Molecular classification of cutaneous malignant melanoma by gene expression profiling

The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.

FGFR2 as a molecular target in endometrial cancer

Although molecularly targeted therapies have been effective in some cancer types, no targeted therapy is approved for use in endometrial cancer. The recent identification of activating mutations in fibroblast growth factor receptor 2 (FGFR2) in endometrial tumors has generated a new avenue for the development of targeted therapeutic agents. The majority of the mutations identified are identical to germline mutations in FGFR2 and FGFR3 that cause craniosynostosis and hypochondroplasia syndromes and result in both ligand-independent and ligand-dependent receptor activation. Mutations that predominantly occur in the endometrioid subtype of endometrial cancer, are mutually exclusive with KRAS mutation, but occur in the presence of PTEN abrogation. In vitro studies have shown that endometrial cancer cell lines with activating FGFR2 mutations are selectively sensitive to a pan-FGFR inhibitor, PD173074. Several agents with activity against FGFRs are currently in clinical trials. Investigation of these agents in endometrial cancer patients with activating FGFR2 mutations is warranted.

Numerical exploration of the defect’s effect on mechanical properties of nanowires under torsion

Molecular dynamics (MD) simulations have been carried out to investigate the defect’s effect on the mechanical properties of single-crystal copper nanowire with different surface defects, under torsion deformation. The torsional rigidity is found insensitive to the surface defects and the critical angle appears an obvious decrease due to the surface defects, the largest decrease is found for the nanowire with surface horizon defect. The deformation mechanism appears different degrees of influence due to surface defects. The surface defects play a role of dislocation sources. Comparing with single intrinsic stacking faults formation for the perfect nanowire, much affluent deformation processes have been activated because of surface defects, for instance, we find the twins formation for the nanowire with a surface 45o defect.

Society, history and research processes

In this reflection on research processes a humanities researcher begins to ask questions about the cultural materialist dimensions of research activities. At the center of this exploration are questions relating to the ways in which personal histories and experiences inform particular research processes and the ways in which a researcher's habits of collecting and working with data are regulated by cultural and social practice. The reflection on personal research processes is located in terms of the ethics work of Michel Foucault that provides reminders about the role of modern bureaucracy in governing what appear to be personal processes.

Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Transglutaminases and receptor tyrosine kinases

Transglutaminases are confounding enzymes which are known to play key roles in various cellular processes. In this paper, we aim to bring together several pieces of evidence from published research and literature that suggest a potentially vital role for transglutaminases in receptor tyrosine kinases (RTK) signalling. We cite literature that confirms and suggests the formation of integrin:RTK:transglutaminase complexes and explores the occurrence and functionality of these complexes in a large fraction of the RTK family.

The molecular structure of the mineral sarmientite Fe2(AsO4,SO4)2(OH)6•5H2O : implications for arsenic accumulation and removal

Sarmientite is an environmental mineral; its formation in soils enables the entrapment and immobilisation of arsenic. The mineral sarmientite is often amorphous making the application of X-ray diffraction difficult. Vibrational spectroscopy has been applied to the study of sarmientite. Bands are attributed to the vibrational units of arsenate, sulphate, hydroxyl and water. Raman bands at 794, 814 and 831 cm−1 are assigned to the ν3 (AsO4)3− antisymmetric stretching modes and the ν1 symmetric stretching mode is observed at 891 cm−1. Raman bands at 1003 and 1106 cm−1 are attributed to vibrations. The Raman band at 484 cm−1 is assigned to the triply degenerate (AsO4)3− bending vibration. The high intensity Raman band observed at 355 cm−1 (both lower and upper) is considered to be due to the (AsO4)3−ν2 bending vibration. Bands attributed to water and OH stretching vibrations are observed.

Boundary weaving : the social structure and processes of organizational boundaries

Boundaries are an important field of study because they mediate almost every aspect of organizational life. They are becoming increasingly more important as organizations change more frequently and yet, despite the endemic use of the boundary metaphor in common organizational parlance, they are poorly understood. Organizational boundaries are under-theorized and researchers in related fields often simply assume their existence, without defining them. The literature on organizational boundaries is fragmented with no unifying theoretical basis. As a result, when it is recognized that an organizational boundary is "dysfunctional". there is little recourse to models on which to base remediating action. This research sets out to develop just such a theoretical model and is guided by the general question: "What is the nature of organizational boundaries?" It is argued that organizational boundaries can be conceptualised through elements of both social structure and of social process. Elements of structure include objects, coupling, properties and identity. Social processes include objectification, identification, interaction and emergence. All of these elements are integrated by a core category, or basic social process, called boundary weaving. An organizational boundary is a complex system of objects and emergent properties that are woven together by people as they interact together, objectifying the world around them, identifying with these objects and creating couplings of varying strength and polarity as well as their own fragmented identity. Organizational boundaries are characterised by the multiplicity of interconnections, a particular domain of objects, varying levels of embodiment and patterns of interaction. The theory developed in this research emerged from an exploratory, qualitative research design employing grounded theory methodology. The field data was collected from the training headquarters of the New Zealand Army using semi-structured interviews and follow up observations. The unit of analysis is an organizational boundary. Only one research context was used because of the richness and multiplicity of organizational boundaries that were present. The model arose, grounded in the data collected, through a process of theoretical memoing and constant comparative analysis. Academic literature was used as a source of data to aid theory development and the saturation of some central categories. The final theory is classified as middle range, being substantive rather than formal, and is generalizable across medium to large organizations in low-context societies. The main limitation of the research arose from the breadth of the research with multiple lines of inquiry spanning several academic disciplines, with some relevant areas such as the role of identity and complexity being addressed at a necessarily high level. The organizational boundary theory developed by this research replaces the typology approaches, typical of previous theory on organizational boundaries and reconceptualises the nature of groups in organizations as well as the role of "boundary spanners". It also has implications for any theory that relies on the concept of boundaries, such as general systems theory. The main contribution of this research is the development of a holistic model of organizational boundaries including an explanation of the multiplicity of boundaries . no organization has a single definable boundary. A significant aspect of this contribution is the integration of aspects of complexity theory and identity theory to explain the emergence of higher-order properties of organizational boundaries and of organizational identity. The core category of "boundary weaving". is a powerful new metaphor that significantly reconceptualises the way organizational boundaries may be understood in organizations. It invokes secondary metaphors such as the weaving of an organization's "boundary fabric". and provides managers with other metaphorical perspectives, such as the management of boundary friction, boundary tension, boundary permeability and boundary stability. Opportunities for future research reside in formalising and testing the theory as well as developing analytical tools that would enable managers in organizations to apply the theory in practice.

The molecular structure of the multianion mineral hidalgoite PbAl3(AsO4)(SO4)(OH)6 : implications for arsenic removal from soils

The objective of this research is to determine the molecular structure of the mineral hidalgoite PbAl3(AsO4)(SO4)(OH)6 using vibrational spectroscopy. The mineral is found in old mine sites. Observed bands are assigned to the stretching and bending vibrations of (SO4)2- and (AsO4)3- units, stretching and bending vibrations of hydrogen bonded (OH)- ions and Al3+-(O,OH) units. The approximate range of O-H...O hydrogen bond lengths is inferred from the Raman and infrared spectra. Values of 2.6989 Å, 2.7682 Å, 2.8659 Å were obtained. The formation of hidalgoite may offer a mechanism for the removal of arsenic from the environment.

Molecular structural studies of the amorphous mineral pitticite Fe, AsO4, SO4, H2O

Some minerals are colloidal and show no X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of these types of mineral. Among this group of minerals is pitticite simply described as Fe, AsO4, SO4, H2O. The objective of this research is to determine the molecular structure of the mineral pitticite using vibrational spectroscopy. Raman microscopy offers a useful method for the analysis of such colloidal minerals. Raman and infrared bands are attributed to the , and water stretching vibrations. The Raman spectrum is dominated by a very intense sharp band at 983 cm−1 assigned to the symmetric stretching mode. A strong Raman band at 1041 cm−1 is observed and is assigned to the antisymmetric stretching mode. Low intensity Raman bands at 757 and 808 cm−1 may be assigned to the antisymmetric and symmetric stretching modes. Raman bands observed at 432 and 465 cm−1 are attributable to the doubly degenerate ν2(SO4)2- bending mode.

Knowledge-based urban development processes of an emerging knowledge city : Brisbane, Australia

In the global knowledge economy, to attract and retain knowledge-intensive industries and workers, cities produce various development strategies. Such strategising is an important development mechanism for cities to complete their transformation into knowledge cities. This paper discusses the critical connections between knowledge city foundations and integrated knowledge-based urban development strategies, and scrutinises Brisbane’s strategies in attracting and retaining investment and talent. The paper introduces a knowledge-based urban development assessment framework and uses this framework to provide a clearer understanding of Brisbane’s knowledge-based development processes and knowledge city transformation experience. The assessment framework particularly focuses on examining Brisbane’s four development processes, institutional, economic, socio-cultural and urban development, in detail. The findings reveal that although Brisbane is still in early stages of its transformation into a fully-fledged knowledge city, global orientation and achievements of Brisbane in strategising knowledge-based urban development are noteworthy.

Iron biogeochemistry and associated greenhouse gas evolution in a forested subtropical Australian coastal catchment : Poona Creek, Southeast Queensland

Iron (Fe) is the fourth most abundant element in the Earth’s crust. Excess Fe mobilization from terrestrial into aquatic systems is of concern for deterioration of water quality via biofouling and nuisance algal blooms in coastal and marine systems. Substantial Fe dissolution and transport involve alternate Fe(II) oxidation followed by Fe(III) reduction, with a diversity of Bacteria and Archaea acting as the key catalyst. Microbially-mediated Fe cycling is of global significance with regard to cycles of carbon (C), sulfur (S) and manganese (Mn). However, knowledge regarding microbial Fe cycling in circumneutral-pH habitats that prevail on Earth has been lacking until recently. In particular, little is known regarding microbial function in Fe cycling and associated Fe mobilization and greenhouse (CO2 and CH4, GHG) evolution in subtropical Australian coastal systems where microbial response to ambient variations such as seasonal flooding and land use changes is of concern. Using the plantation-forested Poona Creek catchment on the Fraser Coast of Southeast Queensland (SEQ), this research aimed to 1) study Fe cycling-associated bacterial populations in diverse terrestrial and aquatic habitats of a representative subtropical coastal circumneutral-pH (4–7) ecosystem; and 2) assess potential impacts of Pinus plantation forestry practices on microbially-mediated Fe mobilization, organic C mineralization and associated GHG evolution in coastal SEQ. A combination of wet-chemical extraction, undisturbed core microcosm, laboratory bacterial cultivation, microscopy and 16S rRNA-based molecular phylogenetic techniques were employed. The study area consisted primarily of loamy sands, with low organic C and dissolved nutrients. Total reactive Fe was abundant and evenly distributed within soil 0–30 cm profiles. Organic complexation primarily controlled Fe bioavailability and forms in well-drained plantation soils and water-logged, native riparian soils, whereas tidal flushing exerted a strong “seawater effect” in estuarine locations and formed a large proportion of inorganic Fe(III) complexes. There was a lack of Fe(II) sources across the catchment terrestrial system. Mature, first-rotation plantation clear-felling and second-rotation replanting significantly decreased organic matter and poorly crystalline Fe in well-drained soils, although variations in labile soil organic C fractions (dissolved organic C, DOC; and microbial biomass C, MBC) were minor. Both well-drained plantation soils and water-logged, native-vegetation soils were inhabited by a variety of cultivable, chemotrophic bacterial populations capable of C, Fe, S and Mn metabolism via lithotrophic or heterotrophic, (micro)aerobic or anaerobic pathways. Neutrophilic Fe(III)-reducing bacteria (FeRB) were most abundant, followed by aerobic, heterotrophic bacteria (heterotrophic plate count, HPC). Despite an abundance of FeRB, cultivable Fe(II)-oxidizing bacteria (FeOB) were absent in associated soils. A lack of links between cultivable Fe, S or Mn bacterial densities and relevant chemical measurements (except for HPC correlated with DOC) was likely due to complex biogeochemical interactions. Neither did variations in cultivable bacterial densities correlate with plantation forestry practices, despite total cultivable bacterial densities being significantly lower in estuarine soils when compared with well-drained plantation soils and water-logged, riparian native-vegetation soils. Given that bacterial Fe(III) reduction is the primary mechanism of Fe oxide dissolution in soils upon saturation, associated Fe mobilization involved several abiotic and biological processes. Abiotic oxidation of dissolved Fe(II) by Mn appeared to control Fe transport and inhibit Fe dissolution from mature, first-rotation plantation soils post-saturation. Such an effect was not observed in clear-felled and replanted soils associated with low SOM and potentially low Mn reactivity. Associated GHG evolution post-saturation mainly involved variable CO2 emissions, with low, but consistently increasing CH4 effluxes in mature, first-rotation plantation soil only. In comparison, water-logged soils in the riparian native-vegetation buffer zone functioned as an important GHG source, with high potentials for Fe mobilization and GHG, particularly CH4 emissions in riparian loam soils associated with high clay and crystalline Fe fractions. Active Fe–C cycling was unlikely to occur in lower-catchment estuarine soils associated with low cultivable bacterial densities and GHG effluxes. As a key component of bacterial Fe cycling, neutrophilic FeOB widely occurred in diverse aquatic, but not terrestrial, habitats of the catchment study area. Stalked and sheathed FeOB resembling Gallionella and Leptothrix were limited to microbial mat material deposited in surface fresh waters associated with a circumneutral-pH seep, and clay-rich soil within riparian buffer zones. Unicellular, Sideroxydans-related FeOB (96% sequence identity) were ubiquitous in surface and subsurface freshwater environments, with highest abundance in estuary-adjacent shallow coastal groundwater water associated with redox transition. The abundance of dissolved C and Fe in the groundwater-dependent system was associated with high numbers of cultivable anaerobic, heterotrophic FeRB, microaerophilic, putatively lithotrophic FeOB and aerobic, heterotrophic bacteria. This research represents the first study of microbial Fe cycling in diverse circumneutral-pH environments (terrestrial–aquatic, freshwater–estuarine, surface–subsurface) of a subtropical coastal ecosystem. It also represents the first study of its kind in the southern hemisphere. This work highlights the significance of bacterial Fe(III) reduction in terrestrial, and bacterial Fe(II) oxidation in aquatic catchment Fe cycling. Results indicate the risk of promotion of Fe mobilization due to plantation clear-felling and replanting, and GHG emissions associated with seasonal water-logging. Additional significant outcomes were also achieved. The first direct evidence for multiple biomineralization patterns of neutrophilic, microaerophilic, unicellular FeOB was presented. A putatively pure culture, which represents the first cultivable neutrophilic FeOB from the southern hemisphere, was obtained as representative FeOB ubiquitous in diverse catchment aquatic habitats.

An approximate Bayesian computation approach for estimating parameters of complex environmental processes in a cellular automata

Modelling an environmental process involves creating a model structure and parameterising the model with appropriate values to accurately represent the process. Determining accurate parameter values for environmental systems can be challenging. Existing methods for parameter estimation typically make assumptions regarding the form of the Likelihood, and will often ignore any uncertainty around estimated values. This can be problematic, however, particularly in complex problems where Likelihoods may be intractable. In this paper we demonstrate an Approximate Bayesian Computational method for the estimation of parameters of a stochastic CA. We use as an example a CA constructed to simulate a range expansion such as might occur after a biological invasion, making parameter estimates using only count data such as could be gathered from field observations. We demonstrate ABC is a highly useful method for parameter estimation, with accurate estimates of parameters that are important for the management of invasive species such as the intrinsic rate of increase and the point in a landscape where a species has invaded. We also show that the method is capable of estimating the probability of long distance dispersal, a characteristic of biological invasions that is very influential in determining spread rates but has until now proved difficult to estimate accurately.

Velocity-jump models with crowding effects

Velocity jump processes are discrete random walk models that have many applications including the study of biological and ecological collective motion. In particular, velocity jump models are often used to represent a type of persistent motion, known as a “run and tumble”, which is exhibited by some isolated bacteria cells. All previous velocity jump processes are non-interacting, which means that crowding effects and agent-to-agent interactions are neglected. By neglecting these agent-to-agent interactions, traditional velocity jump models are only applicable to very dilute systems. Our work is motivated by the fact that many applications in cell biology, such as wound healing, cancer invasion and development, often involve tissues that are densely packed with cells where cell-to-cell contact and crowding effects can be important. To describe these kinds of high cell density problems using a velocity jump process we introduce three different classes of crowding interactions into a one-dimensional model. Simulation data and averaging arguments lead to a suite of continuum descriptions of the interacting velocity jump processes. We show that the resulting systems of hyperbolic partial differential equations predict the mean behavior of the stochastic simulations very well.