish transcriptome, and provides a valuable genomic resource for future selective breeding programs and functional or evolutionary studies of genes that influence salinity tolerance in this important culture species.

Decoupling 2 : technologies, opportunities and policy options

This report was produced by the Decoupling Working Group of the International Resource Panel. It explores technological possibilities and opportunities for both developing and developed countries to accelerate decoupling and reap the environmental and economic benefits of increased resource productivity. It also examines several policy options that have proved to be successful in helping different countries to improve resource productivity in various sectors of their economy, avoiding negative impacts on the environment. It does not seem possible for a global economy based on the current unsustainable patterns of resource use to continue into the future. The economic consequences of these patterns are already apparent in three areas: increases in resource prices, increased price volatility and disruption of environmental systems. The environment impacts of resource use are also leading to potentially irreversible changes to the world’s ecosystems, often with direct effects on people and the economy – for example through damage to health, water shortages, loss of fish stocks or increased storm damage. But there are alternatives to these scary patterns. Many decoupling technologies and techniques that deliver resource productivity increases as high as 5 to 10-fold are already available, allowing countries to pursue their development strategies while significantly reducing their resource footprint and negative impacts on the environment. This report shows that much of the policy design “know-how” needed to achieve decoupling is present in terms of legislation, incentive systems, and institutional reform. Many countries have tried these out with tangible results, encouraging others to study and where appropriate replicate and scale up such practices and successes.

Investor sentiment as conditioning information in asset pricing

This paper assesses whether incorporating investor sentiment as conditioning information in asset-pricing models helps capture the impacts of the size, value, liquidity and momentum effects on risk-adjusted returns of individual stocks. We use survey sentiment measures and a composite index as proxies for investor sentiment. In our conditional framework, the size effect becomes less important in the conditional CAPM and is no longer significant in all the other models examined. Furthermore, the conditional models often capture the value, liquidity and momentum effects.

Creating an enabling legal framework fro REDD+ investments in Kenya

Reducing Emissions from Deforestation and Forest Degradation and the role of conservation, sustainable management of forests and enhancement of forest carbon stocks in developing countries (REDD+) has emerged out of the United Nations Framework Convention on Climate Change (UNFCCC)/Kyoto Protocol negotiations. It is intended to be a mechanism to channel funding (from both public and private sources) for reducing emissions from the forest sector. It is an international climate change policy that relies on national implementation. In order to attract and manage REDD+ investments (both public and private), countries need to decide on their approach to REDD+ implementation through a series of policy choices, and then implement those policy choices through strong legal frameworks. An important question for REDD+ host countries to consider, therefore, is how to develop robust legal structures to facilitate REDD+ implementation. These legal frameworks could be based on existing laws, and/or require new law making.

A regional interpretation of rules and good practice for greenhouse accounting : Northern Australian savanna systems

Land-use change, particularly clearing of forests for agriculture, has contributed significantly to the observed rise in atmospheric carbon dioxide concentration. Concern about the impacts on climate has led to efforts to monitor and curtail the rapid increase in concentrations of carbon dioxide and other greenhouse gases in the atmosphere. Internationally, much of the current focus is on the Kyoto Protocol to the United Nations Framework Convention on Climate Change (UNFCCC). Although electing to not ratify the Protocol, Australia, as a party to the UNFCCC, reports on national greenhouse gas emissions, trends in emissions and abatement measures. In this paper we review the complex accounting rules for human activities affecting greenhouse gas fluxes in the terrestrial biosphere and explore implications and potential opportunities for managing carbon in the savanna ecosystems of northern Australia. Savannas in Australia are managed for grazing as well as for cultural and environmental values against a background of extreme climate variability and disturbance, notably fire. Methane from livestock and non-CO2 emissions from burning are important components of the total greenhouse gas emissions associated with management of savannas. International developments in carbon accounting for the terrestrial biosphere bring a requirement for better attribution of change in carbon stocks and more detailed and spatially explicit data on such characteristics of savanna ecosystems as fire regimes, production and type of fuel for burning, drivers of woody encroachment, rates of woody regrowth, stocking rates and grazing impacts. The benefits of improved biophysical information and of understanding the impacts on ecosystem function of natural factors and management options will extend beyond greenhouse accounting to better land management for multiple objectives.

A review of the potential role of greenhouse gas abatement in native vegetation management in Queensland's rangelands

Concern about the risk of harmful human-induced climate change has resulted in international efforts to reduce greenhouse gas emissions to the atmosphere. We review the international and national context for consideration of greenhouse abatement in native vegetation management and discuss potential options in Queensland. Queensland has large areas of productive or potentially productive land with native woody vegetation cover with approximately 76 million ha with woody cover remaining in 1991. High rates of tree clearing, predominantly to increase pasture productivity, continued throughout the 1990s with an average 345,000 ha/a estimated to have been cleared, including non-remnant (woody regrowth) as well as remnant vegetation. Estimates of greenhouse gas emissions associated with land clearing currently have a high uncertainty but clearing was reported to contribute a significant proportion of Australia's total greenhouse gas emissions from 1990 (21%) to 1999 (13%). In Queensland, greenhouse emissions from land clearing were estimated to have been 54.5 Mt CO(2)-e in 1999. Management of native vegetation for timber harvesting and the proliferation of woody vegetation (vegetation thickening) in the grazed woodlands also represent large carbon fluxes. Forestry (plantations and native forests) in Queensland was reported to be a 4.4 Mt CO(2)-e sink in 1999 but there are a lack of comprehensive data on timber harvesting in private hardwood forests. Vegetation thickening is reported for large areas of the c. 60 million ha grazed woodlands in Queensland. The magnitude of the carbon sink in 27 million ha grazed eucalypt woodlands has been estimated to be 66 Mt CO(2)-e/a but this sink is not currently included in Australia's inventory of anthropogenic greenhouse emissions. Improved understanding of the function and dynamics of natural and managed ecosystems is required to support management of native vegetation to preserve and enhance carbon stocks for greenhouse benefits while meeting objectives of sustainable and productive management and biodiversity protection.

Modeling conditional correlations of asset returns : a smooth transition approach

In this paper we propose a new multivariate GARCH model with time-varying conditional correlation structure. The time-varying conditional correlations change smoothly between two extreme states of constant correlations according to a predetermined or exogenous transition variable. An LM–test is derived to test the constancy of correlations and LM- and Wald tests to test the hypothesis of partially constant correlations. Analytical expressions for the test statistics and the required derivatives are provided to make computations feasible. An empirical example based on daily return series of five frequently traded stocks in the S&P 500 stock index completes the paper.

Dewatering of microalgal culture for biodiesel production : exploring polymer flocculation and tangential flow filtration

Background: Conventional biodiesel production relies on trans-esterification of lipids extracted from vegetable crops. However, the use of valuable vegetable food stocks as raw material for biodiesel production makes it an unfeasibly expensive process. Used cooking oil is a finite resource and requires extra downstream processing, which affects the amount of biodiesel that can be produced and the economics of the process. Lipids extracted from microalgae are considered an alternative raw material for biodiesel production. This is primarily due to the fast growth rate of these species in a simple aquaculture environment. However, the dilute nature of microalgae culture puts a huge economic burden on the dewatering process especially on an industrial scale. This current study explores the performance and economic viability of chemical flocculation and tangential flow filtration (TFF) for the dewatering of Tetraselmis suecicamicroalgae culture. Results: Results show that TFF concentrates the microalgae feedstock up to 148 times by consuming 2.06 kWh m-3 of energy while flocculation consumes 14.81 kWhm-3 to concentrate the microalgae up to 357 times. Economic evaluation demonstrates that even though TFF has higher initial capital investment than polymer flocculation, the payback period for TFF at the upper extreme ofmicroalgae revenue is ∼1.5 years while that of flocculation is ∼3 years. Conclusion: These results illustrate that improved dewatering levels can be achieved more economically by employing TFF. The performances of these two techniques are also compared with other dewatering techniques.

Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

Creation of protein loaded biodegradable microparticles via ultrasonic atomization suitable for nasal delivery

Improved biopharmaceutical delivery may be achieved via the use of biodegradable microspheres as delivery vehicles. Biodegradable microspheres offer the advantages of maintaining sustained protein release over time whilst simultaneously protecting the biopharmaceutical from degradation. Particle samples produced by ultrasonic atomization were studied in order to determine a feed stock capable of producing protein loaded poly-ε-caprolactone (PCL) particles suitable for nasal delivery (i.e., less than 20 μm). A 40 kHz atomization system was used with a 6 mm full wave atomization probe. The effect of solids percent, feed flow rate, volumetric ratio of the polymer stock to the protein stock, and protein concentration in the protein stock on particle size characteristics were determined. It was shown that feed stocks containing 100 parts of 0.5 or 1.0% w/v PCL in acetone with one part 100 mg ml -1 BSA and 15 mg ml -1 PVA produced particles with a mass moment diameter (D[4,3]) of 13.17 μm and 9.10 μm, respectively in addition to displaying high protein encapsulation efficiencies of 93 and 95%, respectively. The biodegradable PCL particles were shown to be able to deliver encapsulated protein in vitro under physiological conditions.

Appendix 8: Quantifying the effects of environmental factors on catch rates in South-East fisheries: 1986-2006

The collection of basic environmental data by industry members was successful and offers a way of overcoming the problems associated with differences in scale between the environment and fisheries datasets. A simple method of collecting environmental data was developed that was only a small time burden on skippers, yet has the potential to provide very useful information on the same scale as the catch and effort data recorded in the logbooks. The success of this trial was aided by the natural interest of fishers to learn more about the environment in which they fish. The archival temperature-depth tags chosen proved robust, reliable and easy to use. While the use of large scale environmental data may not yield significant improvements in stock assessments for most SESSF species, fine-scale data collected from selected vessels using methods developed during this project may, in the longer term, be useful for incorporation into CPUE standardisations in the future...

Demand for ecolabeled seafood in the Japanese market: A conjoint analysis of the impact of information and interaction with other labels

The use of seafood ecolabels is expanding in the world marketplace, but so are labels indicating other product attributes, such as country of origin and wild vs. farmed. The interactive effects of these labels and attributes in evaluating consumers' preferences for ecolabeled seafood are relatively unexplored. In this paper we investigate (1) the direct and interactive effects of seafood ecolabels with other common fish labels, and (2) how consumers' perceptions about the state of marine stocks and the valuation of ecolabels may be affected by different information. We find moderate interactive effects between ecolabels and country of origin labels, whereas the valuation for seafood ecolabels is fairly high. In terms of information, we find that consumers' perceptions about fish stock levels changed (negatively) after receiving information on declining stock levels, and more sensationalized information led to increased change. However, valuation for a seafood ecolabel increases only when the information was perceived positively (credible/interesting); whereas exaggerated information (which was also perceived less credible) had insignificant effects on WTP.

An evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypopthalmus) using an RNA-SEQ approach

The project investigated the molecular response of Tra catfish (Pangasianodon hypophthalmus) to elevated salinity conditions. We employed Next generation sequencing platform to evaluate differential gene expression profiles of key genes under two salinity conditions. Results of the current project can form the basis for further studies to confirm the functional roles of specific genes that influence salinity tolerance in the target species and more broadly in other freshwater teleost fishes. Ultimately, the approach can contribute to developing superior culture stocks of the target species.